Citrus Sinensis ID: 012923

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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---
Protein Sequence
MAKKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDEPILSLLEPFSKDQLVNLLREAAENHRDVASRVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAIDGPKPGKSRHHNAQNPHFQRNEGAGYVGGAGPAAAGPGHLMAPSGPAIPPAAAQALNPALGQALLGTLGSAAGGTAPMQGTYGNQTNVSPSVIGGYANQGGYPNQQMPQGGAGRGQHAAGQYGAPYMGH
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHccHHHHHHHHccccccccHHHHHHHcccccHHHHHHHHHHHHHHcccHHHHHHHccccccccccEEEccccccccHHHHHHHHHcccccEEEEEEEEccccccccEEEEEEccHHHHHHHHHccccEEccEEEEEEccccccccccccccccccccccccccccccHHccccccccccccEEEEEcccccccHHHHHHHHHccccEEEEEEEccccccccccEEEEEEccHHHHHHHHHccccEEccEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccccccccccEEEEcccHHHHcccccccccccccccHcccccccccccccccccHHHHHHHcccccHHHHHHHHHHHHHccccccccccccccccccccEEEEEcccccccHHHHHHHHHHHccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHHccccccccEEEEEEEcccccccccccccccccccccccccccccccccccccccccEEEEEEccccccccHHHHHHHHHHcccEEEEEEEEEccccccccEEEEEEccHHHHHHHHHcccccEcccEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
makkrkhdsktsepteppqkqlqqeppkqeepieeeeyeeeveeegeeegeeeeeeeeeEEEEEEKADQKEDEEEEekadqndeeddepilsllepfsKDQLVNLLREAAENHRDVASRVrqvadedpvhRKIFvhglgwdtKAETLIDAFKQYGEIEDCKAVCdkvsgkskgygFILFKTRSGARKALKEPQkkignrmtacqlasigpattpavastathqhqhqhqhqhqhqhqqhhqqseytQRKIFVsnvgselepQKLLAFFSKygeieegplgidkatgkpkgfCLFVYKTVDAAKKALeephknfegHILNCqraidgpkpgksrhhnaqnphfqrnegagyvggagpaaagpghlmapsgpaippaaAQALNPALGQALLGtlgsaaggtapmqgtygnqtnvspsviggyanqggypnqqmpqggagrgqhaagqygapymgh
Flexible Loop (DISEMBL)
makkrkhdsktsepteppqkqlqqeppkqeepieeeeyeeeveeegeeegeeeeeeeeeeeeeeekadqkedeeeeekadqndeeddePILSLLEPFSKDQLVNLLREAAENHRDVASrvrqvadedpvhrkifvhglgwdtkAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGfilfktrsgarkaLKEPQKKIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGplgidkatgkpKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAIDGPKPGKSRHHNAQNPHFQRNEGAGYVGGAGPAAAGPGHLMAPSGPAIPPAAAQALNPALGQALLGTLGSAAGGTAPMQGTYGNQTNVSPSVIGGYANQGGYPNQQMPQGGAGRGQHAAGQYGAPYMGH
Low Complexity Region (SEG)
MAKKRKHDSKTSepteppqkqlqqeppkqeepieeeeyeeeveeegeeegeeeeeeeeeeeeeeekadqkedeeeeekadqndeeddePILSLLEPFSKDQLVNLLREAAENHRDVASRVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASIGpattpavastathqhqhqhqhqhqhqhqqhhqqSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAIDGPKPGKSRHHNAQNPHFQRNEgagyvggagpaaagpgHLMapsgpaippaaaqalnpalgqallgtlgsaaggtaPMQGTYGNQTNVSPSVIGGYANQGGYPNQQMPqggagrgqhaagqygaPYMGH
Disordered region (IsUnstruct)
*****************************************************************************************************LVNLL****************VADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTR*******************************************************************IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQ*****************************************************************ALLG***************************************************************
Disordered Region (DISOPRED)
*************************************************************************************************************************************FVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASIGP**************************************KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILN**************************************************************************************************************************************
Disordered Region (DISEMBL)
***************************************************************************************EPILSLLEPFSKDQLVNLLREAAENHRDVASRVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASIGPAT********************************YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAIDGP*********AQNPHFQRNEGAGYVGGAGPAAAGPGHLMAPSGPAIPPAAAQALNPALGQALLGTLGSAAGGTAPMQGTYGNQTNVSPSVIGGYANQGGYPNQQM***********AGQYGAPYMGH
Disordered Region (DISPRO)
******************************************EEEGEE************************************EDDEPILSLLEPFSKDQLVNLLREAAEN****************VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASI***********************************EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAIDG***************FQRNEGAGYVGGAGPAAAGPGHLMAPSGPAIPPAAAQALNPALGQALLGTLGSAAGGTAPMQGTYGNQTNVSPSVIGGYANQGGYPNQQMPQGGAGRGQHAAGQY*******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAKKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIExxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxEPILSLLEPFSKDQLVNLLREAAENHRDVASRVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAIDGPKPGKSRHHNAQNPHFQRNEGAGYVGGAGPAAAGPGHLMAPSGPAIPPAAAQALNPALGQALLGTLGSAAGGTAPMQGTYGNQTNVSPSVIGGYANQGGYPNQQMPQGGAGRGQHAAGQYGAPYMGH
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	453	2.2.26 [Sep-21-2011]
O94432	474	Uncharacterized RNA-bindi	yes	no	0.637	0.609	0.25	1e-18
Q99020	285	Heterogeneous nuclear rib	no	no	0.357	0.568	0.299	2e-18
Q14103	355	Heterogeneous nuclear rib	yes	no	0.381	0.487	0.258	5e-18
Q60668	355	Heterogeneous nuclear rib	no	no	0.381	0.487	0.258	7e-18
Q9JJ54	353	Heterogeneous nuclear rib	no	no	0.381	0.490	0.253	1e-17
O14979	420	Heterogeneous nuclear rib	no	no	0.317	0.342	0.267	9e-16
Q6NU14	291	Heterogeneous nuclear rib	N/A	no	0.388	0.604	0.252	2e-15
Q99729	332	Heterogeneous nuclear rib	no	no	0.357	0.487	0.282	2e-15
Q5ZI72	301	Heterogeneous nuclear rib	no	no	0.324	0.488	0.262	4e-15
Q9Z130	301	Heterogeneous nuclear rib	no	no	0.324	0.488	0.262	5e-15

>sp|O94432|YHKF_SCHPO Uncharacterized RNA-binding protein C660.15 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBC660.15 PE=4 SV=1

 Score = 94.7 bits (234), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 90/360 (25%), Positives = 146/360 (40%), Gaps = 71/360 (19%)

Query: 32  PIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEED-DEPI 90
           P +E E  EE+E+ GE   E  +E    EE   +      D++   +A+ N E+D +E  
Sbjct: 38  PTKENEGYEELEKSGEAGAERTKENPFREEPGADFDRSGSDQQYSAEAEANQEDDLNETS 97

Query: 91  LSLLEPFSKDQLVNLLREAA----------------ENHRDVASRVRQVADED------P 128
               +P S D     L  A                 EN   +       ++ED      P
Sbjct: 98  QQAPDPSSYDIRGQALSSATWDNAEDGENSKNDNYNENQSALTGSGAMESNEDNAEETSP 157

Query: 129 VHR---KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGA 185
            +R   K+F+ GL W+T  ++L D F+Q+GE+ DC  + D  +G+S+G+GF+ FK     
Sbjct: 158 FNREDGKMFIGGLNWETTDDSLRDYFEQFGEVLDCTVMRDSTTGRSRGFGFLTFK----- 212

Query: 186 RKALKEPQKKIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEY 245
                    K  N + + +    G    P  A     Q +                    
Sbjct: 213 -------NPKCVNEVMSKEHHLDGKIIDPKRAIPREEQEK-------------------- 245

Query: 246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKA 305
              K+FV  V  +   ++   FF+++G + +  L +DK TG+P+GF    Y+   A +  
Sbjct: 246 -TAKMFVGGVPGDCTEEEFRNFFNQFGRVLDATLMMDKDTGRPRGFGFVTYENESAVEAT 304

Query: 306 LEEPHKNFEGHILNCQRAIDGPKP----GKSRH----HNAQNPHFQRNEGAGYVGGAGPA 357
           + +P+    G  +  +RA   PK        RH    H   NP++ +N      GG  PA
Sbjct: 305 MSQPYITIHGKPVEVKRAT--PKASLRDSHDRHQHGYHGNANPYYAQN--MNMYGGMTPA 360

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

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

 Score = 94.4 bits (233), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 59/197 (29%), Positives = 86/197 (43%), Gaps = 35/197 (17%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K+FV GL WDT  + L D F ++GE+ DC    D  +G+S+G+GFILFK  S   K L +
Sbjct: 76  KMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDSSSVEKVLDQ 135

Query: 192 PQKKIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIF 251
            + ++  R+       I P    A+                               +KIF
Sbjct: 136 KEHRLDGRV-------IDPKKAMAMKKDPV--------------------------KKIF 162

Query: 252 VSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHK 311
           V  +  E   +K+  +F ++GEIE   L ID    K +GF    +K  D  KK LE+   
Sbjct: 163 VGGLNPEATEEKIREYFGQFGEIEAIELPIDPKLNKRRGFVFITFKEEDPVKKVLEKKFH 222

Query: 312 NFEGHILNCQRAIDGPK 328
              G    C+  +  PK
Sbjct: 223 TVSGS--KCEIKVAQPK 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|Q14103|HNRPD_HUMAN Heterogeneous nuclear ribonucleoprotein D0 OS=Homo sapiens GN=HNRNPD PE=1 SV=1

 Score = 92.8 bits (229), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 53/205 (25%), Positives = 90/205 (43%), Gaps = 32/205 (15%)

Query: 108 EAAENHRDVASRVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKV 167
           E  E H + + R  + A       K+F+ GL WDT  + L D F ++GE+ DC    D +
Sbjct: 74  EEDEGHSNSSPRHSEAATAQREEWKMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPI 133

Query: 168 SGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASIGPATTPAVASTATHQHQHQ 227
           +G+S+G+GF+LFK      K + + + K+  ++   + A       P             
Sbjct: 134 TGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRAKAMKTKEPV------------ 181

Query: 228 HQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGK 287
                               +KIFV  +  +   +K+  +F  +GE+E   L +D  T K
Sbjct: 182 --------------------KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNK 221

Query: 288 PKGFCLFVYKTVDAAKKALEEPHKN 312
            +GFC   +K  +  KK +E+ + N
Sbjct: 222 RRGFCFITFKEEEPVKKIMEKKYHN 246

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.

Homo sapiens (taxid: 9606)

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

 Score = 92.0 bits (227), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 53/205 (25%), Positives = 90/205 (43%), Gaps = 32/205 (15%)

Query: 108 EAAENHRDVASRVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKV 167
           E  E H + + R  + A       K+F+ GL WDT  + L D F ++GE+ DC    D +
Sbjct: 74  EEDEGHSNSSPRHTEAAAAQREEWKMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPI 133

Query: 168 SGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASIGPATTPAVASTATHQHQHQ 227
           +G+S+G+GF+LFK      K + + + K+  ++   + A       P             
Sbjct: 134 TGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRAKAMKTKEPV------------ 181

Query: 228 HQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGK 287
                               +KIFV  +  +   +K+  +F  +GE+E   L +D  T K
Sbjct: 182 --------------------KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNK 221

Query: 288 PKGFCLFVYKTVDAAKKALEEPHKN 312
            +GFC   +K  +  KK +E+ + N
Sbjct: 222 RRGFCFITFKEEEPVKKIMEKKYHN 246

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)

>sp|Q9JJ54|HNRPD_RAT Heterogeneous nuclear ribonucleoprotein D0 OS=Rattus norvegicus GN=Hnrnpd PE=1 SV=1

 Score = 91.7 bits (226), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 52/205 (25%), Positives = 90/205 (43%), Gaps = 32/205 (15%)

Query: 108 EAAENHRDVASRVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKV 167
           E  E H + + R  + A       K+F+ GL WDT  + L D F ++G++ DC    D +
Sbjct: 72  EEDEGHSNSSPRHTEAATAQREEWKMFIGGLSWDTTKKDLKDYFSKFGDVVDCTLKLDPI 131

Query: 168 SGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASIGPATTPAVASTATHQHQHQ 227
           +G+S+G+GF+LFK      K + + + K+  ++   + A       P             
Sbjct: 132 TGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRAKAMKTKEPV------------ 179

Query: 228 HQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGK 287
                               +KIFV  +  +   +K+  +F  +GE+E   L +D  T K
Sbjct: 180 --------------------KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNK 219

Query: 288 PKGFCLFVYKTVDAAKKALEEPHKN 312
            +GFC   +K  +  KK +E+ + N
Sbjct: 220 RRGFCFITFKEEEPVKKIMEKKYHN 244

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.

Rattus norvegicus (taxid: 10116)

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

 Score = 85.1 bits (209), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 47/176 (26%), Positives = 81/176 (46%), Gaps = 32/176 (18%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K+F+ GL WDT  + L +   ++GE+ DC    D V+G+S+G+GF+LFK  +   K L+ 
Sbjct: 149 KMFIGGLSWDTSKKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 208

Query: 192 PQKKIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIF 251
            + K+  ++       I P    A+                         + +   +K+F
Sbjct: 209 KEHKLDGKL-------IDPKRAKAL-------------------------KGKEPPKKVF 236

Query: 252 VSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           V  +  +   +++  +F  +GEIE   L +D  T + +GFC   Y   +  KK LE
Sbjct: 237 VGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPVKKLLE 292

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 = 84.3 bits (207), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 54/214 (25%), Positives = 92/214 (42%), Gaps = 38/214 (17%)

Query: 94  LEPFSKDQLVNLLREAAENHRDVASRVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQ 153
           L   ++  LV+ L      H++         D   +  K+F+ GL WDT  + L +   +
Sbjct: 3   LSEITRSTLVSTLSRLLRRHKESN------PDFFLIRSKMFIGGLSWDTSKKDLTEYLSR 56

Query: 154 YGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASIGPATT 213
           +GE+ DC    D V+G+S+G+GF+LFK      K L+  + K+  ++       I P   
Sbjct: 57  FGEVLDCTIKTDPVTGRSRGFGFVLFKDAVSVDKVLETKEHKLDGKL-------IDPKRA 109

Query: 214 PAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGE 273
            A+                         Q +   +K+FV  +  E   +++  +F  +GE
Sbjct: 110 KAL-------------------------QGKEPPKKVFVGGLSPETTEEQIKQYFGGFGE 144

Query: 274 IEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           IE   L +D  T + +GFC   Y   +  +K LE
Sbjct: 145 IENIELPMDTKTNERRGFCFVTYTDEEPVQKLLE 178

Acts as a transcriptional regulator. Binds DNA and RNA.

Xenopus laevis (taxid: 8355)

>sp|Q99729|ROAA_HUMAN Heterogeneous nuclear ribonucleoprotein A/B OS=Homo sapiens GN=HNRNPAB PE=1 SV=2

 Score = 84.0 bits (206), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 56/198 (28%), Positives = 86/198 (43%), Gaps = 36/198 (18%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K+FV GL WDT  + L D F ++GE+ DC    D  +G+S+G+GFILFK  +   K L +
Sbjct: 70  KMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ 129

Query: 192 PQKKIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIF 251
            + ++  R+       I P    A+                               +KIF
Sbjct: 130 KEHRLDGRV-------IDPKKAMAMKKDPV--------------------------KKIF 156

Query: 252 VSNVGSEL-EPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH 310
           V  +  E    +K+  +F ++GEIE   L +D    K +GF    +K  +  KK LE+  
Sbjct: 157 VGGLNPESPTEEKIREYFGEFGEIEAIELPMDPKLNKRRGFVFITFKEEEPVKKVLEKKF 216

Query: 311 KNFEGHILNCQRAIDGPK 328
               G    C+  +  PK
Sbjct: 217 HTVSGS--KCEIKVAQPK 232

Binds single-stranded RNA. Has a high affinity for G-rich and U-rich regions of hnRNA. Also binds to APOB mRNA transcripts around the RNA editing site.

Homo sapiens (taxid: 9606)

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

 Score = 82.8 bits (203), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 47/179 (26%), Positives = 82/179 (45%), Gaps = 32/179 (17%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K+F+ GL WDT  + L +   ++GE+ DC    D V+G+S+G+GF+LFK  +   K L+ 
Sbjct: 31  KMFIGGLSWDTSKKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVEKVLEL 90

Query: 192 PQKKIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIF 251
            + K+  ++       I P    A+                         + +   +K+F
Sbjct: 91  KEHKLDGKL-------IDPKRAKAL-------------------------KGKEPPKKVF 118

Query: 252 VSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH 310
           V  +  +   +++  +F  +GEIE   L +D  T + +GFC   Y   +  KK LE  +
Sbjct: 119 VGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPVKKLLESRY 177

Acts as a transcriptional regulator. Binds DNA and RNA.

Gallus gallus (taxid: 9031)

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

 Score = 82.8 bits (203), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 47/179 (26%), Positives = 82/179 (45%), Gaps = 32/179 (17%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K+F+ GL WDT  + L +   ++GE+ DC    D V+G+S+G+GF+LFK  +   K L+ 
Sbjct: 30  KMFIGGLSWDTSKKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 89

Query: 192 PQKKIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIF 251
            + K+  ++       I P    A+                         + +   +K+F
Sbjct: 90  KEHKLDGKL-------IDPKRAKAL-------------------------KGKEPPKKVF 117

Query: 252 VSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH 310
           V  +  +   +++  +F  +GEIE   L +D  T + +GFC   Y   +  KK LE  +
Sbjct: 118 VGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPVKKLLESRY 176

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)

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	453
225439119	463	PREDICTED: uncharacterized protein LOC10	0.774	0.758	0.622	1e-133
147807511	463	hypothetical protein VITISV_028589 [Viti	0.774	0.758	0.622	1e-133
224137512	477	predicted protein [Populus trichocarpa]	0.962	0.914	0.597	1e-132
255577238	462	Heterogeneous nuclear ribonucleoprotein	0.944	0.926	0.597	1e-130
224086681	474	predicted protein [Populus trichocarpa]	0.944	0.902	0.575	1e-126
449461439	500	PREDICTED: uncharacterized protein LOC10	0.889	0.806	0.545	1e-126
255562178	478	Heterogeneous nuclear ribonucleoprotein	0.953	0.903	0.585	1e-124
312281743	479	unnamed protein product [Thellungiella h	0.777	0.734	0.606	1e-124
15226817	451	RNA recognition motif-containing protein	0.944	0.949	0.550	1e-124
297824045	447	RNA recognition motif-containing protein	0.931	0.944	0.547	1e-123

>gi|225439119|ref|XP_002270568.1| PREDICTED: uncharacterized protein LOC100243393 [Vitis vinifera]

 Score =  480 bits (1235), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 259/416 (62%), Positives = 291/416 (69%), Gaps = 65/416 (15%)

Query: 82  NDEEDDEPILSLLEPFSKDQLVNLLREAAENHRDVASRVRQVADEDPVHRKIFVHGLGWD 141
           +D++D+EPI  +LEPFSKDQL+NLLREAAE H DVA R+R+VADEDPVHRKIFVHGLGWD
Sbjct: 69  DDDDDEEPIQKILEPFSKDQLINLLREAAEKHADVAERLRRVADEDPVHRKIFVHGLGWD 128

Query: 142 TKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMT 201
           T AETLI  FK YGEIEDC+AVCDK+SGKSKGYGFILFKTRSGARKALK+PQKKIGNRMT
Sbjct: 129 TNAETLISVFKDYGEIEDCRAVCDKLSGKSKGYGFILFKTRSGARKALKQPQKKIGNRMT 188

Query: 202 ACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEP 261
           ACQLASIGP  +PAV   A      Q               SEYTQRKI+VSNVG+EL+P
Sbjct: 189 ACQLASIGPVPSPAVGQAAMSVSAAQ-------------SVSEYTQRKIYVSNVGAELDP 235

Query: 262 QKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQ 321
           QKLL FFSKYGEIEEGPLG+DK TGKPKGFCLFVYKT + AKKAL+EPHKNF+GHIL+CQ
Sbjct: 236 QKLLVFFSKYGEIEEGPLGLDKQTGKPKGFCLFVYKTAEGAKKALDEPHKNFDGHILHCQ 295

Query: 322 RAIDGPKPGK-------SRHHNAQNPHFQRNEGAGYVGGAGPAAAGP-GHLMAPSG-PAI 372
           +AIDGPKPGK         HHN  N H+ ++E   ++        GP GHLMAPSG PAI
Sbjct: 296 KAIDGPKPGKQQQLQQQQHHHNLPNTHYTKSEITNFM--------GPQGHLMAPSGPPAI 347

Query: 373 P---PAAAQALNPALGQALLGTLG--------------------------SAAGGTAPMQ 403
           P    +AAQALNPALGQAL   L                           S AG    MQ
Sbjct: 348 PYNQGSAAQALNPALGQALTALLATQGAGLGLTNLLGTLGSASVGAAVNPSVAGAGHGMQ 407

Query: 404 GTYGNQT---NVSPSVIGGYANQGGYPNQQMPQG-GAGRGQHAAGQYG--APYMGH 453
           G Y NQ    N+S  ++GGY +QG Y NQQM QG  +GR QH  G  G  APYMGH
Sbjct: 408 GGYPNQAVAGNISSGMVGGYGSQGAYGNQQMGQGSSSGRSQHGVGHMGGMAPYMGH 463

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147807511|emb|CAN72884.1| hypothetical protein VITISV_028589 [Vitis vinifera]

 Score =  480 bits (1235), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 259/416 (62%), Positives = 291/416 (69%), Gaps = 65/416 (15%)

Query: 82  NDEEDDEPILSLLEPFSKDQLVNLLREAAENHRDVASRVRQVADEDPVHRKIFVHGLGWD 141
           +D++D+EPI  +LEPFSKDQL+NLLREAAE H DVA R+R+VADEDPVHRKIFVHGLGWD
Sbjct: 69  DDDDDEEPIQKILEPFSKDQLINLLREAAEKHADVAERLRRVADEDPVHRKIFVHGLGWD 128

Query: 142 TKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMT 201
           T AETLI  FK YGEIEDC+AVCDK+SGKSKGYGFILFKTRSGARKALK+PQKKIGNRMT
Sbjct: 129 TNAETLISVFKDYGEIEDCRAVCDKLSGKSKGYGFILFKTRSGARKALKQPQKKIGNRMT 188

Query: 202 ACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEP 261
           ACQLASIGP  +PAV   A      Q               SEYTQRKI+VSNVG+EL+P
Sbjct: 189 ACQLASIGPVPSPAVGQAAMSVSAAQ-------------SVSEYTQRKIYVSNVGAELDP 235

Query: 262 QKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQ 321
           QKLL FFSKYGEIEEGPLG+DK TGKPKGFCLFVYKT + AKKAL+EPHKNF+GHIL+CQ
Sbjct: 236 QKLLVFFSKYGEIEEGPLGLDKQTGKPKGFCLFVYKTAEGAKKALDEPHKNFDGHILHCQ 295

Query: 322 RAIDGPKPGK-------SRHHNAQNPHFQRNEGAGYVGGAGPAAAGP-GHLMAPSG-PAI 372
           +AIDGPKPGK         HHN  N H+ ++E   ++        GP GHLMAPSG PAI
Sbjct: 296 KAIDGPKPGKQQQLQQQQHHHNLPNTHYTKSEITNFM--------GPQGHLMAPSGPPAI 347

Query: 373 P---PAAAQALNPALGQALLGTLG--------------------------SAAGGTAPMQ 403
           P    +AAQALNPALGQAL   L                           S AG    MQ
Sbjct: 348 PYNQGSAAQALNPALGQALTALLATQGAGLGLTNLLGTLGSASVGAAVNPSVAGAGHGMQ 407

Query: 404 GTYGNQT---NVSPSVIGGYANQGGYPNQQMPQG-GAGRGQHAAGQYG--APYMGH 453
           G Y NQ    N+S  ++GGY +QG Y NQQM QG  +GR QH  G  G  APYMGH
Sbjct: 408 GGYPNQAVAGNISSGMVGGYGSQGAYGNQQMGQGSSSGRSQHGVGHMGGMAPYMGH 463

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224137512|ref|XP_002322576.1| predicted protein [Populus trichocarpa] gi|222867206|gb|EEF04337.1| predicted protein [Populus trichocarpa]

 Score =  479 bits (1232), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 295/494 (59%), Positives = 343/494 (69%), Gaps = 58/494 (11%)

Query: 1   MAKKRKHDSKTSEPTE-PPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEE 59
           MAKKRKHD+K++EP E PP+KQ QQEPPK+E   E+ E E E  EE EEE  EE EEEEE
Sbjct: 1   MAKKRKHDAKSTEPAEEPPKKQQQQEPPKEELQEEQNEEEVEEVEEEEEEEYEEVEEEEE 60

Query: 60  EEEEEEKAD-QKEDEEEEEKADQNDEEDDEPILSLLEPFSKDQLVNLLREAAENHRDVAS 118
            E+E ++ + Q       E  + +++ED+EP+  LLEPF KDQL+NLLREAA+ HRDVA 
Sbjct: 61  NEDEADEENNQNAQISAGEIQNDDEDEDEEPVEKLLEPFGKDQLINLLREAADAHRDVAE 120

Query: 119 RVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFIL 178
           ++RQVAD+DPVHRKIFVHGLGWDT AE L+ AFK YGEIEDCKAVCDKVSGKSKGYGFIL
Sbjct: 121 KIRQVADQDPVHRKIFVHGLGWDTNAEALMSAFKPYGEIEDCKAVCDKVSGKSKGYGFIL 180

Query: 179 FKTRSGARKALKEPQKKIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQ 238
           FK RSGARKALKEPQKKIGNRMTACQLASIGP            Q             Q 
Sbjct: 181 FKRRSGARKALKEPQKKIGNRMTACQLASIGPVP----------QSSGGQAGPVAAAAQA 230

Query: 239 HHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKT 298
               SEYT RKI+VSNV ++L+PQKL ++FS++GEIEEGPLG+DKATGKPKGFCLFVYK+
Sbjct: 231 QQPVSEYTLRKIYVSNVAADLDPQKLYSYFSEFGEIEEGPLGLDKATGKPKGFCLFVYKS 290

Query: 299 VDAAKKALEEPHKNFEGHILNCQRAIDGPKPGKS-----RHHNAQNPHFQRNEGAGYVGG 353
            + AKKALEEPHK+FEGH+L+CQ+AIDGPKPGK+     +HHN Q+ H+QRN+G     G
Sbjct: 291 SEGAKKALEEPHKSFEGHMLHCQKAIDGPKPGKAQKQPQQHHNLQSSHYQRNDGG----G 346

Query: 354 AGPAAAGPGHLMAP--SGPAI---PPAAAQALNPALGQALLGTL---------------- 392
                +  GHLMAP  SG  I     AA  ALNPALGQAL   L                
Sbjct: 347 YVGGGSRGGHLMAPAASGAGIGFNQGAAGPALNPALGQALTALLATQGAGLGGLTNLLGT 406

Query: 393 ---------GSAAGGTAPMQGTYGNQTNVSPSVIGGYAN----QGGYPNQQMPQGGAGRG 439
                    G  +G    MQG YGNQ ++SP V+G YAN    QGGYPNQQ  QGG+GRG
Sbjct: 407 LGSAAAVNQGGLSGAGHGMQGAYGNQASISPGVMGTYANQGAMQGGYPNQQTGQGGSGRG 466

Query: 440 QHAAGQYGAPYMGH 453
           QH  GQY APYMGH
Sbjct: 467 QH--GQY-APYMGH 477

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255577238|ref|XP_002529501.1| Heterogeneous nuclear ribonucleoprotein A1, putative [Ricinus communis] gi|223531017|gb|EEF32870.1| Heterogeneous nuclear ribonucleoprotein A1, putative [Ricinus communis]

 Score =  473 bits (1217), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 291/487 (59%), Positives = 337/487 (69%), Gaps = 59/487 (12%)

Query: 1   MAKKRKHDSK--TSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEE 58
           MAKKRKHDSK  T+E TEPPQKQ  QE    EE  ++EE  ++  +  EEE EEEEE EE
Sbjct: 1   MAKKRKHDSKATTAEATEPPQKQQHQE----EEKPQQEEEAQKQNQIAEEEEEEEEEIEE 56

Query: 59  EEEEEEEKADQKEDEEEEEKADQNDEEDDEPILSLLEPFSKDQLVNLLREAAENHRDVAS 118
            E+  EE  ++ E EEEEE+ + NDE+DD+PI  LLEPF K+QL+NLLREAA+ HRDVA 
Sbjct: 57  YEQVIEEVEEEVEVEEEEEEEEANDEDDDDPIEKLLEPFGKEQLINLLREAADTHRDVAD 116

Query: 119 RVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFIL 178
            +R++AD DPVHRKIFVHGLGWDT AETL +AFKQYGEIEDCKAVCDKVSGKSKGYGFIL
Sbjct: 117 HIRKIADADPVHRKIFVHGLGWDTSAETLTNAFKQYGEIEDCKAVCDKVSGKSKGYGFIL 176

Query: 179 FKTRSGARKALKEPQKKIGNRMTACQLASIGPA-TTPAVASTATHQHQHQHQHQHQHQHQ 237
           FK RSGARKAL+EPQKKIGNRMTACQLASIGP     A AS  T  H           H 
Sbjct: 177 FKKRSGARKALQEPQKKIGNRMTACQLASIGPVPVGQAAASAVTTSH-----------HP 225

Query: 238 QHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYK 297
           QH Q S+YT+RKI+VSNV ++L+P++L  FFSK+GEIEEGPLG+DK TGKPKGFCLFVYK
Sbjct: 226 QHQQVSDYTRRKIYVSNVAADLDPKELTNFFSKFGEIEEGPLGLDKLTGKPKGFCLFVYK 285

Query: 298 TVDAAKKALEEPHKNFEGHILNCQRAIDGPKPGK-----SRHHNAQNPHFQRNEGAGYVG 352
           + ++AK+ALEEPHK+FEGH+L+CQ+AIDGPK GK      +H+NAQ  HFQRN   GY G
Sbjct: 286 SAESAKRALEEPHKSFEGHMLHCQKAIDGPKHGKPQQQQQQHYNAQKSHFQRNGNPGYSG 345

Query: 353 GAGPAAAGPGHLMAPS--GPAI----PPAAAQALNPALGQALLGTLGS------------ 394
           G    A+GP HLMAP+  GP I      A A ALNPALGQAL   L +            
Sbjct: 346 G---TASGPSHLMAPAAGGPGIGFNEGAAGAPALNPALGQALTALLATQGAGLGLNLLGT 402

Query: 395 ------AAGGTAPMQGTYGNQTNVSPSVIGGYANQGGYPNQQMPQGGAGRGQHAAGQYG- 447
                        MQ  YGNQ        G Y +QG        QG +GRGQH AGQYG 
Sbjct: 403 LGSAAGLPAAAPGMQNPYGNQA-------GSYGHQGVMHGTYPSQGSSGRGQHGAGQYGG 455

Query: 448 -APYMGH 453
             PYMGH
Sbjct: 456 VGPYMGH 462

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224086681|ref|XP_002307930.1| predicted protein [Populus trichocarpa] gi|222853906|gb|EEE91453.1| predicted protein [Populus trichocarpa]

 Score =  457 bits (1177), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 287/499 (57%), Positives = 337/499 (67%), Gaps = 71/499 (14%)

Query: 1   MAKKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEE 60
           MA+KRK DSK++E T     + QQ+  +  +   +EE  E  EEE EE  E EEEEE+ E
Sbjct: 1   MARKRKLDSKSTE-TAEEPPKKQQQQEEPPKEEPQEEEVEVEEEEEEEYEEVEEEEEDNE 59

Query: 61  EEEEEKADQKEDEEEEEKADQNDEEDDEPILSLLEPFSKDQLVNLLREAAENHRDVASRV 120
           ++ + + +Q       E  + +D+ED+EPI  LLEPF KDQL+NLLREAA+ HRDVA ++
Sbjct: 60  DDPDGETNQNAQISAVENLNDDDDEDEEPIEKLLEPFGKDQLINLLREAADGHRDVADKI 119

Query: 121 RQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFK 180
           RQVAD+DPVHRKIFVHGLGWDT AE LI+AFK YGEIEDCKAVCDKV+GKSKGYGFILFK
Sbjct: 120 RQVADQDPVHRKIFVHGLGWDTNAEALINAFKPYGEIEDCKAVCDKVTGKSKGYGFILFK 179

Query: 181 TRSGARKALKEPQKKIGNRMTACQLASIGPA-------TTPAVASTATHQHQHQHQHQHQ 233
            RSGAR ALKEPQKKIGNRM ACQLAS GP        + P  A+  T Q          
Sbjct: 180 KRSGARNALKEPQKKIGNRMAACQLASTGPVPQSSAGPSGPIAAAAQTQQ---------- 229

Query: 234 HQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCL 293
                    SEYT RKI+VSNVG+ L+PQKL++FFS++GEIEEGPLG+DKATGKPKGFCL
Sbjct: 230 -------PVSEYTLRKIYVSNVGANLDPQKLMSFFSEFGEIEEGPLGLDKATGKPKGFCL 282

Query: 294 FVYKTVDAAKKALEEPHKNFEGHILNCQRAIDGPKPGKS-----RHHNAQNPHFQRNEGA 348
           FVYKTV++AKKALEEPHK+FEGHIL+CQ+A+DGPK  KS     +HHN Q+ H+QRN+G 
Sbjct: 283 FVYKTVESAKKALEEPHKSFEGHILHCQKAVDGPKHAKSQKPPQQHHNMQSSHYQRNDGG 342

Query: 349 GYVGGAGPAAAGPGHLMAPSGPAIPPAAAQA-----LNPALGQALLGTLG---------- 393
           GYV   G      GHLMAP+         Q+     LNPALGQAL   L           
Sbjct: 343 GYVASGGRG----GHLMAPAAAGAGIGFNQSAAAPALNPALGQALTALLATQGAGLGGLT 398

Query: 394 -------SAAG---GTAP-----MQGTYGNQTNVSPSVIGGYAN----QGGYPNQQMPQG 434
                  SAA    G  P     MQG YGNQ ++SP VIG YAN    QGGYPNQQM QG
Sbjct: 399 NLLGTLGSAAAVTQGGVPSAAHGMQGAYGNQASISPGVIGAYANQGAMQGGYPNQQMGQG 458

Query: 435 GAGRGQHAAGQYGAPYMGH 453
           G+GRGQH  GQY  PYMGH
Sbjct: 459 GSGRGQH--GQY-TPYMGH 474

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449461439|ref|XP_004148449.1| PREDICTED: uncharacterized protein LOC101211535 [Cucumis sativus] gi|449503048|ref|XP_004161816.1| PREDICTED: uncharacterized protein LOC101228786 [Cucumis sativus]

 Score =  456 bits (1174), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 271/497 (54%), Positives = 328/497 (65%), Gaps = 94/497 (18%)

Query: 1   MAKKRKHDS-KTSEPTEPPQKQLQQ------------EPPKQEEPIEEEEYE-------- 39
           MA+KRK DS KTS+ TEPP+K  QQ            EP K+  P +  +Y+        
Sbjct: 1   MARKRKLDSSKTSDSTEPPKKLQQQPQAPLDEAKPQDEPLKEAVPQDLPQYDVVEEEDDD 60

Query: 40  --------EEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDE-------EEEEKADQNDE 84
                   E   +  ++  EEEEEE+E++E+E+++ D   +             A    +
Sbjct: 61  DNENDNDNENDNDNDDDNDEEEEEEDEDDEDEDDEGDANVNNHHPTPKISTSSAAVATTD 120

Query: 85  EDDEPILSLLEPFSKDQLVNLLREAAENHRDVASRVRQVADEDPVHRKIFVHGLGWDTKA 144
           +DDEPI  LLEPF+KDQL+NLLREAA+ H DVA R+R VAD DP HRKIFVHGLGWDT A
Sbjct: 121 DDDEPIHKLLEPFTKDQLINLLREAADKHVDVAGRIRMVADADPSHRKIFVHGLGWDTNA 180

Query: 145 ETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQ 204
           ETLI+ FKQ+GEIEDCKAVCDKVSGKSKGYGFILFK RSGARKALKEPQKKIGNRMTACQ
Sbjct: 181 ETLINVFKQFGEIEDCKAVCDKVSGKSKGYGFILFKKRSGARKALKEPQKKIGNRMTACQ 240

Query: 205 LASIGPA-TTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQK 263
           LAS+GP  TT AVA+                   Q    SEYTQRKI+VSNVG++++PQK
Sbjct: 241 LASVGPVPTTNAVAAP------------------QVPPASEYTQRKIYVSNVGADVDPQK 282

Query: 264 LLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRA 323
           LLAFFS++GE++EGPLG+DK TGKPKGFCLFVYK++++AKKALEEPHKNFEGH+L+CQ+A
Sbjct: 283 LLAFFSQFGEVDEGPLGLDKMTGKPKGFCLFVYKSIESAKKALEEPHKNFEGHVLHCQKA 342

Query: 324 IDGPKPGKSRH-HNAQNPHFQRNEGAGYVGGAGPAAAGPGHLMAPSGPAI-----PPAAA 377
           IDGPKPGK++H H+  N  FQRN+   Y GG   AA+G GHLMAP+GP +     PP   
Sbjct: 343 IDGPKPGKAQHQHHTPNAPFQRNKNPNYTGG---AASGSGHLMAPAGPGVGYNQGPP--- 396

Query: 378 QALNPALGQALLGTLGS---------------------AAGGTAP-MQGTYGNQTNVSPS 415
           Q LNPA+GQAL   L                       A  G  P +Q  YG+Q N+SP 
Sbjct: 397 QGLNPAIGQALTALLAGQGAGLGLTNLLGTLGTAGLNPAVQGAGPGVQSGYGSQANISPG 456

Query: 416 VIGGYAN----QGGYPN 428
           VI GY +    QGGYPN
Sbjct: 457 VI-GYGSQSGVQGGYPN 472

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255562178|ref|XP_002522097.1| Heterogeneous nuclear ribonucleoprotein A1, putative [Ricinus communis] gi|223538696|gb|EEF40297.1| Heterogeneous nuclear ribonucleoprotein A1, putative [Ricinus communis]

 Score =  452 bits (1162), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 292/499 (58%), Positives = 343/499 (68%), Gaps = 67/499 (13%)

Query: 1   MAKKRKHDSKTS-EPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEE 59
           MAKKRKHDSK S E TEPP+KQ  QE   +++  ++E  EEE EE  + E E EEE+EEE
Sbjct: 1   MAKKRKHDSKASVESTEPPKKQQHQEEETEKQEQKQEIVEEETEEYEQVEEEFEEEQEEE 60

Query: 60  EEEEEEKADQKEDEEEE---EKADQNDEEDDEPILSLLEPFSKDQLVNLLREAAENHRDV 116
           EEEEEE+ D +   + +   +    ND +DD+PI +LLEPF K+QLVNLL+EA++ HRDV
Sbjct: 61  EEEEEEEEDDQNQNQIDGGGQGDVNNDYDDDDPIENLLEPFGKEQLVNLLKEASDKHRDV 120

Query: 117 ASRVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGF 176
           A R+R++AD DP HRKIFVHGLGWD+ AETL +AFKQYGEIEDCKAVCDKVSGKSKGYGF
Sbjct: 121 ADRIRKIADADPAHRKIFVHGLGWDSTAETLTNAFKQYGEIEDCKAVCDKVSGKSKGYGF 180

Query: 177 ILFKTRSGARKALKEPQKKIGNRMTACQLASIGPA-TTPAVASTATHQHQHQHQHQHQHQ 235
           ILFK RSGARKAL+EPQKKIGNRMTACQLAS+GP  T+ A A+T     Q          
Sbjct: 181 ILFKKRSGARKALEEPQKKIGNRMTACQLASMGPVPTSTAPANTPAPGQQ---------- 230

Query: 236 HQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFV 295
                Q SEYTQRKI++SNVG++L+PQ+L +FFSK+GEIEEGPLG+DK TGKPKGFCLFV
Sbjct: 231 -----QVSEYTQRKIYISNVGADLDPQQLTSFFSKFGEIEEGPLGLDKLTGKPKGFCLFV 285

Query: 296 YKTVDAAKKALEEPHKNFEGHILNCQRAIDGPKPGKS----RHHNAQNPHFQRNEGAGYV 351
           YK+V++AKKALEEPHKNFEGHIL+CQ+A+DGPK GKS    +HHN Q  HFQRN  AG  
Sbjct: 286 YKSVESAKKALEEPHKNFEGHILHCQKAVDGPKHGKSQQQQQHHNVQKSHFQRNGNAG-- 343

Query: 352 GGAGPAAAGPGHLMAPSGPAIPP-------AAAQALNPALGQALLGTL------------ 392
           G +G    GP HLMA   PA PP       A A ALNPALGQAL   L            
Sbjct: 344 GYSGRNVPGPAHLMA---PAAPPGIGYQGAAGAPALNPALGQALTALLASQGAGLGLNLL 400

Query: 393 -----------GSAAGGTAPMQGTYGNQTNVSPSVIGGYAN----QGGYPNQQMPQGGAG 437
                      G   G  A MQG YGNQ ++SP VI GY N    QGGY +QQ+ Q  +G
Sbjct: 401 GSLGSAAAVNQGGVPGAAAGMQGAYGNQPSISPGVI-GYGNQGVMQGGYSSQQIGQTSSG 459

Query: 438 R---GQHAAGQYGAPYMGH 453
           R   G         PYMGH
Sbjct: 460 RGQHGGVGQYGGVGPYMGH 478

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|312281743|dbj|BAJ33737.1| unnamed protein product [Thellungiella halophila]

 Score =  451 bits (1159), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 244/402 (60%), Positives = 284/402 (70%), Gaps = 50/402 (12%)

Query: 83  DEEDDEPILSLLEPFSKDQLVNLLREAAENHRDVASRVRQVADEDPVHRKIFVHGLGWDT 142
           D +DDEPI  LLEPFSK+QL+NLL+EAA  H DVA+R+R+VADEDPVHRKIFVHGLGWDT
Sbjct: 97  DTDDDEPIKDLLEPFSKEQLLNLLKEAAGKHLDVANRIREVADEDPVHRKIFVHGLGWDT 156

Query: 143 KAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTA 202
           K ETLI+AFKQYGEIEDCKAV DKVSGKSKGYGFIL+K+RSGAR ALK+PQKKIG+RMTA
Sbjct: 157 KTETLIEAFKQYGEIEDCKAVFDKVSGKSKGYGFILYKSRSGARNALKQPQKKIGSRMTA 216

Query: 203 CQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQ 262
           CQLAS GP       + A      QH +            SE+TQ+KI+VSNVG+EL+PQ
Sbjct: 217 CQLASKGPVFGGNPVAAAASVVPAQHSN------------SEHTQKKIYVSNVGAELDPQ 264

Query: 263 KLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQR 322
           KLLAFFS++GEIEEGPLG+DK TG+PKGFCLFVYK+ ++AK+ALEEPHK FEGHIL+CQ+
Sbjct: 265 KLLAFFSRFGEIEEGPLGLDKFTGRPKGFCLFVYKSPESAKRALEEPHKTFEGHILHCQK 324

Query: 323 AIDGPKPGKSRH---HNAQNPHFQRNEGAGYVGGAGPAAAGPGHLMAPS-------GPAI 372
           AIDGPKPGK +    HN  NP FQRN+  GY      A  G GHLMA +         A+
Sbjct: 325 AIDGPKPGKPQQYNTHNHNNPRFQRNDNNGY-----GAPGGHGHLMAGNQAGMGAPAQAL 379

Query: 373 PPAAAQAL-------------NPALGQALLGTLGSAA----GGTAPMQGTYGNQTNVSPS 415
            PA  QAL             NPA+GQALLG+LG+A     G  A M   Y  Q  ++P 
Sbjct: 380 NPAIGQALTALLASQGAGLAFNPAIGQALLGSLGTATGVNPGAGAGMPSGYATQA-MAPG 438

Query: 416 VIGGYAN----QGGYPNQQMPQGGAGRGQHAAGQYGAPYMGH 453
            I GY      QGGY   Q  QGG+GRGQH   QY +PYMGH
Sbjct: 439 TIPGYGTQPGLQGGYQTPQPGQGGSGRGQHGVNQY-SPYMGH 479

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15226817|ref|NP_181639.1| RNA recognition motif-containing protein [Arabidopsis thaliana] gi|145331087|ref|NP_001078035.1| RNA recognition motif-containing protein [Arabidopsis thaliana] gi|16612302|gb|AAL27512.1|AF439844_1 At2g41060/T3K9.17 [Arabidopsis thaliana] gi|3402711|gb|AAD12005.1| putative RNA-binding protein [Arabidopsis thaliana] gi|22137136|gb|AAM91413.1| At2g41060/T3K9.17 [Arabidopsis thaliana] gi|110742573|dbj|BAE99200.1| putative RNA-binding protein [Arabidopsis thaliana] gi|330254826|gb|AEC09920.1| RNA recognition motif-containing protein [Arabidopsis thaliana] gi|330254827|gb|AEC09921.1| RNA recognition motif-containing protein [Arabidopsis thaliana]

 Score =  450 bits (1158), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 261/474 (55%), Positives = 316/474 (66%), Gaps = 46/474 (9%)

Query: 1   MAKKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEE 60
           M KKRK +S+++E +EP +KQ QQ   ++E+P   E    + + + +E+  E++  +E  
Sbjct: 1   MTKKRKLESESNETSEPTEKQQQQ--CEKEDP---EIRNVDNQRDDDEQVVEQDTLKEMH 55

Query: 61  EEEEEKADQKEDEEEEEKADQNDEEDDEPILS--LLEPFSKDQLVNLLREAAENHRDVAS 118
           EEE +  D  E E      +Q +E+DDE      LLEPFSKDQL+ LL+EAAE HRDVA+
Sbjct: 56  EEEAKGEDNIEAETSSGSGNQGNEDDDEEEPIEDLLEPFSKDQLLILLKEAAERHRDVAN 115

Query: 119 RVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFIL 178
           R+R VADED VHRKIFVHGLGWDTKA++LIDAFKQYGEIEDCK V DKVSG+SKGYGFIL
Sbjct: 116 RIRIVADEDLVHRKIFVHGLGWDTKADSLIDAFKQYGEIEDCKCVVDKVSGQSKGYGFIL 175

Query: 179 FKTRSGARKALKEPQKKIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQ 238
           FK+RSGAR ALK+PQKKIG RMTACQLASIGP     V + A H +              
Sbjct: 176 FKSRSGARNALKQPQKKIGTRMTACQLASIGPVQGNPVVAPAQHFN-------------- 221

Query: 239 HHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKT 298
                E  QRKI+VSNV ++++PQKLL FFS++GEIEEGPLG+DKATG+PKGF LFVY++
Sbjct: 222 ----PENVQRKIYVSNVSADIDPQKLLEFFSRFGEIEEGPLGLDKATGRPKGFALFVYRS 277

Query: 299 VDAAKKALEEPHKNFEGHILNCQRAIDGPKPGKSRHHN----AQNPHFQRNEGAGYV--G 352
           +++AKKALEEPHK FEGH+L+C +A DGPK  K   HN     QN  +QRN+  GY   G
Sbjct: 278 LESAKKALEEPHKTFEGHVLHCHKANDGPKQVKQHQHNHNSHNQNSRYQRNDNNGYGAPG 337

Query: 353 GAGPAAAGPGHLMAPSGPAIPPA---------AAQALNPALGQALLGTLGSAA-GGTAPM 402
           G G   AG    +    PAI  A         A   LN A GQALLGTLG+A+ G    M
Sbjct: 338 GHGHFIAGNNQAVQAFNPAIGQALTALLASQGAGLGLNQAFGQALLGTLGTASPGAVGGM 397

Query: 403 QGTYGNQTNVSPSVIGGYAN----QGGYPNQQMPQGGAGRGQHAAGQYGAPYMG 452
              YG Q N+SP V  GY      QGGY  QQ  QGGAGRGQH AG YG PYMG
Sbjct: 398 PSGYGTQANISPGVYPGYGAQAGYQGGYQTQQPGQGGAGRGQHGAG-YGGPYMG 450

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297824045|ref|XP_002879905.1| RNA recognition motif-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297325744|gb|EFH56164.1| RNA recognition motif-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  447 bits (1151), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 260/475 (54%), Positives = 315/475 (66%), Gaps = 53/475 (11%)

Query: 1   MAKKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEE 60
           MAKKRK +S+++E +EP +KQLQ E   +E+P       E   ++ + + +EE   E+  
Sbjct: 1   MAKKRKLESESNETSEPTEKQLQCE---KEDP-------EFRNDDKQRDHDEEVVGEDAL 50

Query: 61  EEEEEKADQKEDEEEEEKADQND--EEDDEPILSLLEPFSKDQLVNLLREAAENHRDVAS 118
           +EE +  D  E E     A++ +  ++++EPI  LLEPFSKDQL+ LL+EAAE H DVA+
Sbjct: 51  KEEAKGEDNTEAETSSGSANRGNGDDDEEEPIEDLLEPFSKDQLLILLKEAAERHSDVAN 110

Query: 119 RVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFIL 178
           R+R VADED VHRKIFVHGLGWDTKAETLI+AFKQYGEIEDCK V DK+SG+SKGYGFIL
Sbjct: 111 RIRIVADEDSVHRKIFVHGLGWDTKAETLIEAFKQYGEIEDCKCVVDKISGQSKGYGFIL 170

Query: 179 FKTRSGARKALKEPQKKIGNRMTACQLASIGPAT-TPAVASTATHQHQHQHQHQHQHQHQ 237
           FK+RSGAR ALK+PQKKIG RMTACQLASIGP   TP VA                    
Sbjct: 171 FKSRSGARNALKQPQKKIGTRMTACQLASIGPVQGTPVVAPA------------------ 212

Query: 238 QHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYK 297
             H   E  QRKI+VSNV ++L+PQKLL FFS++GEIEEGPLG+DK TG+PKGF LFVY+
Sbjct: 213 -QHFNPENVQRKIYVSNVSADLDPQKLLEFFSRFGEIEEGPLGLDKVTGRPKGFALFVYR 271

Query: 298 TVDAAKKALEEPHKNFEGHILNCQRAIDGPKPGKSRHHN----AQNPHFQRNEGAGYV-- 351
           ++++AKKALEEPHK FEGH+L+C +A DGPK  K   HN     QN  +QRN+  GY   
Sbjct: 272 SLESAKKALEEPHKTFEGHVLHCHKANDGPKQVKQHQHNHNSHNQNSRYQRNDSNGYGAP 331

Query: 352 GGAGPAAAGPGHLMAPSGPAIPPA---------AAQALNPALGQALLGTLGSAA-GGTAP 401
           GG G   AG         PAI  A         A   LN A GQALLGTLG+A+ G    
Sbjct: 332 GGHGHFIAGNNQAAQAFNPAIGQALTALLASQGAGLGLNQAFGQALLGTLGTASPGAVGG 391

Query: 402 MQGTYGNQTNVSPSVIGGYAN----QGGYPNQQMPQGGAGRGQHAAGQYGAPYMG 452
           M  +YG Q N++P V  GYA     QGGY  QQ  QG AGRGQH  G YG PYMG
Sbjct: 392 MPSSYGTQANITPGVYPGYAAQAGFQGGYQTQQPGQGSAGRGQHGVG-YGGPYMG 445

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	453
TAIR|locus:2103670	478	UBA2A "UBP1-associated protein	0.543	0.514	0.676	6.9e-96
TAIR|locus:2063177	451	AT2G41060 [Arabidopsis thalian	0.267	0.268	0.842	2.1e-95
TAIR|locus:2086325	404	AT3G15010 [Arabidopsis thalian	0.258	0.289	0.495	8.7e-49
TAIR|locus:2055956	347	UBA1A [Arabidopsis thaliana (t	0.258	0.337	0.564	1.8e-32
TAIR|locus:2047685	613	AT2G19380 [Arabidopsis thalian	0.260	0.192	0.516	4.9e-28
TAIR|locus:2055951	382	AT2G22100 [Arabidopsis thalian	0.251	0.298	0.517	2.8e-27
UNIPROTKB|F1NIB4	212	HNRNPAB "Uncharacterized prote	0.152	0.325	0.405	4.4e-23
UNIPROTKB|H0YA96	210	HNRNPD "Heterogeneous nuclear	0.152	0.328	0.362	8.6e-22
UNIPROTKB|F1NIB2	263	HNRNPAB "Uncharacterized prote	0.152	0.262	0.405	8.9e-20
ZFIN|ZDB-GENE-030131-185	366	hnrnpab "heterogeneous nuclear	0.150	0.185	0.441	1.8e-19

TAIR|locus:2103670 UBA2A "UBP1-associated protein 2A" [Arabidopsis thaliana (taxid:3702)]

 Score = 916 (327.5 bits), Expect = 6.9e-96, Sum P(2) = 6.9e-96
 Identities = 178/263 (67%), Positives = 209/263 (79%)

Query:    89 PILSLLEPFSKDQLVNLLREAAENHRDVASRVRQVADEDPVHRKIFVHGLGWDTKAETLI 148
             PI  LLEPFSK+Q+++LL+EAAE H DVA+R+R+VADEDPVHRKIFVHGLGWDTK ETLI
Sbjct:    98 PIQDLLEPFSKEQVLSLLKEAAEKHVDVANRIREVADEDPVHRKIFVHGLGWDTKTETLI 157

Query:   149 DAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASI 208
             +AFKQYGEIEDCKAV DK+SGKSKGYGFIL+K+RSGAR ALK+PQKKIG+RMTACQLAS 
Sbjct:   158 EAFKQYGEIEDCKAVFDKISGKSKGYGFILYKSRSGARNALKQPQKKIGSRMTACQLASK 217

Query:   209 GXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSEYTQRKIFVSNVGSELEPQKLLAFF 268
             G                                 SE+TQ+KI+VSNVG+EL+PQKLL FF
Sbjct:   218 GPVFGGAPIAAAAVSAPAQHSN------------SEHTQKKIYVSNVGAELDPQKLLMFF 265

Query:   269 SKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAIDGPK 328
             SK+GEIEEGPLG+DK TG+PKGFCLFVYK+ ++AK+ALEEPHK FEGHIL+CQ+AIDGPK
Sbjct:   266 SKFGEIEEGPLGLDKYTGRPKGFCLFVYKSSESAKRALEEPHKTFEGHILHCQKAIDGPK 325

Query:   329 PGKSR--HHNAQ---NPHFQRNE 346
             PGK +  HHN     NP +QRN+
Sbjct:   326 PGKQQQHHHNPHAYNNPRYQRND 348

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0017091 "AU-rich element binding" evidence=IDA

GO:0048255 "mRNA stabilization" evidence=NAS

GO:0009738 "abscisic acid mediated signaling pathway" evidence=TAS

GO:0006952 "defense response" evidence=IMP

GO:0008219 "cell death" evidence=IMP

GO:0009693 "ethylene biosynthetic process" evidence=IMP

GO:0010150 "leaf senescence" evidence=IMP

GO:0005829 "cytosol" evidence=IDA

TAIR|locus:2063177 AT2G41060 [Arabidopsis thaliana (taxid:3702)]

 Score = 528 (190.9 bits), Expect = 2.1e-95, Sum P(3) = 2.1e-95
 Identities = 102/121 (84%), Positives = 111/121 (91%)

Query:    89 PILSLLEPFSKDQLVNLLREAAENHRDVASRVRQVADEDPVHRKIFVHGLGWDTKAETLI 148
             PI  LLEPFSKDQL+ LL+EAAE HRDVA+R+R VADED VHRKIFVHGLGWDTKA++LI
Sbjct:    86 PIEDLLEPFSKDQLLILLKEAAERHRDVANRIRIVADEDLVHRKIFVHGLGWDTKADSLI 145

Query:   149 DAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASI 208
             DAFKQYGEIEDCK V DKVSG+SKGYGFILFK+RSGAR ALK+PQKKIG RMTACQLASI
Sbjct:   146 DAFKQYGEIEDCKCVVDKVSGQSKGYGFILFKSRSGARNALKQPQKKIGTRMTACQLASI 205

Query:   209 G 209
             G
Sbjct:   206 G 206

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0005634 "nucleus" evidence=IDA

GO:0006952 "defense response" evidence=IMP

GO:0008219 "cell death" evidence=IMP

GO:0009693 "ethylene biosynthetic process" evidence=IMP

GO:0010150 "leaf senescence" evidence=IMP

TAIR|locus:2086325 AT3G15010 [Arabidopsis thaliana (taxid:3702)]

 Score = 282 (104.3 bits), Expect = 8.7e-49, Sum P(2) = 8.7e-49
 Identities = 58/117 (49%), Positives = 74/117 (63%)

Query:    93 LLEPFSKDQLVNLLREAAENHRDVASRVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFK 152
             ++E F+ DQL++LL+EA   H DV   VR  AD D   RK+F+ GL  DT  E L   F 
Sbjct:    37 IIERFTTDQLLDLLQEAIVRHPDVLESVRLTADSDISQRKLFIRGLAADTTTEGLRSLFS 96

Query:   153 QYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASIG 209
              YG++E+   + DKV+GKSKGYGF+ F    GA  ALKEP KKI  R+T  QLA+ G
Sbjct:    97 SYGDLEEAIVILDKVTGKSKGYGFVTFMHVDGALLALKEPSKKIDGRVTVTQLAASG 153

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005730 "nucleolus" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0006952 "defense response" evidence=IMP

GO:0008219 "cell death" evidence=IMP

GO:0009693 "ethylene biosynthetic process" evidence=IMP

GO:0010150 "leaf senescence" evidence=IMP

GO:0005829 "cytosol" evidence=RCA

TAIR|locus:2055956 UBA1A [Arabidopsis thaliana (taxid:3702)]

 Score = 355 (130.0 bits), Expect = 1.8e-32, P = 1.8e-32
 Identities = 66/117 (56%), Positives = 88/117 (75%)

Query:    93 LLEPFSKDQLVNLLREAAENHRDVASRVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFK 152
             LL+P+SKDQLV+L+  A+     + S V + AD D  HRKIFV+GL W+T  ETL+  F+
Sbjct:    66 LLQPYSKDQLVDLVCSASRIGSSIYSAVVEAADRDVTHRKIFVYGLPWETTRETLVGVFE 125

Query:   153 QYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASIG 209
              YGEIE+C  V DK +GK+KG+GF++FKTR GA++ALKEP+K+I NR   CQLAS+G
Sbjct:   126 GYGEIEECTVVIDKATGKAKGFGFVMFKTRKGAKEALKEPKKRILNRTATCQLASMG 182

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0017091 "AU-rich element binding" evidence=IDA

GO:0048255 "mRNA stabilization" evidence=NAS

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

TAIR|locus:2047685 AT2G19380 [Arabidopsis thaliana (taxid:3702)]

 Score = 320 (117.7 bits), Expect = 4.9e-28, P = 4.9e-28
 Identities = 61/118 (51%), Positives = 80/118 (67%)

Query:    90 ILSLLEPFSKDQLVNLLREAAENHRDVASRVRQVADEDPVHRKIFVHGLGWDTKAETLID 149
             I  LL  +SK++LVNL+ + AE    + S + + AD D   R IFV G GWDT  E L  
Sbjct:   367 IKQLLVAYSKEELVNLIYKTAEKGSRLISAILESADRDIAQRNIFVRGFGWDTTQENLKT 426

Query:   150 AFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLAS 207
             AF+ YGEIE+C  V DK +G+ KGYGF++FKTR GAR+ALK P+K++ NR+  C LAS
Sbjct:   427 AFESYGEIEECSVVMDKDTGRGKGYGFVMFKTRKGAREALKRPEKRMYNRIVVCNLAS 484

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2055951 AT2G22100 [Arabidopsis thaliana (taxid:3702)]

 Score = 306 (112.8 bits), Expect = 2.8e-27, P = 2.8e-27
 Identities = 59/114 (51%), Positives = 79/114 (69%)

Query:    90 ILSLLEPFSKDQLVNLLREAAENHRDVASRVRQVADEDPVHRKIFVHGLGWDTKAETLID 149
             I +LLE +SK++L+NL+ + AE    + S V + AD D   R IFV GLGWDT  E L  
Sbjct:   122 IKNLLESYSKEELINLIYKTAEKGSKLISAVFESADRDSSQRNIFVRGLGWDTTHENLKA 181

Query:   150 AFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTAC 203
             AF+ YGEI +C  V DK +G++KG+GF+LFKTR GAR ALK P+K++ NR  +C
Sbjct:   182 AFEVYGEITECSVVMDKDTGRAKGFGFVLFKTRKGARAALKNPEKRMYNRTVSC 235

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

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

UNIPROTKB|F1NIB4 HNRNPAB "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 158 (60.7 bits), Expect = 4.4e-23, Sum P(2) = 4.4e-23
 Identities = 28/69 (40%), Positives = 43/69 (62%)

Query:   132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
             K+FV GL WDT  + L D F ++GE+ DC    D  +G+S+G+GFILFK      K L++
Sbjct:     1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKEPGSVEKVLEQ 60

Query:   192 PQKKIGNRM 200
              + ++  R+
Sbjct:    61 KEHRLDGRL 69

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|H0YA96 HNRNPD "Heterogeneous nuclear ribonucleoprotein D0" [Homo sapiens (taxid:9606)]

 Score = 156 (60.0 bits), Expect = 8.6e-22, Sum P(2) = 8.6e-22
 Identities = 25/69 (36%), Positives = 43/69 (62%)

Query:   132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
             K+F+ GL WDT  + L D F ++GE+ DC    D ++G+S+G+GF+LFK      K + +
Sbjct:     2 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 61

Query:   192 PQKKIGNRM 200
              + K+  ++
Sbjct:    62 KEHKLNGKV 70

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|F1NIB2 HNRNPAB "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 158 (60.7 bits), Expect = 8.9e-20, Sum P(2) = 8.9e-20
 Identities = 28/69 (40%), Positives = 43/69 (62%)

Query:   132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
             K+FV GL WDT  + L D F ++GE+ DC    D  +G+S+G+GFILFK      K L++
Sbjct:     1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKEPGSVEKVLEQ 60

Query:   192 PQKKIGNRM 200
              + ++  R+
Sbjct:    61 KEHRLDGRL 69

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

ZFIN|ZDB-GENE-030131-185 hnrnpab "heterogeneous nuclear ribonucleoprotein A/B" [Danio rerio (taxid:7955)]

 Score = 163 (62.4 bits), Expect = 1.8e-19, Sum P(3) = 1.8e-19
 Identities = 30/68 (44%), Positives = 43/68 (63%)

Query:   132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
             K+FV GL WDT  + L D F ++GE+ DC    D  +G+S+G+GFILFK  SG  K L +
Sbjct:    96 KMFVGGLSWDTSKKDLKDYFSKFGEVTDCTIKMDPNTGRSRGFGFILFKEPSGVDKVLAQ 155

Query:   192 PQKKIGNR 199
              + ++  R
Sbjct:   156 KEHRLDGR 163

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	453
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	4e-29
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-27
smart00360	73	smart00360, RRM, RNA recognition motif	2e-19
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	3e-16
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-14
smart00360	73	smart00360, RRM, RNA recognition motif	4e-14
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	4e-14
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	5e-14
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	6e-14
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	1e-13
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	1e-13
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-13
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	3e-13
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	4e-13
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	7e-13
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	9e-13
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	3e-12
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	4e-12
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	8e-12
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	1e-11
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-11
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-11
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-11
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	3e-11
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	4e-11
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	6e-11
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	8e-11
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	9e-11
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	1e-10
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-10
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	3e-10
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	3e-10
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	5e-10
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	5e-10
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	6e-10
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	6e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	8e-10
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	9e-10
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	9e-10
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-09
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	1e-09
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	1e-09
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-09
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-09
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	2e-09
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	3e-09
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	3e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-09
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	4e-09
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	5e-09
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	5e-09
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	6e-09
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	7e-09
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	1e-08
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	1e-08
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	1e-08
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-08
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-08
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-08
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	3e-08
pfam03344	715	pfam03344, Daxx, Daxx Family	3e-08
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	5e-08
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	5e-08
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	5e-08
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	5e-08
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	6e-08
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	7e-08
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	7e-08
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	8e-08
pfam07133	164	pfam07133, Merozoite_SPAM, Merozoite surface prote	8e-08
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	9e-08
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	9e-08
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	1e-07
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	1e-07
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	1e-07
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	1e-07
pfam03985	431	pfam03985, Paf1, Paf1	1e-07
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-07
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	2e-07
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	2e-07
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	2e-07
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	3e-07
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	3e-07
pfam04147	809	pfam04147, Nop14, Nop14-like family	3e-07
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	4e-07
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	4e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	5e-07
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	5e-07
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	6e-07
pfam11705	221	pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polym	6e-07
pfam03985	431	pfam03985, Paf1, Paf1	7e-07
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	8e-07
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	9e-07
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	1e-06
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	1e-06
pfam04147	809	pfam04147, Nop14, Nop14-like family	1e-06
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	1e-06
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	1e-06
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	1e-06
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	2e-06
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	2e-06
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	2e-06
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	2e-06
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	2e-06
COG5137	279	COG5137, COG5137, Histone chaperone involved in ge	2e-06
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	2e-06
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	2e-06
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	3e-06
COG5137	279	COG5137, COG5137, Histone chaperone involved in ge	3e-06
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	3e-06
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	3e-06
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	3e-06
PHA03089	191	PHA03089, PHA03089, late transcription factor VLTF	3e-06
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	3e-06
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	4e-06
pfam03985	431	pfam03985, Paf1, Paf1	4e-06
pfam04147	809	pfam04147, Nop14, Nop14-like family	4e-06
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	4e-06
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	4e-06
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	4e-06
pfam09756	189	pfam09756, DDRGK, DDRGK domain	4e-06
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	5e-06
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	5e-06
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	5e-06
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	5e-06
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	5e-06
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	5e-06
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	5e-06
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	5e-06
pfam00183	529	pfam00183, HSP90, Hsp90 protein	5e-06
pfam11705	221	pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polym	6e-06
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	6e-06
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	6e-06
pfam11081	172	pfam11081, DUF2890, Protein of unknown function (D	6e-06
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	6e-06
pfam05285	317	pfam05285, SDA1, SDA1	6e-06
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	7e-06
PRK12585	197	PRK12585, PRK12585, putative monovalent cation/H+	7e-06
pfam14153	185	pfam14153, Spore_coat_CotO, Spore coat protein Cot	7e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	8e-06
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	8e-06
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	8e-06
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	8e-06
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	8e-06
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	8e-06
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	9e-06
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	1e-05
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	1e-05
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-05
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	1e-05
pfam05285	317	pfam05285, SDA1, SDA1	1e-05
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-05
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	1e-05
PRK12329	449	PRK12329, nusA, transcription elongation factor Nu	1e-05
PRK12329	449	PRK12329, nusA, transcription elongation factor Nu	1e-05
PRK12329	449	PRK12329, nusA, transcription elongation factor Nu	1e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-05
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	1e-05
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-05
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	1e-05
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	1e-05
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	1e-05
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-05
pfam08553	794	pfam08553, VID27, VID27 cytoplasmic protein	1e-05
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-05
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	2e-05
pfam04147	809	pfam04147, Nop14, Nop14-like family	2e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-05
pfam14153	185	pfam14153, Spore_coat_CotO, Spore coat protein Cot	2e-05
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	2e-05
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-05
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	2e-05
pfam09184	285	pfam09184, PPP4R2, PPP4R2	2e-05
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	2e-05
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-05
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	3e-05
pfam09756	189	pfam09756, DDRGK, DDRGK domain	3e-05
pfam05285	317	pfam05285, SDA1, SDA1	3e-05
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	3e-05
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	3e-05
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	3e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	3e-05
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	3e-05
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	3e-05
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	3e-05
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	4e-05
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	4e-05
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	4e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	4e-05
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	4e-05
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	4e-05
pfam09747	178	pfam09747, DUF2052, Coiled-coil domain containing	4e-05
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	4e-05
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	4e-05
pfam04931	784	pfam04931, DNA_pol_phi, DNA polymerase phi	4e-05
cd12275	71	cd12275, RRM1_MEI2_EAR1_like, RNA recognition moti	4e-05
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	5e-05
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	5e-05
pfam04931	784	pfam04931, DNA_pol_phi, DNA polymerase phi	5e-05
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	5e-05
cd12303	86	cd12303, RRM_spSet1p_like, RNA recognition motif i	5e-05
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	5e-05
pfam02724	583	pfam02724, CDC45, CDC45-like protein	5e-05
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	5e-05
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	6e-05
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	6e-05
pfam04147	809	pfam04147, Nop14, Nop14-like family	6e-05
PRK12329	449	PRK12329, nusA, transcription elongation factor Nu	6e-05
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	6e-05
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	6e-05
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	6e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	6e-05
pfam09538	104	pfam09538, FYDLN_acid, Protein of unknown function	6e-05
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	6e-05
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	6e-05
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	6e-05
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	7e-05
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	7e-05
PRK12329	449	PRK12329, nusA, transcription elongation factor Nu	7e-05
PRK12329	449	PRK12329, nusA, transcription elongation factor Nu	7e-05
pfam09747	178	pfam09747, DUF2052, Coiled-coil domain containing	7e-05
pfam09538	104	pfam09538, FYDLN_acid, Protein of unknown function	7e-05
pfam05758	832	pfam05758, Ycf1, Ycf1	7e-05
pfam05758	832	pfam05758, Ycf1, Ycf1	7e-05
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	7e-05
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	8e-05
pfam00183	529	pfam00183, HSP90, Hsp90 protein	8e-05
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	8e-05
pfam00183	529	pfam00183, HSP90, Hsp90 protein	9e-05
PTZ00415	2849	PTZ00415, PTZ00415, transmission-blocking target a	9e-05
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	9e-05
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	9e-05
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	9e-05
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	1e-04
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	1e-04
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	1e-04
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-04
pfam00183	529	pfam00183, HSP90, Hsp90 protein	1e-04
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	1e-04
pfam14153	185	pfam14153, Spore_coat_CotO, Spore coat protein Cot	1e-04
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	1e-04
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-04
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-04
pfam02724	583	pfam02724, CDC45, CDC45-like protein	1e-04
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	1e-04
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	1e-04
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	1e-04
COG3343	175	COG3343, RpoE, DNA-directed RNA polymerase, delta	1e-04
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	1e-04
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	1e-04
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	1e-04
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	1e-04
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	1e-04
pfam12253	76	pfam12253, CAF1A, Chromatin assembly factor 1 subu	1e-04
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	1e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-04
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	2e-04
pfam03344	715	pfam03344, Daxx, Daxx Family	2e-04
pfam07133	164	pfam07133, Merozoite_SPAM, Merozoite surface prote	2e-04
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	2e-04
pfam11081	172	pfam11081, DUF2890, Protein of unknown function (D	2e-04
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	2e-04
pfam09538	104	pfam09538, FYDLN_acid, Protein of unknown function	2e-04
COG3343	175	COG3343, RpoE, DNA-directed RNA polymerase, delta	2e-04
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	2e-04
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-04
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	2e-04
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	2e-04
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	2e-04
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	2e-04
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	2e-04
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	2e-04
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	2e-04
TIGR02442	633	TIGR02442, Cob-chelat-sub, cobaltochelatase subuni	2e-04
TIGR02442	633	TIGR02442, Cob-chelat-sub, cobaltochelatase subuni	2e-04
pfam10446	449	pfam10446, DUF2457, Protein of unknown function (D	2e-04
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	2e-04
pfam03247	106	pfam03247, Prothymosin, Prothymosin/parathymosin f	2e-04
pfam03247	106	pfam03247, Prothymosin, Prothymosin/parathymosin f	2e-04
pfam11861	154	pfam11861, DUF3381, Domain of unknown function (DU	2e-04
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	2e-04
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	3e-04
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	3e-04
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-04
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	3e-04
pfam09184	285	pfam09184, PPP4R2, PPP4R2	3e-04
pfam04931	784	pfam04931, DNA_pol_phi, DNA polymerase phi	3e-04
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	3e-04
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	3e-04
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	3e-04
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	3e-04
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	3e-04
pfam09507	427	pfam09507, CDC27, DNA polymerase subunit Cdc27	3e-04
PTZ00438	374	PTZ00438, PTZ00438, gamete antigen 27/25-like prot	3e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-04
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	3e-04
COG5406	1001	COG5406, COG5406, Nucleosome binding factor SPN, S	3e-04
PRK02363	129	PRK02363, PRK02363, DNA-directed RNA polymerase su	3e-04
pfam04546	211	pfam04546, Sigma70_ner, Sigma-70, non-essential re	3e-04
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	3e-04
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	3e-04
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	3e-04
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	3e-04
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	3e-04
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	4e-04
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	4e-04
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	4e-04
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	4e-04
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	4e-04
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	4e-04
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	4e-04
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	4e-04
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	4e-04
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	4e-04
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	5e-04
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	5e-04
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	5e-04
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	5e-04
pfam10446	449	pfam10446, DUF2457, Protein of unknown function (D	5e-04
pfam11861	154	pfam11861, DUF3381, Domain of unknown function (DU	5e-04
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	5e-04
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	5e-04
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	5e-04
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	5e-04
pfam04177	335	pfam04177, TAP42, TAP42-like family	5e-04
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	6e-04
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	6e-04
pfam05285	317	pfam05285, SDA1, SDA1	6e-04
pfam05285	317	pfam05285, SDA1, SDA1	6e-04
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	6e-04
COG3343	175	COG3343, RpoE, DNA-directed RNA polymerase, delta	6e-04
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	6e-04
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	6e-04
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	6e-04
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	6e-04
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	6e-04
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	7e-04
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	7e-04
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	7e-04
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	7e-04
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	7e-04
pfam04546	211	pfam04546, Sigma70_ner, Sigma-70, non-essential re	7e-04
PLN03142	1033	PLN03142, PLN03142, Probable chromatin-remodeling	7e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	7e-04
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	8e-04
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	8e-04
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	8e-04
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	8e-04
pfam11861	154	pfam11861, DUF3381, Domain of unknown function (DU	8e-04
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	8e-04
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	8e-04
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	8e-04
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	8e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	8e-04
cd12302	110	cd12302, RRM_scSet1p_like, RNA recognition motif i	9e-04
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	0.001
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	0.001
pfam00183	529	pfam00183, HSP90, Hsp90 protein	0.001
pfam00183	529	pfam00183, HSP90, Hsp90 protein	0.001
pfam14153	185	pfam14153, Spore_coat_CotO, Spore coat protein Cot	0.001
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	0.001
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	0.001
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	0.001
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	0.001
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	0.001
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	0.001
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.001
COG5406	1001	COG5406, COG5406, Nucleosome binding factor SPN, S	0.001
COG5406	1001	COG5406, COG5406, Nucleosome binding factor SPN, S	0.001
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	0.001
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	0.001
PLN03142	1033	PLN03142, PLN03142, Probable chromatin-remodeling	0.001
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	0.001
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	0.001
COG0576	193	COG0576, GrpE, Molecular chaperone GrpE (heat shoc	0.001
COG0576	193	COG0576, GrpE, Molecular chaperone GrpE (heat shoc	0.001
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	0.001
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	0.001
PLN02372	455	PLN02372, PLN02372, violaxanthin de-epoxidase	0.001
PRK06007	542	PRK06007, fliF, flagellar MS-ring protein; Reviewe	0.001
pfam03896	281	pfam03896, TRAP_alpha, Translocon-associated prote	0.001
pfam09805	134	pfam09805, Nop25, Nucleolar protein 12 (25kDa)	0.001
COG5167	776	COG5167, VID27, Protein involved in vacuole import	0.001
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	0.001
PRK14156	177	PRK14156, PRK14156, heat shock protein GrpE; Provi	0.001
COG5117	657	COG5117, NOC3, Protein involved in the nuclear exp	0.001
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	0.001
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	0.002
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	0.002
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	0.002
pfam03344	715	pfam03344, Daxx, Daxx Family	0.002
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	0.002
COG5137	279	COG5137, COG5137, Histone chaperone involved in ge	0.002
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	0.002
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	0.002
pfam00183	529	pfam00183, HSP90, Hsp90 protein	0.002
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	0.002
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	0.002
pfam08553	794	pfam08553, VID27, VID27 cytoplasmic protein	0.002
pfam09184	285	pfam09184, PPP4R2, PPP4R2	0.002
pfam04931	784	pfam04931, DNA_pol_phi, DNA polymerase phi	0.002
pfam02724	583	pfam02724, CDC45, CDC45-like protein	0.002
pfam05758	832	pfam05758, Ycf1, Ycf1	0.002
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	0.002
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	0.002
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	0.002
pfam10446	449	pfam10446, DUF2457, Protein of unknown function (D	0.002
pfam10446	449	pfam10446, DUF2457, Protein of unknown function (D	0.002
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	0.002
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	0.002
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	0.002
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	0.002
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	0.002
COG5167	776	COG5167, VID27, Protein involved in vacuole import	0.002
pfam04156	186	pfam04156, IncA, IncA protein	0.002
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	0.002
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	0.002
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	0.002
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	0.002
pfam02029	431	pfam02029, Caldesmon, Caldesmon	0.002
cd02988	192	cd02988, Phd_like_VIAF, Phosducin (Phd)-like famil	0.002
COG1667	254	COG1667, COG1667, Uncharacterized protein conserve	0.002
pfam04889	241	pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle cont	0.002
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	0.002
pfam06213	282	pfam06213, CobT, Cobalamin biosynthesis protein Co	0.002
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	0.002
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	0.002
cd12535	86	cd12535, RRM_FUS_TAF15, RNA recognition motif in v	0.002
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	0.002
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	0.002
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	0.002
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	0.002
pfam11831	363	pfam11831, Myb_Cef, pre-mRNA splicing factor compo	0.002
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	0.002
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	0.002
TIGR01651	600	TIGR01651, CobT, cobaltochelatase, CobT subunit	0.002
PRK12298	390	PRK12298, obgE, GTPase CgtA; Reviewed	0.002
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	0.003
pfam03985	431	pfam03985, Paf1, Paf1	0.003
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	0.003
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	0.003
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	0.003
pfam11861	154	pfam11861, DUF3381, Domain of unknown function (DU	0.003
PTZ00438	374	PTZ00438, PTZ00438, gamete antigen 27/25-like prot	0.003
PRK02363	129	PRK02363, PRK02363, DNA-directed RNA polymerase su	0.003
PRK02363	129	PRK02363, PRK02363, DNA-directed RNA polymerase su	0.003
pfam04546	211	pfam04546, Sigma70_ner, Sigma-70, non-essential re	0.003
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	0.003
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	0.003
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	0.003
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	0.003
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.003
PRK09202	470	PRK09202, nusA, transcription elongation factor Nu	0.003
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	0.003
PTZ00423	193	PTZ00423, PTZ00423, glideosome-associated protein	0.003
pfam07222	243	pfam07222, PBP_sp32, Proacrosin binding protein sp	0.003
PRK04019	330	PRK04019, rplP0, acidic ribosomal protein P0; Vali	0.003
pfam05340	565	pfam05340, DUF740, Protein of unknown function (DU	0.003
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	0.003
pfam01496	707	pfam01496, V_ATPase_I, V-type ATPase 116kDa subuni	0.003
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	0.004
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	0.004
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	0.004
COG5137	279	COG5137, COG5137, Histone chaperone involved in ge	0.004
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	0.004
pfam09184	285	pfam09184, PPP4R2, PPP4R2	0.004
pfam09184	285	pfam09184, PPP4R2, PPP4R2	0.004
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	0.004
pfam10446	449	pfam10446, DUF2457, Protein of unknown function (D	0.004
pfam10446	449	pfam10446, DUF2457, Protein of unknown function (D	0.004
pfam09507	427	pfam09507, CDC27, DNA polymerase subunit Cdc27	0.004
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.004
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	0.004
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	0.004
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	0.004
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	0.004
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	0.004
PLN03142	1033	PLN03142, PLN03142, Probable chromatin-remodeling	0.004
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	0.004
pfam09805	134	pfam09805, Nop25, Nucleolar protein 12 (25kDa)	0.004
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	0.004
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	0.004
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	0.004
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.004
pfam08597	242	pfam08597, eIF3_subunit, Translation initiation fa	0.004
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	0.004
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	0.004
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	0.004
pfam03286	198	pfam03286, Pox_Ag35, Pox virus Ag35 surface protei	0.004
COG5414	392	COG5414, COG5414, TATA-binding protein-associated	0.004
pfam14283	213	pfam14283, DUF4366, Domain of unknown function (DU	0.004
PLN00152	130	PLN00152, PLN00152, DNA-directed RNA polymerase; P	0.004
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	0.004
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	0.004

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

 Score =  108 bits (272), Expect = 4e-29
 Identities = 24/76 (31%), Positives = 41/76 (53%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
            KIFV  +        L  +FS++GEIEE  +  D+ TGK +G+    +K  ++A++A +
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 308 EPHKNFEGHILNCQRA 323
           +P+   +G   N   A
Sbjct: 61  DPNPIIDGRKANVNLA 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|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score =  104 bits (262), Expect = 1e-27
 Identities = 32/76 (42%), Positives = 45/76 (59%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
            KIFV GL + T  ++L   F Q+GEIE+   + D+ +GKS+GYGF+ FK +  A +A K
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 191 EPQKKIGNRMTACQLA 206
           +P   I  R     LA
Sbjct: 61  DPNPIIDGRKANVNLA 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|214636 smart00360, RRM, RNA recognition motif

 Score = 81.9 bits (203), Expect = 2e-19
 Identities = 26/70 (37%), Positives = 41/70 (58%), Gaps = 1/70 (1%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
            +FV  L  DT  E L + F ++G++E  + V DK +GKSKG+ F+ F++   A KAL+ 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 192 -PQKKIGNRM 200
              K++  R 
Sbjct: 61  LNGKELDGRP 70

Length = 73

>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 = 73.0 bits (180), Expect = 3e-16
 Identities = 25/68 (36%), Positives = 39/68 (57%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           +F+ GL WDT  E+L + F +YGE+ DC  + D ++G+S+G+GF+ F   S   K L   
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 193 QKKIGNRM 200
              +  R 
Sbjct: 61  PHVLDGRE 68

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

 Score = 67.3 bits (165), Expect = 3e-14
 Identities = 28/68 (41%), Positives = 40/68 (58%), Gaps = 2/68 (2%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           +FV  L  DT  E L + F ++GEIE  + V DK  GKSKG+ F+ F++   A KAL+  
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 193 Q-KKIGNR 199
             K++  R
Sbjct: 60  NGKELDGR 67

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|214636 smart00360, RRM, RNA recognition motif

 Score = 66.8 bits (164), Expect = 4e-14
 Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
            +FV N+  +   ++L   FSK+G++E   L  DK TGK KGF    +++ + A+KALE 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 309 PH-KNFEGHILNC 320
            + K  +G  L  
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 66.9 bits (163), Expect = 4e-14
 Identities = 29/69 (42%), Positives = 44/69 (63%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K+FV GL WDT  + L D F ++GE+ DC    D  +G+S+G+GFILFK  S   K L++
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60

Query: 192 PQKKIGNRM 200
            + ++  R+
Sbjct: 61  KEHRLDGRL 69

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|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

 Score = 66.9 bits (164), Expect = 5e-14
 Identities = 31/74 (41%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGAR 186
                +IFV  LG +   E L  AF +Y   +  K V DK +GKSKGYGF+ F   +   
Sbjct: 3   PENDFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYL 62

Query: 187 KALKEPQKK-IGNR 199
           KA+KE   K +GNR
Sbjct: 63  KAMKEMNGKYVGNR 76

This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

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

 Score = 66.1 bits (162), Expect = 6e-14
 Identities = 27/68 (39%), Positives = 40/68 (58%), Gaps = 2/68 (2%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE- 191
           +FV  L  DT  E L D F ++G IE  + V D+ +G+SKG+ F+ F+    A KAL+  
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 192 PQKKIGNR 199
             K++G R
Sbjct: 60  NGKELGGR 67

(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|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 65.7 bits (160), Expect = 1e-13
 Identities = 27/68 (39%), Positives = 43/68 (63%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           +FV GL WDT  + L + F ++GE+ DC    D V+G+S+G+GF+LFK  +   K L + 
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 193 QKKIGNRM 200
           + K+  R+
Sbjct: 61  EHKLDGRV 68

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

 Score = 65.6 bits (160), Expect = 1e-13
 Identities = 26/58 (44%), Positives = 36/58 (62%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           K+FV GL W+T  ETL   F QYGE+ DC  + DK + +S+G+GF+ FK  +     L
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVL 58

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

 Score = 71.8 bits (176), Expect = 2e-13
 Identities = 50/207 (24%), Positives = 84/207 (40%), Gaps = 38/207 (18%)

Query: 127 DPVHRK-----IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKT 181
           DP  R+     IFV  L      + L D F ++G I  CK   D  +GKS+GYGF+ F+ 
Sbjct: 80  DPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEK 138

Query: 182 RSGARKALKEPQKKIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQ 241
              A+ A+++                        V     +  +       +   ++   
Sbjct: 139 EESAKAAIQK------------------------VNGMLLNDKEVYVGRFIKKHEREAAP 174

Query: 242 QSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDA 301
             ++T   ++V N+   +   KL   F+K+GEI    +  D + G+ +GF    ++  + 
Sbjct: 175 LKKFTN--LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGS-GRSRGFAFVNFEKHED 231

Query: 302 AKKALEEPH-----KNFEGHILNCQRA 323
           A KA+EE +        EG  L   RA
Sbjct: 232 AAKAVEEMNGKKIGLAKEGKKLYVGRA 258

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

 Score = 64.2 bits (156), Expect = 3e-13
 Identities = 24/68 (35%), Positives = 42/68 (61%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           +F+ GL WDT  + L D F ++GE+ DC    D ++G+S+G+GF+LFK      K + + 
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 193 QKKIGNRM 200
           + K+  ++
Sbjct: 61  EHKLNGKV 68

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

 Score = 64.6 bits (158), Expect = 4e-13
 Identities = 25/70 (35%), Positives = 39/70 (55%), Gaps = 1/70 (1%)

Query: 127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGAR 186
           DP +  +FV  L   T  ETL + F +YG+I   + V D V+G SKGY F+ ++    A 
Sbjct: 1   DP-YLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDAL 59

Query: 187 KALKEPQKKI 196
           +A ++  K +
Sbjct: 60  RAYRDAHKLV 69

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

 Score = 63.5 bits (154), Expect = 7e-13
 Identities = 25/69 (36%), Positives = 43/69 (62%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K+F+ GL WDT  + L +   ++GE+ DC    D V+G+S+G+GF+LFK  +   K L+ 
Sbjct: 1   KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60

Query: 192 PQKKIGNRM 200
            + K+  ++
Sbjct: 61  KEHKLDGKL 69

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

 Score = 68.4 bits (166), Expect = 9e-13
 Identities = 36/159 (22%), Positives = 67/159 (42%), Gaps = 2/159 (1%)

Query: 34  EEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDEPILSL 93
           E+ E  +  E   +EE    EE   +E   E  + + E E       +    + +     
Sbjct: 19  EDIESGKLTELLLKEEYGGLEEANSKELNLEVNSRKIESEISPPSKKRLLSSERKEENER 78

Query: 94  LEPFSKD-QLVNLLREAAENHRDVASRVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFK 152
                 D +         E  R   S   +   ++  +  +FV  L +D   E L + FK
Sbjct: 79  EMEEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNT-LFVGNLPYDVTEEDLRELFK 137

Query: 153 QYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           ++G ++  + V D+ +GKS+G+ F+ F++   A KA++E
Sbjct: 138 KFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEE 176

Length = 306

>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 = 3e-12
 Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
            + V GL W T  + L D F  +GE+   +   D  +G+SKG+GF+ F       K L +
Sbjct: 1   DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ 60

Query: 192 PQKKIGNRMTACQLA 206
            +  I  R    ++ 
Sbjct: 61  -RHMIDGRWCDVKIP 74

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

 Score = 61.4 bits (150), Expect = 4e-12
 Identities = 24/67 (35%), Positives = 38/67 (56%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           +FV  L +D + E L   F+  G++E  + V D+ +G  KG+G++LFKT+     ALK  
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLN 61

Query: 193 QKKIGNR 199
             K+  R
Sbjct: 62  GIKLKGR 68

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

 Score = 60.4 bits (147), Expect = 8e-12
 Identities = 25/73 (34%), Positives = 40/73 (54%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K+FV  L W   ++ L + F Q+G+++ C    DK +G SKGYGF+ F +R G   AL++
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 192 PQKKIGNRMTACQ 204
            +  +       Q
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|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 60.1 bits (146), Expect = 1e-11
 Identities = 28/68 (41%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           IFV  L  +   ETL  AF  +GEI D + V D  +GKSKGYGF+ F  +  A  A++  
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 193 QKK-IGNR 199
             + +G R
Sbjct: 62  NGQWLGGR 69

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

 Score = 59.9 bits (146), Expect = 1e-11
 Identities = 18/60 (30%), Positives = 36/60 (60%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
            ++V  L ++   E L D F Q+GE+   + + D+ +G+S+G+GF+  +T   A  A+++
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

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

 Score = 65.2 bits (159), Expect = 2e-11
 Identities = 42/195 (21%), Positives = 80/195 (41%), Gaps = 15/195 (7%)

Query: 118 SRVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFI 177
            +  + A        ++V  L      + L + F ++GEI     V    SG+S+G+ F+
Sbjct: 166 KKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAA-VMKDGSGRSRGFAFV 224

Query: 178 LFKTRSGARKALKEPQKKIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQ 237
            F+    A KA++E   K            IG A           Q + + + + + + +
Sbjct: 225 NFEKHEDAAKAVEEMNGK-----------KIGLAKEGKKLYVGRAQKRAEREAELRRKFE 273

Query: 238 QHHQQ--SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFV 295
           +  Q+   +     ++V N+   +  +KL   FS+ GEI    + +D   G  +GF    
Sbjct: 274 ELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVC 332

Query: 296 YKTVDAAKKALEEPH 310
           +   + A +A+ E H
Sbjct: 333 FSNPEEANRAVTEMH 347

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

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

 Score = 59.1 bits (144), Expect = 3e-11
 Identities = 24/61 (39%), Positives = 38/61 (62%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           R +F+  L +D   E L + F Q+GE++  + V DK++G SKG  F+ FKT+  A+K L+
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

Query: 191 E 191
            
Sbjct: 61  A 61

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

 Score = 58.7 bits (142), Expect = 3e-11
 Identities = 20/48 (41%), Positives = 34/48 (70%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFK 180
           +F+ GL W+T  ++L + F Q+GE+ DC  + D  +G+S+G+GF+ FK
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFK 48

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 58.0 bits (141), Expect = 4e-11
 Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 2/70 (2%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE- 308
           +FV N+  +   + L   FSK+G IE   + +   TG+ KGF    ++  + A+KALE  
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRI-VRDETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 309 PHKNFEGHIL 318
             K   G  L
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|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 57.8 bits (140), Expect = 6e-11
 Identities = 19/76 (25%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
            +FV  L W    E L   F+++G +   + + D+ +G+S+G+G++ F++   A+KA++ 
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 192 PQ-KKIGNRMTACQLA 206
              K++  R      +
Sbjct: 61  MDGKELDGRPINVDFS 76

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

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

 Score = 57.8 bits (140), Expect = 8e-11
 Identities = 23/68 (33%), Positives = 40/68 (58%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K+F+ GL ++T  ++L + F Q+GEI DC  + D  + +S+G+GF+ F + S    A+  
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

Query: 192 PQKKIGNR 199
              K+  R
Sbjct: 61  RPHKVDGR 68

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

 Score = 57.4 bits (139), Expect = 9e-11
 Identities = 25/75 (33%), Positives = 38/75 (50%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           KIFV  +  E   +K+  +F K+G I E  L +DK T K +GFC   + + +  KK LE 
Sbjct: 1   KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60

Query: 309 PHKNFEGHILNCQRA 323
                 G  +  ++A
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|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 57.3 bits (139), Expect = 1e-10
 Identities = 30/80 (37%), Positives = 44/80 (55%), Gaps = 6/80 (7%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           +IFV G+  DT  E L D F ++G ++D K + D+ +G SKGYGF+ F+T+  A K L  
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKILAM 62

Query: 192 PQKKIGNRMTACQLASIGPA 211
                  +       +IGPA
Sbjct: 63  GNLNFRGKKL-----NIGPA 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|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 59.3 bits (143), Expect = 1e-10
 Identities = 28/85 (32%), Positives = 46/85 (54%), Gaps = 1/85 (1%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K+F+ GL W T   +L DAF  +G++ D K + D+ +G+S+G+GF+ F     A  A+ E
Sbjct: 36  KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95

Query: 192 PQ-KKIGNRMTACQLASIGPATTPA 215
              K++  R      A+  P+   A
Sbjct: 96  MDGKELNGRHIRVNPANDRPSAPRA 120

Length = 144

>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 = 55.8 bits (135), Expect = 3e-10
 Identities = 22/68 (32%), Positives = 36/68 (52%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           KIFV GL  +T  E + + F ++G I + +   DK + K +G+ FI F +    +K L+ 
Sbjct: 1   KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60

Query: 192 PQKKIGNR 199
               IG +
Sbjct: 61  QFHVIGGK 68

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

 Score = 56.2 bits (135), Expect = 3e-10
 Identities = 23/75 (30%), Positives = 44/75 (58%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K+F+ GL W T  ++L D F ++GEI +C  + D  + +S+G+GF+ F   +   K L +
Sbjct: 1   KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60

Query: 192 PQKKIGNRMTACQLA 206
           P  ++ ++    ++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|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 = 55.6 bits (134), Expect = 5e-10
 Identities = 20/58 (34%), Positives = 37/58 (63%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           K+F+ GL +DT  ++L   F +YG+I +   V D+ + +S+G+GF+ F+    A+ A+
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAM 59

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

 Score = 55.4 bits (133), Expect = 5e-10
 Identities = 22/68 (32%), Positives = 44/68 (64%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K+F+ GL W T  E L + F Q+GE+++C  + D ++ +S+G+GF+ F  ++G  K L +
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 192 PQKKIGNR 199
            + ++ ++
Sbjct: 62  SRHELDSK 69

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

 Score = 55.0 bits (133), Expect = 6e-10
 Identities = 22/58 (37%), Positives = 31/58 (53%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           K+FV GL  D   E L + F QYG +E  + V DK +GK +G+ F+ F       K +
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIV 58

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

 Score = 55.2 bits (133), Expect = 6e-10
 Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           IFV  L  +    TL  AF  +    D + + D  SG+S+GYGF+ F+++  A  A+ E 
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 193 QKK-IGNRMTAC 203
             K +G+R   C
Sbjct: 62  NGKWLGSRPIRC 73

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 54.5 bits (132), Expect = 8e-10
 Identities = 18/69 (26%), Positives = 32/69 (46%), Gaps = 3/69 (4%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           ++V  L      E L + F  YG++E  + V +K   + +G+ F+ F +   A  ALK+ 
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKL 58

Query: 193 QKK-IGNRM 200
               +  R 
Sbjct: 59  NGLVLDGRT 67

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

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

 Score = 59.6 bits (143), Expect = 9e-10
 Identities = 29/107 (27%), Positives = 53/107 (49%), Gaps = 1/107 (0%)

Query: 235 QHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLF 294
           +  +  Q+S+     +FV N+  ++  + L   F K+G ++   L  D+ TGK +GF   
Sbjct: 103 ESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFV 162

Query: 295 VYKTVDAAKKALEE-PHKNFEGHILNCQRAIDGPKPGKSRHHNAQNP 340
            +++ ++A+KA+EE   K  EG  L  Q+A    +P     +N    
Sbjct: 163 EFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDAS 209

Length = 306

>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 = 54.5 bits (132), Expect = 9e-10
 Identities = 25/77 (32%), Positives = 45/77 (58%), Gaps = 1/77 (1%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           K+FVS + +    ++L A FSK+G +EE  L  D  TG+ +GF    +++V+ A  A+ +
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 309 PH-KNFEGHILNCQRAI 324
            + K  EG ++  ++A 
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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 59.9 bits (145), Expect = 1e-09
 Identities = 47/194 (24%), Positives = 78/194 (40%), Gaps = 20/194 (10%)

Query: 114 RDVASRVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKG 173
           R   +    + + +   R +FV  L    +   L + F + G++ D + + D+ S +SKG
Sbjct: 73  RSGRNTKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKG 132

Query: 174 YGFILFKTRSGARKALKEPQKKIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQ 233
             ++ F       KAL    + +  R    Q +    A     A  ATHQ          
Sbjct: 133 VAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQ---AEKNRAAKAATHQ---------- 179

Query: 234 HQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCL 293
                          K++V N+   +  Q+L   F  +G+IE+  L  D  TG+ KGF  
Sbjct: 180 ---PGDIPNF----LKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGF 232

Query: 294 FVYKTVDAAKKALE 307
             +   + AK+ALE
Sbjct: 233 IQFHDAEEAKEALE 246

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

 Score = 54.6 bits (132), Expect = 1e-09
 Identities = 26/70 (37%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           + +FV  L +DT    L   F++YG I+  + V DK +GK +GY FI F+     + A K
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61

Query: 191 EPQ-KKIGNR 199
               KKI  R
Sbjct: 62  YADGKKIDGR 71

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

 Score = 54.0 bits (130), Expect = 1e-09
 Identities = 24/69 (34%), Positives = 39/69 (56%), Gaps = 5/69 (7%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           +F+ GL W T AE L + F ++GEI++C  + D  + +S+G+GF+ F   +   K L + 
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60

Query: 193 -----QKKI 196
                 KKI
Sbjct: 61  PHELDGKKI 69

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

 Score = 53.5 bits (129), Expect = 2e-09
 Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 8/76 (10%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGID---KATGKPKGFCLFVYKTVDAAKKAL 306
           +FV N+  +   + L   FSK+GEIE     +       GK KGF    +++ + A+KAL
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIES----VRIVRDKDGKSKGFAFVEFESPEDAEKAL 56

Query: 307 EEPH-KNFEGHILNCQ 321
           E  + K  +G  L   
Sbjct: 57  EALNGKELDGRKLKVS 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|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 20/59 (33%), Positives = 34/59 (57%)

Query: 135 VHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ 193
           V GL   T    L + F +YG IE  + V D+ +G+S+G+GF+ F++   A++A +   
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLN 62

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

 Score = 53.5 bits (128), Expect = 2e-09
 Identities = 25/76 (32%), Positives = 43/76 (56%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           +KIFV GL  +T  E +   F+Q+G++ED   + DK + + +G+GF+ F+      K  +
Sbjct: 4   KKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCE 63

Query: 191 EPQKKIGNRMTACQLA 206
               +I N+M  C+ A
Sbjct: 64  IHFHEINNKMVECKKA 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|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 53.4 bits (129), Expect = 3e-09
 Identities = 20/64 (31%), Positives = 37/64 (57%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K+FV GL   T  + L   F ++G +E+   + D  +G+S+G+GF+ F++   A  A+++
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 192 PQKK 195
              K
Sbjct: 63  LNGK 66

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

 Score = 53.1 bits (128), Expect = 3e-09
 Identities = 21/68 (30%), Positives = 37/68 (54%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           KIFV GL  D   E   + F Q+G++ D + + D  +G+S+G+GF+ F + S   +    
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60

Query: 192 PQKKIGNR 199
              ++G +
Sbjct: 61  GMLELGGK 68

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|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 = 52.7 bits (127), Expect = 4e-09
 Identities = 22/65 (33%), Positives = 33/65 (50%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           ++FV  L + T  E L + F+ +GEI +     DK + +SKG+ F+ F     A KA  E
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 192 PQKKI 196
               I
Sbjct: 61  LDGSI 65

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

 Score = 52.8 bits (127), Expect = 4e-09
 Identities = 24/65 (36%), Positives = 36/65 (55%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           ++FV  L +  K + L   F ++GE+ +     DK SGKSKG+ ++LF     A KA KE
Sbjct: 4   RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

Query: 192 PQKKI 196
              K+
Sbjct: 64  LDGKV 68

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

 Score = 52.6 bits (127), Expect = 5e-09
 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDC---KAVCDKVSGKSKGYGFILFKTRSGARK 187
           R+I+V  L +    + L   F ++GE+E     K   +K    + G+ F+ FK  S A  
Sbjct: 1   REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60

Query: 188 ALKEPQKKIGNR 199
           AL+    ++G R
Sbjct: 61  ALQLNGTELGGR 72

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

 Score = 52.3 bits (126), Expect = 5e-09
 Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 2/76 (2%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           ++ V  L +      L   F  +G + +   +  K  GK KG+ F+ F +++ A KA+K 
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWEVT-IPRKPDGKKKGFAFVQFTSKADAEKAIKG 59

Query: 192 PQ-KKIGNRMTACQLA 206
              KKI  R  A   A
Sbjct: 60  VNGKKIKGRPVAVDWA 75

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

 Score = 52.3 bits (126), Expect = 6e-09
 Identities = 17/40 (42%), Positives = 27/40 (67%)

Query: 151 FKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           F+  G IE CK V D+++G+S GYGF+ +   + A+KA+ 
Sbjct: 21  FEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

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

 Score = 52.2 bits (126), Expect = 7e-09
 Identities = 22/62 (35%), Positives = 37/62 (59%), Gaps = 2/62 (3%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFV-YKTVDAAKKAL 306
           R +F+ N+  +   ++L   FS++GE++   +  DK TG  KG   FV +KT ++A+K L
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKG-TAFVKFKTKESAQKCL 59

Query: 307 EE 308
           E 
Sbjct: 60  EA 61

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

 Score = 51.6 bits (124), Expect = 1e-08
 Identities = 28/74 (37%), Positives = 41/74 (55%), Gaps = 4/74 (5%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           ++FV N+    +   L   FSK+GE+ E  + IDK +GK KGF   ++   + A KA +E
Sbjct: 4   RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

Query: 309 -PHKNFEG---HIL 318
              K F+G   HIL
Sbjct: 64  LDGKVFQGRLIHIL 77

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|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 21/60 (35%), Positives = 34/60 (56%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
             +++ GL  +T  E L    + +G+I   KA+ DK + K KGYGF+ F +   A KA++
Sbjct: 1   TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60

This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 71

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 56.9 bits (137), Expect = 1e-08
 Identities = 34/92 (36%), Positives = 54/92 (58%), Gaps = 7/92 (7%)

Query: 8   DSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKA 67
            S+T       + +  ++    E   E ++ E+ V+  G  +G + EEEEEEEEEEEE+ 
Sbjct: 818 QSETQADDTEVKDETGEQELNAENQGEAKQDEKGVDGGGGSDGGDSEEEEEEEEEEEEEE 877

Query: 68  DQKEDEEEEEKADQNDEEDDEPILSLLEPFSK 99
           +++E+EEEEE      EE++EP LSL  P ++
Sbjct: 878 EEEEEEEEEE------EENEEP-LSLEWPETR 902

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

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

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 24/63 (38%), Positives = 37/63 (58%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           +FV  L +DT  E L + F + G I+ C  V DK S K +G+G++ F     A++AL+E 
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 193 QKK 195
           +K 
Sbjct: 62  KKT 64

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|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 5/66 (7%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDC-----KAVCDKVSGKSKGYGFILFKTRSGARK 187
           +FV  L + T  ETL   F++ G +        K         S GYGF+ FK++  A+K
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 188 ALKEPQ 193
           ALK  Q
Sbjct: 63  ALKRLQ 68

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|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I polyadenylate-binding proteins

 Score = 50.6 bits (122), Expect = 2e-08
 Identities = 26/70 (37%), Positives = 37/70 (52%), Gaps = 6/70 (8%)

Query: 133 IFVHGL--GWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL- 189
           IF+  L    D KA  L D F  +G I  CK   D+ +G SKGYGF+ F+T   A +A+ 
Sbjct: 5   IFIKNLDKSIDNKA--LYDTFSAFGNILSCKVATDE-NGGSKGYGFVHFETEEAAVRAIE 61

Query: 190 KEPQKKIGNR 199
           K     + ++
Sbjct: 62  KVNGMLLNDK 71

This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 77

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

 Score = 50.4 bits (120), Expect = 3e-08
 Identities = 23/73 (31%), Positives = 42/73 (57%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           KIFV GL  +T  E +   F+Q+G+++D   + DK + + +G+GF+ F++     K  + 
Sbjct: 1   KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 192 PQKKIGNRMTACQ 204
              +I N+M  C+
Sbjct: 61  HFHEINNKMVECK 73

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|217503 pfam03344, Daxx, Daxx Family

 Score = 55.7 bits (134), Expect = 3e-08
 Identities = 34/79 (43%), Positives = 43/79 (54%), Gaps = 4/79 (5%)

Query: 11  TSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQK 70
           +S   E P    Q+   ++      EE EEE EEE EEE E EEEE E+EEEEEE     
Sbjct: 425 SSTSGESPSMASQESEEEESV----EEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADN 480

Query: 71  EDEEEEEKADQNDEEDDEP 89
             EEE E + + D + +EP
Sbjct: 481 GSEEEMEGSSEGDGDGEEP 499

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

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

 Score = 49.7 bits (119), Expect = 5e-08
 Identities = 23/74 (31%), Positives = 41/74 (55%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           KIFV GL  +T  + +   F Q+G++ED   + DK + + +G+GF+ F++     K  + 
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60

Query: 192 PQKKIGNRMTACQL 205
              +I N+M  C+ 
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|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 49.7 bits (118), Expect = 5e-08
 Identities = 22/70 (31%), Positives = 41/70 (58%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           RK+F+ GL ++T  E+L + ++Q+G++ DC  + D  S +S+G+GF+ F   +    A+ 
Sbjct: 3   RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMA 62

Query: 191 EPQKKIGNRM 200
                I  R+
Sbjct: 63  ARPHTIDGRV 72

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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 49.8 bits (119), Expect = 5e-08
 Identities = 26/63 (41%), Positives = 40/63 (63%), Gaps = 1/63 (1%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           +IFV G+ + T    L   F QYG +++ K V D+ +G SKGYGF+ F+T+  A+K L+E
Sbjct: 4   RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQKILQE 62

Query: 192 PQK 194
             +
Sbjct: 63  ANR 65

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

 Score = 49.5 bits (119), Expect = 5e-08
 Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 2/75 (2%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP 309
           ++V N+G +++ +KL   F KYG+I    +  D   GK KGF    ++  +AA+KA+EE 
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 310 H-KNFEGHILNCQRA 323
           + K   G  L   RA
Sbjct: 63  NGKEVNGKKLYVGRA 77

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

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

 Score = 49.4 bits (118), Expect = 6e-08
 Identities = 21/63 (33%), Positives = 32/63 (50%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           +FV  L +    E L D F     I+    V D  +G+S+GYGF+ F     A++AL + 
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 193 QKK 195
           + K
Sbjct: 62  KNK 64

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

 Score = 49.2 bits (118), Expect = 7e-08
 Identities = 21/73 (28%), Positives = 40/73 (54%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           K+FV N+   +  ++L  +FS++G+++   +  DK TG  KG+    + + D  + AL++
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 309 PHKNFEGHILNCQ 321
                EG+ L  Q
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|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 = 49.2 bits (118), Expect = 7e-08
 Identities = 23/71 (32%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           ++FV N+      ++L   F  +GEI E  L +DK T + KGF    +   + A KA  E
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 309 PHKN-FEGHIL 318
              + F+G +L
Sbjct: 61  LDGSIFQGRLL 71

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|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 = 49.2 bits (118), Expect = 8e-08
 Identities = 20/58 (34%), Positives = 32/58 (55%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           +FV  + +D   E LI+ F + G +   + V D+ +GK KGYGF  F+    A  A++
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIR 58

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|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM)

 Score = 51.4 bits (123), Expect = 8e-08
 Identities = 30/90 (33%), Positives = 50/90 (55%), Gaps = 3/90 (3%)

Query: 25  EPPKQEEPIEEEEYEEEVEEEGEEEGEEE-EEEEEEEEEEEEKADQKEDEEEEEKADQND 83
           +  ++++  EEEE EEE+EE  + E EEE  E+EEEEEE+EE     +D E++   D  +
Sbjct: 45  DEKQEDDEEEEEEDEEEIEEPEDIEDEEEIVEDEEEEEEDEEDNVDLKDIEKKNINDIFN 104

Query: 84  EEDDEPILSLLEPFSKDQLVNLLREAAENH 113
              D+   +L+    K    +  ++ AE+ 
Sbjct: 105 STQDDNAQNLISKNYKKNEKS--KKTAEDI 132

This family consists of several Plasmodium falciparum SPAM (secreted polymorphic antigen associated with merozoites) proteins. Variation among SPAM alleles is the result of deletions and amino acid substitutions in non-repetitive sequences within and flanking the alanine heptad-repeat domain. Heptad repeats in which the a and d position contain hydrophobic residues generate amphipathic alpha-helices which give rise to helical bundles or coiled-coil structures in proteins. SPAM is an example of a P. falciparum antigen in which a repetitive sequence has features characteristic of a well-defined structural element. Length = 164

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

 Score = 48.8 bits (117), Expect = 9e-08
 Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 3/78 (3%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEE--GPLGIDKATGKP-KGFCLFVYKTVDAAKK 304
           R+I+V N+  +L+   L   FSK+GE+E    P   D+  G+   GF    +K   +A+ 
Sbjct: 1   REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60

Query: 305 ALEEPHKNFEGHILNCQR 322
           AL+       G  ++   
Sbjct: 61  ALQLNGTELGGRKISVSL 78

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

 Score = 49.1 bits (117), Expect = 9e-08
 Identities = 22/57 (38%), Positives = 33/57 (57%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKA 188
           K+FV GL  D     L + F Q+G +E  + + DK +GK +G+GF+ F+    A KA
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA 57

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

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 24/62 (38%), Positives = 32/62 (51%), Gaps = 5/62 (8%)

Query: 236 HQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFV 295
           H Q+   S Y    I++  +  EL    +L  FS+YGEI +  L  DK TGK KGF    
Sbjct: 3   HDQYKD-SAY----IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLA 57

Query: 296 YK 297
           Y+
Sbjct: 58  YE 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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 19/45 (42%), Positives = 28/45 (62%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFI 177
           I++ GL ++     ++  F QYGEI D   V DK +GKSKG+ F+
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFL 56

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|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           +FV  L +    + L   F + GEI D + V +   GKSKGY ++ F+     ++ALK  
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEALKLD 60

Query: 193 QKKIGNR 199
           ++ I  R
Sbjct: 61  RELIKGR 67

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|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 1/64 (1%)

Query: 128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARK 187
           P + ++F+   G     + L +AF  +GEI+D   V DK + +SKG  ++ F   S A +
Sbjct: 1   PPNSRLFIV-CGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAAR 59

Query: 188 ALKE 191
           A++E
Sbjct: 60  AMEE 63

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|217829 pfam03985, Paf1, Paf1

 Score = 53.2 bits (128), Expect = 1e-07
 Identities = 17/65 (26%), Positives = 30/65 (46%)

Query: 24  QEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQND 83
            +  + +E  +EEE +   E E EE  + EEE  +  E+   ++      + E KAD+  
Sbjct: 365 IDFEEVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQSREDGSSESSSDVGSDSESKADKES 424

Query: 84  EEDDE 88
             D +
Sbjct: 425 ASDSD 429

Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431

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

 Score = 48.6 bits (116), Expect = 1e-07
 Identities = 19/58 (32%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           K+FV GL +    E L   FK++G ++  + V ++ SGK KG  ++ ++  S A +A+
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAV 60

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

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

 Score = 48.1 bits (115), Expect = 2e-07
 Identities = 17/75 (22%), Positives = 36/75 (48%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           KIFV  +  ++  ++   +FS++G++ +  L  D  TG+ +GF    + +  A ++    
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60

Query: 309 PHKNFEGHILNCQRA 323
                 G  +  +RA
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|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 51.3 bits (123), Expect = 2e-07
 Identities = 25/83 (30%), Positives = 46/83 (55%)

Query: 8   DSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKA 67
            S  +   E   K+   +   + E ++EEE E    E+ E++G+ E+E+EE EEE EE+ 
Sbjct: 40  PSDQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEED 99

Query: 68  DQKEDEEEEEKADQNDEEDDEPI 90
           ++  DE E+E  ++ +   ++ I
Sbjct: 100 EESSDENEKETEEKTESNVEKEI 122

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. Length = 214

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

 Score = 48.2 bits (115), Expect = 2e-07
 Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
            K+FV GL   T    L   F +YG++ +C  + D  + +S+G+GFI F +   A +A++
Sbjct: 3   CKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAME 62

Query: 191 -EPQKKIGN 198
            +P    GN
Sbjct: 63  AQPHSIDGN 71

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 = 47.8 bits (113), Expect = 3e-07
 Identities = 21/70 (30%), Positives = 40/70 (57%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           RK+F+ GL ++T  E+L   F+Q+G + DC  + D  + +S+G+GF+ + +      A+ 
Sbjct: 3   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMN 62

Query: 191 EPQKKIGNRM 200
               K+  R+
Sbjct: 63  ARPHKVDGRV 72

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

 Score = 47.8 bits (114), Expect = 3e-07
 Identities = 19/41 (46%), Positives = 25/41 (60%)

Query: 151 FKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           F   GEIE CK + DKV+G+S GYGF+ +     A KA+  
Sbjct: 22  FSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINT 62

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|217927 pfam04147, Nop14, Nop14-like family

 Score = 52.7 bits (127), Expect = 3e-07
 Identities = 29/97 (29%), Positives = 58/97 (59%), Gaps = 3/97 (3%)

Query: 34  EEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDEPILSL 93
            EE+ EEE +   +E+ E+++++ EEEEE+ + +D++EDEE+E+  D++DEE++E     
Sbjct: 319 GEEDEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEKEK 378

Query: 94  LEPFSKDQLVNLLR---EAAENHRDVASRVRQVADED 127
            +  S +   + L       ++H +    ++ V+ ED
Sbjct: 379 KKKKSAESTRSELPFTFPCPKSHEEFLELLKGVSLED 415

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>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 = 46.8 bits (112), Expect = 4e-07
 Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 7/79 (8%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP 309
           +F+  +  +   + L  +FSKYGE+ +  +  D  TG+ +GF    +    +  K L   
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 310 HKNFEGHILNCQRAIDGPK 328
                 H+L+  R ID PK
Sbjct: 61  P-----HVLD-GREID-PK 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|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 46.8 bits (112), Expect = 4e-07
 Identities = 16/67 (23%), Positives = 29/67 (43%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           + + GL +    E + D F       D   +     G+  G  ++ F +   AR+AL++ 
Sbjct: 2   VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKH 61

Query: 193 QKKIGNR 199
             K+G R
Sbjct: 62  NNKMGGR 68

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

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

 Score = 46.4 bits (111), Expect = 5e-07
 Identities = 18/68 (26%), Positives = 36/68 (52%), Gaps = 3/68 (4%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP 309
           ++V N+   +  + L  FFS YG++E   L  +K   +P+GF    + + + A+ AL++ 
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58

Query: 310 H-KNFEGH 316
           +    +G 
Sbjct: 59  NGLVLDGR 66

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

>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 46.6 bits (111), Expect = 5e-07
 Identities = 21/51 (41%), Positives = 31/51 (60%)

Query: 145 ETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK 195
           E L + FK++G+IE    V DK +G+SKG+G++ F   S A  AL+   K 
Sbjct: 15  EDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALENCDKS 65

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

 Score = 46.4 bits (111), Expect = 6e-07
 Identities = 24/59 (40%), Positives = 36/59 (61%), Gaps = 1/59 (1%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           ++V  LG D   E L + F +YG+I   K + D   GKSKG+GF+ F+    A+KA++E
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVEE 61

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|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31

 Score = 49.8 bits (119), Expect = 6e-07
 Identities = 27/87 (31%), Positives = 49/87 (56%), Gaps = 2/87 (2%)

Query: 4   KRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEE 63
           KRK    T E  +  +K       K+ + +E E+ +EE E++ EEE EEEEE+E+ ++++
Sbjct: 136 KRKVGLFTEEEEDIDEKL--SMLEKKLKELEAEDVDEEDEKDEEEEEEEEEEDEDFDDDD 193

Query: 64  EEKADQKEDEEEEEKADQNDEEDDEPI 90
           ++  D    E   +  + +D +DDE +
Sbjct: 194 DDDDDDYNAENYFDNGEDDDYDDDEAV 220

RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. Length = 221

>gnl|CDD|217829 pfam03985, Paf1, Paf1

 Score = 50.9 bits (122), Expect = 7e-07
 Identities = 19/56 (33%), Positives = 30/56 (53%)

Query: 34  EEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDEP 89
           E +E E+E EE+  +E EEEE E+ EEE  + + D   +   +  +D   + D E 
Sbjct: 369 EVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQSREDGSSESSSDVGSDSESKADKES 424

Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431

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

 Score = 46.2 bits (110), Expect = 8e-07
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           +FV  L W  + + L + FK+ GE+ D +   D   G+SKG+G + F T  GA+KAL++ 
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDD-DGRSKGFGHVEFATEEGAQKALEKS 60

Query: 193 QKKIGNRMTACQLA 206
            +++  R     LA
Sbjct: 61  GEELLGREIRVDLA 74

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|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score = 46.1 bits (110), Expect = 9e-07
 Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 1/47 (2%)

Query: 145 ETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           E L + F  +G I   K + D+  G+SKG+GF+ F +   A KA+ E
Sbjct: 16  ERLREEFSPFGTITSAKVMTDE-KGRSKGFGFVCFSSPEEATKAVTE 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|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 46.1 bits (109), Expect = 1e-06
 Identities = 22/76 (28%), Positives = 39/76 (51%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           K+FV  +  ++    L   FS++G +E+  +  DK TGK +GF    ++  D+A KA   
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60

Query: 309 PHKNFEGHILNCQRAI 324
                 GH +  ++A+
Sbjct: 61  KFHPINGHRVEVKKAV 76

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|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP 309
           +FVSN+   +   +L   FSK GEI +  L  +   GK KG+    ++  ++ ++AL+  
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEALKLD 60

Query: 310 HKNFEG 315
            +  +G
Sbjct: 61  RELIKG 66

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|217927 pfam04147, Nop14, Nop14-like family

 Score = 50.8 bits (122), Expect = 1e-06
 Identities = 23/55 (41%), Positives = 38/55 (69%)

Query: 34  EEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
             +  E+E EEE   + E+EE+++++ EEEEE  D  ++EE+EE  D +DE+D+E
Sbjct: 316 LGQGEEDEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEE 370

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 50.3 bits (121), Expect = 1e-06
 Identities = 27/70 (38%), Positives = 48/70 (68%)

Query: 12  SEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKE 71
            + T+  +K +++   K+EE  +E++ +    ++ EEE EEE+E++EEE+EEEE+  ++E
Sbjct: 406 KKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEE 465

Query: 72  DEEEEEKADQ 81
            EEEEEK  +
Sbjct: 466 KEEEEEKKKK 475

Length = 482

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

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 23/64 (35%), Positives = 32/64 (50%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           ++V GL      + L   F  YG I   + +CD V+G S+G GFI F  R  A +A+K  
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 193 QKKI 196
              I
Sbjct: 63  NGTI 66

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|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 45.4 bits (108), Expect = 1e-06
 Identities = 17/65 (26%), Positives = 33/65 (50%), Gaps = 2/65 (3%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYG--EIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           ++V  L W T  E L  A  + G  +++  K    K +GKSKG+ ++ F + + A    +
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 191 EPQKK 195
           + + +
Sbjct: 61  KLEGR 65

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

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

 Score = 45.5 bits (107), Expect = 2e-06
 Identities = 22/62 (35%), Positives = 34/62 (54%)

Query: 130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           H  +FV  L  +   + +  AF  +G I D + V D  +GKSKGYGF+ F  +  A  A+
Sbjct: 1   HFHVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 60

Query: 190 KE 191
           ++
Sbjct: 61  QQ 62

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

 Score = 45.5 bits (107), Expect = 2e-06
 Identities = 23/60 (38%), Positives = 33/60 (55%)

Query: 130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           H  +FV  L  +   E +  AF  +G+I D + V D  +GKSKGYGF+ F  +  A  A+
Sbjct: 1   HFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAI 60

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 5/64 (7%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           R +FV N+ S +E ++L A F ++G+I      +  A  K +GF +  Y  + AA++A  
Sbjct: 2   RTLFVRNINSNVEDEELRALFEQFGDIRT----LYTAC-KHRGFIMVSYYDIRAARRAKR 56

Query: 308 EPHK 311
               
Sbjct: 57  ALQG 60

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

>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 17/47 (36%), Positives = 27/47 (57%)

Query: 142 TKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKA 188
           T  E L   F ++G+I+ C+ + DK +G S  Y FI F+T+    +A
Sbjct: 15  TTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 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|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 45.4 bits (107), Expect = 2e-06
 Identities = 21/64 (32%), Positives = 35/64 (54%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           KIFV  +  +   +K+  +F  +GE+E   L +D  T K +GFC   +K  +  KK +E+
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 309 PHKN 312
            + N
Sbjct: 61  KYHN 64

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|227466 COG5137, COG5137, Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]

 Score = 48.8 bits (116), Expect = 2e-06
 Identities = 27/88 (30%), Positives = 41/88 (46%), Gaps = 5/88 (5%)

Query: 13  EPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKED 72
           +   P Q  +  E  ++ E  +  E EE+ E   +  GE   E  EEEEEE E +D  ED
Sbjct: 165 DEAPPAQPDVDNEEEERLEESDGREEEEDEEVGSDSYGEGNRELNEEEEEEAEGSDDGED 224

Query: 73  EEEEEKADQND-----EEDDEPILSLLE 95
             + E    +      EE +E +++L E
Sbjct: 225 VVDYEGERIDKKQGEEEEMEEEVINLFE 252

Length = 279

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

 Score = 45.0 bits (106), Expect = 2e-06
 Identities = 22/49 (44%), Positives = 33/49 (67%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILF 179
           +KIFV G+  DT+   L D F+QYG+IE  + + D+ SGK +G+ F+ F
Sbjct: 1   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 49

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|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 49.6 bits (119), Expect = 2e-06
 Identities = 13/114 (11%), Positives = 55/114 (48%), Gaps = 2/114 (1%)

Query: 2   AKKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEE 61
            K  K ++   +      K +       ++  ++++ + + ++  +++ +E+++E+++++
Sbjct: 104 KKAEKKNALDKDDDLNYVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDD 163

Query: 62  EEEEKADQKEDEEEEEKADQNDEEDDEPILSLLEPFSKDQLVNLLREAAENHRD 115
           + +++ ++K++ +E EK   +D+   +      E   + +    L   A+  + 
Sbjct: 164 DVDDEDEEKKEAKELEKLSDDDDFVWD--EDDSEALRQARKDAKLTATADPVKA 215

Length = 509

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

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           +IFV  +  +   ++L  FFS++G +++  +  D+A G  KG+    ++T + A+K L  
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRA-GVSKGYGFVTFETQEDAEKILAM 62

Query: 309 PHKNFEGHILNCQRAI 324
            + NF G  LN   AI
Sbjct: 63  GNLNFRGKKLNIGPAI 78

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|227466 COG5137, COG5137, Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]

 Score = 48.1 bits (114), Expect = 3e-06
 Identities = 15/59 (25%), Positives = 27/59 (45%)

Query: 30  EEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
           +   + +E      +   EE E  EE +  EEEE+E+       E   + ++ +EE+ E
Sbjct: 159 DNDEDNDEAPPAQPDVDNEEEERLEESDGREEEEDEEVGSDSYGEGNRELNEEEEEEAE 217

Length = 279

>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 44.9 bits (107), Expect = 3e-06
 Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 2/51 (3%)

Query: 140 WDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
            D     +  AF + GE+   K + +K +GKS GYGF+ F T   A +AL+
Sbjct: 11  MDE--AYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQ 59

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|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional

 Score = 47.8 bits (114), Expect = 3e-06
 Identities = 16/63 (25%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 34 EEEEYEEEVEEEGEEEGEEEEEE-EEEEEEEEEKADQKEDEEEEEKADQNDEEDDEPILS 92
           ++   E +EE+  +E E +EE+  +EE+ E E+ +++E  E+ E++++   E+ +   +
Sbjct: 5  CKDAKHENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKDENN 64

Query: 93 LLE 95
           L+
Sbjct: 65 KLK 67

Length = 211

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

 Score = 45.0 bits (106), Expect = 3e-06
 Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           +KIFV  +  + E   L  +F KYG+IE   +  D+ +GK +GF    +   D   K + 
Sbjct: 1   KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVV 60

Query: 308 EPHKNFEGHILNCQ 321
           + +    GH  NC+
Sbjct: 61  QKYHTINGH--NCE 72

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|222977 PHA03089, PHA03089, late transcription factor VLTF-4; Provisional

 Score = 47.5 bits (113), Expect = 3e-06
 Identities = 17/74 (22%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 13  EPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKED 72
            P++   K+ ++  P++++  ++ + +++ +EE  E   EE  + EE EE ++K D +  
Sbjct: 45  IPSKKTSKK-KKTTPRKKKTTKKTKKKKKEKEEVPELAAEELSDSEENEENDKKVDYELP 103

Query: 73  EEEEEKADQNDEED 86
           + +   A+ N E+ 
Sbjct: 104 KVQNTAAEVNHEDV 117

Length = 191

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

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 26/67 (38%), Positives = 34/67 (50%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           +FV  L +DT AE L+  FK  G     + + DK +GKSKG  F+ F T     KALK  
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62

Query: 193 QKKIGNR 199
              +  R
Sbjct: 63  HTLLKGR 69

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

 Score = 44.2 bits (104), Expect = 4e-06
 Identities = 19/75 (25%), Positives = 43/75 (57%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           K+FV  +  +   + L  +F+K+GE+ +  + +D  TG+ +GF   ++K   + +K LE+
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60

Query: 309 PHKNFEGHILNCQRA 323
                +G +++ ++A
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|217829 pfam03985, Paf1, Paf1

 Score = 48.6 bits (116), Expect = 4e-06
 Identities = 20/77 (25%), Positives = 32/77 (41%), Gaps = 3/77 (3%)

Query: 13  EPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKED 72
            P+    K   +   + +    EE  E+E EEE +   E EEEE E+ EEE     Q  +
Sbjct: 346 NPSTKESKMRDKRRARLDPIDFEEVDEDEDEEEEQRSDEHEEEEGEDSEEEGS---QSRE 402

Query: 73  EEEEEKADQNDEEDDEP 89
           +   E +     + +  
Sbjct: 403 DGSSESSSDVGSDSESK 419

Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 48.8 bits (117), Expect = 4e-06
 Identities = 32/99 (32%), Positives = 55/99 (55%), Gaps = 7/99 (7%)

Query: 30  EEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEE------KADQND 83
           EE   ++E EE+ +++ EEE E+ +  +EEE+EE+E +D ++DEEEEE      K    +
Sbjct: 326 EEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEKEKKKKKSAE 385

Query: 84  EEDDEPILSLLEPFSKDQLVNLLRE-AAENHRDVASRVR 121
               E   +   P S ++ + LL+  + E+   V  R+R
Sbjct: 386 STRSELPFTFPCPKSHEEFLELLKGVSLEDQPTVVQRIR 424

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional

 Score = 47.1 bits (112), Expect = 4e-06
 Identities = 19/59 (32%), Positives = 33/59 (55%)

Query: 28 KQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEED 86
          K+ +  + E  EE+  +E E + E++ +EE+ E EE EK +  ED EE  +    + +D
Sbjct: 3  KECKDAKHENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKD 61

Length = 211

>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 = 44.5 bits (106), Expect = 4e-06
 Identities = 24/63 (38%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFV-YKTVDAAKKALE 307
           K+FV  +      + + A F +YG IEE  +  DK TG+ KG C FV + + + A+KA+E
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKG-CAFVKFSSREEAQKAIE 59

Query: 308 EPH 310
             H
Sbjct: 60  ALH 62

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

 Score = 45.3 bits (107), Expect = 4e-06
 Identities = 20/58 (34%), Positives = 31/58 (53%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           +FV  L +D   E+L   F ++G +     V DK +G++KG GF+ FK +      LK
Sbjct: 4   LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLK 61

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|220383 pfam09756, DDRGK, DDRGK domain

 Score = 47.0 bits (112), Expect = 4e-06
 Identities = 33/130 (25%), Positives = 60/130 (46%), Gaps = 4/130 (3%)

Query: 2   AKKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEE 61
            K+ +   + +E  E  +++  +E  + E   EEE  EE  +++ EEE +E EE+  +E+
Sbjct: 13  EKQARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKEREEQARKEQ 72

Query: 62  EEEEKADQKEDEEEEEKADQNDEEDDEPILSLLEPFSKDQLVNLLREAAEN----HRDVA 117
           EE EK       EEE     + +E+   +L     + K + V  L E +        DV 
Sbjct: 73  EEYEKLKSSFVVEEEGTDKLSADEESNELLEDFINYIKLKKVVNLEELSAEFGLKTEDVI 132

Query: 118 SRVRQVADED 127
            R++ +  + 
Sbjct: 133 ERIQDLEAQG 142

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

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

 Score = 43.8 bits (103), Expect = 5e-06
 Identities = 18/74 (24%), Positives = 41/74 (55%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP 309
           +F+  +  +   + L  +FSK+GE+ +  L +D  TG+ +GF   ++K  ++  K +++ 
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 310 HKNFEGHILNCQRA 323
                G +++ +RA
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|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 43.8 bits (104), Expect = 5e-06
 Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKA-LE 307
           K+FV  +  ++  + L  +FS+YG +E   +  DK TGK +GF    +   D   K  L+
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

Query: 308 EPH 310
           + H
Sbjct: 61  KYH 63

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

 Score = 44.0 bits (104), Expect = 5e-06
 Identities = 18/74 (24%), Positives = 36/74 (48%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           KIFV  + +      +  +FS++G++E+  L  DK T + +GF    +++ D   K  E 
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60

Query: 309 PHKNFEGHILNCQR 322
                   ++ C++
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|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 48.4 bits (116), Expect = 5e-06
 Identities = 19/59 (32%), Positives = 42/59 (71%)

Query: 28  KQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEED 86
            ++   + EE ++E +++     ++EEEEEEE+E++EE+ +++E+E EEEK ++ +++ 
Sbjct: 416 VEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKK 474

Length = 482

>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 49.2 bits (117), Expect = 5e-06
 Identities = 21/90 (23%), Positives = 44/90 (48%), Gaps = 10/90 (11%)

Query: 4    KRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEE---E 60
            K + D++  EP +       ++P ++   ++E+  +++  +  E++ +  E+  EE   E
Sbjct: 4020 KEEADAEKDEPMQ------DEDPLEENNTLDEDIQQDDFSDLAEDDEKMNEDGFEENVQE 4073

Query: 61   EEEEEKADQKEDEEEEEKADQNDEE-DDEP 89
             EE  +   K DEE E+     D+  D+ P
Sbjct: 4074 NEESTEDGVKSDEELEQGEVPEDQAIDNHP 4103

Length = 4600

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

 Score = 43.8 bits (104), Expect = 5e-06
 Identities = 21/57 (36%), Positives = 30/57 (52%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           IFV  + + T  E L + FK  G I     +CDK +G+ KG+ +I F  +S    AL
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|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 44.1 bits (105), Expect = 5e-06
 Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 2/52 (3%)

Query: 141 DTKAETLIDAFKQYGEIEDCKAVC-DKVSGKSKGYGFILFKTRSGARKALKE 191
           D     L + F   G +   + VC D ++ +S GY ++ F+  + A +AL  
Sbjct: 10  DVTEAMLYEIFSPAGPVLSIR-VCRDLITRRSLGYAYVNFQNPADAERALDT 60

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

 Score = 43.9 bits (104), Expect = 5e-06
 Identities = 25/70 (35%), Positives = 34/70 (48%), Gaps = 4/70 (5%)

Query: 132 KIFVHG----LGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARK 187
            IFV G    LG D    +L + F   GEI       D+ +G SKG+ +I FK+  G  K
Sbjct: 1   TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60

Query: 188 ALKEPQKKIG 197
           AL+     +G
Sbjct: 61  ALELDGSDLG 70

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|215774 pfam00183, HSP90, Hsp90 protein

 Score = 48.2 bits (115), Expect = 5e-06
 Identities = 22/47 (46%), Positives = 33/47 (70%)

Query: 30 EEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEE 76
          E P EEEE E+E ++E EE+  ++EEE +EEEE+EEK  + +  +E 
Sbjct: 34 EVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKET 80

Length = 529

>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31

 Score = 47.1 bits (112), Expect = 6e-06
 Identities = 25/75 (33%), Positives = 45/75 (60%)

Query: 14  PTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDE 73
             +   K+L     K++  +  EE E+  E+    E + +E E E+ +EE+EK +++E+E
Sbjct: 122 INKKAGKKLALSKFKRKVGLFTEEEEDIDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEE 181

Query: 74  EEEEKADQNDEEDDE 88
           EEEE  D +D++DD+
Sbjct: 182 EEEEDEDFDDDDDDD 196

RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. Length = 221

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 48.4 bits (116), Expect = 6e-06
 Identities = 24/54 (44%), Positives = 43/54 (79%)

Query: 28  KQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQ 81
           ++EE  E+++     +++ EEE EE+E++EEE+EEEEE+A+++++EEEE+K  Q
Sbjct: 423 REEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKKKQ 476

Length = 482

>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 44.0 bits (103), Expect = 6e-06
 Identities = 22/57 (38%), Positives = 35/57 (61%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           +++ GL   T  + L+   + YG+I   KA+ DK + K KGYGF+ F + S A+KA+
Sbjct: 4   LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 60

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 75

>gnl|CDD|220972 pfam11081, DUF2890, Protein of unknown function (DUF2890)

 Score = 46.1 bits (109), Expect = 6e-06
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 20 KQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKA 79
          K+L+  PP  ++  EEE+++ + EE  E+E E E+ E+  +EE+EE     E+ EEE  A
Sbjct: 8  KKLKVRPPPTKD--EEEDWDSQAEEVEEDEEEMEDWEDSLDEEDEE----AEEVEEETAA 61

Query: 80 DQNDEEDDEPILSL 93
                      S 
Sbjct: 62 SSKAPSSSSKSSSQ 75

This family is conserved in dsDNA adenoviruses of vertebrates. The function is not known. Length = 172

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

 Score = 43.8 bits (103), Expect = 6e-06
 Identities = 25/68 (36%), Positives = 36/68 (52%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           +KIFV  +  E   +K+  +F ++GEIE   L +D  T K +GF    +K  D  KK LE
Sbjct: 5   KKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLE 64

Query: 308 EPHKNFEG 315
           +   N  G
Sbjct: 65  KKFHNVSG 72

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|218538 pfam05285, SDA1, SDA1

 Score = 47.7 bits (114), Expect = 6e-06
 Identities = 18/54 (33%), Positives = 35/54 (64%)

Query: 35  EEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
           E+  EEE +++  E+G E +++++EEEE E + D+  D+E E    ++D+E + 
Sbjct: 76  EKWKEEERKKKEAEQGLESDDDDDEEEEWEVEEDEDSDDEGEWIDVESDKEIES 129

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 48.5 bits (115), Expect = 7e-06
 Identities = 26/40 (65%), Positives = 28/40 (70%)

Query: 39  EEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEK 78
           EEE EEE EEE EEEEEEEEEEEEE E+    E  E  +K
Sbjct: 865 EEEEEEEEEEEEEEEEEEEEEEEEENEEPLSLEWPETRQK 904

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|183610 PRK12585, PRK12585, putative monovalent cation/H+ antiporter subunit G; Reviewed

 Score = 46.2 bits (109), Expect = 7e-06
 Identities = 27/84 (32%), Positives = 47/84 (55%)

Query: 5   RKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEE 64
           +K D K  +     Q+Q+++   ++EE  E  E+E   E+  E E +EE+E E EE+  E
Sbjct: 111 KKDDIKKKKSLIIRQEQIEKARQEREELEERMEWERREEKIDEREDQEEQEREREEQTIE 170

Query: 65  EKADQKEDEEEEEKADQNDEEDDE 88
           E++D  E E  E+   + + +DD+
Sbjct: 171 EQSDDSEHEIIEQDESETESDDDK 194

Length = 197

>gnl|CDD|222571 pfam14153, Spore_coat_CotO, Spore coat protein CotO

 Score = 46.0 bits (109), Expect = 7e-06
 Identities = 25/78 (32%), Positives = 39/78 (50%)

Query: 1   MAKKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEE 60
           + KK     +  E ++   K  ++E   + E  E+E+   E E E   E +E+EE  +EE
Sbjct: 32  IIKKADEKEEEKENSDEHVKSKEEEQKIEYEEAEKEKEAGEPEREDIAEQQEKEEIAQEE 91

Query: 61  EEEEEKADQKEDEEEEEK 78
           E+EEE  D K+ E    K
Sbjct: 92  EKEEEAEDVKQQEVFSFK 109

Bacillus spores are protected by a protein shell consisting of over 50 different polypeptides, known as the coat. This family of proteins has an important morphogenetic role in coat assembly, it is involved in the assembly of at least 5 different coat proteins including CotB, CotG, CotS, CotSA and CotW. It is likely to act at a late stage of coat assembly. Length = 185

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

 Score = 47.9 bits (114), Expect = 8e-06
 Identities = 30/166 (18%), Positives = 47/166 (28%), Gaps = 30/166 (18%)

Query: 145 ETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE------------- 191
           E L + F + GEI   K + D+  G S+G+GF+ F     A +A+ E             
Sbjct: 300 EKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYV 358

Query: 192 --PQKKIGNRMTACQL-------ASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQ 242
              Q+K   R                 P  +P   +     +  Q   Q  +       +
Sbjct: 359 ALAQRKEQRRAHLQDQFMQLQPRMRQLPMGSPMGGAMGQPPYYGQGPQQQFNGQPLGWPR 418

Query: 243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKP 288
                        G  L P       +    +         A  KP
Sbjct: 419 M---SMMPTPMGPGGPLRPN----GLAPMNAVRAPSRNAQNAAQKP 457

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|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 47.6 bits (114), Expect = 8e-06
 Identities = 20/57 (35%), Positives = 41/57 (71%)

Query: 33  IEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDEP 89
              E+ E++ EEE +E+ ++    +++EEEEEE+ ++KE+E+EEE+ +  +E+++E 
Sbjct: 414 KIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEE 470

Length = 482

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

 Score = 43.4 bits (102), Expect = 8e-06
 Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           +KIFV  +  + E   L  +F +YG+IE   +  D+ +GK +GF    +   D+  K + 
Sbjct: 1   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 60

Query: 308 EPHKNFEGHILNCQ 321
           + +    GH  NC+
Sbjct: 61  QKYHTVNGH--NCE 72

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|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 43.6 bits (103), Expect = 8e-06
 Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           RK+FV  L        +   F  +G IE+C  + D+ +G+S+G  F+ F +R  A  A+K
Sbjct: 2   RKLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQ-NGQSRGCAFVTFASRQCALNAIK 60

Query: 191 E 191
            
Sbjct: 61  A 61

This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 81

>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 43.4 bits (103), Expect = 8e-06
 Identities = 28/83 (33%), Positives = 37/83 (44%), Gaps = 9/83 (10%)

Query: 133 IFVHGLGWDTKAETLIDAFKQ-YGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           IFV  L  D     L + F+  Y  +   K V D V+G+SKGYGF+ F       +AL E
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 192 PQKK-IGNR-MTACQLASIGPAT 212
                  +R M       + PAT
Sbjct: 64  MNGVYCSSRPMR------VSPAT 80

This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 80

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

 Score = 43.6 bits (102), Expect = 8e-06
 Identities = 19/70 (27%), Positives = 40/70 (57%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           RK+F+ GL ++T  ++L + F+++G + DC  + D  + +S+G+GF+ +        A+ 
Sbjct: 3   RKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMS 62

Query: 191 EPQKKIGNRM 200
               K+  R+
Sbjct: 63  ARPHKVDGRV 72

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|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 43.2 bits (102), Expect = 9e-06
 Identities = 19/60 (31%), Positives = 30/60 (50%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           +FV  L ++T  + L   F + G I   + +  + SGK KG+ F+ F+    A  ALK  
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60

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|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 42.9 bits (101), Expect = 1e-05
 Identities = 20/74 (27%), Positives = 42/74 (56%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP 309
           +FV  +  +   + L  +FSK+GE+ +  + ID  TG+ +GF   ++K   + +K L++ 
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 310 HKNFEGHILNCQRA 323
               +G +++ +RA
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|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 42.7 bits (100), Expect = 1e-05
 Identities = 18/75 (24%), Positives = 39/75 (52%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           K+F+  +  +   + L  + S++GE+ +  +  D  TG+ +GF   ++K   +  K LE 
Sbjct: 1   KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60

Query: 309 PHKNFEGHILNCQRA 323
                +G +++ +RA
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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 47.2 bits (112), Expect = 1e-05
 Identities = 44/219 (20%), Positives = 80/219 (36%), Gaps = 32/219 (14%)

Query: 2   AKKRKHDSKTSE---PTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEE 58
           ++ R    +  +         +   + P +   P  +  Y  +    G    E   E E 
Sbjct: 28  SRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYRPRGDRSYRRDDRRSGRNTKEPLTEAER 87

Query: 59  EE-----EEEEEKADQKEDEEEEEKA----------DQN-------------DEEDDEPI 90
           ++      +   KA +++  E   K           D+N             D E     
Sbjct: 88  DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKA 147

Query: 91  LSLLEPFSKDQLVNLLREAAENHRDVASRVRQVADEDPVHRKIFVHGLGWDTKAETLIDA 150
           L+L       + + +    AE +R  A        + P   K++V  L ++   + L   
Sbjct: 148 LALTGQMLLGRPIIVQSSQAEKNR-AAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQI 206

Query: 151 FKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           F+ +G+IED +   D  +G+SKG+GFI F     A++AL
Sbjct: 207 FEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEAL 245

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

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 20/57 (35%), Positives = 27/57 (47%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKAL 306
           IFV NV     P++L   F   G I    +  DK TG+PKGF    +    + + AL
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|218538 pfam05285, SDA1, SDA1

 Score = 47.0 bits (112), Expect = 1e-05
 Identities = 19/68 (27%), Positives = 36/68 (52%), Gaps = 2/68 (2%)

Query: 22  LQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQ 81
           L++   ++ +  E E+  E  +++ EEE  E EE+E+ ++E E    + + E E    D 
Sbjct: 75  LEKWKEEERKKKEAEQGLESDDDDDEEEEWEVEEDEDSDDEGEWIDVESDKEIESS--DS 132

Query: 82  NDEEDDEP 89
            DEE+ + 
Sbjct: 133 EDEEEKDE 140

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

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

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 13/71 (18%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEE--------GPLGIDKATGKPKGFCLFVYKTVD 300
           ++++ N+ S L    LL  FSKYG+I++        GPL      G+P+G+C   ++T +
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPL-----KGQPRGYCFVTFETKE 55

Query: 301 AAKKALEEPHK 311
            A+KAL+  + 
Sbjct: 56  EAEKALKSLNG 66

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|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 8/63 (12%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           ++V  L   T  E L + F +YGE+E  K        K K Y F+ F+ R  A KA++E 
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVK--------KIKDYAFVHFEERDDAVKAMEEM 55

Query: 193 QKK 195
             K
Sbjct: 56  NGK 58

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|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 47.0 bits (112), Expect = 1e-05
 Identities = 19/45 (42%), Positives = 34/45 (75%)

Query: 34  EEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEK 78
           +EE+ EE +E+  EEE E++  E E+E+EE+E  +++ED++E +K
Sbjct: 275 DEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDDDEGDK 319

Length = 319

>gnl|CDD|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional

 Score = 47.5 bits (113), Expect = 1e-05
 Identities = 15/61 (24%), Positives = 29/61 (47%)

Query: 28  KQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDD 87
            ++  + E   + E EE  + E EE  E E+ E  EE+   ++     E++ +  DE ++
Sbjct: 380 AEDAKVAELISQREEEEALQREAEERLEAEQAERAEEDARLRELYPLPEDEFEDEDELEE 439

Query: 88  E 88
            
Sbjct: 440 A 440

Length = 449

>gnl|CDD|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional

 Score = 47.1 bits (112), Expect = 1e-05
 Identities = 16/67 (23%), Positives = 28/67 (41%)

Query: 19  QKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEK 78
           +     E   Q E  E  + E E   E E+    EE+    E     + + ++++E EE 
Sbjct: 381 EDAKVAELISQREEEEALQREAEERLEAEQAERAEEDARLRELYPLPEDEFEDEDELEEA 440

Query: 79  ADQNDEE 85
             + +EE
Sbjct: 441 QPEEEEE 447

Length = 449

>gnl|CDD|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional

 Score = 47.1 bits (112), Expect = 1e-05
 Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 2/68 (2%)

Query: 19  QKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEK 78
             ++ +   ++EE  EE    E  E    E+ E  EE+    E      D+ EDE+E E+
Sbjct: 382 DAKVAELISQREE--EEALQREAEERLEAEQAERAEEDARLRELYPLPEDEFEDEDELEE 439

Query: 79  ADQNDEED 86
           A   +EE+
Sbjct: 440 AQPEEEEE 447

Length = 449

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

 Score = 46.9 bits (111), Expect = 1e-05
 Identities = 48/237 (20%), Positives = 69/237 (29%), Gaps = 63/237 (26%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE- 191
           ++V GL        L   F  +G+I   + + D V+G SKG GFI F  R  A +A+K  
Sbjct: 92  LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTL 151

Query: 192 -------------------PQKKIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQ- 231
                              P       + +   A   P TT    ST          H  
Sbjct: 152 NGTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHA 211

Query: 232 ---------------HQHQHQQHHQQSEYTQRK--------------------------- 249
                             Q Q    Q    QR                            
Sbjct: 212 AARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYC 271

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKAL 306
           IFV N+  + +   L   F  +G ++   +  D  T + KG+        D A  A+
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAI 328

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|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 44.6 bits (105), Expect = 1e-05
 Identities = 18/64 (28%), Positives = 29/64 (45%)

Query: 25  EPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDE 84
            P        E   E E  +  E+  E  E +  +E +EEE+ D+  DE  +E   + +E
Sbjct: 61  GPAAAATAAAEAAEEAEAADADEDADEAAEADAADEADEEEETDEAVDETADEADAEAEE 120

Query: 85  EDDE 88
            D+E
Sbjct: 121 ADEE 124

Length = 131

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

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 19/59 (32%), Positives = 32/59 (54%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           +FV N+  + +   +   F +YGEI    L  D  +G+PKGF    + + +AA+ AL+ 
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDA 59

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

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 21/61 (34%), Positives = 36/61 (59%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP 309
           IFV+ V  E + + +   F+++GEI+   L +D+ TG  KG+ L  Y+T   A+ A+E  
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 310 H 310
           +
Sbjct: 69  N 69

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

>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 3/60 (5%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           R ++V N+  ++  ++L   F KYG I +  +G  K T   +G    VY+ +  AK A +
Sbjct: 3   RILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYDAKNACD 59

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 1/67 (1%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK-E 191
           +FV  L    +   L + F + G++ D + + D+ S +SKG  ++ F        AL   
Sbjct: 2   VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGLT 61

Query: 192 PQKKIGN 198
            Q+ +G 
Sbjct: 62  GQRLLGQ 68

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

 Score = 42.5 bits (101), Expect = 1e-05
 Identities = 12/40 (30%), Positives = 21/40 (52%)

Query: 151 FKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           F  YG ++D     D+     +GY ++ F++   A KA+K
Sbjct: 19  FSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIK 58

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|219900 pfam08553, VID27, VID27 cytoplasmic protein

 Score = 47.1 bits (112), Expect = 1e-05
 Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 1/59 (1%)

Query: 30  EEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEE-EEEKADQNDEEDD 87
            +     E E+   E  +EE E+EEEEEEE+E+E    +  +DEE EE+  +   E+ D
Sbjct: 373 LDAFSALEIEDANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKYEDSD 431

This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794

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

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 18/59 (30%), Positives = 33/59 (55%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           IFV ++  E++ + L A F+ +GEI +  +  D  TGK KG+    +   + A+ A++ 
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQS 60

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|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 47.3 bits (112), Expect = 2e-05
 Identities = 27/73 (36%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 16  EPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEE 75
           E   ++++ E   + E  E+E  E E  EEGEE  +E E E E + E E + D+KE E E
Sbjct: 709 ETEAEEVEHEGETEAEGTEDEG-EIETGEEGEEVEDEGEGEAEGKHEVETEGDRKETEHE 767

Query: 76  EEKADQNDEEDDE 88
            E   +  E++DE
Sbjct: 768 GETEAEGKEDEDE 780

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 46.9 bits (112), Expect = 2e-05
 Identities = 19/69 (27%), Positives = 44/69 (63%)

Query: 20  KQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKA 79
           K+L+ E  ++    EE++ EEE  +E  ++ ++E E ++++     + ++ E+EEE+   
Sbjct: 272 KKLEAERLRRMRGEEEDDEEEEDSKESADDLDDEFEPDDDDNFGLGQGEEDEEEEEDGVD 331

Query: 80  DQNDEEDDE 88
           D+++E+DD+
Sbjct: 332 DEDEEDDDD 340

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 46.5 bits (111), Expect = 2e-05
 Identities = 22/66 (33%), Positives = 44/66 (66%)

Query: 28  KQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDD 87
           K  E  E++  EE+ E++ +    +++EEEEEEE+E+++ +++E+EEE E+  + +EE  
Sbjct: 414 KIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKK 473

Query: 88  EPILSL 93
           +   +L
Sbjct: 474 KKQATL 479

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 46.1 bits (110), Expect = 2e-05
 Identities = 20/72 (27%), Positives = 50/72 (69%)

Query: 7   HDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEK 66
              K ++  +   ++ +++  ++++  +++ +  + +EE EEE +E++EEE+EEEEEE +
Sbjct: 404 GSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAE 463

Query: 67  ADQKEDEEEEEK 78
            +++E+EE+++K
Sbjct: 464 EEKEEEEEKKKK 475

Length = 482

>gnl|CDD|222571 pfam14153, Spore_coat_CotO, Spore coat protein CotO

 Score = 45.2 bits (107), Expect = 2e-05
 Identities = 23/81 (28%), Positives = 42/81 (51%)

Query: 1   MAKKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEE 60
            A  +K         +  +K+   E  K +E  ++ EYEE  +E+   E E E+  E++E
Sbjct: 24  KANMQKTFIIKKADEKEEEKENSDEHVKSKEEEQKIEYEEAEKEKEAGEPEREDIAEQQE 83

Query: 61  EEEEEKADQKEDEEEEEKADQ 81
           +EE  + ++KE+E E+ K  +
Sbjct: 84  KEEIAQEEEKEEEAEDVKQQE 104

Bacillus spores are protected by a protein shell consisting of over 50 different polypeptides, known as the coat. This family of proteins has an important morphogenetic role in coat assembly, it is involved in the assembly of at least 5 different coat proteins including CotB, CotG, CotS, CotSA and CotW. It is likely to act at a late stage of coat assembly. Length = 185

>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 1/67 (1%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           +++  L WD   + + + FK   EI   +   DK +G+ KG+G + F        ALK  
Sbjct: 2   VYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALKLD 60

Query: 193 QKKIGNR 199
              +  R
Sbjct: 61  GTVLCGR 67

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

 Score = 42.1 bits (100), Expect = 2e-05
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 9/77 (11%)

Query: 252 VSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHK 311
           V+N+  + +   L   F  +G I    L  DK TG+ +GF    + T + A++A+    +
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAI----E 59

Query: 312 NFEGH-----ILNCQRA 323
              G      IL+ + A
Sbjct: 60  KLNGFGYDNLILSVEWA 76

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

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

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 18/76 (23%), Positives = 37/76 (48%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           +KIFV  +   +    L  +FS++G + E  +  D    +P+GF    +++ D+  + + 
Sbjct: 3   KKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVN 62

Query: 308 EPHKNFEGHILNCQRA 323
           E   +  G  +  +RA
Sbjct: 63  EHFHDINGKKVEVKRA 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|220135 pfam09184, PPP4R2, PPP4R2

 Score = 45.6 bits (108), Expect = 2e-05
 Identities = 17/75 (22%), Positives = 42/75 (56%)

Query: 15  TEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEE 74
           ++   K L++   K+       + +     + + +  ++EE+++++ +  E+ + KEDEE
Sbjct: 211 SQDKNKSLEEYYEKESSDAAASQDDGPKGSDVKNKKSDDEEDDDQDGDYVEEKELKEDEE 270

Query: 75  EEEKADQNDEEDDEP 89
           EEE  ++ +EED++ 
Sbjct: 271 EEETEEEEEEEDEDE 285

PPP4R2 (protein phosphatase 4 core regulatory subunit R2) is the regulatory subunit of the histone H2A phosphatase complex. It has been shown to confer resistance to the anticancer drug cisplatin in yeast, and may confer resistance in higher eukaryotes. Length = 285

>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 145 ETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           E L  AF Q+GE+E    + D   G+S G G + F  + GA+ A+K 
Sbjct: 14  ELLEQAFSQFGEVERAVVIVD-DRGRSTGEGIVEFSRKPGAQAAIKR 59

This subfamily corresponds to the RRM2 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. The family 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 contains 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 = 80

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

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 20/45 (44%), Positives = 27/45 (60%)

Query: 145 ETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           + L   F+ +GEIE  +   D  +G+SKGYGFI F     A+KAL
Sbjct: 13  DDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKAL 57

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

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 5/85 (5%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP 309
           +FV  +  +   + L   FS+YG+I    L  D  TG  KG+    Y+    A +A  + 
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 310 HKNF-EGHIL----NCQRAIDGPKP 329
           HK   +G  +      +R + G  P
Sbjct: 66  HKLVIDGSEIFVDFERERTLPGWIP 90

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|220383 pfam09756, DDRGK, DDRGK domain

 Score = 44.3 bits (105), Expect = 3e-05
 Identities = 27/70 (38%), Positives = 41/70 (58%)

Query: 19 QKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEK 78
           K+  +   KQ    + E  EEE EE  + E + E E +EEEE EEE+  +KE+EE +E+
Sbjct: 5  AKKRAKLEEKQARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKER 64

Query: 79 ADQNDEEDDE 88
           +Q  +E +E
Sbjct: 65 EEQARKEQEE 74

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 45.4 bits (108), Expect = 3e-05
 Identities = 25/78 (32%), Positives = 45/78 (57%), Gaps = 8/78 (10%)

Query: 20  KQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGE--------EEEEEEEEEEEEEEKADQKE 71
           K+ +Q     ++  EEEE+E E +E+ ++EGE        E E  + E+EEE+++A +K 
Sbjct: 86  KEAEQGLESDDDDDEEEEWEVEEDEDSDDEGEWIDVESDKEIESSDSEDEEEKDEAAKKA 145

Query: 72  DEEEEEKADQNDEEDDEP 89
            E+ +E+  + DEE+   
Sbjct: 146 KEDSDEELSEEDEEEAAE 163

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 41.7 bits (98), Expect = 3e-05
 Identities = 19/65 (29%), Positives = 31/65 (47%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP 309
           +FV N+  E    +L A F + G I    +   + +GK KGF    ++ ++ A  AL+  
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60

Query: 310 HKNFE 314
           H N  
Sbjct: 61  HLNGR 65

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

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 145 ETLIDAFKQYGEIEDCKAVCDKV---SGKSKGYGFILFKTRSGARKALKEPQKKI 196
             L+  F +YG+I+    +  K     G+ +GY F+ F+T+  A KALK    K 
Sbjct: 14  FHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKALKSLNGKT 68

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

 Score = 42.0 bits (99), Expect = 3e-05
 Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 4/69 (5%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIE--DCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           ++V G+ + +  + +   F   GEIE  D     D  +G+ +G  FI FKT   A++AL 
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPD--TGRFRGIAFITFKTEEAAKRALA 58

Query: 191 EPQKKIGNR 199
              + +G R
Sbjct: 59  LDGEDMGGR 67

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|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 41.9 bits (99), Expect = 3e-05
 Identities = 22/57 (38%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 151 FKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE-PQKKIGNRMTACQLA 206
           F +YG++     V DK + KSKG  FILF  R  A K +K    K++  R   C +A
Sbjct: 22  FSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNNKELFGRTLKCSIA 78

This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. . Length = 78

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 45.9 bits (109), Expect = 3e-05
 Identities = 17/59 (28%), Positives = 36/59 (61%), Gaps = 1/59 (1%)

Query: 28  KQEEPIE-EEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEE 85
           +QE   E  ++ ++  ++ GE + E +  EE E + +EEK  Q+E+E+++++    D+E
Sbjct: 367 RQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADEDKE 425

Length = 434

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

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 16/55 (29%), Positives = 29/55 (52%)

Query: 135 VHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           V  L + T  + L   F++YGE+ D     D+ + +S+G+ F+ F  +  A  A+
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAM 57

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

 Score = 45.8 bits (108), Expect = 3e-05
 Identities = 28/87 (32%), Positives = 42/87 (48%)

Query: 222 HQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGI 281
               HQ Q     Q QQ  QQ+     +++V ++  EL    +   F  +G I+   +  
Sbjct: 82  QTKAHQQQQLENQQRQQQRQQALAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSW 141

Query: 282 DKATGKPKGFCLFVYKTVDAAKKALEE 308
           D ATGK KGF    Y+  +AA+ ALE+
Sbjct: 142 DPATGKHKGFAFVEYEVPEAAQLALEQ 168

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

 Score = 41.6 bits (97), Expect = 4e-05
 Identities = 18/76 (23%), Positives = 38/76 (50%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           +KIFV  + +    + +  +F ++G++E+  L  DK T + +GF    ++  D  +K  E
Sbjct: 4   KKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCE 63

Query: 308 EPHKNFEGHILNCQRA 323
                    ++ C++A
Sbjct: 64  IHFHEINNKMVECKKA 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|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 = 41.5 bits (98), Expect = 4e-05
 Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 4/70 (5%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP 309
           +FV N+  +   ++L+  FS+ G +    L  D+ TGKPKG+    ++ ++ A  A+   
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAI--- 57

Query: 310 HKNFEGHILN 319
            +N  G+  N
Sbjct: 58  -RNLNGYEFN 66

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

 Score = 41.1 bits (96), Expect = 4e-05
 Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           KIFV GL  DT  E + + F  +GE+E  +   D  + K +G+ FI FK     +K +++
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 192 PQKKIGNRMTACQL 205
               +G  ++ C++
Sbjct: 61  KYHNVG--LSKCEI 72

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

 Score = 45.3 bits (107), Expect = 4e-05
 Identities = 61/276 (22%), Positives = 90/276 (32%), Gaps = 61/276 (22%)

Query: 151 FKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASIGP 210
           F   GEIE CK V DKV+G+S GYGF+ +     A KA+        N +   +L +   
Sbjct: 24  FTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAV--------NSLNGLRLQNKTI 75

Query: 211 ATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSK 270
             + A  S+ + +  +                       ++VS +   +   +L + FS 
Sbjct: 76  KVSYARPSSDSIKGAN-----------------------LYVSGLPKTMTQHELESIFSP 112

Query: 271 YGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHI-LNCQRAI----- 324
           +G+I    +  D  TG  KG     +   D A +A+    K   G     C   I     
Sbjct: 113 FGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAI----KTLNGTTPSGCTEPITVKFA 168

Query: 325 -----DGPKPGKSRHHNAQNPHFQRNEGA--GYVGGAGPAAAG-------PGHLMA---- 366
                   K   S+    QNP   R   +      G GP            G   A    
Sbjct: 169 NNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAH 228

Query: 367 --PSGPAIPPAAAQALNPALGQALLGTLGSAAGGTA 400
                      AAQ  +P         L + A   A
Sbjct: 229 QQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAA 264

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

 Score = 41.4 bits (98), Expect = 4e-05
 Identities = 16/50 (32%), Positives = 28/50 (56%)

Query: 141 DTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           D   + L + F+ +G I       DK +G+S+G+ F+ F TR  A +A++
Sbjct: 10  DADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIE 59

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

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

 Score = 41.6 bits (98), Expect = 4e-05
 Identities = 19/76 (25%), Positives = 34/76 (44%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           +KIFV GL  +     L   F Q+G + +   + D    + +G+GFI F++     + + 
Sbjct: 3   KKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVN 62

Query: 191 EPQKKIGNRMTACQLA 206
           E    I  +    + A
Sbjct: 63  EHFHDINGKKVEVKRA 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|220377 pfam09747, DUF2052, Coiled-coil domain containing protein (DUF2052)

 Score = 43.9 bits (104), Expect = 4e-05
 Identities = 25/66 (37%), Positives = 34/66 (51%), Gaps = 2/66 (3%)

Query: 19  QKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEK 78
            +    E  ++EE  EEEE  E+ EEE EEE EE +     EEEEE+     E    EE+
Sbjct: 69  ARLELLEQQEEEESAEEEE--EDPEEENEEEEEEYQRGPFGEEEEEDGDSYDELPTPEER 126

Query: 79  ADQNDE 84
            +  +E
Sbjct: 127 EELREE 132

This entry is of sequences of two conserved domains separated by a region of low complexity, spanning some 200 residues. The function is unknown. Length = 178

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

 Score = 41.4 bits (98), Expect = 4e-05
 Identities = 17/57 (29%), Positives = 32/57 (56%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKAL 306
           ++V N+      +++   FS+ G+I+   +G+D+ T  P GFC   Y T + A+ A+
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAV 57

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|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 41.8 bits (99), Expect = 4e-05
 Identities = 17/74 (22%), Positives = 33/74 (44%), Gaps = 6/74 (8%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYG--EIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           + + GL   T  E ++ A        I+D + + DK++G S+G+ F+ F +   A + + 
Sbjct: 5   LILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMD 64

Query: 191 EPQK----KIGNRM 200
                    I  R+
Sbjct: 65  ALNNLDPFVIDGRV 78

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|218333 pfam04931, DNA_pol_phi, DNA polymerase phi

 Score = 45.6 bits (108), Expect = 4e-05
 Identities = 18/66 (27%), Positives = 33/66 (50%)

Query: 30  EEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDEP 89
           EE  E++  E + +E+  E  E+ E E E + E+ E+ +Q++D E  E     D+     
Sbjct: 648 EEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDAEANEGVVPIDKAVRRA 707

Query: 90  ILSLLE 95
           +  +L 
Sbjct: 708 LPKVLN 713

This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784

>gnl|CDD|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 41.0 bits (96), Expect = 4e-05
 Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 5/61 (8%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           R +FV NV  ++    L   F  YG++     G+       +G     +  +  AK+A+ 
Sbjct: 2   RSLFVINVPRDVTESTLRRLFEVYGDVR----GVQTER-ISEGIVTVHFYDIRDAKRAVR 56

Query: 308 E 308
           E
Sbjct: 57  E 57

This subfamily corresponds to the RRM1 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding protein family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

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

 Score = 41.1 bits (97), Expect = 5e-05
 Identities = 15/60 (25%), Positives = 31/60 (51%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
            ++V N+   +  + L   F ++GE+    +  D+ TG+ +GF     +T + A  A+E+
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

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|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 45.8 bits (108), Expect = 5e-05
 Identities = 20/79 (25%), Positives = 35/79 (44%)

Query: 10  KTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQ 69
             +E     +   + E   + E   E E E E+  E + E E E E E +E + + + + 
Sbjct: 653 TEAEGENGEESGGEAEQEGETETKGENESEGEIPAERKGEQEGEGEIEAKEADHKGETEA 712

Query: 70  KEDEEEEEKADQNDEEDDE 88
           +E E E E   +  E++ E
Sbjct: 713 EEVEHEGETEAEGTEDEGE 731

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi

 Score = 45.2 bits (107), Expect = 5e-05
 Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 6/78 (7%)

Query: 20  KQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKA 79
           K  + +   Q+    EEE E+++EE  ++E E E  E+ E E E +  D +EDE+E+   
Sbjct: 633 KADENKSRHQQLFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQED--- 689

Query: 80  DQNDEEDDEPILSLLEPF 97
              D E +E ++ + +  
Sbjct: 690 ---DAEANEGVVPIDKAV 704

This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784

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

 Score = 41.3 bits (96), Expect = 5e-05
 Identities = 23/57 (40%), Positives = 32/57 (56%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           + V+ L  +   E L   F   GEIE CK V DK++G+S GYGF+ +     A KA+
Sbjct: 7   LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 63

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|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast Schizosaccharomyces pombe SET domain-containing protein 1 (spSet1p) and similar proteins

 Score = 41.6 bits (98), Expect = 5e-05
 Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 8/65 (12%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYK--------TVDA 301
           I ++ +     P+++   F  +GEIEE  L +D  TG+  G C   ++          +A
Sbjct: 1   ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPLRPSAAHEA 60

Query: 302 AKKAL 306
           AK A+
Sbjct: 61  AKAAV 65

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|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 41.3 bits (96), Expect = 5e-05
 Identities = 21/57 (36%), Positives = 36/57 (63%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           +++ GL  +T  + L+   + YG+I   KA+ DK + K KGYGF+ F + + A+KA+
Sbjct: 10  LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAV 66

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein

 Score = 45.4 bits (108), Expect = 5e-05
 Identities = 15/56 (26%), Positives = 35/56 (62%)

Query: 29  QEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDE 84
           Q+EP  ++ Y +  E++ ++E  +EE+EE  + E++E  D  +D+++    +++ E
Sbjct: 111 QDEPRYDDAYRDLEEDDDDDEESDEEDEESSKSEDDEDDDDDDDDDDIATRERSLE 166

CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583

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

 Score = 41.2 bits (96), Expect = 5e-05
 Identities = 20/49 (40%), Positives = 34/49 (69%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILF 179
           +K+FV G+  DT+   L D F++YG+I+  + + D+ SGK +G+GF+ F
Sbjct: 1   KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTF 49

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

 Score = 40.8 bits (96), Expect = 6e-05
 Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
            +FV N+   ++ + L A F K+G +    +  D+ TG+ +GF    +++ + AKKA+E 
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 309 PH-KNFEGHILNCQRA 323
              K  +G  +N   +
Sbjct: 61  MDGKELDGRPINVDFS 76

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

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

 Score = 40.7 bits (96), Expect = 6e-05
 Identities = 16/43 (37%), Positives = 28/43 (65%)

Query: 268 FSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH 310
           FS+YG IE+  +  D+ TG+ +GF    +++V+ AK+A E  +
Sbjct: 20  FSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLN 62

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|217927 pfam04147, Nop14, Nop14-like family

 Score = 45.4 bits (108), Expect = 6e-05
 Identities = 25/56 (44%), Positives = 41/56 (73%), Gaps = 2/56 (3%)

Query: 35  EEEYEEEVEEE-GEEEGEEEEEEEEEEEEEEEKADQKED-EEEEEKADQNDEEDDE 88
           ++E+E + ++  G  +GEE+EEEEE+  ++E++ D  +D EEEEE  D +DEE+DE
Sbjct: 303 DDEFEPDDDDNFGLGQGEEDEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDE 358

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional

 Score = 44.8 bits (106), Expect = 6e-05
 Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 24  QEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQND 83
            E  K  E I + E EE ++ E EE   E E+ E  EE+   +      E+E E  D+ +
Sbjct: 380 AEDAKVAELISQREEEEALQREAEER-LEAEQAERAEEDARLRELYPLPEDEFEDEDELE 438

Query: 84  EEDDEP 89
           E   E 
Sbjct: 439 EAQPEE 444

Length = 449

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

 Score = 41.0 bits (97), Expect = 6e-05
 Identities = 19/59 (32%), Positives = 35/59 (59%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           IFV G+  + + E + D F ++GEI++     D+ +G  KGY  I ++T+  A+ A++ 
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEG 67

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

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 44.8 bits (106), Expect = 6e-05
 Identities = 16/70 (22%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 20  KQLQQEPPKQEEPIEE--EEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEE 77
            + Q+   +  + +++  ++  E  +E    E  E + +EE+ ++EE +  QKE  +E++
Sbjct: 365 DKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADEDK 424

Query: 78  KADQNDEEDD 87
           +  Q DE   
Sbjct: 425 EKRQKDERKK 434

Length = 434

>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 41.1 bits (97), Expect = 6e-05
 Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 2/66 (3%)

Query: 133 IFVHGLGWDTKAETLIDAF-KQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           +FV  L  D     L + F K+Y   +  K V D+ +G S+GYGF+ F   S  ++AL E
Sbjct: 4   LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQ-NGNSRGYGFVRFSDESEQKRALTE 62

Query: 192 PQKKIG 197
            Q   G
Sbjct: 63  MQGASG 68

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

>gnl|CDD|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 = 40.7 bits (96), Expect = 6e-05
 Identities = 16/59 (27%), Positives = 30/59 (50%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           +F++ L  +   + L   F  +G +   K   DK +G+SK +GF+ +     A+ A+K 
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKA 59

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

>gnl|CDD|220284 pfam09538, FYDLN_acid, Protein of unknown function (FYDLN_acid)

 Score = 41.5 bits (98), Expect = 6e-05
 Identities = 13/53 (24%), Positives = 29/53 (54%)

Query: 36 EEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
          EE   EV +      + E+  +++E+EE+E     +D+++++  D   + DD+
Sbjct: 34 EEVPPEVAKSRAPAADAEDAAKKDEDEEDEDDVVLDDDDDDDDDDDLPDLDDD 86

Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown. Length = 104

>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 41.2 bits (97), Expect = 6e-05
 Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 3/77 (3%)

Query: 247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKAL 306
           +  IFV  +  ++  ++L   FS++G+I E  L I +A      F    ++   AA +A+
Sbjct: 3   KYSIFVGQLSPDVTKEELNERFSRHGKILEVNL-IKRANHTN-AFAFIKFEREQAAARAV 60

Query: 307 E-EPHKNFEGHILNCQR 322
           E E H   +   ++ Q 
Sbjct: 61  ESENHSMLKNKTMHVQY 77

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

 Score = 40.9 bits (96), Expect = 6e-05
 Identities = 27/71 (38%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           ++F+ N+      + L   FSKYG + E  L IDK T KPKGF    Y   + A KA  E
Sbjct: 4   RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63

Query: 309 -PHKNFEGHIL 318
                F+G +L
Sbjct: 64  LDGTVFQGRLL 74

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|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 41.3 bits (96), Expect = 6e-05
 Identities = 22/57 (38%), Positives = 31/57 (54%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           + V+ L  +   E     F   GEIE CK V DK++G+S GYGF+ +     A KA+
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

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

 Score = 40.8 bits (95), Expect = 7e-05
 Identities = 19/71 (26%), Positives = 34/71 (47%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           K+F+  +  +  P  L  +FSK+GEI E  +  D  T + +GF    +    +  K L +
Sbjct: 1   KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60

Query: 309 PHKNFEGHILN 319
           PH   +   ++
Sbjct: 61  PHHELDSKTID 71

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

 Score = 41.1 bits (96), Expect = 7e-05
 Identities = 21/49 (42%), Positives = 33/49 (67%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILF 179
           +KIFV G+  DT+   L D F++YG+IE  + + D+ SGK +G+ F+ F
Sbjct: 1   KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTF 49

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|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional

 Score = 44.8 bits (106), Expect = 7e-05
 Identities = 17/61 (27%), Positives = 29/61 (47%)

Query: 17  PPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEE 76
             Q++ ++   ++ E   E E  E  EE+          E+E E+E+E +  Q E+EEE 
Sbjct: 389 ISQREEEEALQREAEERLEAEQAERAEEDARLRELYPLPEDEFEDEDELEEAQPEEEEEA 448

Query: 77  E 77
            
Sbjct: 449 R 449

Length = 449

>gnl|CDD|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional

 Score = 44.8 bits (106), Expect = 7e-05
 Identities = 17/73 (23%), Positives = 36/73 (49%)

Query: 6   KHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEE 65
             +++ ++  E   ++ ++E  ++E     E  + E  EE     E     E+E E+E+E
Sbjct: 377 DQEAEDAKVAELISQREEEEALQREAEERLEAEQAERAEEDARLRELYPLPEDEFEDEDE 436

Query: 66  KADQKEDEEEEEK 78
             + + +EEEE +
Sbjct: 437 LEEAQPEEEEEAR 449

Length = 449

>gnl|CDD|220377 pfam09747, DUF2052, Coiled-coil domain containing protein (DUF2052)

 Score = 43.2 bits (102), Expect = 7e-05
 Identities = 28/63 (44%), Positives = 33/63 (52%), Gaps = 4/63 (6%)

Query: 30  EEPIEEEEYEEEVEEEGEEEG----EEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEE 85
           E  ++ EE   E+ E+ EEE     EEE+ EEE EEEEEE       EEEEE  D  DE 
Sbjct: 61  ESSLDREEARLELLEQQEEEESAEEEEEDPEEENEEEEEEYQRGPFGEEEEEDGDSYDEL 120

Query: 86  DDE 88
              
Sbjct: 121 PTP 123

This entry is of sequences of two conserved domains separated by a region of low complexity, spanning some 200 residues. The function is unknown. Length = 178

>gnl|CDD|220284 pfam09538, FYDLN_acid, Protein of unknown function (FYDLN_acid)

 Score = 41.5 bits (98), Expect = 7e-05
 Identities = 13/65 (20%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

Query: 25  EPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEE-EEKADQND 83
           E  K   P  + E   + +E+ E+E +   +++++++++++  D  +D+ + ++  D   
Sbjct: 39  EVAKSRAPAADAEDAAKKDEDEEDEDDVVLDDDDDDDDDDDLPDLDDDDVDLDDDDDDFL 98

Query: 84  EEDDE 88
           E+DD+
Sbjct: 99  EDDDD 103

Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown. Length = 104

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 45.0 bits (107), Expect = 7e-05
 Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 5/77 (6%)

Query: 27  PKQEEPIEEEEYEEEVEEEGEEE--GEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDE 84
            K+    EE E E +VE E   E  G ++E+E   EE+    +++KED ++ E  D+ + 
Sbjct: 226 LKETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLDKLEI 285

Query: 85  ---EDDEPILSLLEPFS 98
              + DE +    +P+ 
Sbjct: 286 LKEKKDEELFWFEKPWP 302

The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 45.0 bits (107), Expect = 7e-05
 Identities = 26/85 (30%), Positives = 39/85 (45%), Gaps = 6/85 (7%)

Query: 26  PPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEE 85
             K +E  E EE EEE + E E   E +  ++E+E   EE  D     EE+E  D+ ++ 
Sbjct: 223 TKKLKETSETEEREEETDVEIETTSETKGTKQEQEGSTEE--DPSLFSEEKEDPDKTEDL 280

Query: 86  DDEPILSLLEP---FSKDQ-LVNLL 106
           D   IL   +    F  ++    LL
Sbjct: 281 DKLEILKEKKDEELFWFEKPWPTLL 305

The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 44.2 bits (104), Expect = 7e-05
 Identities = 54/249 (21%), Positives = 89/249 (35%), Gaps = 49/249 (19%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           + V+ L  D     L   F+  G I  C+ + D  +G S GY F+ F + + +++A+K  
Sbjct: 110 LIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNL 169

Query: 193 QK-KIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIF 251
               + N+      A  G                                        ++
Sbjct: 170 NGITVRNKRLKVSYARPG--------------------------------GESIKDTNLY 197

Query: 252 VSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHK 311
           V+N+   +   +L   F KYG+I +  +  DK TG P+G     +   + A++A+     
Sbjct: 198 VTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISA--- 254

Query: 312 NFEGHILNCQRAIDGPKPGKSR----HHNAQNPHFQRNEGAGYVGGAGPAAAG-PGHLMA 366
                 LN      G +P   R    H  A+  H+    G G +G  G    G  G   +
Sbjct: 255 ------LNNVIPEGGSQPLTVRLAEEHGKAKAHHYMSQMGHGNMGNMGHGNMGMAGG--S 306

Query: 367 PSGPAIPPA 375
              P  PPA
Sbjct: 307 GMNPPNPPA 315

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|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 45.0 bits (106), Expect = 8e-05
 Identities = 25/81 (30%), Positives = 39/81 (48%), Gaps = 3/81 (3%)

Query: 10  KTSEPTEPPQKQLQQEPPK---QEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEK 66
           +T E  E P +   +   +   + E   E E + E E EGE   E + E+E E E E ++
Sbjct: 644 RTGEEGERPTEAEGENGEESGGEAEQEGETETKGENESEGEIPAERKGEQEGEGEIEAKE 703

Query: 67  ADQKEDEEEEEKADQNDEEDD 87
           AD K + E EE   + + E +
Sbjct: 704 ADHKGETEAEEVEHEGETEAE 724

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 44.8 bits (106), Expect = 8e-05
 Identities = 21/46 (45%), Positives = 37/46 (80%)

Query: 33 IEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEK 78
          +E+E  +E  +EE EEE EE++EEEE+  ++EE+ D++E++EE++K
Sbjct: 27 VEKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKK 72

Length = 529

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 40.3 bits (95), Expect = 8e-05
 Identities = 22/72 (30%), Positives = 31/72 (43%), Gaps = 9/72 (12%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           ++V GLG     + L D F Q+GEI     V        +   F+ F TR  A KA +  
Sbjct: 4   LYVGGLGERVTEKDLRDHFYQFGEIRSITVV------PRQQCAFVTFTTREAAEKAAERL 57

Query: 193 QKKI---GNRMT 201
             K+   G R+ 
Sbjct: 58  FNKLIINGRRLK 69

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|215774 pfam00183, HSP90, Hsp90 protein

 Score = 44.4 bits (105), Expect = 9e-05
 Identities = 21/59 (35%), Positives = 40/59 (67%)

Query: 30 EEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
          E+ +E+E  +EE EEE EE+ EEEE+  ++EEE +E+ +++E +++ +K  +   E + 
Sbjct: 28 EKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEWEL 86

Length = 529

>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230; Provisional

 Score = 44.7 bits (105), Expect = 9e-05
 Identities = 30/125 (24%), Positives = 56/125 (44%)

Query: 3   KKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEE 62
           K    D           + L +E     +    ++ +E+ +E+ ++E ++EEEEEEEEE 
Sbjct: 121 KAEIGDLDMIIIKRRRARHLAEEDMSPRDNFVIDDDDEDEDEDDDDEEDDEEEEEEEEEI 180

Query: 63  EEEKADQKEDEEEEEKADQNDEEDDEPILSLLEPFSKDQLVNLLREAAENHRDVASRVRQ 122
           +    + +EDE  E+   +  E D       +E  + D + + + EA E        V Q
Sbjct: 181 KGFDDEDEEDEGGEDFTYEKSEVDKTDCFKFIEAGAGDDVFDKIDEAFETTEKGDGAVLQ 240

Query: 123 VADED 127
            +D++
Sbjct: 241 ASDDE 245

Length = 2849

>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 40.5 bits (94), Expect = 9e-05
 Identities = 19/39 (48%), Positives = 26/39 (66%)

Query: 151 FKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           F   GEIE CK V DK++G+S GYGF+ +   + A KA+
Sbjct: 24  FGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAI 62

This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

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

 Score = 40.3 bits (95), Expect = 9e-05
 Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 3/56 (5%)

Query: 153 QYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP--QKKIGNRMTACQLA 206
            +G +E C  V  + +G+SKGYGF+ + +++ A KA K     K+IG R      A
Sbjct: 22  PFGAVERCFLVYSESTGESKGYGFVEYASKASALKA-KNQLDGKQIGGRKLQVDWA 76

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

>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)

 Score = 44.2 bits (104), Expect = 9e-05
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 12  SEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKE 71
           ++P E   K   + P K E   +E+  E E EE+ EEEG   ++ ++ ++ + +K    +
Sbjct: 295 NDPEEREDKLSPEIPAKPEIEQDEDSEESE-EEKNEEEGGLSKKGKKLKKLKGKKNGLDK 353

Query: 72  DEEEEEKADQNDEEDDE 88
           D+ +      + + D E
Sbjct: 354 DDSDSGDDSDDSDIDGE 370

Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II. Length = 528

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 44.6 bits (105), Expect = 1e-04
 Identities = 23/68 (33%), Positives = 33/68 (48%)

Query: 23  QQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQN 82
           + E P + E    EE   E E+EGE E + E E E E   E +   + E E E ++AD  
Sbjct: 648 EGERPTEAEGENGEESGGEAEQEGETETKGENESEGEIPAERKGEQEGEGEIEAKEADHK 707

Query: 83  DEEDDEPI 90
            E + E +
Sbjct: 708 GETEAEEV 715

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 43.2 bits (102), Expect = 1e-04
 Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 17  PPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEE-EEEKADQKEDEEE 75
           P     Q    +QE    +++   E+EE  EEE E    E++E++   E++ ++ E+E E
Sbjct: 37  PSSPSDQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENE 96

Query: 76  EEKADQNDEEDDEP 89
           EE  + +DE + E 
Sbjct: 97  EEDEESSDENEKET 110

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. Length = 214

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 43.8 bits (104), Expect = 1e-04
 Identities = 23/64 (35%), Positives = 46/64 (71%)

Query: 20  KQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKA 79
           K++++   K E+  EEE+ E++ +    ++ EEEEEEE+E++EEE++ +++E EEE+E+ 
Sbjct: 410 KKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEE 469

Query: 80  DQND 83
           ++  
Sbjct: 470 EEKK 473

Length = 482

>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 = 40.2 bits (95), Expect = 1e-04
 Identities = 22/59 (37%), Positives = 35/59 (59%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           K+FV  L      E +   F++YG IE+   + DK +G+SKG  F+ F +R  A+KA++
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIE 59

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|215774 pfam00183, HSP90, Hsp90 protein

 Score = 44.0 bits (104), Expect = 1e-04
 Identities = 22/62 (35%), Positives = 40/62 (64%)

Query: 20 KQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKA 79
          K++++E P +EE  E+EE +EE E+  ++E E +EEEE+EE++++ K  ++   E E   
Sbjct: 29 KEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEWELLN 88

Query: 80 DQ 81
            
Sbjct: 89 KT 90

Length = 529

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

 Score = 40.0 bits (93), Expect = 1e-04
 Identities = 24/66 (36%), Positives = 38/66 (57%), Gaps = 1/66 (1%)

Query: 126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGA 185
           +DPV +KIFV GL  +   E + + F ++GEIE  +   D  + K +G+ FI FK     
Sbjct: 1   KDPV-KKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPV 59

Query: 186 RKALKE 191
           +K L++
Sbjct: 60  KKVLEK 65

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|222571 pfam14153, Spore_coat_CotO, Spore coat protein CotO

 Score = 42.1 bits (99), Expect = 1e-04
 Identities = 21/81 (25%), Positives = 44/81 (54%), Gaps = 1/81 (1%)

Query: 19  QKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEK 78
            ++ +++    E    +EE ++   EE E+E E  E E E+  E++EK +  ++EE+EE+
Sbjct: 37  DEKEEEKENSDEHVKSKEEEQKIEYEEAEKEKEAGEPEREDIAEQQEKEEIAQEEEKEEE 96

Query: 79  ADQNDEEDDEPILSLLEPFSK 99
           A+   +++        +PF +
Sbjct: 97  AEDVKQQEVFSFKR-KKPFKE 116

Bacillus spores are protected by a protein shell consisting of over 50 different polypeptides, known as the coat. This family of proteins has an important morphogenetic role in coat assembly, it is involved in the assembly of at least 5 different coat proteins including CotB, CotG, CotS, CotSA and CotW. It is likely to act at a late stage of coat assembly. Length = 185

>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 43.9 bits (104), Expect = 1e-04
 Identities = 20/55 (36%), Positives = 33/55 (60%), Gaps = 3/55 (5%)

Query: 23  QQEPPK---QEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEE 74
            +  P+    +E   EE  E+  EEE E++  E E+E+EE+E+EEE+ D  E ++
Sbjct: 265 VKGEPEVVGGDEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDDDEGDK 319

Length = 319

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

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 20/62 (32%), Positives = 35/62 (56%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           +FV  L +D   +++ +AF +YGEI   +   D  SG+ KG+G++ F ++  A+ AL   
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 193 QK 194
             
Sbjct: 61  GG 62

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 20/58 (34%), Positives = 29/58 (50%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           ++V N+   +    L   F  +GEIE   L  D  TG+ KG+    +   + AKKALE
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALE 58

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|217203 pfam02724, CDC45, CDC45-like protein

 Score = 43.8 bits (104), Expect = 1e-04
 Identities = 18/56 (32%), Positives = 35/56 (62%), Gaps = 3/56 (5%)

Query: 33  IEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
           IEEE  +E   ++   + EE+++++EE +EE+E   +    E++E  D +D++DD 
Sbjct: 106 IEEELQDEPRYDDAYRDLEEDDDDDEESDEEDE---ESSKSEDDEDDDDDDDDDDI 158

CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583

>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 44.3 bits (105), Expect = 1e-04
 Identities = 24/37 (64%), Positives = 25/37 (67%)

Query: 24  QEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEE 60
           + PP   EP EEEE EEEV EE EEE EEEE   EEE
Sbjct: 297 RPPPSPPEPEEEEEEEEEVPEEEEEEEEEEERTFEEE 333

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 43.9 bits (104), Expect = 1e-04
 Identities = 24/38 (63%), Positives = 24/38 (63%), Gaps = 2/38 (5%)

Query: 26  PPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEE 63
           PP    P E EE EEE EE  EEE EEEEEEE   EEE
Sbjct: 298 PP--PSPPEPEEEEEEEEEVPEEEEEEEEEEERTFEEE 333

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

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

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 16/45 (35%), Positives = 23/45 (51%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFI 177
           IFV+ L  D     L   F  +G + + K + D  + K KGYGF+
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFV 48

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

>gnl|CDD|225880 COG3343, RpoE, DNA-directed RNA polymerase, delta subunit [Transcription]

 Score = 42.4 bits (100), Expect = 1e-04
 Identities = 22/83 (26%), Positives = 49/83 (59%), Gaps = 2/83 (2%)

Query: 8   DSKTSEPTEPPQKQLQQEPPKQEEPIEEEE--YEEEVEEEGEEEGEEEEEEEEEEEEEEE 65
           D +    TE    + + +     E  +E+E  Y+E+ EEE ++E +  ++E ++E+E+++
Sbjct: 88  DEEIQAMTEKKDIKAKDKEVDAFEEGDEDELDYDEDKEEEEDDEVDSLDDENDDEDEDDD 147

Query: 66  KADQKEDEEEEEKADQNDEEDDE 88
           +  +   E++E   D++D+ED+E
Sbjct: 148 EIVEILIEDDEVDEDEDDDEDEE 170

Length = 175

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

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 19/58 (32%), Positives = 32/58 (55%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           +FV  + ++   E L D F + G +   + V D+ +GK KGYGF  +K +  A  A++
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMR 58

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

>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 20/57 (35%), Positives = 28/57 (49%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           ++V  + + + AE L   F   G I     +CDK SG  KGY +I F TR     A+
Sbjct: 2   VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAV 58

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 16/57 (28%), Positives = 30/57 (52%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           ++V GL  +   + L  AF  +G+I+D +   D  + K +G+ F+ F+    A  A+
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAI 57

This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. . Length = 73

>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 1/59 (1%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           ++ V  L    K + L   F+ +G I D +    K  GK + +GF+ +KT   A+KALK
Sbjct: 2   RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTK-DGKFRKFGFVGYKTEEEAQKALK 59

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|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 39.9 bits (93), Expect = 1e-04
 Identities = 19/48 (39%), Positives = 26/48 (54%)

Query: 144 AETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
            E   +  + YG IE C  V  +V+G SKGYGF+ +  +  A KA  E
Sbjct: 13  LEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLE 60

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

>gnl|CDD|221490 pfam12253, CAF1A, Chromatin assembly factor 1 subunit A

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 22/54 (40%), Positives = 34/54 (62%)

Query: 15 TEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKAD 68
          T+P    L + P  Q+ P  + +Y+ + E E EEEGE+ E E+EE+EEE++  D
Sbjct: 19 TKPSSVILPRNPLSQDLPGLDYDYDSDAEWEEEEEGEDLESEDEEDEEEDDDDD 72

The CAF-1 or chromatin assembly factor-1 consists of three subunits, and this is the first, or A. The A domain is uniquely required for the progression of S phase in mouse cells, independent of its ability to promote histone deposition but dependent on its ability to interact with HP1 - heterochromatin protein 1-rich heterochromatin domains next to centromeres that are crucial for chromosome segregation during mitosis. This HP1-CAF-1 interaction module functions as a built-in replication control for heterochromatin, which, like a control barrier, has an impact on S-phase progression in addition to DNA-based checkpoints. Length = 76

>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 42.3 bits (100), Expect = 1e-04
 Identities = 22/55 (40%), Positives = 30/55 (54%)

Query: 29 QEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQND 83
          + E +EEE  E EVEE  E+E EEE  EEE E E  ++   K  E E +  +  +
Sbjct: 4  KNEQVEEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQAKIAELEAKLDELEE 58

Length = 191

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

 Score = 43.3 bits (102), Expect = 2e-04
 Identities = 46/216 (21%), Positives = 83/216 (38%), Gaps = 46/216 (21%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           ++V  L  D     L D FK +G +   +   D V+ +S GYG++ F+  + A +AL+  
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 193 Q-KKIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRK-- 249
             K++G +      +   P+                                    R+  
Sbjct: 63  NFKRLGGKPIRIMWSQRDPSL-----------------------------------RRSG 87

Query: 250 ---IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKAL 306
              IFV N+   ++ + L   FSK+G I    +  D+  GK +G+    ++  ++AK A+
Sbjct: 88  VGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAI 146

Query: 307 EEPHKNFEGHILNCQRAIDGPKPGKSRHHNAQNPHF 342
           ++      G +LN +    G    K     A    F
Sbjct: 147 QK----VNGMLLNDKEVYVGRFIKKHEREAAPLKKF 178

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|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 43.4 bits (102), Expect = 2e-04
 Identities = 25/42 (59%), Positives = 27/42 (64%)

Query: 30  EEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKE 71
           EE  EEEE EEE EEE EEE EEEEE EE    E  +  QK+
Sbjct: 864 EEEEEEEEEEEEEEEEEEEEEEEEEENEEPLSLEWPETRQKQ 905

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 43.7 bits (103), Expect = 2e-04
 Identities = 31/96 (32%), Positives = 47/96 (48%), Gaps = 7/96 (7%)

Query: 10  KTSEPTEPPQKQLQQEPPKQEEPIEEEEYEE----EVEEEGEEEGEEEEEEEEEEEEEEE 65
               P+   Q+  ++E  ++EE  EEEE EE    E EE  +EE EEEE E +   EEE 
Sbjct: 428 SGESPSMASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEE-EEEEVEADNGSEEEM 486

Query: 66  KADQKEDEEEEEKADQNDEEDDEPILSLLEPFSKDQ 101
           +   + D + EE  +  D E     ++ +   S+ Q
Sbjct: 487 EGSSEGDGDGEEPEE--DAERRNSEMAGISRMSEGQ 520

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM)

 Score = 41.4 bits (97), Expect = 2e-04
 Identities = 22/50 (44%), Positives = 40/50 (80%), Gaps = 1/50 (2%)

Query: 40 EEVEEEGEEEGEEEEEEEEEE-EEEEEKADQKEDEEEEEKADQNDEEDDE 88
          E+V++E +E+ EEEEEE+EEE EE E+  D++E  E+EE+ ++++E++ +
Sbjct: 41 EDVKDEKQEDDEEEEEEDEEEIEEPEDIEDEEEIVEDEEEEEEDEEDNVD 90

This family consists of several Plasmodium falciparum SPAM (secreted polymorphic antigen associated with merozoites) proteins. Variation among SPAM alleles is the result of deletions and amino acid substitutions in non-repetitive sequences within and flanking the alanine heptad-repeat domain. Heptad repeats in which the a and d position contain hydrophobic residues generate amphipathic alpha-helices which give rise to helical bundles or coiled-coil structures in proteins. SPAM is an example of a P. falciparum antigen in which a repetitive sequence has features characteristic of a well-defined structural element. Length = 164

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 42.4 bits (100), Expect = 2e-04
 Identities = 24/77 (31%), Positives = 47/77 (61%), Gaps = 1/77 (1%)

Query: 14  PTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDE 73
           P+ P  +    E   ++   +E    EEV+EE +E    E++E++ + E+E++  ++E+E
Sbjct: 37  PSSPSDQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENE 96

Query: 74  EE-EEKADQNDEEDDEP 89
           EE EE +D+N++E +E 
Sbjct: 97  EEDEESSDENEKETEEK 113

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. Length = 214

>gnl|CDD|220972 pfam11081, DUF2890, Protein of unknown function (DUF2890)

 Score = 41.8 bits (98), Expect = 2e-04
 Identities = 24/70 (34%), Positives = 34/70 (48%), Gaps = 2/70 (2%)

Query: 1  MAKKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEE 60
          M  K    +K  +   PP K  +++   Q E +EE+E E E  E+  +E +EE EE EEE
Sbjct: 1  MPPKGN--AKKLKVRPPPTKDEEEDWDSQAEEVEEDEEEMEDWEDSLDEEDEEAEEVEEE 58

Query: 61 EEEEEKADQK 70
               KA   
Sbjct: 59 TAASSKAPSS 68

This family is conserved in dsDNA adenoviruses of vertebrates. The function is not known. Length = 172

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

 Score = 39.7 bits (92), Expect = 2e-04
 Identities = 19/77 (24%), Positives = 38/77 (49%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           +K+FV  +  + E   L  +F +YG+I+   +  D+ +GK +GF    +   D   K + 
Sbjct: 1   KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVL 60

Query: 308 EPHKNFEGHILNCQRAI 324
           + +    GH    ++A+
Sbjct: 61  QKYHTINGHNAEVRKAL 77

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|220284 pfam09538, FYDLN_acid, Protein of unknown function (FYDLN_acid)

 Score = 40.4 bits (95), Expect = 2e-04
 Identities = 7/60 (11%), Positives = 35/60 (58%)

Query: 24  QEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQND 83
                 E+  +++E EE+ ++   ++ ++++++++  + +++  D  +D+++  + D ++
Sbjct: 45  APAADAEDAAKKDEDEEDEDDVVLDDDDDDDDDDDLPDLDDDDVDLDDDDDDFLEDDDDE 104

Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown. Length = 104

>gnl|CDD|225880 COG3343, RpoE, DNA-directed RNA polymerase, delta subunit [Transcription]

 Score = 42.0 bits (99), Expect = 2e-04
 Identities = 20/55 (36%), Positives = 34/55 (61%), Gaps = 5/55 (9%)

Query: 35  EEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDEP 89
           EEE ++EV+   +E  +E+E+++E  E   E  +  EDE+++E     DEED+E 
Sbjct: 125 EEEEDDEVDSLDDENDDEDEDDDEIVEILIEDDEVDEDEDDDE-----DEEDEED 174

Length = 175

>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 1/65 (1%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           ++ V N+   ++  KL   F  +G I +  L   K  GK + F    YKT + A+KAL+ 
Sbjct: 2   RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTK-DGKFRKFGFVGYKTEEEAQKALKH 60

Query: 309 PHKNF 313
            + +F
Sbjct: 61  FNNSF 65

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 39.0 bits (92), Expect = 2e-04
 Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 6/54 (11%)

Query: 147 LIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE-PQKKIGNR 199
           L   F  +G +E  K     +  K  G+ F+ F T   A KA++       G R
Sbjct: 1   LYKLFSPFGNVEKIK-----LLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGR 49

(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|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 24/89 (26%), Positives = 36/89 (40%), Gaps = 17/89 (19%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIE----------EGPLGIDKATGKPK-----GFC 292
           R +FV N+    + + L   F ++G IE          E  L    A  K K        
Sbjct: 1   RTVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNV 60

Query: 293 LF--VYKTVDAAKKALEEPHKNFEGHILN 319
               V+K  ++A+KAL+     FEGH + 
Sbjct: 61  NAYVVFKEEESAEKALKLNGTEFEGHHIR 89

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|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 7/73 (9%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK- 190
           +IFV  +  D   + L+  F++ G I D + + D ++G ++GY F+ F T+  A++A+K 
Sbjct: 3   EIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKL 62

Query: 191 ------EPQKKIG 197
                  P K IG
Sbjct: 63  YNNHEIRPGKHIG 75

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

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 18/59 (30%), Positives = 31/59 (52%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           K+FV  +  +   +++  +F  +GEIE   L +D  T + +GFC   Y   +  +K LE
Sbjct: 1   KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLE 59

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|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 39.8 bits (92), Expect = 2e-04
 Identities = 21/57 (36%), Positives = 35/57 (61%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           +++ GL   T  + LI   + YG+I   KA+ DK + + KGYGF+ F + + A+KA+
Sbjct: 7   LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAV 63

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 19/59 (32%), Positives = 36/59 (61%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           ++FV  +  D   + L+  F++ G I D + + D +SG+++GY FI F  +  A++A+K
Sbjct: 3   EVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVK 61

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|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 43.7 bits (103), Expect = 2e-04
 Identities = 26/82 (31%), Positives = 44/82 (53%), Gaps = 4/82 (4%)

Query: 11  TSEPT--EPPQKQLQQEPPKQEEPIEEEEYEEEVEE-EGEEEGEEEEEEEEEEEEEEEKA 67
            +E T  +  ++   +E    ++P   E+ E   EE EG +E EE+E E  + E EE + 
Sbjct: 218 MAEETGDDGIEEDADEEDGDDDQPDNNEDSEAGREESEGSDESEEDEAEATDGEGEEGEM 277

Query: 68  DQKEDEEEEEKADQNDEEDDEP 89
           D  E  E+ E +D++DE+ + P
Sbjct: 278 DAAEASEDSE-SDESDEDTETP 298

Length = 620

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

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 18/76 (23%), Positives = 31/76 (40%), Gaps = 1/76 (1%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           KIF+  + + L   ++      +G+++   L  D ATG  KG+    Y       +A+  
Sbjct: 2   KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61

Query: 309 PH-KNFEGHILNCQRA 323
            +        L  QRA
Sbjct: 62  LNGMQLGDKKLTVQRA 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|233870 TIGR02442, Cob-chelat-sub, cobaltochelatase subunit

 Score = 43.5 bits (103), Expect = 2e-04
 Identities = 14/72 (19%), Positives = 30/72 (41%)

Query: 16  EPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEE 75
           +P ++   ++    EE  EE   + E  +EGE++ E+           +++ +    EE 
Sbjct: 312 KPFEQPQGKDEKDLEEKPEEPGPDPEKPDEGEDDAEQSGPRGHPTPGNDDEKEPDPQEEA 371

Query: 76  EEKADQNDEEDD 87
           + +    D   D
Sbjct: 372 DGQGSSTDPAGD 383

Cobaltochelatase is responsible for the insertion of cobalt into the corrin ring of coenzyme B12 during its biosynthesis. Two versions have been well described. CbiK/CbiX is a monomeric, anaerobic version which acts early in the biosynthesis (pfam06180). CobNST is a trimeric, ATP-dependent, aerobic version which acts late in the biosynthesis (TIGR02257/TIGR01650/TIGR01651). A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis. Length = 633

>gnl|CDD|233870 TIGR02442, Cob-chelat-sub, cobaltochelatase subunit

 Score = 43.5 bits (103), Expect = 2e-04
 Identities = 22/98 (22%), Positives = 43/98 (43%), Gaps = 3/98 (3%)

Query: 22  LQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQ 81
            +++P +Q +  +E++ EE+ EE G +   E+ +E E++ E+           ++EK   
Sbjct: 309 RRRKPFEQPQGKDEKDLEEKPEEPGPDP--EKPDEGEDDAEQSGPRGHPTPGNDDEKEPD 366

Query: 82  NDEEDDEPILSLLEPFSKDQLVNLLREAAENHRDVASR 119
             EE D    S  +P      + +L       R  + R
Sbjct: 367 PQEEADGQG-SSTDPAGDIFRIRVLAPPQARARGASGR 403

Cobaltochelatase is responsible for the insertion of cobalt into the corrin ring of coenzyme B12 during its biosynthesis. Two versions have been well described. CbiK/CbiX is a monomeric, anaerobic version which acts early in the biosynthesis (pfam06180). CobNST is a trimeric, ATP-dependent, aerobic version which acts late in the biosynthesis (TIGR02257/TIGR01650/TIGR01651). A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis. Length = 633

>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457)

 Score = 43.1 bits (101), Expect = 2e-04
 Identities = 19/39 (48%), Positives = 30/39 (76%)

Query: 50 GEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
          G+E EEE  EEE+++E+ D  +D+E+E+  D +D+EDDE
Sbjct: 42 GKEAEEEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDE 80

This is a family of uncharacterized proteins. Length = 449

>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated

 Score = 43.2 bits (103), Expect = 2e-04
 Identities = 31/136 (22%), Positives = 53/136 (38%), Gaps = 30/136 (22%)

Query: 30  EEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEE-------------- 75
            +P  EE+      E  E + +E+EEEEE+E ++   AD+ E  E+              
Sbjct: 174 VDPNAEEDPAHVGSELEELDDDEDEEEEEDENDDSLAADESELPEKVLEKFKALAKQYKK 233

Query: 76  ----EEKADQNDEEDDEPILSLLE----------PFSK--DQLVNLLREAAENHRDVASR 119
               +EK  +      +    L E            SK  D+LV  LR+  +  R     
Sbjct: 234 LRKAQEKKVEGRLAQHKKYAKLREKLKEELKSLRLTSKQIDELVEQLRDINKRVRGQERE 293

Query: 120 VRQVADEDPVHRKIFV 135
           + ++ +   + RK F+
Sbjct: 294 LLRLVERLKMPRKDFL 309

Length = 619

>gnl|CDD|217450 pfam03247, Prothymosin, Prothymosin/parathymosin family

 Score = 39.9 bits (93), Expect = 2e-04
 Identities = 32/87 (36%), Positives = 48/87 (55%), Gaps = 1/87 (1%)

Query: 3   KKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEE-GEEEEEEEEEEE 61
           +K++   +       P    + E    +E  +E E EEEV+E+ EEE GE EEEE EEEE
Sbjct: 18  EKKEVVEEKENGKNAPANGNENEENGAQEGDDEMEEEEEVDEDDEEEEGEGEEEEGEEEE 77

Query: 62  EEEEKADQKEDEEEEEKADQNDEEDDE 88
           E E    ++  E+EE+ A+   ++ DE
Sbjct: 78  ETEGATGKRAAEDEEDDAETKKQKTDE 104

Prothymosin alpha and parathymosin are two ubiquitous small acidic nuclear proteins that are thought to be involved in cell cycle progression, proliferation, and cell differentiation. Length = 106

>gnl|CDD|217450 pfam03247, Prothymosin, Prothymosin/parathymosin family

 Score = 39.9 bits (93), Expect = 2e-04
 Identities = 26/63 (41%), Positives = 37/63 (58%)

Query: 24  QEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQND 83
            +    E   EEE  E++ EEEGE E EE EEEEE E    ++A + E+++ E K  + D
Sbjct: 44  AQEGDDEMEEEEEVDEDDEEEEGEGEEEEGEEEEETEGATGKRAAEDEEDDAETKKQKTD 103

Query: 84  EED 86
           E+D
Sbjct: 104 EDD 106

Prothymosin alpha and parathymosin are two ubiquitous small acidic nuclear proteins that are thought to be involved in cell cycle progression, proliferation, and cell differentiation. Length = 106

>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381)

 Score = 41.1 bits (97), Expect = 2e-04
 Identities = 20/52 (38%), Positives = 32/52 (61%), Gaps = 1/52 (1%)

Query: 33  IEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDE 84
           ++++E EEE EEE E E E +EEE+ +E  E+E A  K ++  E +  Q + 
Sbjct: 96  LDKKEKEEEEEEEVEVE-ELDEEEQIDELLEKELAKLKREKRRENERKQKEI 146

This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 156 to 174 amino acids in length. This domain is found associated with pfam07780, pfam01728. Length = 154

>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 = 2e-04
 Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 5/69 (7%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           R +FV G    T  E L+D F  +G + +   + DK  G    Y  + F ++ G  K L 
Sbjct: 3   RSVFVSGFKRGTSEEQLMDYFSAFGPVMN--VIMDKDKGV---YAIVEFDSKEGVDKVLS 57

Query: 191 EPQKKIGNR 199
           EPQ  +   
Sbjct: 58  EPQHTLNGH 66

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

 Score = 40.8 bits (95), Expect = 3e-04
 Identities = 25/116 (21%), Positives = 45/116 (38%), Gaps = 4/116 (3%)

Query: 245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKK 304
               K+F+  +    +   L   F+ +G++ +  + +D+ TG+ +GF    +    AA  
Sbjct: 32  LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATA 91

Query: 305 ALEEPHKNFEGHILNCQRAIDGPKPGKSRHHNAQNPHFQRNEGAGYVGGAGPAAAG 360
           A+ E     +G  LN +     P   +     A       + G G  GG G    G
Sbjct: 92  AISE----MDGKELNGRHIRVNPANDRPSAPRAYGGGGGYSGGGGGYGGGGDGGGG 143

Length = 144

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 43.1 bits (101), Expect = 3e-04
 Identities = 23/87 (26%), Positives = 38/87 (43%), Gaps = 13/87 (14%)

Query: 15  TEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQK---- 70
                K   +   +  E  E E   E   ++ E + E  E+E   E + E K D+K    
Sbjct: 795 EGAEGKVEHEGETEAGEKDEHEGQSETQADDTEVKDETGEQELNAENQGEAKQDEKGVDG 854

Query: 71  ---------EDEEEEEKADQNDEEDDE 88
                    E+EEEEE+ ++ +EE++E
Sbjct: 855 GGGSDGGDSEEEEEEEEEEEEEEEEEE 881

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 42.6 bits (101), Expect = 3e-04
 Identities = 28/69 (40%), Positives = 42/69 (60%)

Query: 2   AKKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEE 61
            KK K   + +E     +K+ +++     +  EEEE EE+ ++E E+E EEEE EEE+EE
Sbjct: 409 TKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEE 468

Query: 62  EEEEKADQK 70
           EEE+K  Q 
Sbjct: 469 EEEKKKKQA 477

Length = 482

>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 42.3 bits (100), Expect = 3e-04
 Identities = 20/45 (44%), Positives = 31/45 (68%)

Query: 43  EEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDD 87
           +EE  EE  E+ EEEEEE++  E  D+ E++E+EE+ + +DE D 
Sbjct: 275 DEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDDDEGDK 319

Length = 319

>gnl|CDD|220135 pfam09184, PPP4R2, PPP4R2

 Score = 42.1 bits (99), Expect = 3e-04
 Identities = 14/77 (18%), Positives = 43/77 (55%), Gaps = 2/77 (2%)

Query: 14  PTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEE--EEKADQKE 71
            +   + +  +E  ++E        ++  +    +  + ++EE+++++ +  EEK  +++
Sbjct: 209 DSSQDKNKSLEEYYEKESSDAAASQDDGPKGSDVKNKKSDDEEDDDQDGDYVEEKELKED 268

Query: 72  DEEEEEKADQNDEEDDE 88
           +EEEE + ++ +E++DE
Sbjct: 269 EEEEETEEEEEEEDEDE 285

PPP4R2 (protein phosphatase 4 core regulatory subunit R2) is the regulatory subunit of the histone H2A phosphatase complex. It has been shown to confer resistance to the anticancer drug cisplatin in yeast, and may confer resistance in higher eukaryotes. Length = 285

>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi

 Score = 42.9 bits (101), Expect = 3e-04
 Identities = 16/85 (18%), Positives = 40/85 (47%)

Query: 28  KQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDD 87
           K +E     +   E EEE E++ EE +++E+E E  E+   + E + E+ + D+ +++ +
Sbjct: 633 KADENKSRHQQLFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDAE 692

Query: 88  EPILSLLEPFSKDQLVNLLREAAEN 112
                +    +  + +  +    + 
Sbjct: 693 ANEGVVPIDKAVRRALPKVLNLPDA 717

This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784

>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 43.1 bits (102), Expect = 3e-04
 Identities = 23/39 (58%), Positives = 23/39 (58%), Gaps = 2/39 (5%)

Query: 26  PPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEE 64
            P    P  EEE  EE EEE  EE EEEEEEEE   EEE
Sbjct: 297 RPPPSPPEPEEE--EEEEEEVPEEEEEEEEEEERTFEEE 333

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

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

 Score = 38.7 bits (91), Expect = 3e-04
 Identities = 14/63 (22%), Positives = 35/63 (55%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP 309
           ++V  +  E++ + L A F  +G+I++  + +D  T K +GF    ++  + A  A++  
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 310 HKN 312
           +++
Sbjct: 61  NES 63

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|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 41.5 bits (98), Expect = 3e-04
 Identities = 23/52 (44%), Positives = 32/52 (61%)

Query: 28 KQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKA 79
          + EE +EE E EE VE+E EEE  EEE E E  +EE+ K  + E + +E + 
Sbjct: 7  QVEEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQAKIAELEAKLDELEE 58

Length = 191

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 43.1 bits (102), Expect = 3e-04
 Identities = 32/107 (29%), Positives = 49/107 (45%), Gaps = 36/107 (33%)

Query: 21  QLQQEPPKQ--EEPIEEEEYEEEVEEEGEEEGE-------------------------EE 53
           QL++E  ++  EEP E +E EE  + EG E  E                          E
Sbjct: 286 QLEEEEEEEEEEEPAERDELEENPDFEGLEVRELADSLDNWVHHVQHILPQGRCTWVNPE 345

Query: 54  EEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDEPILSLLEPFSKD 100
           +++EEEE+E+EE+ +++E+ EE E          E    LL P S+D
Sbjct: 346 QKDEEEEQEDEEEEEEEEEPEEPEP---------EEGPPLLTPISED 383

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 39.3 bits (91), Expect = 3e-04
 Identities = 22/58 (37%), Positives = 32/58 (55%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           ++V GL      + L   F QYG I   + + D+V+G S+G GFI F  R  A +A+K
Sbjct: 5   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 62

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27

 Score = 42.9 bits (101), Expect = 3e-04
 Identities = 23/90 (25%), Positives = 47/90 (52%), Gaps = 2/90 (2%)

Query: 2   AKKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEE 61
            +    + +++EPT   + + + EP    E  + EE  EE E+E  +  ++  E+E+E+E
Sbjct: 250 KRDVILEDESAEPTGLDEDEDEDEPKPSGERSDSEEETEEKEKEKRKRLKKMMEDEDEDE 309

Query: 62  EEEEKAD--QKEDEEEEEKADQNDEEDDEP 89
           E E   +   +E+E EE +     ++++E 
Sbjct: 310 EMEIVPESPVEEEESEEPEPPPLPKKEEEK 339

This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterized by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif. Length = 427

>gnl|CDD|185618 PTZ00438, PTZ00438, gamete antigen 27/25-like protein; Provisional

 Score = 42.7 bits (100), Expect = 3e-04
 Identities = 30/91 (32%), Positives = 45/91 (49%), Gaps = 24/91 (26%)

Query: 22  LQQEPPKQEEPIEEEEY----------------EEEVEEEG--------EEEGEEEEEEE 57
            +Q+  +  + I  EEY                E +VE EG        EE G ++EEEE
Sbjct: 52  EEQDLSEACDYIAIEEYSACGNVASIANDKSDNENDVELEGLNIIVKNEEERGTQKEEEE 111

Query: 58  EEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
           +E+ EE E+ ++ E  EEE   D++ E+DDE
Sbjct: 112 DEDVEEIEEVEEVEVVEEEYDDDEDSEKDDE 142

Length = 374

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 43.2 bits (101), Expect = 3e-04
 Identities = 25/88 (28%), Positives = 50/88 (56%)

Query: 1    MAKKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEE 60
             AKK + D K +E  +  ++  ++     ++  EE +  EE++++  EE ++ EE ++ E
Sbjct: 1666 EAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAE 1725

Query: 61   EEEEEKADQKEDEEEEEKADQNDEEDDE 88
            EE + KA++ + E EE+K    + + DE
Sbjct: 1726 EENKIKAEEAKKEAEEDKKKAEEAKKDE 1753

Length = 2084

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 43.1 bits (101), Expect = 3e-04
 Identities = 19/86 (22%), Positives = 39/86 (45%), Gaps = 1/86 (1%)

Query: 27  PKQEEPIEEEEYEEEVEEEGEEE-GEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEE 85
            K ++    E+  +  + + E+   +EEEEEE+E  E+E   D+ E +   E     ++ 
Sbjct: 92  AKLQDSESHEDGSDGSDMDSEDSADDEEEEEEDESLEDEMIDDEDEADLFNESESSLEDL 151

Query: 86  DDEPILSLLEPFSKDQLVNLLREAAE 111
            D+      E   +++     +E+ E
Sbjct: 152 SDDETEDDEEKKMEEEEAGEEKESVE 177

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]

 Score = 43.1 bits (101), Expect = 3e-04
 Identities = 22/53 (41%), Positives = 31/53 (58%)

Query: 34  EEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEED 86
           E +E EEEV E      +E +E +E+EE +E   D  EDE E + +D+ D ED
Sbjct: 930 ESDESEEEVSEYEASSDDESDETDEDEESDESSEDLSEDESENDSSDEEDGED 982

Length = 1001

>gnl|CDD|235033 PRK02363, PRK02363, DNA-directed RNA polymerase subunit delta; Reviewed

 Score = 40.4 bits (95), Expect = 3e-04
 Identities = 14/56 (25%), Positives = 31/56 (55%), Gaps = 2/56 (3%)

Query: 33  IEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
           I+EE    E + + +++   + +++  +++     D  E++ +EE  D  DEED+E
Sbjct: 76  IDEEIIPLEEKFDKKKKKFMDGDDDIIDDDILPDDDFDEEDLDEE--DDEDEEDEE 129

Length = 129

>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region

 Score = 41.4 bits (98), Expect = 3e-04
 Identities = 15/66 (22%), Positives = 24/66 (36%), Gaps = 12/66 (18%)

Query: 36 EEYEEEVEEEG------------EEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQND 83
          E+Y+     EG                        E E +EE  +  +D++E+E  D  +
Sbjct: 10 EQYDRVEAGEGRLSDLISGFIDPNAAAAAATAAAIESELDEEDLEDDDDDDEDEDEDDEE 69

Query: 84 EEDDEP 89
          E D  P
Sbjct: 70 EADLGP 75

The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. Length = 211

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 39.2 bits (91), Expect = 3e-04
 Identities = 20/62 (32%), Positives = 32/62 (51%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           K+FV +V   +  Q++   F ++G + E  +  DK TG  +G C   Y T D A +A+  
Sbjct: 1   KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60

Query: 309 PH 310
            H
Sbjct: 61  LH 62

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

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 19/60 (31%), Positives = 32/60 (53%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           +++V ++  EL    +   FS +G I+   +  D  T K KGF    Y+  +AA+ ALE+
Sbjct: 2   RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61

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|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 40.8 bits (96), Expect = 3e-04
 Identities = 19/60 (31%), Positives = 36/60 (60%), Gaps = 3/60 (5%)

Query: 25 EPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDE---EEEEKADQ 81
          +  + EE  EE+E +E  +EE  +  ++E++EE + EEE+    ++E+E   E E + D+
Sbjct: 9  DGEEDEELPEEDEDDESSDEEEVDLPDDEQDEESDSEEEQIFVTRQEEEVDPEAEAEFDR 68

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 42.9 bits (100), Expect = 3e-04
 Identities = 33/109 (30%), Positives = 50/109 (45%), Gaps = 2/109 (1%)

Query: 6    KHDSKTSEPTEPPQKQLQQEPPKQEEPIEE--EEYEEEVEEEGEEEGEEEEEEEEEEEEE 63
            K  ++ +   +  +   +      EE +EE  EE  EE  EE  EE  EE  EE  EE  
Sbjct: 940  KEHAEANIEEDAEENVEEDAEENVEENVEENVEENVEENVEENVEENVEENVEENVEENV 999

Query: 64   EEKADQKEDEEEEEKADQNDEEDDEPILSLLEPFSKDQLVNLLREAAEN 112
            EE  ++  +E  EE  ++N EE DE  +  +E   ++     + E  EN
Sbjct: 1000 EENIEENVEENVEENIEENVEEYDEENVEEVEENVEEYDEENVEEIEEN 1048

Length = 1136

>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 26/61 (42%), Positives = 36/61 (59%), Gaps = 4/61 (6%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           + +FV GL  DT  ETL ++F   G I   + V D+ +G SKG+GF+ F +   A KA K
Sbjct: 1   KTLFVKGLSEDTTEETLKESFD--GSIA-ARIVTDRDTGSSKGFGFVDFSSEEDA-KAAK 56

Query: 191 E 191
           E
Sbjct: 57  E 57

This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 78

>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

 Score = 38.7 bits (91), Expect = 4e-04
 Identities = 20/60 (33%), Positives = 34/60 (56%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           +IFV ++G+E+  + L   FSKY   ++  +  DK TGK KG+    +   +   KA++E
Sbjct: 8   RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKE 67

This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

>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 = 38.7 bits (90), Expect = 4e-04
 Identities = 19/75 (25%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP 309
           +F+  +  E     L  +F ++GE+ +  +  D ATG+ +GF    +K   +  + +++ 
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 310 HKNFEGHILNCQRAI 324
           H   +G I++ +RAI
Sbjct: 61  H-ILDGKIIDPKRAI 74

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

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE- 308
           +FV N+  +   ++L  FFS+ G I+   +  DK + K +GF    +   + AK+ALEE 
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 309 PHKNFEGHILNCQRA 323
               F G  ++ + A
Sbjct: 62  KKTKFGGRKIHVEFA 76

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|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 42.3 bits (100), Expect = 4e-04
 Identities = 17/110 (15%), Positives = 51/110 (46%)

Query: 2   AKKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEE 61
            K     SK +E      K       K  + + + + +++ +++ + + ++ ++++++E+
Sbjct: 96  LKDELDSSKKAEKKNALDKDDDLNYVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDED 155

Query: 62  EEEEKADQKEDEEEEEKADQNDEEDDEPILSLLEPFSKDQLVNLLREAAE 111
           ++E+  D   D+E+EEK +  + E        +      + +   R+ A+
Sbjct: 156 DDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDSEALRQARKDAK 205

Length = 509

>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 = 38.4 bits (90), Expect = 4e-04
 Identities = 15/59 (25%), Positives = 31/59 (52%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           +F+ ++ +E   Q L   F+ +G +    + +DK TG+ K F    Y   ++A+ A++ 
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKA 59

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

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 40.8 bits (96), Expect = 4e-04
 Identities = 16/59 (27%), Positives = 30/59 (50%)

Query: 30 EEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
           E   ++  E+E   E +E+ E  +EEE +  ++E+  +   +EE+     Q +E D E
Sbjct: 3  SESESDDGEEDEELPEEDEDDESSDEEEVDLPDDEQDEESDSEEEQIFVTRQEEEVDPE 61

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 42.5 bits (99), Expect = 4e-04
 Identities = 31/85 (36%), Positives = 45/85 (52%), Gaps = 2/85 (2%)

Query: 30   EEPIEE--EEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDD 87
            EE +EE  EE  EE  EE  EE  EE  EE  EE  EE  ++  +E  EE  ++ DEE+ 
Sbjct: 968  EENVEENVEENVEENVEENVEENVEENVEENVEENIEENVEENVEENIEENVEEYDEENV 1027

Query: 88   EPILSLLEPFSKDQLVNLLREAAEN 112
            E +   +E + ++ +  +   A EN
Sbjct: 1028 EEVEENVEEYDEENVEEIEENAEEN 1052

Length = 1136

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

 Score = 38.9 bits (91), Expect = 4e-04
 Identities = 23/75 (30%), Positives = 34/75 (45%), Gaps = 1/75 (1%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE- 308
           ++V NV     P  L   F KYG I +  + +D  T +P+GF    ++ V  A+ AL   
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 309 PHKNFEGHILNCQRA 323
               F G  +  Q A
Sbjct: 63  DRTRFLGREIEIQFA 77

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

>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 38.9 bits (90), Expect = 4e-04
 Identities = 19/54 (35%), Positives = 29/54 (53%)

Query: 135 VHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKA 188
           V GL   T    L + F +YG I D   V D+ S +S+G+ F+ F+    A++A
Sbjct: 14  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 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|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 39.1 bits (91), Expect = 4e-04
 Identities = 20/42 (47%), Positives = 27/42 (64%)

Query: 45 EGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEED 86
          E EE  E +EEEEEEEEEE+E   +   ++EE + +  D ED
Sbjct: 56 EAEESEENDEEEEEEEEEEDEGEIEYVSDDEELEEEIEDLED 97

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional

 Score = 40.9 bits (96), Expect = 5e-04
 Identities = 15/57 (26%), Positives = 32/57 (56%)

Query: 39 EEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDEPILSLLE 95
           E+  ++ + E  EE+  +E E +EE+K  +++ E EE + ++  E+ +E     +E
Sbjct: 1  MEKECKDAKHENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIE 57

Length = 211

>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional

 Score = 40.9 bits (96), Expect = 5e-04
 Identities = 20/70 (28%), Positives = 30/70 (42%)

Query: 7  HDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEK 66
                   E  ++   +E   +EE   +EE  E  E E EE  E+ EE  E + EE + 
Sbjct: 2  EKECKDAKHENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKD 61

Query: 67 ADQKEDEEEE 76
           + K  EE +
Sbjct: 62 ENNKLKEENK 71

Length = 211

>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 41.6 bits (98), Expect = 5e-04
 Identities = 21/43 (48%), Positives = 32/43 (74%)

Query: 46  GEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
           G+EE  EE  E+ EEEEEE+   + EDE+EE++ ++ +E+DDE
Sbjct: 274 GDEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDDDE 316

Length = 319

>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 41.6 bits (98), Expect = 5e-04
 Identities = 17/44 (38%), Positives = 33/44 (75%)

Query: 34  EEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEE 77
            +EE  EE+ E+ EEE EE++  E E+E+EE++ +++E++++E 
Sbjct: 274 GDEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDDDEG 317

Length = 319

>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457)

 Score = 41.9 bits (98), Expect = 5e-04
 Identities = 16/46 (34%), Positives = 33/46 (71%)

Query: 40 EEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEE 85
          +E EEE  EE +++EE+++++++E+E  D  +D+E++E  D +D  
Sbjct: 43 KEAEEEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDDDST 88

This is a family of uncharacterized proteins. Length = 449

>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381)

 Score = 40.0 bits (94), Expect = 5e-04
 Identities = 16/49 (32%), Positives = 28/49 (57%)

Query: 40  EEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
           + +  + +E+ EEEEEE E EE +EE+   +  E+E  K  +    ++E
Sbjct: 92  KLLGLDKKEKEEEEEEEVEVEELDEEEQIDELLEKELAKLKREKRRENE 140

This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 156 to 174 amino acids in length. This domain is found associated with pfam07780, pfam01728. Length = 154

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 42.1 bits (98), Expect = 5e-04
 Identities = 32/83 (38%), Positives = 43/83 (51%), Gaps = 2/83 (2%)

Query: 8    DSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEE--EEEEEEEEEE 65
            +    E  E   ++  +E  ++ E   EE  EE VEE  EE  EE EE  EE  EE  EE
Sbjct: 1050 EENVEENIEENIEEYDEENVEEIEENIEENIEENVEENVEENVEEIEENVEENVEENAEE 1109

Query: 66   KADQKEDEEEEEKADQNDEEDDE 88
             A++  +E  EE  D+N EE +E
Sbjct: 1110 NAEENAEENAEEYDDENPEEHNE 1132

Length = 1136

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

 Score = 38.4 bits (90), Expect = 5e-04
 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 5/59 (8%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEI--EDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           IFV  L +    + L D F++ G +   D K   D   G+SKG+G +LF++   A++A+
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDND---GRSKGFGTVLFESPEDAQRAI 56

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

>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 38.4 bits (89), Expect = 5e-04
 Identities = 24/67 (35%), Positives = 36/67 (53%), Gaps = 2/67 (2%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK-- 190
           ++V GL      + +   F QYG I   + + D+V+G S+G GFI F  R  A +A+K  
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63

Query: 191 EPQKKIG 197
             QK +G
Sbjct: 64  NGQKPLG 70

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 38.4 bits (90), Expect = 5e-04
 Identities = 18/59 (30%), Positives = 32/59 (54%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           +I+V  +  D   + +   F+ +G+I+ C    D  +GK KGYGFI ++    A+ A+ 
Sbjct: 2   RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

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|217940 pfam04177, TAP42, TAP42-like family

 Score = 41.5 bits (98), Expect = 5e-04
 Identities = 21/56 (37%), Positives = 32/56 (57%), Gaps = 2/56 (3%)

Query: 35  EEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDE-EDDEP 89
           +E  E+E++  G  +G  E     EEEE++E  ++ +D EE  KA   DE +DD P
Sbjct: 281 DEYLEQEMKRGGVPQGGGEAAASAEEEEDDEDDEEDDD-EETLKARAWDEFKDDNP 335

The TOR signalling pathway activates a cell-growth program in response to nutrients. TIP41 (pfam04176) interacts with TAP42 and negatively regulates the TOR signaling pathway. Length = 335

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

 Score = 38.3 bits (89), Expect = 6e-04
 Identities = 27/86 (31%), Positives = 40/86 (46%), Gaps = 9/86 (10%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE- 307
           K+FV  +  E   + L  +FS+YGE+ +  +  DK T + +GF    +K  +     L  
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60

Query: 308 EPHKNFEGHILNCQRAIDGPKPGKSR 333
            PH   +G      R ID PKP   R
Sbjct: 61  GPH-TLDG------RTID-PKPCTPR 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|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 41.9 bits (98), Expect = 6e-04
 Identities = 32/90 (35%), Positives = 44/90 (48%), Gaps = 6/90 (6%)

Query: 2   AKKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGE------EEGEEEEE 55
           AK+  H  +T       + + + E  + E  IE  E  EEVE+EGE       E E E +
Sbjct: 701 AKEADHKGETEAEEVEHEGETEAEGTEDEGEIETGEEGEEVEDEGEGEAEGKHEVETEGD 760

Query: 56  EEEEEEEEEEKADQKEDEEEEEKADQNDEE 85
            +E E E E +A+ KEDE+E E     D E
Sbjct: 761 RKETEHEGETEAEGKEDEDEGEIQAGEDGE 790

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 41.6 bits (98), Expect = 6e-04
 Identities = 20/70 (28%), Positives = 39/70 (55%), Gaps = 4/70 (5%)

Query: 30  EEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEE----EEKADQKEDEEEEEKADQNDEE 85
           +E  ++E    +VE + E E  + E+EEE++E      E+  ++  +E+EEE A++ + E
Sbjct: 109 DEDSDDEGEWIDVESDKEIESSDSEDEEEKDEAAKKAKEDSDEELSEEDEEEAAEEEEAE 168

Query: 86  DDEPILSLLE 95
            ++   S L 
Sbjct: 169 AEKEKASELA 178

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 41.6 bits (98), Expect = 6e-04
 Identities = 23/63 (36%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 30  EEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDEP 89
           E   +++E EE   EE E+  +E E  + E ++E E +D  EDEEE+++A +  +ED + 
Sbjct: 93  ESDDDDDEEEEWEVEEDEDSDDEGEWIDVESDKEIESSDS-EDEEEKDEAAKKAKEDSDE 151

Query: 90  ILS 92
            LS
Sbjct: 152 ELS 154

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 38.1 bits (89), Expect = 6e-04
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 2/61 (3%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
             IFV  L  D   E L + F ++G+I +   +  K +  +  + FI F+    A +A++
Sbjct: 4   YSIFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARAVE 61

Query: 191 E 191
            
Sbjct: 62  S 62

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|225880 COG3343, RpoE, DNA-directed RNA polymerase, delta subunit [Transcription]

 Score = 40.1 bits (94), Expect = 6e-04
 Identities = 18/49 (36%), Positives = 31/49 (63%), Gaps = 1/49 (2%)

Query: 29  QEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEE 77
           +EE  E +  ++E ++E +E+ +E  E   E++E +E  D  EDEE+EE
Sbjct: 126 EEEDDEVDSLDDENDDE-DEDDDEIVEILIEDDEVDEDEDDDEDEEDEE 173

Length = 175

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 42.1 bits (98), Expect = 6e-04
 Identities = 29/64 (45%), Positives = 38/64 (59%), Gaps = 5/64 (7%)

Query: 30   EEPIEE---EEYEEEVEEEGE--EEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDE 84
            EE IEE   E  EE VEE  E  EE  EE  EE  EE  EE A++  +E ++E  ++++E
Sbjct: 1073 EENIEENIEENVEENVEENVEEIEENVEENVEENAEENAEENAEENAEEYDDENPEEHNE 1132

Query: 85   EDDE 88
            E DE
Sbjct: 1133 EYDE 1136

Length = 1136

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 40.0 bits (94), Expect = 6e-04
 Identities = 16/36 (44%), Positives = 25/36 (69%)

Query: 29  QEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEE 64
           Q     EE+  ++ EE+ EEE +EE+++E+E EEEE
Sbjct: 104 QHLVASEEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

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

 Score = 38.1 bits (88), Expect = 6e-04
 Identities = 19/57 (33%), Positives = 30/57 (52%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           + V+ L  +   + L   F   GE+E  K + DKV+G S GYGF+ +     A +A+
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAI 60

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

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 41.8 bits (98), Expect = 6e-04
 Identities = 24/86 (27%), Positives = 44/86 (51%), Gaps = 2/86 (2%)

Query: 6   KHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEE--EGEEEGEEEEEEEEEEEEE 63
           K   K        + +  +EP  +    EE+E E+  EE  + +E+ +EE ++ + +EE 
Sbjct: 78  KRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEA 137

Query: 64  EEKADQKEDEEEEEKADQNDEEDDEP 89
           +EK   KE E+E+EK  +   + +E 
Sbjct: 138 KEKRPPKEKEKEKEKKVEEPRDREEE 163

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen B (HuB)

 Score = 38.6 bits (89), Expect = 6e-04
 Identities = 22/58 (37%), Positives = 32/58 (55%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           ++V GL      + L   F QYG I   + + D+V+G S+G GFI F  R  A +A+K
Sbjct: 8   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 65

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

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

 Score = 38.4 bits (90), Expect = 7e-04
 Identities = 16/50 (32%), Positives = 27/50 (54%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYK 297
           + +FV+ +  +    KL   F +YG I+   L  DK TGKP+G+    ++
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFE 51

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

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

 Score = 38.1 bits (89), Expect = 7e-04
 Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 1/74 (1%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP 309
           +FV N+    E   L  FF + GE+ +  +  D   G+ KGF    + T + A+KALE+ 
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALEKS 60

Query: 310 HKNFEGHILNCQRA 323
            +   G  +    A
Sbjct: 61  GEELLGREIRVDLA 74

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

 Score = 37.7 bits (88), Expect = 7e-04
 Identities = 24/70 (34%), Positives = 33/70 (47%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP 309
           +FV N+  +   + LLA F   G      L  DK TGK KG     + T +A  KAL+  
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62

Query: 310 HKNFEGHILN 319
           H   +G  +N
Sbjct: 63  HTLLKGRKIN 72

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|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)

 Score = 41.9 bits (98), Expect = 7e-04
 Identities = 17/90 (18%), Positives = 43/90 (47%), Gaps = 4/90 (4%)

Query: 3   KKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYE-EEVEEEGEEE---GEEEEEEEE 58
            + K   K  +  +  +K    +  K+    + +EY+ ++ ++EG EE    +      +
Sbjct: 237 DEEKSKKKKKKLAKNKKKLDDDKKGKRGGDDDADEYDSDDGDDEGREEDYISDSSASGND 296

Query: 59  EEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
            EE E++ + +   + E E+ + ++E ++E
Sbjct: 297 PEEREDKLSPEIPAKPEIEQDEDSEESEEE 326

Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II. Length = 528

>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 37.9 bits (88), Expect = 7e-04
 Identities = 20/69 (28%), Positives = 34/69 (49%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP 309
           ++V NV      ++L A FS  G I    +  DK +G PKG+    + T D+ + A+   
Sbjct: 2   VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVALD 61

Query: 310 HKNFEGHIL 318
             +F G ++
Sbjct: 62  ESSFRGRVI 70

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|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region

 Score = 40.6 bits (96), Expect = 7e-04
 Identities = 13/46 (28%), Positives = 26/46 (56%)

Query: 30 EEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEE 75
                     E E + E+  ++++++E+E+E++EE+AD   D EE
Sbjct: 34 AAAAAATAAAIESELDEEDLEDDDDDDEDEDEDDEEEADLGPDPEE 79

The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. Length = 211

>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase chain; Provisional

 Score = 42.1 bits (99), Expect = 7e-04
 Identities = 16/56 (28%), Positives = 29/56 (51%)

Query: 29 QEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDE 84
          +EE +  +  EEE EEE E        + +++E   E  D+ E+++EE ++    E
Sbjct: 1  EEEQVNTQANEEEDEEELEAVARSAGSDSDDDEVPAEDEDEDEEDDEEAESPAKAE 56

Length = 1033

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

 Score = 37.6 bits (88), Expect = 7e-04
 Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 6/57 (10%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKA 188
           ++FV  L  D   E   + F +YGE+ +          K KG+GFI   TR+ A KA
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKYGEVSEV------FLNKEKGFGFIRLDTRTNAEKA 53

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

 Score = 37.6 bits (88), Expect = 8e-04
 Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           ++ V N+  +     L   FS +G + E  +   K  GK KGF    + +   A+KA++ 
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIP-RKPDGKKKGFAFVQFTSKADAEKAIKG 59

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|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 41.4 bits (98), Expect = 8e-04
 Identities = 14/62 (22%), Positives = 40/62 (64%)

Query: 27  PKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEED 86
            K+     ++  E+  ++  EE+ E++++    +++EEE+ ++KE +EEE++ ++ + E+
Sbjct: 405 SKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEE 464

Query: 87  DE 88
           ++
Sbjct: 465 EK 466

Length = 482

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

 Score = 37.8 bits (88), Expect = 8e-04
 Identities = 24/63 (38%), Positives = 29/63 (46%), Gaps = 4/63 (6%)

Query: 249 KIFVSNVGSELEPQK----LLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKK 304
            IFV    S L        L   FS  GEI    +  D+ TG  KGF    +K+VD  +K
Sbjct: 1   TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60

Query: 305 ALE 307
           ALE
Sbjct: 61  ALE 63

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

 Score = 37.5 bits (88), Expect = 8e-04
 Identities = 12/40 (30%), Positives = 25/40 (62%)

Query: 268 FSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           FS YG +++  L ID+    P+G+    +++ + A+KA++
Sbjct: 19  FSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIK 58

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|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381)

 Score = 39.6 bits (93), Expect = 8e-04
 Identities = 16/50 (32%), Positives = 29/50 (58%)

Query: 29  QEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEK 78
             +  E+EE EEE  E  E + EE+ +E  E+E  + K +++ + E ++K
Sbjct: 95  GLDKKEKEEEEEEEVEVEELDEEEQIDELLEKELAKLKREKRRENERKQK 144

This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 156 to 174 amino acids in length. This domain is found associated with pfam07780, pfam01728. Length = 154

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 39.2 bits (92), Expect = 8e-04
 Identities = 14/39 (35%), Positives = 27/39 (69%)

Query: 42  VEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKAD 80
             EE E + +EE+EEEE++EE++++ + +E+E   +K  
Sbjct: 108 ASEEDESDDDEEDEEEEDDEEDDDEDESEEEESPVKKVK 146

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>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 = 37.6 bits (88), Expect = 8e-04
 Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 2/63 (3%)

Query: 260 EPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKN-FEGHIL 318
           EP+ L  +FS++G +    L   K TGK KG+    +++ + AK   E  +       +L
Sbjct: 13  EPE-LRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLL 71

Query: 319 NCQ 321
            C+
Sbjct: 72  KCK 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|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in azoospermia-like (DAZL) proteins

 Score = 37.9 bits (88), Expect = 8e-04
 Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 7/79 (8%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           +FV G+        +   F +YG +++ K + D+ +G SKGYGF+ F      +K ++  
Sbjct: 8   VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDDVDVQKIVESQ 66

Query: 193 QKKIGNRMTACQLASIGPA 211
               G ++       +GPA
Sbjct: 67  INFHGKKL------KLGPA 79

This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. 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 = 82

>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 = 8e-04
 Identities = 21/58 (36%), Positives = 32/58 (55%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           ++V GL      + L   F QYG I   + + D+++G S+G GFI F  R  A +A+K
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

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|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 37.6 bits (88), Expect = 8e-04
 Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           +I V  L      + L + F+  GE+ D K +  +  GKS+ +GF+ FK+   A++A+K 
Sbjct: 2   RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTR-DGKSRRFGFVGFKSEEDAQQAVKY 60

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|240748 cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast Saccharomyces cerevisiae SET domain-containing protein 1 (scSet1p) and similar proteins

 Score = 38.5 bits (90), Expect = 9e-04
 Identities = 20/60 (33%), Positives = 25/60 (41%), Gaps = 5/60 (8%)

Query: 267 FFSKYGEIEEGPLGIDKATGKPKGFCLFVY-----KTVDAAKKALEEPHKNFEGHILNCQ 321
           +FS +GEI E     D  T  P G  L  Y     K   AAK AL+   K  +  I   +
Sbjct: 22  YFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYGSPGKPDRAAKAALKAVRKAQDCRIGGAE 81

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

 Score = 37.4 bits (87), Expect = 0.001
 Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 6/79 (7%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKT---VDAAKKA 305
           K+F+  +  E     L  +FS++GEI +  +  D  T + +GF    + +   VDAA  A
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

Query: 306 LEEPHKNFEGHILNCQRAI 324
              PHK  +G  +  +RA+
Sbjct: 61  --RPHK-VDGREVEPKRAV 76

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|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 40.7 bits (96), Expect = 0.001
 Identities = 13/61 (21%), Positives = 39/61 (63%)

Query: 28  KQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDD 87
             ++  ++ +   E  E+  EE ++E++++    +++E+ +++E E++EE+ ++ +EE +
Sbjct: 404 GSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAE 463

Query: 88  E 88
           E
Sbjct: 464 E 464

Length = 482

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 21/47 (44%), Positives = 33/47 (70%), Gaps = 4/47 (8%)

Query: 42 VEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
          VE+E E+E  +EEEEEE+EE++EE+    + EEE ++    +EE +E
Sbjct: 27 VEKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDE----EEEKEE 69

Length = 529

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 40.5 bits (95), Expect = 0.001
 Identities = 17/45 (37%), Positives = 32/45 (71%)

Query: 45 EGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDEP 89
          E E E E  +EEEEEE+EE+++ ++K  ++EEE  ++ ++E+ + 
Sbjct: 28 EKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKK 72

Length = 529

>gnl|CDD|222571 pfam14153, Spore_coat_CotO, Spore coat protein CotO

 Score = 39.8 bits (93), Expect = 0.001
 Identities = 16/63 (25%), Positives = 34/63 (53%)

Query: 8   DSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKA 67
             K+ E  +  + +  ++  +  EP  E+  E++ +EE  +E E+EEE E+ +++E    
Sbjct: 49  HVKSKEEEQKIEYEEAEKEKEAGEPEREDIAEQQEKEEIAQEEEKEEEAEDVKQQEVFSF 108

Query: 68  DQK 70
            +K
Sbjct: 109 KRK 111

Bacillus spores are protected by a protein shell consisting of over 50 different polypeptides, known as the coat. This family of proteins has an important morphogenetic role in coat assembly, it is involved in the assembly of at least 5 different coat proteins including CotB, CotG, CotS, CotSA and CotW. It is likely to act at a late stage of coat assembly. Length = 185

>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 40.8 bits (96), Expect = 0.001
 Identities = 15/42 (35%), Positives = 32/42 (76%)

Query: 47  EEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
           EE+ EE  E+ EEEEEE++ ++ ++++EE+E  ++ +++D+ 
Sbjct: 276 EEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDDDEG 317

Length = 319

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

 Score = 37.4 bits (87), Expect = 0.001
 Identities = 17/60 (28%), Positives = 29/60 (48%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           ++F+  L +    E L   F +YG + +     DK++ K KG+ F+ +     A KA  E
Sbjct: 4   RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 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|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 41.2 bits (97), Expect = 0.001
 Identities = 19/34 (55%), Positives = 21/34 (61%)

Query: 40  EEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDE 73
               E  EEE EEEE  EEEEEEEEE+    E+E
Sbjct: 300 PSPPEPEEEEEEEEEVPEEEEEEEEEEERTFEEE 333

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

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

 Score = 37.1 bits (86), Expect = 0.001
 Identities = 24/70 (34%), Positives = 36/70 (51%), Gaps = 4/70 (5%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP 309
           +FV N+  E   ++L   FS+ G +    L  D+ TGKPKG+    YK  + A  A+   
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAM--- 57

Query: 310 HKNFEGHILN 319
            +N  G+ LN
Sbjct: 58  -RNLNGYELN 66

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

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

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 20/67 (29%), Positives = 36/67 (53%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K+FV GL  DT  E + + F  +GEIE+ +   D  + + +G+ F+ +      +K L+ 
Sbjct: 1   KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60

Query: 192 PQKKIGN 198
              +IG+
Sbjct: 61  RYHQIGS 67

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|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 40.4 bits (95), Expect = 0.001
 Identities = 23/97 (23%), Positives = 40/97 (41%), Gaps = 27/97 (27%)

Query: 16  EPPQKQLQQEPPKQEEPIEEEEYEEE---------------------------VEEEGEE 48
           E  +++ ++EP +++E  E  ++E                             V  E ++
Sbjct: 289 EEEEEEEEEEPAERDELEENPDFEGLEVRELADSLDNWVHHVQHILPQGRCTWVNPEQKD 348

Query: 49  EGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEE 85
           E EE+E+EEEEEEEEE +  + E+          D  
Sbjct: 349 EEEEQEDEEEEEEEEEPEEPEPEEGPPLLTPISEDAP 385

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 41.7 bits (97), Expect = 0.001
 Identities = 22/89 (24%), Positives = 53/89 (59%), Gaps = 2/89 (2%)

Query: 2    AKKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEE 61
            AKK +     +E  +  +++ ++    +++  EE++  EE+++  EE   +  EE ++ E
Sbjct: 1612 AKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAE 1671

Query: 62   EEEEKADQ--KEDEEEEEKADQNDEEDDE 88
            E+++KA++  K +E+E++ A+   +E +E
Sbjct: 1672 EDKKKAEEAKKAEEDEKKAAEALKKEAEE 1700

Length = 2084

>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]

 Score = 41.5 bits (97), Expect = 0.001
 Identities = 19/55 (34%), Positives = 32/55 (58%)

Query: 34  EEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
            ++E +E  EE  E E   ++E +E +E+EE     ++  E+E + D +DEED E
Sbjct: 927 SDDESDESEEEVSEYEASSDDESDETDEDEESDESSEDLSEDESENDSSDEEDGE 981

Length = 1001

>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]

 Score = 40.8 bits (95), Expect = 0.001
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 4/64 (6%)

Query: 30  EEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEE-EEEEKADQKEDEEEEEKADQNDEE--- 85
           E   E  EYE   ++E +E  E+EE +E  E+  E+E  +   DEE+ E  D+ + +   
Sbjct: 933 ESEEEVSEYEASSDDESDETDEDEESDESSEDLSEDESENDSSDEEDGEDWDELESKAAY 992

Query: 86  DDEP 89
           D  P
Sbjct: 993 DSRP 996

Length = 1001

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 39.3 bits (92), Expect = 0.001
 Identities = 17/50 (34%), Positives = 32/50 (64%), Gaps = 1/50 (2%)

Query: 37 EYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEED 86
             E   ++GEE+ E  EE+E++E  +EE+ D   D+E++E++D  +E+ 
Sbjct: 1  SGSESESDDGEEDEELPEEDEDDESSDEEEVD-LPDDEQDEESDSEEEQI 49

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 38.8 bits (91), Expect = 0.001
 Identities = 13/33 (39%), Positives = 24/33 (72%)

Query: 38  YEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQK 70
             EE E + +EE EEEE++EE+++E+E + ++ 
Sbjct: 108 ASEEDESDDDEEDEEEEDDEEDDDEDESEEEES 140

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase chain; Provisional

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 20/51 (39%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 43 EEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEE-KADQNDEEDDEPILS 92
          EEE       EEE+EEE E     A    D++E   + +  DEEDDE   S
Sbjct: 1  EEEQVNTQANEEEDEEELEAVARSAGSDSDDDEVPAEDEDEDEEDDEEAES 51

Length = 1033

>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 37.5 bits (87), Expect = 0.001
 Identities = 25/82 (30%), Positives = 38/82 (46%), Gaps = 7/82 (8%)

Query: 133 IFVHGLGWDTKAETLIDAFK-QYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           IFV  L  +     L+  F+ ++   +  K + D V+G S+GYGF+ F   +  ++AL E
Sbjct: 4   IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63

Query: 192 PQKKI-GNRMTACQLASIGPAT 212
            Q    G R        I  AT
Sbjct: 64  MQGVYCGGRPM-----RISTAT 80

This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 80

>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)

 Score = 40.8 bits (96), Expect = 0.001
 Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 19  QKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEE--EEEKADQKEDEEEE 76
           Q+ LQ+E  K+ +  ++ +  E VEE+  E+   E    +E  E   EE  D  E+E ++
Sbjct: 196 QELLQEEYEKEVKAEKKRQELERVEEKKLEKMAPEASRLDEMSEGLLEESDDDGEEESDD 255

Query: 77  EKADQNDEEDDEP 89
           E A +  E + EP
Sbjct: 256 ESAWEGFESEYEP 268

This nucleolar family of proteins are involved in 60S ribosomal biogenesis. They are specifically involved in the processing beyond the 27S stage of 25S rRNA maturation. This family contains sequences that bear similarity to the glioma tumour suppressor candidate region gene 2 protein (p60). This protein has been found to interact with herpes simplex type 1 regulatory proteins. Length = 387

>gnl|CDD|223649 COG0576, GrpE, Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]

 Score = 39.6 bits (93), Expect = 0.001
 Identities = 23/54 (42%), Positives = 29/54 (53%)

Query: 30 EEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQND 83
          +E   EE   EE EE  + E EE EEEE EEE E E+  Q+  E E +  +  D
Sbjct: 4  KEQKTEEPDAEETEEAEKSEEEEAEEEEPEEENELEEEQQEIAELEAQLEELKD 57

Length = 193

>gnl|CDD|223649 COG0576, GrpE, Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]

 Score = 39.6 bits (93), Expect = 0.001
 Identities = 24/54 (44%), Positives = 32/54 (59%)

Query: 34 EEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDD 87
          +E++ EE   EE EE  + EEEE EEEE EEE   ++E +E  E   Q +E  D
Sbjct: 4  KEQKTEEPDAEETEEAEKSEEEEAEEEEPEEENELEEEQQEIAELEAQLEELKD 57

Length = 193

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

 Score = 37.6 bits (87), Expect = 0.001
 Identities = 16/57 (28%), Positives = 27/57 (47%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           ++V  L      + L   F+ YG I  C  + DK +G  +G  F+ +  R  A+ A+
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAI 59

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|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 4/75 (5%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE- 191
           +FV  +  D   + L+  F++ G I + + + D  SG ++GY F+ +  +  A++A+K+ 
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMD-FSGLNRGYAFVTYTNKEAAQRAVKQL 62

Query: 192 PQKKI--GNRMTACQ 204
              +I  G R+  C 
Sbjct: 63  HNYEIRPGKRLGVCI 77

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

>gnl|CDD|215212 PLN02372, PLN02372, violaxanthin de-epoxidase

 Score = 41.0 bits (96), Expect = 0.001
 Identities = 32/89 (35%), Positives = 47/89 (52%), Gaps = 6/89 (6%)

Query: 25  EPPKQEEPIEE--EEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQN 82
           EPP  E  +E+  EE E+ + +E  +  EE E+E E+  +EEE   ++   EE  K  + 
Sbjct: 359 EPPLLER-LEKDVEEGEKTIVKEARQIEEELEKEVEKLGKEEESLFKRVALEEGLKELEQ 417

Query: 83  DEEDDEPILSLLEPFSKDQLVNLLREAAE 111
           DEE+    LS  E   K+ L  L  EA+E
Sbjct: 418 DEENFLKELSKEE---KELLEKLKMEASE 443

Length = 455

>gnl|CDD|235668 PRK06007, fliF, flagellar MS-ring protein; Reviewed

 Score = 41.0 bits (97), Expect = 0.001
 Identities = 24/96 (25%), Positives = 38/96 (39%), Gaps = 22/96 (22%)

Query: 28  KQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDD 87
            +    EEE  EEE   E     E+EE   E E  ++E+ ++++ EEE +  D       
Sbjct: 462 LRPLLPEEELAEEEAAAEEAALEEDEEAALEVELSDDEELEEEKAEEELKYEDL------ 515

Query: 88  EPILSLLEPFSKDQLVNLLREAAENH-RDVASRVRQ 122
                          +  LRE A+    +VA  +R 
Sbjct: 516 ---------------LKRLRELAKEDPEEVAQVLRT 536

Length = 542

>gnl|CDD|217783 pfam03896, TRAP_alpha, Translocon-associated protein (TRAP), alpha subunit

 Score = 40.1 bits (94), Expect = 0.001
 Identities = 21/54 (38%), Positives = 30/54 (55%), Gaps = 7/54 (12%)

Query: 29 QEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQN 82
          Q+   +EE  ++ V+E+ E+E   EE+E E  EEE       EDEE E KA  +
Sbjct: 32 QDLTEDEEAEDDVVDEDEEDEAVVEEDENELTEEE-------EDEEGEVKASPD 78

The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane. Length = 281

>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa)

 Score = 38.5 bits (90), Expect = 0.001
 Identities = 17/60 (28%), Positives = 30/60 (50%)

Query: 28  KQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDD 87
           ++E   E E+  +E +E  +   EE ++EE+ E E+ E  +  E E   E    + EE+ 
Sbjct: 58  REERKQELEKQLKERKEALKLLEEENDDEEDAETEDTEDVEDDEWEGFPEPTVTDYEEEY 117

Members of this family of proteins are part of the yeast nuclear pore complex-associated pre-60S ribosomal subunit. The family functions as a highly conserved exonuclease that is required for the 5'-end maturation of 5.8S and 25S rRNAs, demonstrating that 5'-end processing also has a redundant pathway. Nop25 binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery; and there is evidence for both physical and functional links between late 60S subunit processing and export. Length = 134

>gnl|CDD|227496 COG5167, VID27, Protein involved in vacuole import and degradation [Intracellular trafficking and secretion]

 Score = 40.7 bits (95), Expect = 0.001
 Identities = 21/81 (25%), Positives = 35/81 (43%), Gaps = 2/81 (2%)

Query: 8   DSKTSEPTEPPQKQLQQEPPKQEEPIEEEEY--EEEVEEEGEEEGEEEEEEEEEEEEEEE 65
           +   +E  E     L       E+  ++  Y  + E+E    EE E EEE E+ E+E + 
Sbjct: 339 EKWGNEEAERKDYILDSSSVPLEKQFDDILYFEKMEIENRNPEESEHEEEVEDYEDENDH 398

Query: 66  KADQKEDEEEEEKADQNDEED 86
                +D+E E      DE++
Sbjct: 399 SKRICDDDELENHFRAADEKN 419

Length = 776

>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 = 36.8 bits (86), Expect = 0.001
 Identities = 21/72 (29%), Positives = 31/72 (43%), Gaps = 10/72 (13%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K+FV  L   T +E L   F++YG + +C  V        K YGF+  +    A  A+K 
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTVTECDVV--------KNYGFVHMEEEEDAEDAIKA 52

Query: 192 PQKKI--GNRMT 201
                  G R+ 
Sbjct: 53  LNGYEFMGKRIN 64

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|237628 PRK14156, PRK14156, heat shock protein GrpE; Provisional

 Score = 39.0 bits (91), Expect = 0.001
 Identities = 22/46 (47%), Positives = 27/46 (58%)

Query: 30 EEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEE 75
           E I+ EE EEEVE    EE  EE  EE  E+ E E A+++ DE E
Sbjct: 2  SEEIKNEEVEEEVEATETEETVEEVVEETPEKSELELANERADEFE 47

Length = 177

>gnl|CDD|227447 COG5117, NOC3, Protein involved in the nuclear export of pre-ribosomes [Translation, ribosomal structure and biogenesis / Intracellular trafficking and secretion]

 Score = 40.8 bits (95), Expect = 0.001
 Identities = 23/93 (24%), Positives = 41/93 (44%), Gaps = 4/93 (4%)

Query: 5   RKHDSKTSEPTEP-PQK---QLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEE 60
           R   S  +E     P K    +  +    EE + E E E  +E + + + E+++  EE++
Sbjct: 63  RVSSSWNNESYNRLPIKTKDNVVADVNNGEEFLSESESEASLEIDSDIKDEKQKSLEEQK 122

Query: 61  EEEEEKADQKEDEEEEEKADQNDEEDDEPILSL 93
              E    Q+ D E+E  A    +  +EP  +L
Sbjct: 123 IAPEIPVKQQIDSEKERIASICTKIIEEPEENL 155

Length = 657

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 40.3 bits (94), Expect = 0.001
 Identities = 6/63 (9%), Positives = 9/63 (14%)

Query: 27  PKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEED 86
           P             E       E                  +    E      +Q     
Sbjct: 107 PSGSAEELASGLSPENTSGSSPESPASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSF 166

Query: 87  DEP 89
            +P
Sbjct: 167 LQP 169

Length = 413

>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 = 16/60 (26%), Positives = 27/60 (45%), Gaps = 1/60 (1%)

Query: 262 QKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQ 321
           Q L  +FS +GE+    +  D  TG+ KGF    +   +   K L + H   +G   + +
Sbjct: 14  QDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQRH-MIDGRWCDVK 72

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|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 = 36.8 bits (85), Expect = 0.002
 Identities = 19/58 (32%), Positives = 31/58 (53%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKAL 306
           K+F+  +  +   Q L   FSKYG+I E  +  D+ T + +GF    ++  D AK A+
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAM 59

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|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 40.4 bits (94), Expect = 0.002
 Identities = 23/42 (54%), Positives = 26/42 (61%)

Query: 28  KQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQ 69
           ++EE  EEEE EEE EEE EEE EEE EE    E  E +  Q
Sbjct: 864 EEEEEEEEEEEEEEEEEEEEEEEEEENEEPLSLEWPETRQKQ 905

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 40.7 bits (95), Expect = 0.002
 Identities = 33/140 (23%), Positives = 53/140 (37%), Gaps = 12/140 (8%)

Query: 6   KHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEE---------EEE 56
           + +    E  E  +++ ++E   +EE  E+EE EEEVE +   E E E         EE 
Sbjct: 440 EEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGEEP 499

Query: 57  EEEEEEEEEKADQKEDEEEEEKADQNDEEDDEPILSLLEPFSKDQLV---NLLREAAENH 113
           EE+ E    +        E ++   +  + + P    L+P S D          E     
Sbjct: 500 EEDAERRNSEMAGISRMSEGQQPRGSSVQPESPQEEPLQPESMDAESVGEESDEELLAEE 559

Query: 114 RDVASRVRQVADEDPVHRKI 133
             ++S         PV  KI
Sbjct: 560 SPLSSHTELEGVATPVETKI 579

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 36.7 bits (85), Expect = 0.002
 Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 2/77 (2%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           +IFV  +  +     L  FFS+YG ++E  +  D+A G  KG+    ++T + A+K L+E
Sbjct: 4   RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRA-GVSKGYGFVTFETQEDAQKILQE 62

Query: 309 PHK-NFEGHILNCQRAI 324
            ++  F    LN  +AI
Sbjct: 63  ANRLCFRDKKLNIGQAI 79

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|227466 COG5137, COG5137, Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]

 Score = 40.0 bits (93), Expect = 0.002
 Identities = 26/92 (28%), Positives = 41/92 (44%), Gaps = 6/92 (6%)

Query: 3   KKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEE------ 56
           ++R  +S   E  E  +           E  EEEE E E  ++GE+  + E E       
Sbjct: 179 EERLEESDGREEEEDEEVGSDSYGEGNRELNEEEEEEAEGSDDGEDVVDYEGERIDKKQG 238

Query: 57  EEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
           EEEE EEE     + + EEE  +++    ++E
Sbjct: 239 EEEEMEEEVINLFEIEWEEESPSEEVPRNNEE 270

Length = 279

>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 40.4 bits (94), Expect = 0.002
 Identities = 19/96 (19%), Positives = 41/96 (42%), Gaps = 15/96 (15%)

Query: 8    DSKTSEPT-EPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEE--EEEE 64
            D    E   E  QK  +Q     E  +  +E + +  E+ + + +E+EEE  ++   ++E
Sbjct: 3909 DEPNEEDLLETEQKSNEQSAANNESDLVSKEDDNKALEDKDRQEKEDEEEMSDDVGIDDE 3968

Query: 65   EKADQKEDEE------------EEEKADQNDEEDDE 88
             + D +E+              E+ K D+ + +  +
Sbjct: 3969 IQPDIQENNSQPPPENEDLDLPEDLKLDEKEGDVSK 4004

Length = 4600

>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 40.4 bits (94), Expect = 0.002
 Identities = 24/112 (21%), Positives = 48/112 (42%), Gaps = 2/112 (1%)

Query: 16   EPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEE 75
            EP ++ L +   K  E        + V +E + +  E+++ +E+E+EEE   D   D+E 
Sbjct: 3910 EPNEEDLLETEQKSNEQSAANNESDLVSKEDDNKALEDKDRQEKEDEEEMSDDVGIDDEI 3969

Query: 76   EEKADQNDEEDDEPILSLLEPFSKDQLVNLLREAAENHRDVASRVRQVADED 127
            +    +N+ +       L  P  +D  ++          D+     + ADE+
Sbjct: 3970 QPDIQENNSQPPPENEDLDLP--EDLKLDEKEGDVSKDSDLEDMDMEAADEN 4019

Length = 4600

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 39.8 bits (93), Expect = 0.002
 Identities = 19/57 (33%), Positives = 36/57 (63%)

Query: 29 QEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEE 85
          +E   E  + EEE E+E ++E EE+  ++EEE +EEE+ ++K+ + ++ K    + E
Sbjct: 29 KEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEWE 85

Length = 529

>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 39.6 bits (93), Expect = 0.002
 Identities = 16/47 (34%), Positives = 31/47 (65%)

Query: 42  VEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
           V  + E+  E  E+ EEEEEE++    + EDEE+E++ ++ D+++ +
Sbjct: 272 VGGDEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDDDEGD 318

Length = 319

>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 3/62 (4%)

Query: 129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKA 188
           V+R ++V  L +   +E L D F +YG I   +    K   +++G  F++++    A+ A
Sbjct: 1   VNRILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTK---ETRGTAFVVYEDIYDAKNA 57

Query: 189 LK 190
             
Sbjct: 58  CD 59

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|219900 pfam08553, VID27, VID27 cytoplasmic protein

 Score = 40.1 bits (94), Expect = 0.002
 Identities = 23/51 (45%), Positives = 31/51 (60%)

Query: 22  LQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKED 72
           L+ E    E   EEEE EEE EEE E+EG  +E  ++EE EE++   + ED
Sbjct: 379 LEIEDANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKYED 429

This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794

>gnl|CDD|220135 pfam09184, PPP4R2, PPP4R2

 Score = 39.8 bits (93), Expect = 0.002
 Identities = 17/57 (29%), Positives = 32/57 (56%)

Query: 9   SKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEE 65
              +   + P+    +     +E  ++++ +   E+E +E+ EEEE EEEEEEE+E+
Sbjct: 228 DAAASQDDGPKGSDVKNKKSDDEEDDDQDGDYVEEKELKEDEEEEETEEEEEEEDED 284

PPP4R2 (protein phosphatase 4 core regulatory subunit R2) is the regulatory subunit of the histone H2A phosphatase complex. It has been shown to confer resistance to the anticancer drug cisplatin in yeast, and may confer resistance in higher eukaryotes. Length = 285

>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi

 Score = 40.2 bits (94), Expect = 0.002
 Identities = 20/64 (31%), Positives = 31/64 (48%)

Query: 17  PPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEE 76
             + Q   E  +++E   EE  ++E E E  E+ E E E + E+ EE+E+ D  E  E  
Sbjct: 638 KSRHQQLFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDAEANEGV 697

Query: 77  EKAD 80
              D
Sbjct: 698 VPID 701

This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784

>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein

 Score = 40.4 bits (95), Expect = 0.002
 Identities = 14/55 (25%), Positives = 38/55 (69%), Gaps = 1/55 (1%)

Query: 36  EEYEEEVEEEGE-EEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDEP 89
            + EEE+++E   ++   + EE+++++EE ++ D++  + E+++ D +D++DD+ 
Sbjct: 104 GDIEEELQDEPRYDDAYRDLEEDDDDDEESDEEDEESSKSEDDEDDDDDDDDDDI 158

CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 40.4 bits (95), Expect = 0.002
 Identities = 21/84 (25%), Positives = 42/84 (50%), Gaps = 3/84 (3%)

Query: 14  PTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDE 73
            T+  ++  + E  ++E  +E E   E    + E+EG  EE+     EE+E+    ++ +
Sbjct: 222 FTKKLKETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLD 281

Query: 74  EEEEKADQNDEE---DDEPILSLL 94
           + E   ++ DEE    ++P  +LL
Sbjct: 282 KLEILKEKKDEELFWFEKPWPTLL 305

The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832

>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 40.0 bits (94), Expect = 0.002
 Identities = 18/27 (66%), Positives = 18/27 (66%)

Query: 39  EEEVEEEGEEEGEEEEEEEEEEEEEEE 65
               E E EEE EEE  EEEEEEEEEE
Sbjct: 300 PSPPEPEEEEEEEEEVPEEEEEEEEEE 326

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 40.0 bits (94), Expect = 0.002
 Identities = 19/27 (70%), Positives = 19/27 (70%)

Query: 39  EEEVEEEGEEEGEEEEEEEEEEEEEEE 65
             E EEE EEE E  EEEEEEEEEEE 
Sbjct: 302 PPEPEEEEEEEEEVPEEEEEEEEEEER 328

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 38.8 bits (91), Expect = 0.002
 Identities = 21/55 (38%), Positives = 33/55 (60%)

Query: 34 EEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
           EE+ E+  EE  E E EE  E+E EEE  EE+++ +  +EE+ K  + + + DE
Sbjct: 1  MEEKNEQVEEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQAKIAELEAKLDE 55

Length = 191

>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457)

 Score = 40.4 bits (94), Expect = 0.002
 Identities = 20/53 (37%), Positives = 33/53 (62%)

Query: 48  EEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDEPILSLLEPFSKD 100
           +E EEE  EEE+++EE++  D  EDE++++  D  D+ED++   S L   S  
Sbjct: 43  KEAEEEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDDDSTLHDDSSA 95

This is a family of uncharacterized proteins. Length = 449

>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457)

 Score = 40.0 bits (93), Expect = 0.002
 Identities = 14/55 (25%), Positives = 37/55 (67%)

Query: 34 EEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
          +E E E   EE+ +EE ++++++E+E++++++  +  EDE++++    +D   D+
Sbjct: 43 KEAEEEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDDDSTLHDDSSADD 97

This is a family of uncharacterized proteins. Length = 449

>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated

 Score = 40.2 bits (95), Expect = 0.002
 Identities = 15/45 (33%), Positives = 22/45 (48%)

Query: 34  EEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEK 78
             +   EE       E EE +++E+EEEEE+E  D    +E E  
Sbjct: 173 FVDPNAEEDPAHVGSELEELDDDEDEEEEEDENDDSLAADESELP 217

Length = 619

>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated

 Score = 40.2 bits (95), Expect = 0.002
 Identities = 24/88 (27%), Positives = 34/88 (38%), Gaps = 11/88 (12%)

Query: 37  EYEEEVEEEGE--------EEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
           E+ + +E                  EE+      E E+ D  EDEEEEE  + +    DE
Sbjct: 154 EWYDRLENGERRLRELIDGFVDPNAEEDPAHVGSELEELDDDEDEEEEEDENDDSLAADE 213

Query: 89  PIL--SLLEPFSK-DQLVNLLREAAENH 113
             L   +LE F    +    LR+A E  
Sbjct: 214 SELPEKVLEKFKALAKQYKKLRKAQEKK 241

Length = 619

>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 5/77 (6%)

Query: 247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKAL 306
           +R +FVS        ++L+ +FS +G +    + +DK  G    + +  + + +   K L
Sbjct: 2   ERSVFVSGFKRGTSEEQLMDYFSAFGPVMN--VIMDKDKGV---YAIVEFDSKEGVDKVL 56

Query: 307 EEPHKNFEGHILNCQRA 323
            EP     GH L  +  
Sbjct: 57  SEPQHTLNGHRLRVRPR 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|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 15/60 (25%), Positives = 33/60 (55%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           +++V  + ++   +T+  AF  +G I+      D V+ K KG+ F+ ++    A+ AL++
Sbjct: 2   RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61

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|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 40.2 bits (93), Expect = 0.002
 Identities = 30/88 (34%), Positives = 46/88 (52%), Gaps = 5/88 (5%)

Query: 6    KHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEE 65
            ++D +  E  E   ++  +E  ++ E   EE  EE +EE  EE  EE  EE EE  EE  
Sbjct: 1021 EYDEENVEEVEENVEEYDEENVEEIEENAEENVEENIEENIEEYDEENVEEIEENIEENI 1080

Query: 66   KADQKEDEEE-----EEKADQNDEEDDE 88
            + + +E+ EE     EE  ++N EE+ E
Sbjct: 1081 EENVEENVEENVEEIEENVEENVEENAE 1108

Length = 1136

>gnl|CDD|227496 COG5167, VID27, Protein involved in vacuole import and degradation [Intracellular trafficking and secretion]

 Score = 40.7 bits (95), Expect = 0.002
 Identities = 17/68 (25%), Positives = 32/68 (47%), Gaps = 3/68 (4%)

Query: 25  EPPKQEEPIEE---EEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQ 81
           E  ++++ I +      E++ ++    E  E E    EE E EE+ +  EDE +  K   
Sbjct: 344 EEAERKDYILDSSSVPLEKQFDDILYFEKMEIENRNPEESEHEEEVEDYEDENDHSKRIC 403

Query: 82  NDEEDDEP 89
           +D+E +  
Sbjct: 404 DDDELENH 411

Length = 776

>gnl|CDD|217933 pfam04156, IncA, IncA protein

 Score = 39.4 bits (92), Expect = 0.002
 Identities = 20/120 (16%), Positives = 48/120 (40%), Gaps = 4/120 (3%)

Query: 18  PQKQLQQEPPKQEEPIEEE----EYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDE 73
              + Q+    Q E  E +    E +EE+E+  E   E E E E+ +E+ +   +  +  
Sbjct: 67  QSVRPQKLEELQGELSELKQQLSELQEELEDLEERIAELESELEDLKEDLQLLRELLKSL 126

Query: 74  EEEEKADQNDEEDDEPILSLLEPFSKDQLVNLLREAAENHRDVASRVRQVADEDPVHRKI 133
           EE  ++ +   ++    L  L    ++++  L  E      ++      + +   +  ++
Sbjct: 127 EERLESLEESIKELAKELRELRQDLREEVEELREELERLQENLQRLQEAIQELQSLLEQL 186

Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Length = 186

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

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 15/46 (32%), Positives = 28/46 (60%)

Query: 145 ETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           E     F   G +++CK V DK +G S G+GF+ +++   A++A++
Sbjct: 15  EEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIR 60

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

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

 Score = 37.3 bits (86), Expect = 0.002
 Identities = 17/59 (28%), Positives = 32/59 (54%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           +++ GL      + + D F ++G I + + + D+ +G S+G  FI F  RS A +A+  
Sbjct: 3   LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61

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

>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 12/71 (16%), Positives = 47/71 (66%)

Query: 14  PTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDE 73
             E  + + +++   +E    ++EYEE+ + + +++  ++++++++++++++K D+ E +
Sbjct: 54  DAEYTEAKKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKK 113

Query: 74  EEEEKADQNDE 84
           +E+E  D+ ++
Sbjct: 114 DEKEAEDKLED 124

This is a family of fungal proteins of unknown function. Length = 182

>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 10/65 (15%)

Query: 131 RKIFVHGLGWDTKAETLIDAF-----KQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGA 185
             +FV  +      E + D F     ++ G++   K V D  +GK K +GF  F+   GA
Sbjct: 1   TTVFVGNI-----PEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGA 55

Query: 186 RKALK 190
            +AL+
Sbjct: 56  LRALR 60

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 40.4 bits (94), Expect = 0.002
 Identities = 31/117 (26%), Positives = 48/117 (41%), Gaps = 1/117 (0%)

Query: 3   KKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEE 62
           K    D   SEP+   Q+    E    EE  E+EE  EE EE  E EG  + E++ +  +
Sbjct: 85  KPTSTDQSLSEPSRRMQEDSGAENETVEEE-EKEESREEREEVEETEGVTKSEQKNDWRD 143

Query: 63  EEEKADQKEDEEEEEKADQNDEEDDEPILSLLEPFSKDQLVNLLREAAENHRDVASR 119
            EE   ++++ E EE+        +E     +    K       R  AE  +  A +
Sbjct: 144 AEECQKEEKEPEPEEEEKPKRGSLEENNGEFMTHKLKHTENTFSRGGAEGAQVEAGK 200

Length = 431

>gnl|CDD|239286 cd02988, Phd_like_VIAF, Phosducin (Phd)-like family, Viral inhibitor of apoptosis (IAP)-associated factor (VIAF) subfamily; VIAF is a Phd-like protein that functions in caspase activation during apoptosis

 Score = 39.2 bits (92), Expect = 0.002
 Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 7/54 (12%)

Query: 26 PPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKA 79
          PPK   P EEEE   E+  +   E   E++  +E +EE        DEEE+++ 
Sbjct: 14 PPKPPSPKEEEEEALELAIQEAHENALEKKLLDELDEE-------LDEEEDDRF 60

It was identified as an IAP binding protein through a screen of a human B-cell library using a prototype IAP. VIAF lacks a consensus IAP binding motif and while it does not function as an IAP antagonist, it still plays a regulatory role in the complete activation of caspases. VIAF itself is a substrate for IAP-mediated ubiquitination, suggesting that it may be a target of IAPs in the prevention of cell death. The similarity of VIAF to Phd points to a potential role distinct from apoptosis regulation. Phd functions as a cytosolic regulator of G protein by specifically binding to G protein betagamma (Gbg)-subunits. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain. Length = 192

>gnl|CDD|224581 COG1667, COG1667, Uncharacterized protein conserved in archaea [Function unknown]

 Score = 39.9 bits (93), Expect = 0.002
 Identities = 24/100 (24%), Positives = 42/100 (42%), Gaps = 4/100 (4%)

Query: 31  EPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEE--KADQNDEEDDE 88
            PI EEE E E+EE    E EE  E+      E E+ ++  DE       +++ +E   E
Sbjct: 116 VPITEEEVENEMEELKSSEREELLEKYGIRVPEIEEIERILDEAVGSDYFSEEIEEPSRE 175

Query: 89  PILSLLEPFSKDQ--LVNLLREAAENHRDVASRVRQVADE 126
            +L  L     D+  +  +L+       ++     ++  E
Sbjct: 176 ELLKKLGIKEPDENWVETILKVFRGVDEELEEEKERILSE 215

Length = 254

>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein

 Score = 39.7 bits (93), Expect = 0.002
 Identities = 15/95 (15%), Positives = 39/95 (41%), Gaps = 8/95 (8%)

Query: 13  EPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEE--------EEEEEEE 64
           E     ++  +       +  +     +  +++ +++  E+E           ++E  EE
Sbjct: 102 EDEIKRKRIEEDARNSDADDSDSSSDSDSSDDDSDDDDSEDETAALLRELEKIKKERAEE 161

Query: 65  EKADQKEDEEEEEKADQNDEEDDEPILSLLEPFSK 99
           ++ +++E   EEEKA + +     P+L+    F  
Sbjct: 162 KEREEEEKAAEEEKAREEEILTGNPLLNTSGDFKV 196

This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing. Length = 241

>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 16/56 (28%), Positives = 31/56 (55%)

Query: 135 VHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           V GL   T    L + F +YG +     V D+ +G+S+G+ F+ F+    +++A++
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAME 59

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|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT

 Score = 39.8 bits (93), Expect = 0.002
 Identities = 18/83 (21%), Positives = 34/83 (40%), Gaps = 1/83 (1%)

Query: 7   HDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGE-EEEEEEEEEEEEEE 65
            D  +S           +    ++   E++  E+E +++GEEE     +   E+ +   E
Sbjct: 200 RDMLSSMDMAEELGDEPESADSEDNEDEDDPKEDEDDDQGEEEESGSSDSLSEDSDASSE 259

Query: 66  KADQKEDEEEEEKADQNDEEDDE 88
           + +  E E  E  AD   + DD 
Sbjct: 260 EMESGEMEAAEASADDTPDSDDA 282

This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. Length = 282

>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 37.0 bits (85), Expect = 0.002
 Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 1/60 (1%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           RK+F+  +        +   F  +G+IE+C+ +     G S+G  F+ F TR+ A+ A+K
Sbjct: 2   RKLFIGMVSKKCNENDIRVMFSPFGQIEECR-ILRGPDGLSRGCAFVTFTTRAMAQTAIK 60

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it preferentially binds to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 81

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

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 19/58 (32%), Positives = 28/58 (48%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           ++V  L  +   E L   F +YG +        K +G  KG+ FI F+T   A+KA K
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACK 59

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|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused in Ewing's sarcoma protein (FUS), TATA-binding protein-associated factor 15 (TAF15) and similar proteins

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 23/65 (35%), Positives = 31/65 (47%), Gaps = 8/65 (12%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAV--------CDKVSGKSKGYGFILFKTRSG 184
           IFV GLG D   E++ D FKQ G I+  K           D+ +GK KG   + F     
Sbjct: 5   IFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 64

Query: 185 ARKAL 189
           A+ A+
Sbjct: 65  AKAAI 69

This subgroup corresponds to the RRM of FUS and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed 75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS (Translocated in liposarcoma), is a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multi-functional protein and has been implicated in pre-mRNA splicing, chromosome stability, cell spreading, and transcription. FUS was originally identified in human myxoid and round cell liposarcomas as an oncogenic fusion with the stress-induced DNA-binding transcription factor CHOP (CCAAT enhancer-binding homologous protein) and later as hnRNP P2, a component of hnRNP H complex assembled on pre-mRNA. It can form ternary complexes with hnRNP A1 and hnRNP C1/C2. Additional research indicates that FUS binds preferentially to GGUG-containing RNAs. In the presence of Mg2+, it can bind both single- and double-stranded DNA (ssDNA/dsDNA) and promote ATP-independent annealing of complementary ssDNA and D-loop formation in superhelical dsDNA. FUS has been shown to be recruited by single stranded noncoding RNAs to the regulatory regions of target genes such as cyclin D1, where it represses transcription by disrupting complex formation. TAF15 (TAFII68), also termed TATA-binding protein-associated factor 2N (TAF2N), or RNA-binding protein 56 (RBP56), originally identified as a TAF in the general transcription initiation TFIID complex, is a novel RNA/ssDNA-binding protein with homology to the proto-oncoproteins FUS and EWS (also termed EWSR1), belonging to the FET family as well. TAF15 likely functions in RNA polymerase II (RNAP II) transcription by interacting with TFIID and subunits of RNAP II itself. TAF15 is also associated with U1 snRNA, chromatin and RNA, in a complex distinct from the Sm-containing U1 snRNP that functions in splicing. Like other members in the FET family, both FUS and TAF15 contain an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. . Length = 86

>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein

 Score = 39.7 bits (93), Expect = 0.002
 Identities = 22/59 (37%), Positives = 35/59 (59%), Gaps = 5/59 (8%)

Query: 30 EEPIEEEEYEEEVEEEGEEEGE-----EEEEEEEEEEEEEEKADQKEDEEEEEKADQND 83
          EE  ++EE+E E EEE EE        E++E E ++EEE EK  Q+E+  +++K  +  
Sbjct: 35 EEEEDDEEFEIEEEEEEEEVDSDFDDSEDDEPESDDEEEGEKELQREERLKKKKRVKTK 93

The proteins in this family are designated YL1. These proteins have been shown to be DNA-binding and may be a transcription factor. Length = 238

>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 27/71 (38%), Positives = 40/71 (56%), Gaps = 4/71 (5%)

Query: 19 QKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEE---EEEEKADQKEDEEE 75
          +K L++E  + E       +EEE E++ E E EEEEEEEE +    + E+   + +DEEE
Sbjct: 15 KKLLEEELEEDEFFWTYLLFEEE-EDDEEFEIEEEEEEEEVDSDFDDSEDDEPESDDEEE 73

Query: 76 EEKADQNDEED 86
           EK  Q +E  
Sbjct: 74 GEKELQREERL 84

The proteins in this family are designated YL1. These proteins have been shown to be DNA-binding and may be a transcription factor. Length = 238

>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 249 KIFVSNVGSELEPQKLLAFF-SKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           ++F+SN+  +L+ Q L   F  K GE+    L  D   GK +G  +  +K  ++ +KALE
Sbjct: 1   RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKD-EEGKSRGCGVVEFKDKESVQKALE 59

Query: 308 EPHK 311
             ++
Sbjct: 60  TMNR 63

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 36.6 bits (84), Expect = 0.002
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           R ++V GL   T+A  L + F +YG++   K V +  S  ++ YGF+   T   A K + 
Sbjct: 2   RNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCIN 61

Query: 191 EPQK-KIGNRMTACQ 204
              + ++  RM + +
Sbjct: 62  HLHRTELHGRMISVE 76

This subgroup corresponds to RRM of SAFB1, also termed scaffold attachment factor B (SAF-B), heat-shock protein 27 estrogen response element ERE and TATA-box-binding protein (HET), or heterogeneous nuclear ribonucleoprotein hnRNP A1- associated protein (HAP), a large multi-domain protein with well-described functions in transcriptional repression, RNA splicing and metabolism, and a proposed role in chromatin organization. Based on the numerous functions, SAFB1 has been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. SAFB1 specifically binds to AT-rich scaffold or matrix attachment region DNA elements (S/MAR DNA) by using its N-terminal scaffold attachment factor-box (SAF-box, also known as SAP domain), a homeodomain-like DNA binding motif. The central region of SAFB1 is composed of an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a nuclear localization signal (NLS). The C-terminus of SAFB1 contains Glu/Arg- and Gly-rich regions that might be involved in protein-protein interaction. Additional studies indicate that the C-terminal region contains a potent and transferable transcriptional repression domain. Another family member is SAFB2, a homolog of SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed and share very high sequence similarity, suggesting that they might function in a similar manner. However, unlike SAFB1, exclusively existing in the nucleus, SAFB2 is also present in the cytoplasm. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1. Length = 76

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 40.5 bits (95), Expect = 0.002
 Identities = 27/100 (27%), Positives = 45/100 (45%), Gaps = 5/100 (5%)

Query: 28  KQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDD 87
            + E +EE   E + + E  +E  EE E   EE E+     ++  EE EEK     EE +
Sbjct: 316 NELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELE 375

Query: 88  EPILSLLEPFSKDQLVNLLREAAENHRDVASRVRQVADED 127
           E   +L     +++L  L  E AE   ++    R++   +
Sbjct: 376 ELFEAL-----REELAELEAELAEIRNELEELKREIESLE 410

Length = 1163

>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 17/57 (29%), Positives = 29/57 (50%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           ++V GL   TKA  L   F +YG++   K V +  S  ++ +GF+   +   A K +
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCI 58

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

>gnl|CDD|221250 pfam11831, Myb_Cef, pre-mRNA splicing factor component

 Score = 39.7 bits (93), Expect = 0.002
 Identities = 18/48 (37%), Positives = 29/48 (60%)

Query: 32  PIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKA 79
           P  + E+E E+ EE EEE EE EEE EE+  + +   +  +E +E++ 
Sbjct: 139 PKPKNEFELELPEEEEEEPEEMEEELEEDAADRDARKRAAEEAKEQEE 186

This family is a region of the Myb-Related Cdc5p/Cef1 proteins, in fungi, and is part of the pre-mRNA splicing factor complex. Length = 363

>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 5/60 (8%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K++V  LG       L D F++YG +         V+    G+ F+ F+    A  A++ 
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSV-----WVARNPPGFAFVEFEDPRDAEDAVRA 55

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|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 1/60 (1%)

Query: 130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
            RK+FV  L      + +   F+ +G IE+C  +     G SKG  F+ F + + A+ A+
Sbjct: 1   DRKLFVGMLSKQQTEDDVRRLFEPFGTIEEC-TILRGPDGNSKGCAFVKFSSHAEAQAAI 59

This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 81

>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit

 Score = 39.9 bits (93), Expect = 0.002
 Identities = 16/82 (19%), Positives = 38/82 (46%)

Query: 8   DSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKA 67
             + +E      +   +E    ++P E E+ E+   E   +EG   +E E  + E E   
Sbjct: 196 SMELAEEMGDDTESEDEEDGDDDQPTENEQEEQGEGEGEGQEGSAPQESEATDRESESGE 255

Query: 68  DQKEDEEEEEKADQNDEEDDEP 89
           ++    ++++  D++D++ + P
Sbjct: 256 EEMVQSDQDDLPDESDDDSETP 277

This model describes Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit that functions in cobalamin biosynthesis. Cobalamin (vitamin B12) can be synthesized via several pathways, including an aerobic pathway (found in Pseudomonas denitrificans) and an anaerobic pathway (found in P. shermanii and Salmonella typhimurium). These pathways differ in the point of cobalt insertion during corrin ring formation. There are apparently a number of variations on these two pathways, where the major differences seem to be concerned with the process of ring contraction. Confusion regarding the functions of enzymes found in the aerobic vs. anaerobic pathways has arisen because nonhomologous genes in these different pathways were given the same gene symbols. Thus, cobT in the aerobic pathway (P. denitrificans) is not a homolog of cobT in the anaerobic pathway (S. typhimurium). It should be noted that E. coli synthesizes cobalamin only when it is supplied with the precursor cobinamide, which is a complex intermediate. Additionally, all E. coli cobalamin synthesis genes (cobU, cobS and cobT) were named after their Salmonella typhimurium homologs which function in the anaerobic cobalamin synthesis pathway. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]. Length = 600

>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed

 Score = 39.9 bits (94), Expect = 0.002
 Identities = 17/50 (34%), Positives = 29/50 (58%)

Query: 39  EEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
           EE   EE EE    E+ E   ++   E+ ++ E+E++++  D  DE+DDE
Sbjct: 333 EENPREEAEEAEAPEKVEFMWDDYHREQLEEVEEEDDDDWDDDWDEDDDE 382

Length = 390

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

 Score = 36.0 bits (84), Expect = 0.003
 Identities = 20/66 (30%), Positives = 35/66 (53%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP 309
           +FV N+  ++E ++L   F   G++E   +  D+ TG  KGF   ++KT D+   AL+  
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLN 61

Query: 310 HKNFEG 315
               +G
Sbjct: 62  GIKLKG 67

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|217829 pfam03985, Paf1, Paf1

 Score = 39.3 bits (92), Expect = 0.003
 Identities = 13/78 (16%), Positives = 31/78 (39%)

Query: 3   KKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEE 62
            + K  ++          + + E  +Q     EEE  E+ EEEG +  E+   E   +  
Sbjct: 354 MRDKRRARLDPIDFEEVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQSREDGSSESSSDVG 413

Query: 63  EEEKADQKEDEEEEEKAD 80
            + ++   ++   +  ++
Sbjct: 414 SDSESKADKESASDSDSE 431

Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431

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

 Score = 36.6 bits (84), Expect = 0.003
 Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 2/78 (2%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           RK+F+  +  E   + L + F ++G + +  +  D  T + +GF    Y +V+    A+ 
Sbjct: 3   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMN 62

Query: 308 -EPHKNFEGHILNCQRAI 324
             PHK  +G ++  +RA+
Sbjct: 63  ARPHK-VDGRVVEPKRAV 79

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|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 40.0 bits (93), Expect = 0.003
 Identities = 20/86 (23%), Positives = 43/86 (50%), Gaps = 8/86 (9%)

Query: 34   EEEEYEEEVEEEGEEE--GEEEEEEEEEEEEEEE----KADQKEDEEEEEKADQNDEEDD 87
             +EE + E +E  ++E   EE    +E+ ++++     + D+K +E+  E+  Q +EE  
Sbjct: 4019 NKEEADAEKDEPMQDEDPLEENNTLDEDIQQDDFSDLAEDDEKMNEDGFEENVQENEEST 4078

Query: 88   EPILSLLEPFSKDQLVNLLREAAENH 113
            E  +   E   + ++     +A +NH
Sbjct: 4079 EDGVKSDEELEQGEVPE--DQAIDNH 4102

Length = 4600

>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 37.6 bits (87), Expect = 0.003
 Identities = 17/55 (30%), Positives = 31/55 (56%)

Query: 34  EEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
           E  + +E+ +E  E +  +E +EEEE +E  ++   + D E EE  ++ DEE + 
Sbjct: 77  EAADADEDADEAAEADAADEADEEEETDEAVDETADEADAEAEEADEEEDEEAEA 131

Length = 131

>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381)

 Score = 38.0 bits (89), Expect = 0.003
 Identities = 17/63 (26%), Positives = 34/63 (53%)

Query: 20  KQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKA 79
           K L  +  ++EE  EEE   EE++EE + +   E+E  + + E+  + ++K+ E  +E+ 
Sbjct: 92  KLLGLDKKEKEEEEEEEVEVEELDEEEQIDELLEKELAKLKREKRRENERKQKEILKEQM 151

Query: 80  DQN 82
              
Sbjct: 152 KML 154

This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 156 to 174 amino acids in length. This domain is found associated with pfam07780, pfam01728. Length = 154

>gnl|CDD|185618 PTZ00438, PTZ00438, gamete antigen 27/25-like protein; Provisional

 Score = 39.3 bits (91), Expect = 0.003
 Identities = 25/73 (34%), Positives = 41/73 (56%)

Query: 23  QQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQN 82
           ++E   Q+E  E+E+ EE  E E  E  EEE +++E+ E+++EK    E +E E   +  
Sbjct: 100 EEERGTQKEEEEDEDVEEIEEVEEVEVVEEEYDDDEDSEKDDEKESDAEGDENELAGEYI 159

Query: 83  DEEDDEPILSLLE 95
            EE D+ +  L E
Sbjct: 160 IEEVDDDVAILNE 172

Length = 374

>gnl|CDD|235033 PRK02363, PRK02363, DNA-directed RNA polymerase subunit delta; Reviewed

 Score = 37.3 bits (87), Expect = 0.003
 Identities = 11/52 (21%), Positives = 30/52 (57%), Gaps = 5/52 (9%)

Query: 23  QQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEE 74
            +E   +++    +  ++ ++++   + + +EE+ +EE++E+E     EDEE
Sbjct: 83  LEEKFDKKKKKFMDGDDDIIDDDILPDDDFDEEDLDEEDDEDE-----EDEE 129

Length = 129

>gnl|CDD|235033 PRK02363, PRK02363, DNA-directed RNA polymerase subunit delta; Reviewed

 Score = 37.3 bits (87), Expect = 0.003
 Identities = 11/53 (20%), Positives = 29/53 (54%)

Query: 8   DSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEE 60
           D +     E   K+ ++     ++ I+++   ++  +E + + E++E+EE+EE
Sbjct: 77  DEEIIPLEEKFDKKKKKFMDGDDDIIDDDILPDDDFDEEDLDEEDDEDEEDEE 129

Length = 129

>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region

 Score = 38.7 bits (91), Expect = 0.003
 Identities = 11/46 (23%), Positives = 23/46 (50%)

Query: 27 PKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKED 72
                       E  EE+ E++ +++E+E+E++EEE +     E+
Sbjct: 34 AAAAAATAAAIESELDEEDLEDDDDDDEDEDEDDEEEADLGPDPEE 79

The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. Length = 211

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 37.7 bits (88), Expect = 0.003
 Identities = 16/41 (39%), Positives = 27/41 (65%)

Query: 39  EEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKA 79
           +  V  E +E  ++EE+EEEE++EE++  D+ E+EE   K 
Sbjct: 104 QHLVASEEDESDDDEEDEEEEDDEEDDDEDESEEEESPVKK 144

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

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

 Score = 36.0 bits (84), Expect = 0.003
 Identities = 13/36 (36%), Positives = 21/36 (58%)

Query: 151 FKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGAR 186
           F Q+G +   +    K +GKSKGY F+ F++   A+
Sbjct: 20  FSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAK 55

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|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 36.0 bits (84), Expect = 0.003
 Identities = 15/65 (23%), Positives = 32/65 (49%), Gaps = 1/65 (1%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           +I V N+   +   +L   F   GE+ +  + +    GK + F    +K+ + A++A++ 
Sbjct: 2   RIIVKNLPKYVTEDRLREHFESKGEVTDVKV-MRTRDGKSRRFGFVGFKSEEDAQQAVKY 60

Query: 309 PHKNF 313
            +K F
Sbjct: 61  FNKTF 65

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|218737 pfam05764, YL1, YL1 nuclear protein

 Score = 38.9 bits (91), Expect = 0.003
 Identities = 24/58 (41%), Positives = 34/58 (58%), Gaps = 3/58 (5%)

Query: 34 EEEEYEEEVEEEG---EEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
          EE E +E         EEE +EE E EEEEEEEE  +D  + E++E ++D  +E + E
Sbjct: 20 EELEEDEFFWTYLLFEEEEDDEEFEIEEEEEEEEVDSDFDDSEDDEPESDDEEEGEKE 77

The proteins in this family are designated YL1. These proteins have been shown to be DNA-binding and may be a transcription factor. Length = 238

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 40.1 bits (94), Expect = 0.003
 Identities = 22/109 (20%), Positives = 44/109 (40%)

Query: 19  QKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEK 78
           ++  ++E   +E      E EE  EE  E+     EE EE  E   E+  + E E  E +
Sbjct: 337 EELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALREELAELEAELAEIR 396

Query: 79  ADQNDEEDDEPILSLLEPFSKDQLVNLLREAAENHRDVASRVRQVADED 127
            +  + + +   L        ++L +L  E  E   ++     ++ + +
Sbjct: 397 NELEELKREIESLEERLERLSERLEDLKEELKELEAELEELQTELEELN 445

Length = 1163

>gnl|CDD|236410 PRK09202, nusA, transcription elongation factor NusA; Validated

 Score = 39.9 bits (94), Expect = 0.003
 Identities = 11/65 (16%), Positives = 30/65 (46%)

Query: 19  QKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEK 78
           +++ ++    +    EE+  ++ +  EG +     +  E+  +  E+ A+Q  DE  + +
Sbjct: 406 RERAKEALETEALAQEEKLADDLLSLEGLDRELAFKLAEKGIKTLEDLAEQAVDELIDIE 465

Query: 79  ADQND 83
            D+  
Sbjct: 466 GDEEK 470

Length = 470

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 36.4 bits (84), Expect = 0.003
 Identities = 21/63 (33%), Positives = 32/63 (50%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           +FV  LG++   E L   F + G IE  + V D  +   KG+ ++ FK  +   KAL   
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLN 61

Query: 193 QKK 195
           +KK
Sbjct: 62  EKK 64

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|240413 PTZ00423, PTZ00423, glideosome-associated protein 45; Provisional

 Score = 38.6 bits (89), Expect = 0.003
 Identities = 26/91 (28%), Positives = 49/91 (53%), Gaps = 3/91 (3%)

Query: 10  KTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQ 69
           + ++  EP ++ + +   +++   E EE  E+  E+  EE E++ EE  E+EEE E   +
Sbjct: 6   RKNKAKEPKRRDIDELAEREKLKKEVEEIPEQKPEDIVEELEDQPEEPPEQEEENE---E 62

Query: 70  KEDEEEEEKADQNDEEDDEPILSLLEPFSKD 100
           ++ +EE +   Q ++  DE  L  LE  + D
Sbjct: 63  QKPKEEIDYPIQENKSFDEKNLDDLERSNSD 93

Length = 193

>gnl|CDD|148682 pfam07222, PBP_sp32, Proacrosin binding protein sp32

 Score = 38.9 bits (90), Expect = 0.003
 Identities = 19/57 (33%), Positives = 35/57 (61%), Gaps = 2/57 (3%)

Query: 19  QKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEE 75
             Q++   PKQE+ + + +  E ++E   EE + +EE+EEEE EEE K ++ +  ++
Sbjct: 189 SVQVKAPKPKQEQLLSKLQ--EYLQEHKTEEKQPQEEQEEEEVEEEAKQEEGQGTDD 243

This family consists of several mammalian specific proacrosin binding protein sp32 sequences. sp32 is a sperm specific protein which is known to bind with with 55- and 53-kDa proacrosins and the 49-kDa acrosin intermediate. The exact function of sp32 is unclear, it is thought however that the binding of sp32 to proacrosin may be involved in packaging the acrosin zymogen into the acrosomal matrix. Length = 243

>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated

 Score = 39.1 bits (92), Expect = 0.003
 Identities = 17/40 (42%), Positives = 19/40 (47%)

Query: 26  PPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEE 65
             K     E +E      +    E EEEEEEEEEEEE  E
Sbjct: 279 ADKDALDEELKEVLSAQAQAAAAEEEEEEEEEEEEEEPSE 318

Length = 330

>gnl|CDD|218561 pfam05340, DUF740, Protein of unknown function (DUF740)

 Score = 39.6 bits (92), Expect = 0.003
 Identities = 29/99 (29%), Positives = 49/99 (49%), Gaps = 8/99 (8%)

Query: 6   KHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEE-----EEEEEEE 60
           + +  +S    PP+   +   P   + + EEE E E+EE+ EE  E+E     +E+ EEE
Sbjct: 114 EENLPSSIA--PPEIDPEPRKPIVPDLVLEEEEEVEMEED-EEYYEKEPGKVVDEKSEEE 170

Query: 61  EEEEEKADQKEDEEEEEKADQNDEEDDEPILSLLEPFSK 99
           EEEE K  +   + E +    + +++ +   S    FSK
Sbjct: 171 EEEELKTMKDFIDLESQTKKPSVKDNGKSFWSAASVFSK 209

This family consists of several uncharacterized plant proteins of unknown function. Length = 565

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 36.1 bits (83), Expect = 0.003
 Identities = 17/60 (28%), Positives = 34/60 (56%), Gaps = 1/60 (1%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           +IF+  L  D   + LI   ++ G+I + + + D  +G ++GY F+ F  +  A+ A+K+
Sbjct: 3   EIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQ 61

This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 78

>gnl|CDD|216531 pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family

 Score = 39.7 bits (93), Expect = 0.003
 Identities = 40/179 (22%), Positives = 57/179 (31%), Gaps = 36/179 (20%)

Query: 5   RKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGE--EEGEEEEEEEEEEEE 62
           +K      +    P     +E    EE  E  + E E++E  E  E  E+E  E EE   
Sbjct: 48  KKLGIPLKDTGGKPDVPPSKEFLDLEE--EILDLEAEIKEVEENLESLEKEINELEEWLN 105

Query: 63  EEEKADQKEDEEEEEKADQNDEEDDEPILSLLEPFSKDQLVNLL----------REAAEN 112
             ++     DE  EE            + +L   F   +    L          RE  E 
Sbjct: 106 VLDEEKSFLDENLEEL---------SELSNLDIDFKYLRGAEGLKLGFVAGVINREKLEA 156

Query: 113 HRDVASRV-----RQV----ADEDPVHRK--IFVHGLGWDTKAETLIDAFKQYGEIEDC 160
                 R      RQ       EDP      IF  G     K + ++D+F    E+ D 
Sbjct: 157 FERELWRACRGYIRQAEIEEPLEDPKKTVFIIFFVGKEDLDKVKKILDSFG--FELYDV 213

This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1. Length = 707

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

 Score = 35.8 bits (82), Expect = 0.004
 Identities = 16/74 (21%), Positives = 36/74 (48%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           KIFV  +      + +  +F ++G++++  L  DK T + +GF    +++ D  +K  E 
Sbjct: 1   KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 309 PHKNFEGHILNCQR 322
                   ++ C++
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|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 36.0 bits (83), Expect = 0.004
 Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE- 308
           +FV N+   +  + L  FFS    I+   +  D  TG+ +G+    +  ++ A++AL + 
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 309 PHKNFEGHIL 318
            +K   G IL
Sbjct: 62  KNKKLHGRIL 71

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

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 6/70 (8%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           R +FV  +  + + E L   F+Q+G+I      C     K +G+  + +     AR+A +
Sbjct: 2   RTLFVRNINSNVEDEELRALFEQFGDIRTLYTAC-----KHRGFIMVSYYDIRAARRAKR 56

Query: 191 EPQKK-IGNR 199
             Q   +G R
Sbjct: 57  ALQGTELGGR 66

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

>gnl|CDD|227466 COG5137, COG5137, Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]

 Score = 38.8 bits (90), Expect = 0.004
 Identities = 16/60 (26%), Positives = 31/60 (51%), Gaps = 1/60 (1%)

Query: 30  EEPIEEE-EYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
           E+P         + +E+ +E    + + + EEEE  E++D +E+EE+EE    +  E + 
Sbjct: 147 EKPRVTRFNIVWDNDEDNDEAPPAQPDVDNEEEERLEESDGREEEEDEEVGSDSYGEGNR 206

Length = 279

>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 39.6 bits (92), Expect = 0.004
 Identities = 17/60 (28%), Positives = 38/60 (63%), Gaps = 7/60 (11%)

Query: 36   EEYEEEVEEEGEEEGEEEEEEEE-----EEEEEEEKADQKEDEEE--EEKADQNDEEDDE 88
            +E +EE + E +E  ++E+  EE     E+ ++++ +D  ED+E+  E+  ++N +E++E
Sbjct: 4017 DENKEEADAEKDEPMQDEDPLEENNTLDEDIQQDDFSDLAEDDEKMNEDGFEENVQENEE 4076

Length = 4600

>gnl|CDD|220135 pfam09184, PPP4R2, PPP4R2

 Score = 38.7 bits (90), Expect = 0.004
 Identities = 18/63 (28%), Positives = 37/63 (58%)

Query: 7   HDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEK 66
           ++ ++S+         +    K ++  +EE+ +++ +   E+E +E+EEEEE EEEEEE+
Sbjct: 222 YEKESSDAAASQDDGPKGSDVKNKKSDDEEDDDQDGDYVEEKELKEDEEEEETEEEEEEE 281

Query: 67  ADQ 69
            + 
Sbjct: 282 DED 284

PPP4R2 (protein phosphatase 4 core regulatory subunit R2) is the regulatory subunit of the histone H2A phosphatase complex. It has been shown to confer resistance to the anticancer drug cisplatin in yeast, and may confer resistance in higher eukaryotes. Length = 285

>gnl|CDD|220135 pfam09184, PPP4R2, PPP4R2

 Score = 38.7 bits (90), Expect = 0.004
 Identities = 21/59 (35%), Positives = 33/59 (55%)

Query: 7   HDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEE 65
            D+  S+   P    ++ +    EE  +++    E +E  E+E EEE EEEEEEE+E+E
Sbjct: 227 SDAAASQDDGPKGSDVKNKKSDDEEDDDQDGDYVEEKELKEDEEEEETEEEEEEEDEDE 285

PPP4R2 (protein phosphatase 4 core regulatory subunit R2) is the regulatory subunit of the histone H2A phosphatase complex. It has been shown to confer resistance to the anticancer drug cisplatin in yeast, and may confer resistance in higher eukaryotes. Length = 285

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

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 1/75 (1%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP 309
           + V N+  E   ++     S +G +E   L   ++TG+ KG+    Y +  +A KA  + 
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 310 HKN-FEGHILNCQRA 323
                 G  L    A
Sbjct: 62  DGKQIGGRKLQVDWA 76

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

>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457)

 Score = 39.2 bits (91), Expect = 0.004
 Identities = 22/81 (27%), Positives = 44/81 (54%), Gaps = 12/81 (14%)

Query: 28  KQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQK------------EDEEE 75
            +EE +EEE+ +EE +++ ++E E++++++++E++E+E  D              E + E
Sbjct: 45  AEEEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDDDSTLHDDSSADDGNETDNE 104

Query: 76  EEKADQNDEEDDEPILSLLEP 96
              AD +DE DD        P
Sbjct: 105 AGFADSDDESDDGSEYVFWAP 125

This is a family of uncharacterized proteins. Length = 449

>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457)

 Score = 39.2 bits (91), Expect = 0.004
 Identities = 15/61 (24%), Positives = 41/61 (67%)

Query: 28  KQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDD 87
           + EE   EEE ++E +++ +++ +E++++++++E++E++ D      ++  AD  +E D+
Sbjct: 44  EAEEEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDDDSTLHDDSSADDGNETDN 103

Query: 88  E 88
           E
Sbjct: 104 E 104

This is a family of uncharacterized proteins. Length = 449

>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27

 Score = 39.0 bits (91), Expect = 0.004
 Identities = 21/89 (23%), Positives = 45/89 (50%)

Query: 2   AKKRKHDSKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEE 61
            K ++   K        +++ ++E  K++  +E+E  E    +E E+E E +   E  + 
Sbjct: 224 KKTKEKKEKKEASESTVKEESEEESGKRDVILEDESAEPTGLDEDEDEDEPKPSGERSDS 283

Query: 62  EEEEKADQKEDEEEEEKADQNDEEDDEPI 90
           EEE +  +KE  +  +K  ++++ED+E  
Sbjct: 284 EEETEEKEKEKRKRLKKMMEDEDEDEEME 312

This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterized by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif. Length = 427

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 39.7 bits (92), Expect = 0.004
 Identities = 27/90 (30%), Positives = 54/90 (60%), Gaps = 5/90 (5%)

Query: 2    AKKRKHDSKTSE---PTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEE 58
            AKK + D K +      E  + +  +E  K+E   EE++  EE+++  EE   + EE ++
Sbjct: 1680 AKKAEEDEKKAAEALKKEAEEAKKAEELKKKEA--EEKKKAEELKKAEEENKIKAEEAKK 1737

Query: 59   EEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
            E EE+++KA++ + +EEE+K   + ++++E
Sbjct: 1738 EAEEDKKKAEEAKKDEEEKKKIAHLKKEEE 1767

Length = 2084

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 39.4 bits (91), Expect = 0.004
 Identities = 31/63 (49%), Positives = 39/63 (61%), Gaps = 4/63 (6%)

Query: 30   EEPIEE---EEYEEEVEEEGEEEGEEEEEEEEEEEEEE-EKADQKEDEEEEEKADQNDEE 85
            EE +EE   E  EE VEE  EE  EE +EE  EE EE  E+ D++  EE EE A++N EE
Sbjct: 996  EENVEENIEENVEENVEENIEENVEEYDEENVEEVEENVEEYDEENVEEIEENAEENVEE 1055

Query: 86   DDE 88
            + E
Sbjct: 1056 NIE 1058

Length = 1136

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 39.4 bits (91), Expect = 0.004
 Identities = 33/109 (30%), Positives = 50/109 (45%), Gaps = 7/109 (6%)

Query: 26   PPKQEEPIE---EEEYEEEVE---EEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKA 79
                EE +E   EE  EE VE   EE  EE  EE  EE  EE  EE  ++  +E  EE  
Sbjct: 948  EEDAEENVEEDAEENVEENVEENVEENVEENVEENVEENVEENVEENVEENVEENIEENV 1007

Query: 80   DQNDEED-DEPILSLLEPFSKDQLVNLLREAAENHRDVASRVRQVADED 127
            ++N EE+ +E +    E   ++   N+     EN  ++     +  +E+
Sbjct: 1008 EENVEENIEENVEEYDEENVEEVEENVEEYDEENVEEIEENAEENVEEN 1056

Length = 1136

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 39.4 bits (91), Expect = 0.004
 Identities = 32/105 (30%), Positives = 51/105 (48%), Gaps = 2/105 (1%)

Query: 13   EPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEE--EEEEEEEEEEEEEKADQK 70
            E  +    +  +E  ++ +    EE EE  EE  EE  EE  EE +EE  EE EE  ++ 
Sbjct: 1020 EEYDEENVEEVEENVEEYDEENVEEIEENAEENVEENIEENIEEYDEENVEEIEENIEEN 1079

Query: 71   EDEEEEEKADQNDEEDDEPILSLLEPFSKDQLVNLLREAAENHRD 115
             +E  EE  ++N EE +E +   +E  +++       E AE + D
Sbjct: 1080 IEENVEENVEENVEEIEENVEENVEENAEENAEENAEENAEEYDD 1124

Length = 1136

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 39.4 bits (91), Expect = 0.004
 Identities = 32/116 (27%), Positives = 55/116 (47%), Gaps = 4/116 (3%)

Query: 16   EPPQKQLQQEPPKQEEPIEEEEYEEEVEE---EGEEEGEEEEEEEEEEEEEEEKADQKED 72
            E  ++  +    +  E   EE+ EE VEE   E  EE  EE  EE  EE  EE  ++  +
Sbjct: 937  EHLKEHAEANIEEDAEENVEEDAEENVEENVEENVEENVEENVEENVEENVEENVEENVE 996

Query: 73   EEEEEKADQNDEED-DEPILSLLEPFSKDQLVNLLREAAENHRDVASRVRQVADED 127
            E  EE  ++N EE+ +E I   +E + ++ +  +     E   +    + + A+E+
Sbjct: 997  ENVEENIEENVEENVEENIEENVEEYDEENVEEVEENVEEYDEENVEEIEENAEEN 1052

Length = 1136

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

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 17/59 (28%), Positives = 32/59 (54%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           +I+V++V  +L    + + F  +G+I+   L  D  TGK KG+    Y+   +A+ A+ 
Sbjct: 2   RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

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|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase chain; Provisional

 Score = 39.4 bits (92), Expect = 0.004
 Identities = 17/48 (35%), Positives = 27/48 (56%)

Query: 41 EVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDE 88
          E E+   +  EEE+EEE E       +D  +DE   E  D+++E+D+E
Sbjct: 1  EEEQVNTQANEEEDEEELEAVARSAGSDSDDDEVPAEDEDEDEEDDEE 48

Length = 1033

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 35.6 bits (83), Expect = 0.004
 Identities = 20/66 (30%), Positives = 36/66 (54%), Gaps = 2/66 (3%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP 309
           +FV  +  +L   +L+  F K G I E  L +D + G  +G+    Y   +AA++A+++ 
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFS-GLNRGYAFVTYTNKEAAQRAVKQL 62

Query: 310 HKNFEG 315
           H N+E 
Sbjct: 63  H-NYEI 67

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa)

 Score = 36.9 bits (86), Expect = 0.004
 Identities = 17/69 (24%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 19  QKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEK 78
           +K++++E  KQE   + +E +E ++   EE  +EE+ E E+ E+ E+   +   E     
Sbjct: 54  RKRIREER-KQELEKQLKERKEALKLLEEENDDEEDAETEDTEDVEDDEWEGFPEPTVTD 112

Query: 79  ADQNDEEDD 87
            ++   ++D
Sbjct: 113 YEEEYIDED 121

Members of this family of proteins are part of the yeast nuclear pore complex-associated pre-60S ribosomal subunit. The family functions as a highly conserved exonuclease that is required for the 5'-end maturation of 5.8S and 25S rRNAs, demonstrating that 5'-end processing also has a redundant pathway. Nop25 binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery; and there is evidence for both physical and functional links between late 60S subunit processing and export. Length = 134

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 39.2 bits (91), Expect = 0.004
 Identities = 19/84 (22%), Positives = 28/84 (33%), Gaps = 2/84 (2%)

Query: 8   DSKTSEPTEPPQKQLQQEP--PKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEE 65
            +  S P  PP      EP  P+   P   ++    ++   E+  EE E    E E +  
Sbjct: 131 PASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSP 190

Query: 66  KADQKEDEEEEEKADQNDEEDDEP 89
              Q E            +E  EP
Sbjct: 191 GPPQSETPTSSPPPQSPPDEPGEP 214

Length = 413

>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 38.1 bits (89), Expect = 0.004
 Identities = 17/66 (25%), Positives = 39/66 (59%), Gaps = 2/66 (3%)

Query: 26  PPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEE--EEEEEEEKADQKEDEEEEEKADQND 83
           P    E  E ++ ++E+ EE E+  +E EE+++   ++++ +K   K+ +++++K D   
Sbjct: 51  PIYDAEYTEAKKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKS 110

Query: 84  EEDDEP 89
           E+ DE 
Sbjct: 111 EKKDEK 116

This is a family of fungal proteins of unknown function. Length = 182

>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 37.7 bits (88), Expect = 0.004
 Identities = 11/63 (17%), Positives = 46/63 (73%), Gaps = 2/63 (3%)

Query: 28  KQEEPIEEE--EYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEE 85
           K+++ + EE  + ++E EE+ + + ++++ ++++++++++K D+K+D+ E++   + +++
Sbjct: 62  KKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAEDK 121

Query: 86  DDE 88
            ++
Sbjct: 122 LED 124

This is a family of fungal proteins of unknown function. Length = 182

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 39.3 bits (92), Expect = 0.004
 Identities = 23/69 (33%), Positives = 34/69 (49%)

Query: 20  KQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKA 79
           ++L++   + +E IE  + E E  E   EE E+   E EE +EE E+      EE EE  
Sbjct: 319 EELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELF 378

Query: 80  DQNDEEDDE 88
           +   EE  E
Sbjct: 379 EALREELAE 387

Length = 1163

>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3 subunit

 Score = 38.5 bits (90), Expect = 0.004
 Identities = 17/63 (26%), Positives = 33/63 (52%)

Query: 13  EPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKED 72
           E  E  + ++  +   ++    + E +E+ + E EE+G  E EE+  E+E  EK   ++ 
Sbjct: 43  EEKEEEKAKVAAKAKAKKALKAKIEEKEKAKREKEEKGLRELEEDTPEDELAEKLRLRKL 102

Query: 73  EEE 75
           +EE
Sbjct: 103 QEE 105

This is a family of proteins which are subunits of the eukaryotic translation initiation factor 3 (eIF3). In yeast it is called Hcr1. The Saccharomyces cerevisiae protein eIF3j (HCR1) has been shown to be required for processing of 20S pre-rRNA and binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p. Length = 242

>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein MRN1 and similar proteins

 Score = 35.9 bits (83), Expect = 0.004
 Identities = 12/28 (42%), Positives = 18/28 (64%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIE 275
           R +++ N+   L  +KL   FS+YGEIE
Sbjct: 4   RNVYIGNIDDSLTEEKLRNDFSQYGEIE 31

This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 36.1 bits (83), Expect = 0.004
 Identities = 16/60 (26%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           ++FV  +  D   + L+  F+  G I + + + D   GK++GY F+++  +  A++A++E
Sbjct: 3   EVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMD-FDGKNRGYAFVMYTQKHEAKRAVRE 61

This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

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

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 20/60 (33%), Positives = 27/60 (45%), Gaps = 2/60 (3%)

Query: 132 KIFVHGLGWDTKAETLIDAF-KQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           ++ V  L        L + F K  GEI D K +     GKS+   FI +KT   A+KA  
Sbjct: 2   RLIVKNLPASLTEAELKEHFSKHGGEITDVK-LLRTEDGKSRRIAFIGYKTEEEAQKAKD 60

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|217476 pfam03286, Pox_Ag35, Pox virus Ag35 surface protein

 Score = 38.2 bits (89), Expect = 0.004
 Identities = 17/79 (21%), Positives = 32/79 (40%)

Query: 9   SKTSEPTEPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKAD 68
            K  +   P   +      K ++  +E+  EEE + E +++  EE E + +  EE   + 
Sbjct: 48  PKQPKKKRPTTPRKPATTKKSKKKDKEKLTEEEKKPESDDDKTEENENDPDNNEESGDSQ 107

Query: 69  QKEDEEEEEKADQNDEEDD 87
           +          D  D+ DD
Sbjct: 108 ESASANSLSDIDNEDDMDD 126

Length = 198

>gnl|CDD|227701 COG5414, COG5414, TATA-binding protein-associated factor [Transcription]

 Score = 38.9 bits (90), Expect = 0.004
 Identities = 18/49 (36%), Positives = 28/49 (57%)

Query: 36  EEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDE 84
           E   +EV E  +E+ +EE E  E  +EE +     E  EE+E+ D+N+E
Sbjct: 283 EIENKEVSEGDKEQQQEEVENAEAHKEEVQSDRPDEIGEEKEEDDENEE 331

Length = 392

>gnl|CDD|222648 pfam14283, DUF4366, Domain of unknown function (DUF4366)

 Score = 38.1 bits (89), Expect = 0.004
 Identities = 22/97 (22%), Positives = 29/97 (29%), Gaps = 32/97 (32%)

Query: 25  EPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEE-------------------- 64
           E      P         V        E E E E EEE E+                    
Sbjct: 115 EEEDAAAPTCSCCPVCSVNMTECTGPEPEPEPEPEEEPEKKSGMGPLLLVLAVALIGGGA 174

Query: 65  ------------EKADQKEDEEEEEKADQNDEEDDEP 89
                       EK    +D +E +  D+++EEDDEP
Sbjct: 175 YYYFKFYKPKQQEKGAPDDDLDEYDYGDEDEEEDDEP 211

This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 227 and 387 amino acids in length. Length = 213

>gnl|CDD|177755 PLN00152, PLN00152, DNA-directed RNA polymerase; Provisional

 Score = 37.2 bits (86), Expect = 0.004
 Identities = 16/44 (36%), Positives = 23/44 (52%)

Query: 37 EYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKAD 80
           YE+E  E   EEG EE+ E    +E +    + ED+EE+E   
Sbjct: 8  GYEDEPSEPEIEEGAEEDSESNNNDEVKGSIGENEDKEEQEPVQ 51

Length = 130

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 36.3 bits (83), Expect = 0.004
 Identities = 12/34 (35%), Positives = 29/34 (85%)

Query: 45 EGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEK 78
          EGEE+ + + +EEE++++E+E+ D ++D+E++++
Sbjct: 7  EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 35.4 bits (81), Expect = 0.004
 Identities = 24/63 (38%), Positives = 30/63 (47%), Gaps = 8/63 (12%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           +FV  L      E L  AF Q+G++E  K        K K Y FI F  R GA KA++E 
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVK--------KLKDYAFIHFDERDGAVKAMEEM 55

Query: 193 QKK 195
             K
Sbjct: 56  NGK 58

This subgroup corresponds to the RRM3 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 that is 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 = 72

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	453
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	100.0
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.97
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.97
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.97
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.97
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.97
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.97
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.96
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.96
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.96
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.95
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.95
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.95
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.95
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.95
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.95
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.94
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.94
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.94
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.92
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.92
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.91
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.9
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.9
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.9
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.89
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.89
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.88
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.85
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.84
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.83
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.8
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.79
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.78
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.77
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.75
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.75
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.73
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.73
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.7
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.69
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.69
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.68
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.65
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.63
KOG0122	270	consensus Translation initiation factor 3, subunit	99.63
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.63
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.6
KOG0122	270	consensus Translation initiation factor 3, subunit	99.6
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.6
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.59
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.59
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.58
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.58
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.56
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.56
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.56
PLN03120	260	nucleic acid binding protein; Provisional	99.55
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.55
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.55
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.54
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.54
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.53
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.53
PLN03120	260	nucleic acid binding protein; Provisional	99.53
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.53
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.53
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.53
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.51
PLN03213	759	repressor of silencing 3; Provisional	99.5
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.5
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.49
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.49
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.47
PLN03121	243	nucleic acid binding protein; Provisional	99.47
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.47
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.46
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.45
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.45
PLN03213	759	repressor of silencing 3; Provisional	99.45
KOG4210	285	consensus Nuclear localization sequence binding pr	99.44
PLN03121	243	nucleic acid binding protein; Provisional	99.42
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.42
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.42
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.41
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.4
smart00362	72	RRM_2 RNA recognition motif.	99.4
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.39
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.39
smart00362	72	RRM_2 RNA recognition motif.	99.39
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.38
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.38
smart00360	71	RRM RNA recognition motif.	99.36
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.35
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.34
smart00360	71	RRM RNA recognition motif.	99.33
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	99.31
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.3
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.29
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.29
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.27
smart00361	70	RRM_1 RNA recognition motif.	99.27
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.25
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.22
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	99.18
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.18
smart00361	70	RRM_1 RNA recognition motif.	99.18
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.18
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.18
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.17
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.14
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.14
KOG0226	290	consensus RNA-binding proteins [General function p	99.13
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	99.12
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.09
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.09
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.04
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.03
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	99.0
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.0
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.98
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.96
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.94
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.93
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.89
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.8
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.8
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.75
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.74
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.71
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.7
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.66
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.63
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.62
KOG0226	290	consensus RNA-binding proteins [General function p	98.61
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.6
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.54
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.52
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.49
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.49
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.46
KOG0151	877	consensus Predicted splicing regulator, contains R	98.43
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.41
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.32
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.27
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.25
KOG0151	877	consensus Predicted splicing regulator, contains R	98.21
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.17
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.07
KOG3152	278	consensus TBP-binding protein, activator of basal	98.07
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.05
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.0
KOG4210	285	consensus Nuclear localization sequence binding pr	97.86
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.8
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.77
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.73
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.59
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.58
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.44
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.4
KOG2314	698	consensus Translation initiation factor 3, subunit	97.36
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.33
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.19
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.17
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.13
KOG3152	278	consensus TBP-binding protein, activator of basal	97.12
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.08
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.06
KOG2314	698	consensus Translation initiation factor 3, subunit	97.02
KOG1996	378	consensus mRNA splicing factor [RNA processing and	97.0
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.97
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	96.93
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.91
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.74
KOG1999	1024	consensus RNA polymerase II transcription elongati	96.71
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.71
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	96.62
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.58
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	96.52
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.51
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.38
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.33
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.2
PF10446	458	DUF2457: Protein of unknown function (DUF2457); In	96.14
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.95
KOG1996	378	consensus mRNA splicing factor [RNA processing and	95.86
PF10446	458	DUF2457: Protein of unknown function (DUF2457); In	95.46
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	95.38
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	94.8
KOG4483	528	consensus Uncharacterized conserved protein [Funct	94.79
KOG2591	684	consensus c-Mpl binding protein, contains La domai	94.78
KOG2236	483	consensus Uncharacterized conserved protein [Funct	94.72
KOG2135	526	consensus Proteins containing the RNA recognition	94.5
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.37
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	94.18
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	94.09
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	93.96
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	93.95
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	93.67
KOG2591	684	consensus c-Mpl binding protein, contains La domai	93.67
KOG2068	327	consensus MOT2 transcription factor [Transcription	93.41
COG5180	654	PBP1 Protein interacting with poly(A)-binding prot	93.01
KOG1999	1024	consensus RNA polymerase II transcription elongati	92.66
KOG2135	526	consensus Proteins containing the RNA recognition	92.6
PF04147	840	Nop14: Nop14-like family ; InterPro: IPR007276 Emg	92.43
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	92.41
KOG3973	465	consensus Uncharacterized conserved glycine-rich p	92.33
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	91.65
KOG2068	327	consensus MOT2 transcription factor [Transcription	91.22
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	91.21
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	90.76
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	90.1
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	89.96
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	89.53
KOG2318	650	consensus Uncharacterized conserved protein [Funct	88.82
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	88.32
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	85.87
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	85.54
COG5180	654	PBP1 Protein interacting with poly(A)-binding prot	85.5
KOG2141	822	consensus Protein involved in high osmolarity sign	85.42
KOG4594	354	consensus Sequence-specific single-stranded-DNA-bi	85.21
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	83.9
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	82.97
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	80.58
KOG0262	1640	consensus RNA polymerase I, large subunit [Transcr	80.16
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	80.12

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=3.2e-37  Score=289.33  Aligned_cols=173  Identities=24%  Similarity=0.403  Sum_probs=153.9

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ......++|||+|||+++|+++|+++|+.||.|++|+|++|+.+++++|||||+|.+.++|.+||+.|+ ..|.++.|+|
T Consensus       102 ~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V  181 (346)
T TIGR01659       102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKV  181 (346)
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeee
Confidence            445567899999999999999999999999999999999999999999999999999999999999888 5589999999


Q ss_pred             EecccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccC
Q 012923          204 QLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDK  283 (453)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~  283 (453)
                      .++.....                                ....++|||+|||+.+|+++|+++|++||.|+.|+|++++
T Consensus       182 ~~a~p~~~--------------------------------~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~  229 (346)
T TIGR01659       182 SYARPGGE--------------------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDK  229 (346)
T ss_pred             eccccccc--------------------------------ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecC
Confidence            98753211                                0123589999999999999999999999999999999999


Q ss_pred             CCCCCceEEEEEECCHHHHHHHHHcCC-CccCC--eEEEEEEccCCCCC
Q 012923          284 ATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEG--HILNCQRAIDGPKP  329 (453)
Q Consensus       284 ~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g--~~l~v~~a~~~~~~  329 (453)
                      .+++++|||||+|.+.++|.+||+.|| ..|.+  ++|.|.++....+.
T Consensus       230 ~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~~~  278 (346)
T TIGR01659       230 LTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGKA  278 (346)
T ss_pred             CCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCccccc
Confidence            999999999999999999999999999 66655  78999999765443

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).

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=100.00  E-value=1.1e-34  Score=263.19  Aligned_cols=198  Identities=19%  Similarity=0.318  Sum_probs=153.2

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc--cCCeEeEEEe
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK--IGNRMTACQL  205 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~--~~gr~~~v~~  205 (453)
                      +..|-|||+.||.++.|++|..||++.|+|.++||++|+.+|.+||||||+|.+.+.|+.||+.+|..  -.|+.|.|..
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            66889999999999999999999999999999999999999999999999999999999999999843  4789998888


Q ss_pred             cccCCCCCCCcCcccccccc--------------------------c------------------cccc----ccc----
Q 012923          206 ASIGPATTPAVASTATHQHQ--------------------------H------------------QHQH----QHQ----  233 (453)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~--------------------------~------------------~~~~----~~~----  233 (453)
                      +....+...-.....+...+                          .                  +...    +..    
T Consensus       161 Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~  240 (506)
T KOG0117|consen  161 SVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAI  240 (506)
T ss_pred             eeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcc
Confidence            75443221000000000000                          0                  0000    000    


Q ss_pred             -----cccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHc
Q 012923          234 -----HQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE  308 (453)
Q Consensus       234 -----~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~  308 (453)
                           ..............+.|||+||+.++|++.|+++|+.||.|++|+.++|        ||||+|.+.++|.+|++.
T Consensus       241 tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~  312 (506)
T KOG0117|consen  241 TVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKE  312 (506)
T ss_pred             eeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHH
Confidence                 0000011223444589999999999999999999999999999998866        999999999999999999


Q ss_pred             CC-CccCCeEEEEEEccCCCCCCCCC
Q 012923          309 PH-KNFEGHILNCQRAIDGPKPGKSR  333 (453)
Q Consensus       309 ~~-~~l~g~~l~v~~a~~~~~~~~~~  333 (453)
                      +| ..|+|..|.|.+|++..+....|
T Consensus       313 ~ngkeldG~~iEvtLAKP~~k~k~~r  338 (506)
T KOG0117|consen  313 TNGKELDGSPIEVTLAKPVDKKKKER  338 (506)
T ss_pred             hcCceecCceEEEEecCChhhhccch
Confidence            99 99999999999998776555443

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=1.3e-35  Score=252.51  Aligned_cols=184  Identities=26%  Similarity=0.444  Sum_probs=158.4

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~  204 (453)
                      ....+.-|||+.|...++-++|++.|.+||+|.+++|++|..|+++|||+||.|.+.++|+.||..|++ .|.+|.|+..
T Consensus        58 t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTN  137 (321)
T KOG0148|consen   58 TSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTN  137 (321)
T ss_pred             ccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecc
Confidence            334466799999999999999999999999999999999999999999999999999999999999995 5899999999


Q ss_pred             ecccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCC
Q 012923          205 LASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKA  284 (453)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~  284 (453)
                      |+..++......                ...............++|||+|++..+|+++||+.|++||.|..|||+++  
T Consensus       138 WATRKp~e~n~~----------------~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~--  199 (321)
T KOG0148|consen  138 WATRKPSEMNGK----------------PLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD--  199 (321)
T ss_pred             ccccCccccCCC----------------CccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc--
Confidence            998776221110                01111222344556789999999999999999999999999999999998  


Q ss_pred             CCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCCCCCC
Q 012923          285 TGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGPKPGK  331 (453)
Q Consensus       285 ~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~~~~~  331 (453)
                          +||+||.|.++++|.+||..+| ..|.|+.|+|.|.+.......
T Consensus       200 ----qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~~~~  243 (321)
T KOG0148|consen  200 ----QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDDGIN  243 (321)
T ss_pred             ----cceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCCCCCC
Confidence                8999999999999999999999 999999999999987654433

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=100.00  E-value=1.1e-32  Score=271.50  Aligned_cols=181  Identities=20%  Similarity=0.415  Sum_probs=155.3

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~  205 (453)
                      ....++|||+|||+++++++|+++|.+||.|.+|+|++|+.+++++|||||+|.+.++|.+||+.+++ .|.||.|+|.+
T Consensus       104 ~~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~r  183 (612)
T TIGR01645       104 LAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  183 (612)
T ss_pred             hcCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecc
Confidence            34568999999999999999999999999999999999999999999999999999999999998884 58999999985


Q ss_pred             cccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCC
Q 012923          206 ASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKAT  285 (453)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~  285 (453)
                      ....+......                     ..........++|||+||++.+++++|+++|+.||.|.+|+|++++.+
T Consensus       184 p~~~p~a~~~~---------------------~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~t  242 (612)
T TIGR01645       184 PSNMPQAQPII---------------------DMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTG  242 (612)
T ss_pred             ccccccccccc---------------------ccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCC
Confidence            43221110000                     000011123469999999999999999999999999999999999999


Q ss_pred             CCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCCC
Q 012923          286 GKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGPK  328 (453)
Q Consensus       286 g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~~  328 (453)
                      +++||||||+|.+.++|.+||..|| ..|+|+.|+|.++...+.
T Consensus       243 gksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~pP~  286 (612)
T TIGR01645       243 RGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPD  286 (612)
T ss_pred             CCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCCcc
Confidence            9999999999999999999999999 899999999999986553

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.

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

Probab=99.97  E-value=4.8e-31  Score=269.20  Aligned_cols=185  Identities=23%  Similarity=0.400  Sum_probs=152.5

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccC----CeEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIG----NRMT  201 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~----gr~~  201 (453)
                      ....++|||+|||.++|+++|+++|+.||.|.+|+|+++. +++++|||||+|.+.++|.+|++.+++ .|.    ++.|
T Consensus       175 ~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~-~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l  253 (562)
T TIGR01628       175 LKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKL  253 (562)
T ss_pred             ccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceee
Confidence            3456789999999999999999999999999999999987 789999999999999999999999885 477    8888


Q ss_pred             EEEecccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeec
Q 012923          202 ACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGI  281 (453)
Q Consensus       202 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~  281 (453)
                      .|.++............              ...............++|||+||++.+|+++|+++|+.||.|.+|+|++
T Consensus       254 ~v~~a~~k~er~~~~~~--------------~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~  319 (562)
T TIGR01628       254 YVGRAQKRAEREAELRR--------------KFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVML  319 (562)
T ss_pred             EeecccChhhhHHHHHh--------------hHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEE
Confidence            88876543222100000              0000000111233456899999999999999999999999999999999


Q ss_pred             cCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCC
Q 012923          282 DKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGP  327 (453)
Q Consensus       282 d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~  327 (453)
                      + .+|+++|||||+|.+.++|.+||..+| ..|+|++|.|.++..+.
T Consensus       320 d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~  365 (562)
T TIGR01628       320 D-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKE  365 (562)
T ss_pred             C-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCcH
Confidence            8 689999999999999999999999999 89999999999997653

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.97  E-value=4.1e-30  Score=253.09  Aligned_cols=192  Identities=19%  Similarity=0.307  Sum_probs=141.1

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-cc-CCeEeEEEe
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KI-GNRMTACQL  205 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~-~gr~~~v~~  205 (453)
                      ...++|||+|||+++++++|+++|++||.|.+|+|++| .+++++|||||+|.+.++|++||+.|+. .| .++.|.|.+
T Consensus        56 ~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~  134 (578)
T TIGR01648        56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCI  134 (578)
T ss_pred             CCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccc
Confidence            34689999999999999999999999999999999999 5999999999999999999999999984 34 467766654


Q ss_pred             cccCCCC---------C---------CC---cC--cc---cccccccc------------------ccc-------ccc-
Q 012923          206 ASIGPAT---------T---------PA---VA--ST---ATHQHQHQ------------------HQH-------QHQ-  233 (453)
Q Consensus       206 ~~~~~~~---------~---------~~---~~--~~---~~~~~~~~------------------~~~-------~~~-  233 (453)
                      +......         .         ..   ..  ..   ........                  ...       ... 
T Consensus       135 S~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I  214 (578)
T TIGR01648       135 SVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVI  214 (578)
T ss_pred             cccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceE
Confidence            4211100         0         00   00  00   00000000                  000       000 


Q ss_pred             -----cccccccccccccccEEEEecCCCCccHHHHHHHHhcc--CCcceeeeeccCCCCCCceEEEEEECCHHHHHHHH
Q 012923          234 -----HQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKY--GEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKAL  306 (453)
Q Consensus       234 -----~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al  306 (453)
                           ..............++|||+||++.+|+++|+++|+.|  |.|++|+++        ++||||+|.+.++|.+||
T Consensus       215 ~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s~e~A~kAi  286 (578)
T TIGR01648       215 AVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDREDAVKAM  286 (578)
T ss_pred             EEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCCHHHHHHHH
Confidence                 00000001122335789999999999999999999999  999999875        459999999999999999


Q ss_pred             HcCC-CccCCeEEEEEEccCCCC
Q 012923          307 EEPH-KNFEGHILNCQRAIDGPK  328 (453)
Q Consensus       307 ~~~~-~~l~g~~l~v~~a~~~~~  328 (453)
                      ..|| ..|+|+.|+|.|+.+...
T Consensus       287 ~~lnG~~i~Gr~I~V~~Akp~~~  309 (578)
T TIGR01648       287 DELNGKELEGSEIEVTLAKPVDK  309 (578)
T ss_pred             HHhCCCEECCEEEEEEEccCCCc
Confidence            9999 899999999999976543

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.

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

Probab=99.97  E-value=3.7e-31  Score=239.22  Aligned_cols=170  Identities=24%  Similarity=0.364  Sum_probs=147.0

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC--CccCCe--Ee
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ--KKIGNR--MT  201 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~--~~~~gr--~~  201 (453)
                      .+.+.-+|||+-||..|+|.||+++|++||.|.+|.|++|+.++.++|||||.|.+.++|.+|+..++  .+|.|-  .|
T Consensus        30 ~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pv  109 (510)
T KOG0144|consen   30 PDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPV  109 (510)
T ss_pred             CCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcce
Confidence            34556689999999999999999999999999999999999999999999999999999999999988  346665  45


Q ss_pred             EEEecccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeec
Q 012923          202 ACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGI  281 (453)
Q Consensus       202 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~  281 (453)
                      .|+++.......                               ...++|||+-|+..+||.+|+++|++||.|++|.|+|
T Consensus       110 qvk~Ad~E~er~-------------------------------~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilr  158 (510)
T KOG0144|consen  110 QVKYADGERERI-------------------------------VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILR  158 (510)
T ss_pred             eecccchhhhcc-------------------------------ccchhhhhhhccccccHHHHHHHHHhhCccchhhhee
Confidence            555554332211                               1235899999999999999999999999999999999


Q ss_pred             cCCCCCCceEEEEEECCHHHHHHHHHcCC--CccCC--eEEEEEEccCCC
Q 012923          282 DKATGKPKGFCLFVYKTVDAAKKALEEPH--KNFEG--HILNCQRAIDGP  327 (453)
Q Consensus       282 d~~~g~~kg~afV~F~~~~~A~~Al~~~~--~~l~g--~~l~v~~a~~~~  327 (453)
                      |. .+.+||||||+|.+.+.|..||+.||  .++.|  .+|.|+||....
T Consensus       159 d~-~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqk  207 (510)
T KOG0144|consen  159 DP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQK  207 (510)
T ss_pred             cc-cccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCC
Confidence            85 79999999999999999999999999  56655  789999997653

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.97  E-value=2e-30  Score=250.28  Aligned_cols=202  Identities=20%  Similarity=0.296  Sum_probs=153.8

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCC--eEeEE
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGN--RMTAC  203 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~g--r~~~v  203 (453)
                      ....++|||+|||..+++++|+.+|.+||.|..++|+.+..++.++|||||+|.+.++|..||+.|++. +.+  +.|.|
T Consensus        86 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v  165 (352)
T TIGR01661        86 SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITV  165 (352)
T ss_pred             ccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEE
Confidence            345678999999999999999999999999999999999888999999999999999999999999854 544  67788


Q ss_pred             EecccCCCCCCCcCcc------------c------------cccc---ccc----------------ccccc----ccc-
Q 012923          204 QLASIGPATTPAVAST------------A------------THQH---QHQ----------------HQHQH----QHQ-  235 (453)
Q Consensus       204 ~~~~~~~~~~~~~~~~------------~------------~~~~---~~~----------------~~~~~----~~~-  235 (453)
                      .++.............            .            +...   ...                .....    ... 
T Consensus       166 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (352)
T TIGR01661       166 KFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRAS  245 (352)
T ss_pred             EECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCC
Confidence            8775332110000000            0            0000   000                00000    000 


Q ss_pred             ------------cccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHH
Q 012923          236 ------------HQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAK  303 (453)
Q Consensus       236 ------------~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~  303 (453)
                                  ...........+.+|||+|||+.+++++|+++|++||.|.+|+|++|+.|+.+||||||+|.+.++|.
T Consensus       246 ~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~  325 (352)
T TIGR01661       246 PPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAA  325 (352)
T ss_pred             CccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHH
Confidence                        00000011222347999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHcCC-CccCCeEEEEEEccCCCC
Q 012923          304 KALEEPH-KNFEGHILNCQRAIDGPK  328 (453)
Q Consensus       304 ~Al~~~~-~~l~g~~l~v~~a~~~~~  328 (453)
                      +||..|| ..|+||.|+|.|+..+..
T Consensus       326 ~Ai~~lnG~~~~gr~i~V~~~~~~~~  351 (352)
T TIGR01661       326 MAILSLNGYTLGNRVLQVSFKTNKAY  351 (352)
T ss_pred             HHHHHhCCCEECCeEEEEEEccCCCC
Confidence            9999999 899999999999987653

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.97  E-value=7.7e-30  Score=246.23  Aligned_cols=166  Identities=25%  Similarity=0.408  Sum_probs=148.7

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~~~~  208 (453)
                      .++|||+|||+++|+++|+++|++||+|.+|+|++|+.+|+++|||||+|.+.++|.+||+.+++ .|.|+.|.|.++..
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            47999999999999999999999999999999999999999999999999999999999998884 59999999998753


Q ss_pred             CCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCC
Q 012923          209 GPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKP  288 (453)
Q Consensus       209 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~  288 (453)
                      ...                                ....++|||+|||..+++++|+.+|+.||.|..++++++..++.+
T Consensus        83 ~~~--------------------------------~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~  130 (352)
T TIGR01661        83 SSD--------------------------------SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLS  130 (352)
T ss_pred             ccc--------------------------------ccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCc
Confidence            211                                112358999999999999999999999999999999999888999


Q ss_pred             ceEEEEEECCHHHHHHHHHcCC-CccCC--eEEEEEEccCCC
Q 012923          289 KGFCLFVYKTVDAAKKALEEPH-KNFEG--HILNCQRAIDGP  327 (453)
Q Consensus       289 kg~afV~F~~~~~A~~Al~~~~-~~l~g--~~l~v~~a~~~~  327 (453)
                      +|||||+|.+.++|..||..|| ..+.|  ++|.|.++....
T Consensus       131 ~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~~  172 (352)
T TIGR01661       131 KGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPS  172 (352)
T ss_pred             CcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCCC
Confidence            9999999999999999999999 66666  678888886443

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.97  E-value=3e-30  Score=257.55  Aligned_cols=182  Identities=25%  Similarity=0.380  Sum_probs=155.8

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQ  204 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~  204 (453)
                      ..+...++|||+|||+.+|+++|+++|++||.|..|+|++|+.+++++|||||+|.+.++|.+||...+..|.|+.|.|.
T Consensus        84 ~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~  163 (457)
T TIGR01622        84 EAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQ  163 (457)
T ss_pred             ccccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEe
Confidence            34456789999999999999999999999999999999999999999999999999999999999977788999999998


Q ss_pred             ecccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCC
Q 012923          205 LASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKA  284 (453)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~  284 (453)
                      +.............                    .........++|||+|||+.+|+++|+++|+.||.|..|.|+++..
T Consensus       164 ~~~~~~~~~~~~~~--------------------~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~  223 (457)
T TIGR01622       164 SSQAEKNRAAKAAT--------------------HQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPE  223 (457)
T ss_pred             ecchhhhhhhhccc--------------------ccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCC
Confidence            76432211100000                    0000112257999999999999999999999999999999999999


Q ss_pred             CCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCC
Q 012923          285 TGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDG  326 (453)
Q Consensus       285 ~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~  326 (453)
                      +|+++|||||+|.+.++|.+||..|| ..|.|++|.|.|+...
T Consensus       224 ~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~  266 (457)
T TIGR01622       224 TGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDS  266 (457)
T ss_pred             CCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccCC
Confidence            99999999999999999999999999 8999999999998743

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.

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

Probab=99.96  E-value=1e-28  Score=252.14  Aligned_cols=163  Identities=25%  Similarity=0.444  Sum_probs=146.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCCeEeEEEecccCC
Q 012923          132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGNRMTACQLASIGP  210 (453)
Q Consensus       132 ~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~~~v~~~~~~~  210 (453)
                      +|||+|||+++|+++|+++|++||.|.+|+|++|..+++++|||||+|.+.++|.+||+.++.. |.|+.|+|.|+...+
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~~~~   81 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDP   81 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccc
Confidence            7999999999999999999999999999999999999999999999999999999999999855 999999999875332


Q ss_pred             CCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCce
Q 012923          211 ATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKG  290 (453)
Q Consensus       211 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg  290 (453)
                      ...                              .....+|||+|||.++++++|+++|+.||.|..|+|+++. +|+++|
T Consensus        82 ~~~------------------------------~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~-~g~skg  130 (562)
T TIGR01628        82 SLR------------------------------RSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRG  130 (562)
T ss_pred             ccc------------------------------ccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecC-CCCccc
Confidence            211                              1123479999999999999999999999999999999874 788999


Q ss_pred             EEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          291 FCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       291 ~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      ||||+|.+.++|.+||..+| ..++++.|.|.....
T Consensus       131 ~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~  166 (562)
T TIGR01628       131 YGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIK  166 (562)
T ss_pred             EEEEEECCHHHHHHHHHHhcccEecCceEEEecccc
Confidence            99999999999999999999 889999999976543

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.96  E-value=3.4e-28  Score=205.96  Aligned_cols=205  Identities=21%  Similarity=0.285  Sum_probs=160.3

Q ss_pred             cccCCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCcc---CC
Q 012923          122 QVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKI---GN  198 (453)
Q Consensus       122 ~~~~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~---~g  198 (453)
                      +...+......|||.+||..+|..+|..+|++||.|..-+|+.|..+|.+||.+||.|....+|+.||..+|+..   +-
T Consensus       119 RPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~t  198 (360)
T KOG0145|consen  119 RPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCT  198 (360)
T ss_pred             cCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCC
Confidence            334555666789999999999999999999999999999999999999999999999999999999999999653   56


Q ss_pred             eEeEEEecccCCCCCCCcCccc-------------cccccccc------ccccc------------cccccccccccccc
Q 012923          199 RMTACQLASIGPATTPAVASTA-------------THQHQHQH------QHQHQ------------HQHQQHHQQSEYTQ  247 (453)
Q Consensus       199 r~~~v~~~~~~~~~~~~~~~~~-------------~~~~~~~~------~~~~~------------~~~~~~~~~~~~~~  247 (453)
                      ..|.|+++..............             ....++..      ++...            .......+......
T Consensus       199 epItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g  278 (360)
T KOG0145|consen  199 EPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGG  278 (360)
T ss_pred             CCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCCCCe
Confidence            7899998864332211110000             00000000      00000            00000112334446


Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCC
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDG  326 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~  326 (453)
                      .+|||-||.+++++.-|+++|.+||.|..|+|++|..|.++|||+||...+-++|..||..|| ..|.+|.|.|.+...+
T Consensus       279 ~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  279 WCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             eEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecCC
Confidence            899999999999999999999999999999999999999999999999999999999999999 8999999999998654

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.96  E-value=5.8e-28  Score=224.56  Aligned_cols=192  Identities=22%  Similarity=0.351  Sum_probs=155.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecccC
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASIG  209 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~~  209 (453)
                      .||||++||+.++.++|.++|+.+|+|..|.++.++.++.+|||+||+|+-.++++.|++..+ ..+.||.|.|..+..+
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R   85 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKR   85 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccccc
Confidence            699999999999999999999999999999999999999999999999999999999999988 5699999999998766


Q ss_pred             CCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCc
Q 012923          210 PATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPK  289 (453)
Q Consensus       210 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~k  289 (453)
                      ...................+      .............+|+|+||||.|...+|+.+|+.||.|..|.|++... |+-.
T Consensus        86 ~r~e~~~~~e~~~veK~~~q------~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~d-gklc  158 (678)
T KOG0127|consen   86 ARSEEVEKGENKAVEKPIEQ------KRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKD-GKLC  158 (678)
T ss_pred             ccchhcccccchhhhccccc------CCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCC-CCcc
Confidence            55432111110000000000      0000011122257999999999999999999999999999999998765 4445


Q ss_pred             eEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCCCC
Q 012923          290 GFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGPKP  329 (453)
Q Consensus       290 g~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~~~  329 (453)
                      |||||+|....+|..||+.+| ..|+||+|-|.||.++...
T Consensus       159 GFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~y  199 (678)
T KOG0127|consen  159 GFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTY  199 (678)
T ss_pred             ceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccccc
Confidence            999999999999999999999 9999999999999877554

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.95  E-value=1.4e-27  Score=222.05  Aligned_cols=196  Identities=23%  Similarity=0.368  Sum_probs=152.3

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~  208 (453)
                      .-+|.|+||||.|...+|+.+|+.||.|.+|.|.+.+ .|+-.|||||+|....+|..||+.+| ..|.||+|.|.|+..
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~-dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~  195 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK-DGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVD  195 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC-CCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecc
Confidence            4589999999999999999999999999999999877 55555999999999999999999999 669999999999976


Q ss_pred             CCCCCCCcCcc---------------------c----------ccccc--cc----------c-----ccccc-----cc
Q 012923          209 GPATTPAVAST---------------------A----------THQHQ--HQ----------H-----QHQHQ-----HQ  235 (453)
Q Consensus       209 ~~~~~~~~~~~---------------------~----------~~~~~--~~----------~-----~~~~~-----~~  235 (453)
                      +..........                     .          .....  ..          .     .....     ..
T Consensus       196 Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~  275 (678)
T KOG0127|consen  196 KDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKE  275 (678)
T ss_pred             cccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccccccccccccCc
Confidence            65432211000                     0          00000  00          0     00000     00


Q ss_pred             c---ccc--cccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC
Q 012923          236 H---QQH--HQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH  310 (453)
Q Consensus       236 ~---~~~--~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~  310 (453)
                      .   ...  .........+|||+|||+++|++.|.+.|++||.|.++.|+.++.|+.++|.|||.|.+..+|..||....
T Consensus       276 ~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~As  355 (678)
T KOG0127|consen  276 SDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAAS  355 (678)
T ss_pred             ccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcC
Confidence            0   000  01222334899999999999999999999999999999999999999999999999999999999999872


Q ss_pred             -------CccCCeEEEEEEccCC
Q 012923          311 -------KNFEGHILNCQRAIDG  326 (453)
Q Consensus       311 -------~~l~g~~l~v~~a~~~  326 (453)
                             ..|.||.|.|..|..+
T Consensus       356 pa~e~g~~ll~GR~Lkv~~Av~R  378 (678)
T KOG0127|consen  356 PASEDGSVLLDGRLLKVTLAVTR  378 (678)
T ss_pred             ccCCCceEEEeccEEeeeeccch
Confidence                   3579999999999865

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.95  E-value=1.3e-27  Score=202.45  Aligned_cols=168  Identities=24%  Similarity=0.404  Sum_probs=151.2

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~  205 (453)
                      +...+.|.|--||.++|+++|+.+|...|+|++|++++|+.+|.+.||+||.|-++++|++|+..+|+ .|..+.|+|.+
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy  117 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY  117 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEe
Confidence            34457899999999999999999999999999999999999999999999999999999999999995 49999999999


Q ss_pred             cccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCC
Q 012923          206 ASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKAT  285 (453)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~  285 (453)
                      +.....                                .+....|||.+||..+|..+|.++|++||.|..-+|+.|..|
T Consensus       118 ARPSs~--------------------------------~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvt  165 (360)
T KOG0145|consen  118 ARPSSD--------------------------------SIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVT  165 (360)
T ss_pred             ccCChh--------------------------------hhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhccc
Confidence            864322                                233458999999999999999999999999999999999999


Q ss_pred             CCCceEEEEEECCHHHHHHHHHcCC-CccCC--eEEEEEEccCC
Q 012923          286 GKPKGFCLFVYKTVDAAKKALEEPH-KNFEG--HILNCQRAIDG  326 (453)
Q Consensus       286 g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g--~~l~v~~a~~~  326 (453)
                      |.+||.+||.|+...+|+.||..|| ..--|  .+|.|+++...
T Consensus       166 g~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannP  209 (360)
T KOG0145|consen  166 GLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNP  209 (360)
T ss_pred             ceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCc
Confidence            9999999999999999999999999 44433  68999998644

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.95  E-value=4.6e-27  Score=213.47  Aligned_cols=175  Identities=27%  Similarity=0.540  Sum_probs=159.7

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEeccc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASI  208 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~~  208 (453)
                      +.++|||++|++++|++.|+++|.+||+|.+|.+++|+.+++++||+||+|.+.+.+.++|....+.|.|+.|.+..+..
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            56899999999999999999999999999999999999999999999999999999999999999999999999999886


Q ss_pred             CCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCC
Q 012923          209 GPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKP  288 (453)
Q Consensus       209 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~  288 (453)
                      +........                          ....++|||++||..+++++|++.|.+||.|..+.++.|..+.++
T Consensus        85 r~~~~~~~~--------------------------~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~  138 (311)
T KOG4205|consen   85 REDQTKVGR--------------------------HLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRP  138 (311)
T ss_pred             ccccccccc--------------------------ccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeeccccccc
Confidence            655433211                          114569999999999999999999999999999999999999999


Q ss_pred             ceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEccCCCCC
Q 012923          289 KGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAIDGPKP  329 (453)
Q Consensus       289 kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a~~~~~~  329 (453)
                      +||+||.|.+.+++.+++...-+.|+++.+.|..|.++...
T Consensus       139 rgFgfv~~~~e~sVdkv~~~~f~~~~gk~vevkrA~pk~~~  179 (311)
T KOG4205|consen  139 RGFGFVTFDSEDSVDKVTLQKFHDFNGKKVEVKRAIPKEVM  179 (311)
T ss_pred             ccceeeEeccccccceecccceeeecCceeeEeeccchhhc
Confidence            99999999999999999988779999999999999876543

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.95  E-value=7e-28  Score=193.82  Aligned_cols=168  Identities=25%  Similarity=0.359  Sum_probs=151.6

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~  208 (453)
                      ..||||+||+..++++-|.++|-+.|+|.+++|.+|+.+...+|||||+|.+.++|+-|++.++ -+|.||+|+|..+..
T Consensus         9 d~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas~   88 (203)
T KOG0131|consen    9 DATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKASA   88 (203)
T ss_pred             CceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEeccc
Confidence            4699999999999999999999999999999999999999999999999999999999999999 459999999998862


Q ss_pred             CCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCccee-eeeccCCCCC
Q 012923          209 GPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEG-PLGIDKATGK  287 (453)
Q Consensus       209 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v-~i~~d~~~g~  287 (453)
                      .....                               ..+.+|||+||.+.+++..|..+|+.||.|... .|+++..||.
T Consensus        89 ~~~nl-------------------------------~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~  137 (203)
T KOG0131|consen   89 HQKNL-------------------------------DVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGN  137 (203)
T ss_pred             ccccc-------------------------------cccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCC
Confidence            22211                               122589999999999999999999999998764 8899999999


Q ss_pred             CceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCCC
Q 012923          288 PKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGPK  328 (453)
Q Consensus       288 ~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~~  328 (453)
                      ++||+||.|.+.+.+.+||..+| ..++.++|.|.++..+..
T Consensus       138 ~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~  179 (203)
T KOG0131|consen  138 PKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDT  179 (203)
T ss_pred             CCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCC
Confidence            99999999999999999999999 888999999999976553

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.95  E-value=2.6e-26  Score=232.50  Aligned_cols=194  Identities=18%  Similarity=0.261  Sum_probs=142.2

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhcc------------CCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcC
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQY------------GEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP  192 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~------------G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~  192 (453)
                      ..+...++|||+|||+++|+++|++||..|            +.|..+.+      .+.+|||||+|.+.++|..||...
T Consensus       170 ~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al~l~  243 (509)
T TIGR01642       170 QATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAMALD  243 (509)
T ss_pred             cCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhhcCC
Confidence            445668999999999999999999999975            23444443      356799999999999999999644


Q ss_pred             CCccCCeEeEEEecccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccC
Q 012923          193 QKKIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYG  272 (453)
Q Consensus       193 ~~~~~gr~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G  272 (453)
                      ...|.|+.|.|................   .........................++|||+|||+.+|+++|+++|+.||
T Consensus       244 g~~~~g~~l~v~r~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G  320 (509)
T TIGR01642       244 SIIYSNVFLKIRRPHDYIPVPQITPEV---SQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFG  320 (509)
T ss_pred             CeEeeCceeEecCccccCCccccCCCC---CCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC
Confidence            456899999887543221110000000   00000000000000001111223457999999999999999999999999


Q ss_pred             CcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCC
Q 012923          273 EIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGP  327 (453)
Q Consensus       273 ~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~  327 (453)
                      .|..+.|+++..+|.++|||||+|.+.++|..||..|| ..|.|+.|.|.++....
T Consensus       321 ~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~  376 (509)
T TIGR01642       321 DLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGA  376 (509)
T ss_pred             CeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCC
Confidence            99999999999999999999999999999999999999 89999999999986543

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.95  E-value=3.5e-27  Score=208.92  Aligned_cols=181  Identities=20%  Similarity=0.412  Sum_probs=156.9

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEecc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQLAS  207 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~~~  207 (453)
                      .-|+|||+.|.+.+.|+.|+..|.+||+|.+|.+..|+.|++++|||||+|.-++.|+.|++.+|+ .+.||.|+|.+..
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPs  191 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  191 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCC
Confidence            458999999999999999999999999999999999999999999999999999999999999995 5899999998654


Q ss_pred             cCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCC
Q 012923          208 IGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGK  287 (453)
Q Consensus       208 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~  287 (453)
                      ..+.......                     ........-.+|||..+.+++++++|+.+|+.||.|++|.+.+++..+.
T Consensus       192 NmpQAQpiID---------------------~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~  250 (544)
T KOG0124|consen  192 NMPQAQPIID---------------------MVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRG  250 (544)
T ss_pred             CCcccchHHH---------------------HHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCC
Confidence            3332211100                     0011122235999999999999999999999999999999999998899


Q ss_pred             CceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCCCCC
Q 012923          288 PKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGPKPG  330 (453)
Q Consensus       288 ~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~~~~  330 (453)
                      +|||+||+|.+..+-..||..|| +.|+|..|+|..+...|..-
T Consensus       251 HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vTPP~aL  294 (544)
T KOG0124|consen  251 HKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPDAL  294 (544)
T ss_pred             ccceeeEEeccccchHHHhhhcchhhcccceEecccccCCCchh
Confidence            99999999999999999999999 99999999999998776543

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.94  E-value=2.4e-25  Score=221.51  Aligned_cols=192  Identities=15%  Similarity=0.182  Sum_probs=142.0

Q ss_pred             CCCcCeEEEcCCCC-CCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEE
Q 012923          127 DPVHRKIFVHGLGW-DTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQ  204 (453)
Q Consensus       127 ~~~~~~lfV~nLp~-~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~  204 (453)
                      .+.+++|||+|||+ .+|+++|+++|+.||.|..|+|++++     +|||||+|.+.++|..||..|++ .|.|+.|.|.
T Consensus       272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~  346 (481)
T TIGR01649       272 GGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVC  346 (481)
T ss_pred             CCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEE
Confidence            34678999999998 69999999999999999999999863     68999999999999999998885 5999999999


Q ss_pred             ecccCCCCCCCcCcccccc-----cccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCC--ccee
Q 012923          205 LASIGPATTPAVASTATHQ-----HQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGE--IEEG  277 (453)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~--i~~v  277 (453)
                      ++.................     .......................+.+|||+|||..+|+++|+++|+.||.  |..|
T Consensus       347 ~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~i  426 (481)
T TIGR01649       347 PSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKF  426 (481)
T ss_pred             EcccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEE
Confidence            8754332111100000000     00000000000000000112345679999999999999999999999998  8888


Q ss_pred             eeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeE------EEEEEccC
Q 012923          278 PLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHI------LNCQRAID  325 (453)
Q Consensus       278 ~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~------l~v~~a~~  325 (453)
                      +++... + ..+++|||+|.+.++|.+||..|| ..|.++.      |+|.++++
T Consensus       427 k~~~~~-~-~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~  479 (481)
T TIGR01649       427 KFFPKD-N-ERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTS  479 (481)
T ss_pred             EEecCC-C-CcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccC
Confidence            886543 2 358999999999999999999999 8898885      88888754

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).

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.94  E-value=1.8e-24  Score=215.24  Aligned_cols=167  Identities=13%  Similarity=0.134  Sum_probs=136.3

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcC--C-CccCCeEeEEEec
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP--Q-KKIGNRMTACQLA  206 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~--~-~~~~gr~~~v~~~  206 (453)
                      +++|||+|||+++|+++|+++|++||.|..|+|+++      +|||||+|.+.++|.+||..+  + ..|.|+.|.|.++
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s   75 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYS   75 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEec
Confidence            689999999999999999999999999999998853      579999999999999999864  3 5699999999998


Q ss_pred             ccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCC
Q 012923          207 SIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATG  286 (453)
Q Consensus       207 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g  286 (453)
                      ............                    ..........+|||.||++.+|+++|+++|+.||.|.+|.|+++..  
T Consensus        76 ~~~~~~~~~~~~--------------------~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~--  133 (481)
T TIGR01649        76 TSQEIKRDGNSD--------------------FDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNN--  133 (481)
T ss_pred             CCcccccCCCCc--------------------ccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCC--
Confidence            654322111000                    0000111235899999999999999999999999999999987642  


Q ss_pred             CCceEEEEEECCHHHHHHHHHcCC-CccCC--eEEEEEEccCC
Q 012923          287 KPKGFCLFVYKTVDAAKKALEEPH-KNFEG--HILNCQRAIDG  326 (453)
Q Consensus       287 ~~kg~afV~F~~~~~A~~Al~~~~-~~l~g--~~l~v~~a~~~  326 (453)
                        +++|||+|.+.++|.+|+..|| ..|.+  +.|+|.|+...
T Consensus       134 --~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~  174 (481)
T TIGR01649       134 --VFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKPT  174 (481)
T ss_pred             --ceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecCC
Confidence              4789999999999999999999 77754  58999998654

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).

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.94  E-value=2.4e-25  Score=225.52  Aligned_cols=190  Identities=18%  Similarity=0.233  Sum_probs=146.6

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~~~~  208 (453)
                      .++|||+|||+.+|+++|+++|..||.|..|.|+++..+|.++|||||+|.+.++|..||..|++ .|.|+.|.|.++..
T Consensus       295 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~  374 (509)
T TIGR01642       295 KDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACV  374 (509)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECcc
Confidence            47899999999999999999999999999999999998999999999999999999999999884 59999999999865


Q ss_pred             CCCCCCCcCcc-cccccccccccccccccccccccccccccEEEEecCCCCc----------cHHHHHHHHhccCCccee
Q 012923          209 GPATTPAVAST-ATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSEL----------EPQKLLAFFSKYGEIEEG  277 (453)
Q Consensus       209 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~----------t~~~l~~~F~~~G~i~~v  277 (453)
                      ........... ........   .  .............+++|+|.||....          ..++|+++|++||.|+.|
T Consensus       375 ~~~~~~~~~~~~~~~~~~~~---~--~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v  449 (509)
T TIGR01642       375 GANQATIDTSNGMAPVTLLA---K--ALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINI  449 (509)
T ss_pred             CCCCCCcccccccccccccc---c--cchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEE
Confidence            43322111000 00000000   0  00000001123356799999996421          236899999999999999


Q ss_pred             eeeccC---CCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          278 PLGIDK---ATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       278 ~i~~d~---~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      .|+++.   .++.++|++||+|.+.++|.+||..|| ..|+|+.|.|.|..
T Consensus       450 ~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~  500 (509)
T TIGR01642       450 VIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYG  500 (509)
T ss_pred             EeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeC
Confidence            998753   345678999999999999999999999 89999999999874

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.92  E-value=5.3e-25  Score=189.82  Aligned_cols=148  Identities=21%  Similarity=0.410  Sum_probs=135.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEecccCC
Q 012923          132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQLASIGP  210 (453)
Q Consensus       132 ~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~~~~~~  210 (453)
                      +|||+|||..+++.+|+.+|++||+|.+|.|+++        |+||..++...|..||..|++ +|+|..|.|+.+..+.
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs   75 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS   75 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEeccccC
Confidence            6999999999999999999999999999999986        899999999999999998885 5999999999886552


Q ss_pred             CCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCce
Q 012923          211 ATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKG  290 (453)
Q Consensus       211 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg  290 (453)
                      .                                  ..++|+|+||.+.++.++|+..|++||.|..+.|++        +
T Consensus        76 k----------------------------------~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk--------d  113 (346)
T KOG0109|consen   76 K----------------------------------ASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK--------D  113 (346)
T ss_pred             C----------------------------------CccccccCCCCccccCHHHhhhhcccCCceeeeeec--------c
Confidence            2                                  235899999999999999999999999999999985        4


Q ss_pred             EEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCCCC
Q 012923          291 FCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGPKP  329 (453)
Q Consensus       291 ~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~~~  329 (453)
                      |+||+|.-.++|..||+.|+ ..|.|++++|++..++-+.
T Consensus       114 y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrlrt  153 (346)
T KOG0109|consen  114 YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRT  153 (346)
T ss_pred             eeEEEEeeccchHHHHhcccccccccceeeeeeecccccc
Confidence            99999999999999999999 9999999999999877443

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.92  E-value=1.6e-23  Score=209.29  Aligned_cols=194  Identities=21%  Similarity=0.294  Sum_probs=144.5

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~~  206 (453)
                      +..++|||+|||+.+|+++|+++|++||.|..|.|+++..+++++|||||+|.+.++|.+||..|++ .|.|+.|.|.++
T Consensus       184 p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a  263 (457)
T TIGR01622       184 PNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYA  263 (457)
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEc
Confidence            3468999999999999999999999999999999999998899999999999999999999998885 599999999997


Q ss_pred             ccCCCCCCCcCccccc-----------------------------------ccc-------cccc-------------cc
Q 012923          207 SIGPATTPAVASTATH-----------------------------------QHQ-------HQHQ-------------HQ  231 (453)
Q Consensus       207 ~~~~~~~~~~~~~~~~-----------------------------------~~~-------~~~~-------------~~  231 (453)
                      ................                                   ...       ....             ..
T Consensus       264 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  343 (457)
T TIGR01622       264 QDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGA  343 (457)
T ss_pred             cCCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhccccccccccccccccccccc
Confidence            5221110000000000                                   000       0000             00


Q ss_pred             ccc---ccccccccccccccEEEEecCCCCcc----------HHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECC
Q 012923          232 HQH---QHQQHHQQSEYTQRKIFVSNVGSELE----------PQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKT  298 (453)
Q Consensus       232 ~~~---~~~~~~~~~~~~~~~l~V~nLp~~~t----------~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~  298 (453)
                      ...   .............++|+|.||....+          .++|++.|++||.|+.|.|..    ..+.|++||+|.+
T Consensus       344 ~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~----~~~~G~~fV~F~~  419 (457)
T TIGR01622       344 LAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDT----KNSAGKIYLKFSS  419 (457)
T ss_pred             cccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeC----CCCceeEEEEECC
Confidence            000   00000011235678999999965544          368999999999999998863    3458999999999


Q ss_pred             HHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          299 VDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       299 ~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      +++|.+|+..|| ..|+|+.|.|.+...
T Consensus       420 ~e~A~~A~~~lnGr~f~gr~i~~~~~~~  447 (457)
T TIGR01622       420 VDAALAAFQALNGRYFGGKMITAAFVVN  447 (457)
T ss_pred             HHHHHHHHHHhcCcccCCeEEEEEEEcH
Confidence            999999999999 899999999998753

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.

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.91  E-value=2e-24  Score=183.84  Aligned_cols=198  Identities=19%  Similarity=0.312  Sum_probs=151.9

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC--ccCC--eEeEEE
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK--KIGN--RMTACQ  204 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~--~~~g--r~~~v~  204 (453)
                      +.|+|||+-|...-.|+|++.+|..||.|.+|.+++.+ .|.+||||||.|.+..+|+.||..|++  ++.|  ..|.|+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            56899999999999999999999999999999999988 899999999999999999999999984  4554  456677


Q ss_pred             ecccCCCC------------------------------------------------------------------------
Q 012923          205 LASIGPAT------------------------------------------------------------------------  212 (453)
Q Consensus       205 ~~~~~~~~------------------------------------------------------------------------  212 (453)
                      ++.-...+                                                                        
T Consensus        97 ~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~angl~A  176 (371)
T KOG0146|consen   97 FADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNANGLAA  176 (371)
T ss_pred             eccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhccccc
Confidence            76422211                                                                        


Q ss_pred             CCCcCcccccc-------------------------ccccccc-----------cccc----------------------
Q 012923          213 TPAVASTATHQ-------------------------HQHQHQH-----------QHQH----------------------  234 (453)
Q Consensus       213 ~~~~~~~~~~~-------------------------~~~~~~~-----------~~~~----------------------  234 (453)
                      .+.........                         .+...+.           ....                      
T Consensus       177 ~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y~Aa  256 (371)
T KOG0146|consen  177 APVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQYAAA  256 (371)
T ss_pred             CCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHHhhh
Confidence            00000000000                         0000000           0000                      


Q ss_pred             ----------------ccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECC
Q 012923          235 ----------------QHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKT  298 (453)
Q Consensus       235 ----------------~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~  298 (453)
                                      ..-..........+.|||-.||....+.+|.++|-+||.|++.+++.|+.|+.+|+|+||.|++
T Consensus       257 ypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDN  336 (371)
T KOG0146|consen  257 YPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDN  336 (371)
T ss_pred             cchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCC
Confidence                            0000002345667999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHcCC-CccCCeEEEEEEccCCC
Q 012923          299 VDAAKKALEEPH-KNFEGHILNCQRAIDGP  327 (453)
Q Consensus       299 ~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~  327 (453)
                      ..+|..||.+|| +.|+-++|+|.+.+++.
T Consensus       337 p~SaQaAIqAMNGFQIGMKRLKVQLKRPkd  366 (371)
T KOG0146|consen  337 PASAQAAIQAMNGFQIGMKRLKVQLKRPKD  366 (371)
T ss_pred             chhHHHHHHHhcchhhhhhhhhhhhcCccc
Confidence            999999999999 89999999999886543

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.90  E-value=7.7e-24  Score=203.76  Aligned_cols=174  Identities=25%  Similarity=0.352  Sum_probs=146.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCC---CCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVS---GKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~---g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ++|||.||++++|.++|..+|...|.|.+|.|...+..   -.|.|||||+|.+.++|+.|++.|+ ..|.|+.|.|.++
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S  595 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKIS  595 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEec
Confidence            34999999999999999999999999999988765522   1466999999999999999999999 5699999999998


Q ss_pred             ccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCC
Q 012923          207 SIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATG  286 (453)
Q Consensus       207 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g  286 (453)
                      ...+.....                       ........++.|+|+|||+..+..+|+++|..||.|.+|+|+.....+
T Consensus       596 ~~k~~~~~g-----------------------K~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~  652 (725)
T KOG0110|consen  596 ENKPASTVG-----------------------KKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKG  652 (725)
T ss_pred             cCccccccc-----------------------cccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcch
Confidence            722221110                       001111225799999999999999999999999999999999876667


Q ss_pred             CCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCC
Q 012923          287 KPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGP  327 (453)
Q Consensus       287 ~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~  327 (453)
                      .++|||||+|-++.+|..|+.+|. ..|.||.|.+.|+....
T Consensus       653 a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d~  694 (725)
T KOG0110|consen  653 AHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSDN  694 (725)
T ss_pred             hhccceeeeccCcHHHHHHHHhhcccceechhhheehhccch
Confidence            789999999999999999999999 88999999999997643

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

Probab=99.90  E-value=2.5e-23  Score=188.72  Aligned_cols=200  Identities=24%  Similarity=0.333  Sum_probs=155.6

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc--c--CCeEeEE
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK--I--GNRMTAC  203 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~--~--~gr~~~v  203 (453)
                      ...++|||+-|+..+||.+|+++|++||.|++|+|++|. .+.+||||||.|.+.+.|..||+.+|+.  +  +..+|.|
T Consensus       122 ~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVV  200 (510)
T KOG0144|consen  122 VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVV  200 (510)
T ss_pred             ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecc-cccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEE
Confidence            346889999999999999999999999999999999998 8999999999999999999999999954  4  5568899


Q ss_pred             EecccCCCCC-----------------------------------------------------CCc--------------
Q 012923          204 QLASIGPATT-----------------------------------------------------PAV--------------  216 (453)
Q Consensus       204 ~~~~~~~~~~-----------------------------------------------------~~~--------------  216 (453)
                      +|+.......                                                     ...              
T Consensus       201 kFADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~g~~~L~~l~a~~~qq~~~~  280 (510)
T KOG0144|consen  201 KFADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLGGLPPLGPLNATQLQQAAAL  280 (510)
T ss_pred             EecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccccccCCCCcchhHHHHHHHh
Confidence            9985333220                                                     000              


Q ss_pred             -----------Ccccc--cccccccc---cc--c------c---------------------------------------
Q 012923          217 -----------ASTAT--HQHQHQHQ---HQ--H------Q---------------------------------------  233 (453)
Q Consensus       217 -----------~~~~~--~~~~~~~~---~~--~------~---------------------------------------  233 (453)
                                 .+...  ...+....   ..  .      .                                       
T Consensus       281 ~~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t~~~~n~~~~~a~a~~~sp~  360 (510)
T KOG0144|consen  281 AAAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGTPANYNLAGGMAGAGTTSPV  360 (510)
T ss_pred             hhhcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCCchhcccccccccccccCcc
Confidence                       00000  00000000   00  0      0                                       


Q ss_pred             --------------------------------------------------cccccccccccccccEEEEecCCCCccHHH
Q 012923          234 --------------------------------------------------HQHQQHHQQSEYTQRKIFVSNVGSELEPQK  263 (453)
Q Consensus       234 --------------------------------------------------~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~  263 (453)
                                                                        ................|||.+||.+.-+.+
T Consensus       361 aa~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eGpeGanlfiyhlPqefgdq~  440 (510)
T KOG0144|consen  361 AASLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEGPEGANLFIYHLPQEFGDQD  440 (510)
T ss_pred             cccccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccCCCccceeeeeCchhhhhHH
Confidence                                                              000000033455568899999999999999


Q ss_pred             HHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCCC
Q 012923          264 LLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGPK  328 (453)
Q Consensus       264 l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~~  328 (453)
                      |-..|..||.|++.++..|+.|+-+|.|+||.|++..+|..||..|| ..|+.++|+|....++..
T Consensus       441 l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk~~~~n  506 (510)
T KOG0144|consen  441 LIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLKRDRNN  506 (510)
T ss_pred             HHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEeeeccCC
Confidence            99999999999999999999999999999999999999999999999 899999999999876643

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.90  E-value=2.8e-24  Score=201.44  Aligned_cols=191  Identities=20%  Similarity=0.345  Sum_probs=160.7

Q ss_pred             hcccCCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeE
Q 012923          121 RQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRM  200 (453)
Q Consensus       121 ~~~~~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~  200 (453)
                      ......+.+.+|||+--|+..++..+|.+||+.+|.|.+|+||.|+.+++++|.|||+|.+.+++..||...+..+.|-+
T Consensus       170 ~~l~~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~p  249 (549)
T KOG0147|consen  170 RILSPEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVP  249 (549)
T ss_pred             ccCCchHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccCce
Confidence            34556677889999999999999999999999999999999999999999999999999999999999988888899999


Q ss_pred             eEEEecccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeee
Q 012923          201 TACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLG  280 (453)
Q Consensus       201 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~  280 (453)
                      |.|+..............                  .........+-.+|||+||.+++|+++|+.+|++||.|..|.+.
T Consensus       250 v~vq~sEaeknr~a~~s~------------------a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~  311 (549)
T KOG0147|consen  250 VIVQLSEAEKNRAANASP------------------ALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLT  311 (549)
T ss_pred             eEecccHHHHHHHHhccc------------------cccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeec
Confidence            999887533222100000                  00001111222349999999999999999999999999999999


Q ss_pred             ccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCCCC
Q 012923          281 IDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGPKP  329 (453)
Q Consensus       281 ~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~~~  329 (453)
                      +|..||+++||+||+|.+.++|.+|+..|| ..|.|+.|+|.....+-..
T Consensus       312 ~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~~  361 (549)
T KOG0147|consen  312 KDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERVDT  361 (549)
T ss_pred             cccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeeccc
Confidence            999999999999999999999999999999 9999999999888765443

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.89  E-value=1.1e-22  Score=192.09  Aligned_cols=151  Identities=21%  Similarity=0.388  Sum_probs=138.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEecccC
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQLASIG  209 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~~~~~  209 (453)
                      ..|||+   +++|+..|.++|+++|.|.+|+|++|. +  +.|||||.|.++++|.+||..+|. .+.|+.|++.|+...
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd   75 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD   75 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC
Confidence            369999   999999999999999999999999998 6  999999999999999999999995 599999999998643


Q ss_pred             CCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCc
Q 012923          210 PATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPK  289 (453)
Q Consensus       210 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~k  289 (453)
                      +.                                     .|||.||+..++...|.++|+.||.|++|++.++. .| ++
T Consensus        76 ~~-------------------------------------~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~k  116 (369)
T KOG0123|consen   76 PS-------------------------------------LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SK  116 (369)
T ss_pred             Cc-------------------------------------eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ce
Confidence            22                                     39999999999999999999999999999999985 44 89


Q ss_pred             eEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCC
Q 012923          290 GFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGP  327 (453)
Q Consensus       290 g~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~  327 (453)
                      || ||+|.+.++|.+||..+| ..+.++.|.|.....+.
T Consensus       117 g~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~  154 (369)
T KOG0123|consen  117 GY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKE  154 (369)
T ss_pred             ee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchh
Confidence            99 999999999999999999 88899999998876553

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.89  E-value=8.9e-23  Score=174.41  Aligned_cols=139  Identities=19%  Similarity=0.366  Sum_probs=118.9

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecc
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLAS  207 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~  207 (453)
                      ..-|||||+||..++||+-|..||.+.|.|..|+||.+.                                  |.|.++.
T Consensus         4 ~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~e----------------------------------~~v~wa~   49 (321)
T KOG0148|consen    4 DEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFDE----------------------------------LKVNWAT   49 (321)
T ss_pred             CCCceEEeeccChhhHHHHHHHHHHhccccccceeehhh----------------------------------hcccccc
Confidence            345899999999999999999999999999999999872                                  3454544


Q ss_pred             cCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCC
Q 012923          208 IGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGK  287 (453)
Q Consensus       208 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~  287 (453)
                      .......                           .....+-.|||+-|...++-++||+.|.+||+|.+++|+||..|++
T Consensus        50 ~p~nQsk---------------------------~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~K  102 (321)
T KOG0148|consen   50 APGNQSK---------------------------PTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGK  102 (321)
T ss_pred             CcccCCC---------------------------CccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCc
Confidence            2211110                           0111134799999999999999999999999999999999999999


Q ss_pred             CceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCC
Q 012923          288 PKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGP  327 (453)
Q Consensus       288 ~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~  327 (453)
                      +|||+||.|-+.++|+.||..|| .+|++|.|+-.||..++
T Consensus       103 sKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp  143 (321)
T KOG0148|consen  103 SKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKP  143 (321)
T ss_pred             ccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCc
Confidence            99999999999999999999999 99999999999998777

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.88  E-value=8.3e-21  Score=175.88  Aligned_cols=172  Identities=18%  Similarity=0.311  Sum_probs=139.4

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecc
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLAS  207 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~  207 (453)
                      ....-|.+++|||+||++||.+||+.| .|+++.+.+.  +|+..|-|||+|.+.+++++||+.....+..|.|.|..+.
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~   84 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPRR--NGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAG   84 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcC-ceeEEEEecc--CCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccC
Confidence            345679999999999999999999999 5777665554  7999999999999999999999999899999999998886


Q ss_pred             cCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcce-eeeeccCCCC
Q 012923          208 IGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEE-GPLGIDKATG  286 (453)
Q Consensus       208 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~-v~i~~d~~~g  286 (453)
                      ..........                     ...........|.+++||+.||+++|.+||+..-.|.. |.++.+ ..+
T Consensus        85 ~~e~d~~~~~---------------------~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d-~rg  142 (510)
T KOG4211|consen   85 GAEADWVMRP---------------------GGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMD-QRG  142 (510)
T ss_pred             CccccccccC---------------------CCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeecc-CCC
Confidence            5443211100                     00111123458999999999999999999998865555 444454 478


Q ss_pred             CCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEcc
Q 012923          287 KPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAI  324 (453)
Q Consensus       287 ~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a~  324 (453)
                      ++.|-|||+|.+.+.|++||......|+.|.|.|..+.
T Consensus       143 R~tGEAfVqF~sqe~ae~Al~rhre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  143 RPTGEAFVQFESQESAEIALGRHRENIGHRYIEVFRSS  180 (510)
T ss_pred             CcccceEEEecCHHHHHHHHHHHHHhhccceEEeehhH
Confidence            89999999999999999999998888999999998775

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.85  E-value=2.6e-20  Score=153.22  Aligned_cols=84  Identities=23%  Similarity=0.464  Sum_probs=78.7

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|++||.|.+|.|++|+.+++++|||||+|.+.++|.+||..|| ..|+|+.|+|.|+
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a  111 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPA  111 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeC
Confidence            345699999999999999999999999999999999999999999999999999999999999998 8999999999999


Q ss_pred             cCCCC
Q 012923          324 IDGPK  328 (453)
Q Consensus       324 ~~~~~  328 (453)
                      ..++.
T Consensus       112 ~~~~~  116 (144)
T PLN03134        112 NDRPS  116 (144)
T ss_pred             CcCCC
Confidence            76543

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.84  E-value=2.3e-20  Score=176.41  Aligned_cols=176  Identities=26%  Similarity=0.425  Sum_probs=149.1

Q ss_pred             cccCCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCCeE
Q 012923          122 QVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGNRM  200 (453)
Q Consensus       122 ~~~~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~  200 (453)
                      .+....++.+.|||.||+.++|..+|.++|+.||.|.+|++.++. +| ++|| ||+|.+.++|.+|++.+|+. +.++.
T Consensus        68 rim~s~rd~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kk  144 (369)
T KOG0123|consen   68 RIMWSQRDPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKK  144 (369)
T ss_pred             EeehhccCCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCe
Confidence            334444455559999999999999999999999999999999998 66 9999 99999999999999999965 89999


Q ss_pred             eEEEecccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeee
Q 012923          201 TACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLG  280 (453)
Q Consensus       201 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~  280 (453)
                      |.|.....+.....+...                        ....-+.++|.|++..++++.|..+|..+|.|..+.++
T Consensus       145 i~vg~~~~~~er~~~~~~------------------------~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~  200 (369)
T KOG0123|consen  145 IYVGLFERKEEREAPLGE------------------------YKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVM  200 (369)
T ss_pred             eEEeeccchhhhcccccc------------------------hhhhhhhhheeccccccchHHHHHhhcccCcceEEEEe
Confidence            999887654443222111                        11223589999999999999999999999999999999


Q ss_pred             ccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          281 IDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       281 ~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      ++. .+++++|+||.|.++++|..|+..++ ..+.+..+.|..+..
T Consensus       201 ~~~-~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqk  245 (369)
T KOG0123|consen  201 RDS-IGKSKGFGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQK  245 (369)
T ss_pred             ecC-CCCCCCccceeecChhHHHHHHHhccCCcCCccceeeccccc
Confidence            975 66799999999999999999999999 777889999988765

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.83  E-value=2.4e-19  Score=177.45  Aligned_cols=80  Identities=20%  Similarity=0.364  Sum_probs=75.3

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCCeEeEEEecc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGNRMTACQLAS  207 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~~~v~~~~  207 (453)
                      ..++|||+|||+++++++|+++|+.||.|.+|+|++++.+++++|||||+|.+.++|.+||+.+|.. |.|+.|+|.++.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            4579999999999999999999999999999999999989999999999999999999999999954 999999999876


Q ss_pred             c
Q 012923          208 I  208 (453)
Q Consensus       208 ~  208 (453)
                      .
T Consensus       283 ~  283 (612)
T TIGR01645       283 T  283 (612)
T ss_pred             C
Confidence            4

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.

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.80  E-value=7.5e-18  Score=136.16  Aligned_cols=180  Identities=17%  Similarity=0.201  Sum_probs=132.9

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~~~v~~~  206 (453)
                      ..+++|||+|||.++.+.+|.++|-+||.|..|.|...+   ..-.||||+|.+..+|+.||..-++. +.|..|+|.++
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            456899999999999999999999999999999876543   34579999999999999999987754 99999999998


Q ss_pred             ccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCC
Q 012923          207 SIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATG  286 (453)
Q Consensus       207 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g  286 (453)
                      ..................      ..........+.......+|.|.+||.+.++++|+.+....|.|-...+.+|    
T Consensus        81 rggr~s~~~~G~y~gggr------gGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD----  150 (241)
T KOG0105|consen   81 RGGRSSSDRRGSYSGGGR------GGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD----  150 (241)
T ss_pred             cCCCcccccccccCCCCC------CCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc----
Confidence            755422111110000000      0000000111222334468999999999999999999999999999888875    


Q ss_pred             CCceEEEEEECCHHHHHHHHHcCC-Ccc--CCeEEEEEEc
Q 012923          287 KPKGFCLFVYKTVDAAKKALEEPH-KNF--EGHILNCQRA  323 (453)
Q Consensus       287 ~~kg~afV~F~~~~~A~~Al~~~~-~~l--~g~~l~v~~a  323 (453)
                         |++.|+|...++..-||.+|. ..+  .|-...+...
T Consensus       151 ---g~GvV~~~r~eDMkYAvr~ld~~~~~seGe~~yirv~  187 (241)
T KOG0105|consen  151 ---GVGVVEYLRKEDMKYAVRKLDDQKFRSEGETAYIRVR  187 (241)
T ss_pred             ---cceeeeeeehhhHHHHHHhhccccccCcCcEeeEEec
Confidence               479999999999999999988 433  4544444433

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.79  E-value=5.5e-18  Score=142.86  Aligned_cols=186  Identities=19%  Similarity=0.241  Sum_probs=139.2

Q ss_pred             cCeEEEcCCCCCCCHHHHHH----HHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCCeEeEEE
Q 012923          130 HRKIFVHGLGWDTKAETLID----AFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGNRMTACQ  204 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~----~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~~~v~  204 (453)
                      +.||||.||+..+..++|+.    +|++||.|..|...+   +.+.||=|||.|.+.+.|..|+..|++. +.|+.++|+
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriq   85 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQ   85 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhhee
Confidence            44999999999999999998    999999999987766   6689999999999999999999999976 899999999


Q ss_pred             ecccCCCCCCCcCccccccccc-----cc---c---ccc------ccccccc-cccccccccEEEEecCCCCccHHHHHH
Q 012923          205 LASIGPATTPAVASTATHQHQH-----QH---Q---HQH------QHQHQQH-HQQSEYTQRKIFVSNVGSELEPQKLLA  266 (453)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~~~~-----~~---~---~~~------~~~~~~~-~~~~~~~~~~l~V~nLp~~~t~~~l~~  266 (453)
                      ++..+.................     ..   +   ...      ....... ..........||+.|||..++.+.|..
T Consensus        86 yA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~~  165 (221)
T KOG4206|consen   86 YAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLSD  165 (221)
T ss_pred             cccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHHH
Confidence            9975543321111000000000     00   0   000      0000000 123355678999999999999999999


Q ss_pred             HHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccC-CeEEEEEEc
Q 012923          267 FFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFE-GHILNCQRA  323 (453)
Q Consensus       267 ~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~-g~~l~v~~a  323 (453)
                      +|.+|.....|+++...     +++|||+|.+...|..|...+. ..|- ...+.|.++
T Consensus       166 lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a  219 (221)
T KOG4206|consen  166 LFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFA  219 (221)
T ss_pred             HHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEeccc
Confidence            99999999999998754     8899999999999999998887 5553 677777665

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.78  E-value=8e-19  Score=165.03  Aligned_cols=189  Identities=20%  Similarity=0.313  Sum_probs=138.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCCeEeEEEecccC
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGNRMTACQLASIG  209 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~~~v~~~~~~  209 (453)
                      .+|||+||.+++|+++|+.+|++||.|..|.+.+|..+|.++||+||+|.+.++|.+|++.+|+. |.||.|+|......
T Consensus       279 ~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  279 RRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             hhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            34999999999999999999999999999999999999999999999999999999999999964 89999998765433


Q ss_pred             CCCCCCcCcccc-------------cc-ccccc-------------------c-------ccccccccccc-------cc
Q 012923          210 PATTPAVASTAT-------------HQ-HQHQH-------------------Q-------HQHQHQHQQHH-------QQ  242 (453)
Q Consensus       210 ~~~~~~~~~~~~-------------~~-~~~~~-------------------~-------~~~~~~~~~~~-------~~  242 (453)
                      ............             .. .+...                   .       ...........       +.
T Consensus       359 ~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~  438 (549)
T KOG0147|consen  359 VDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADASPA  438 (549)
T ss_pred             cccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCccccccc
Confidence            222111000000             00 00000                   0       00000000001       11


Q ss_pred             ccccccEEEEecCCCCcc----------HHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-C
Q 012923          243 SEYTQRKIFVSNVGSELE----------PQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-K  311 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t----------~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~  311 (453)
                      -.+.+.|+.|.|+-...|          .++|.+-|.+||.|..|.|.+.     +-|+.||.|.+.+.|..|+.+|| .
T Consensus       439 ~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~n-----s~g~VYvrc~s~~~A~~a~~alhgr  513 (549)
T KOG0147|consen  439 FDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKN-----SAGCVYVRCPSAEAAGTAVKALHGR  513 (549)
T ss_pred             cCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccC-----CCceEEEecCcHHHHHHHHHHHhhh
Confidence            125677888888843322          2678888999999998887543     24999999999999999999999 9


Q ss_pred             ccCCeEEEEEEcc
Q 012923          312 NFEGHILNCQRAI  324 (453)
Q Consensus       312 ~l~g~~l~v~~a~  324 (453)
                      +|.|+.|.+.|-.
T Consensus       514 WF~gr~Ita~~~~  526 (549)
T KOG0147|consen  514 WFAGRMITAKYLP  526 (549)
T ss_pred             hhccceeEEEEee
Confidence            9999999998864

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.77  E-value=8.1e-18  Score=153.18  Aligned_cols=195  Identities=19%  Similarity=0.289  Sum_probs=147.0

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHh-ccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFK-QYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~-~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      ....|.|||.|||+++.+.+|++||. +.|+|+.|.|+.|. +|++||||.|+|++++.+++|++.|+ ..+.||.|.|+
T Consensus        41 ~~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vK  119 (608)
T KOG4212|consen   41 AARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVK  119 (608)
T ss_pred             ccccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEe
Confidence            34457799999999999999999996 68999999999998 99999999999999999999999999 55999999997


Q ss_pred             ecccCCCCC--------------------------------------CCcCccccccc-------c--c-----cccccc
Q 012923          205 LASIGPATT--------------------------------------PAVASTATHQH-------Q--H-----QHQHQH  232 (453)
Q Consensus       205 ~~~~~~~~~--------------------------------------~~~~~~~~~~~-------~--~-----~~~~~~  232 (453)
                      --.......                                      .+.......+.       .  .     ......
T Consensus       120 Ed~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl  199 (608)
T KOG4212|consen  120 EDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGL  199 (608)
T ss_pred             ccCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccc
Confidence            653211100                                      00000000000       0  0     000000


Q ss_pred             -ccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-
Q 012923          233 -QHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-  310 (453)
Q Consensus       233 -~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-  310 (453)
                       .......+-...+...++||.||.+.+....|.+.|.-.|.|..|.+-.|+ .|.++|||.|+|..+-.|..||..++ 
T Consensus       200 ~~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idK-eG~s~G~~vi~y~hpveavqaIsml~~  278 (608)
T KOG4212|consen  200 SASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDK-EGNSRGFAVIEYDHPVEAVQAISMLDR  278 (608)
T ss_pred             hhhhhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeecc-ccccCCeeEEEecchHHHHHHHHhhcc
Confidence             001111112344556799999999999999999999999999999998886 56999999999999999999999999 


Q ss_pred             CccCCeEEEEEEc
Q 012923          311 KNFEGHILNCQRA  323 (453)
Q Consensus       311 ~~l~g~~l~v~~a  323 (453)
                      .-+..++..+++.
T Consensus       279 ~g~~~~~~~~Rl~  291 (608)
T KOG4212|consen  279 QGLFDRRMTVRLD  291 (608)
T ss_pred             CCCccccceeecc
Confidence            6677888777764

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.75  E-value=9.5e-18  Score=138.02  Aligned_cols=85  Identities=32%  Similarity=0.656  Sum_probs=78.1

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ...+++|||+|||+++|+++|+++|.+||.|.+|+|+.|+.+++++|||||+|.+.++|++||+.++ ..|.|+.|+|.+
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            3456799999999999999999999999999999999999999999999999999999999999877 569999999999


Q ss_pred             cccCCC
Q 012923          206 ASIGPA  211 (453)
Q Consensus       206 ~~~~~~  211 (453)
                      +..++.
T Consensus       111 a~~~~~  116 (144)
T PLN03134        111 ANDRPS  116 (144)
T ss_pred             CCcCCC
Confidence            875543

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.75  E-value=4.2e-17  Score=144.74  Aligned_cols=194  Identities=15%  Similarity=0.239  Sum_probs=143.6

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeE--------EEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccC
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIED--------CKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIG  197 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~--------v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~  197 (453)
                      ...++.|||.|||.++|-+++.++|++||.|..        |+|.++. .|+.+|-|+|.|-..+++..|+..|+ ..|.
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCccccc
Confidence            344678999999999999999999999998753        7888888 69999999999999999999999999 4589


Q ss_pred             CeEeEEEecccCCCCCCCcCccccccc----cccccccccc--ccccccccccccccEEEEecCCCC----cc-------
Q 012923          198 NRMTACQLASIGPATTPAVASTATHQH----QHQHQHQHQH--QHQQHHQQSEYTQRKIFVSNVGSE----LE-------  260 (453)
Q Consensus       198 gr~~~v~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~--~~~~~~~~~~~~~~~l~V~nLp~~----~t-------  260 (453)
                      |+.|+|..+.....-............    ....+.....  .............++|.|+||-..    .+       
T Consensus       210 g~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dl  289 (382)
T KOG1548|consen  210 GKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDL  289 (382)
T ss_pred             CcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHH
Confidence            999999998744332211111111011    0111111100  111123455556789999998421    22       


Q ss_pred             HHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          261 PQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       261 ~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .++|++-+++||.|.+|.|.-    ..+.|.+-|.|.+.++|..||..|+ ++|+||.|..+..-.
T Consensus       290 kedl~eec~K~G~v~~vvv~d----~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG  351 (382)
T KOG1548|consen  290 KEDLTEECEKFGQVRKVVVYD----RHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDG  351 (382)
T ss_pred             HHHHHHHHHHhCCcceEEEec----cCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCC
Confidence            467778899999999998853    2348999999999999999999999 999999999887643

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.73  E-value=4.2e-16  Score=144.96  Aligned_cols=192  Identities=15%  Similarity=0.191  Sum_probs=135.5

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeE-EEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIED-CKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLAS  207 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~-v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~  207 (453)
                      ..-.|.+++||+.||++||.+||+..-.|.. |.++.+. .+++.|-|||+|++.+.|++||..++..|..|.|.|..+.
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~rhre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGRHRENIGHRYIEVFRSS  180 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHHHHHhhccceEEeehhH
Confidence            4468999999999999999999998765555 4455555 7889999999999999999999999999999999998775


Q ss_pred             cCCCCCCC----------c---C----cc----cccccccc---------------------------------c---cc
Q 012923          208 IGPATTPA----------V---A----ST----ATHQHQHQ---------------------------------H---QH  230 (453)
Q Consensus       208 ~~~~~~~~----------~---~----~~----~~~~~~~~---------------------------------~---~~  230 (453)
                      ........          .   .    ..    ........                                 .   ..
T Consensus       181 ~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~gs~~~~~~~~~~  260 (510)
T KOG4211|consen  181 RAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFGSYGGGRDPNYP  260 (510)
T ss_pred             HHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCccccccccccccccccccccC
Confidence            21111000          0   0    00    00000000                                 0   00


Q ss_pred             c---ccccccccc-ccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHH
Q 012923          231 Q---HQHQHQQHH-QQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKAL  306 (453)
Q Consensus       231 ~---~~~~~~~~~-~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al  306 (453)
                      .   .+....... .........++.++||+..+..+|..+|+..-.+ .|.|-.. .+|+..|-|+|+|.|+++|..|+
T Consensus       261 ~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~-~v~i~ig-~dGr~TGEAdveF~t~edav~Am  338 (510)
T KOG4211|consen  261 VSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPY-RVHIEIG-PDGRATGEADVEFATGEDAVGAM  338 (510)
T ss_pred             CCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCce-eEEEEeC-CCCccCCcceeecccchhhHhhh
Confidence            0   000000000 1112223789999999999999999999977544 6666553 58999999999999999999999


Q ss_pred             HcCCCccCCeEEEEEEc
Q 012923          307 EEPHKNFEGHILNCQRA  323 (453)
Q Consensus       307 ~~~~~~l~g~~l~v~~a  323 (453)
                      .+-+..+..+.|.+...
T Consensus       339 skd~anm~hrYVElFln  355 (510)
T KOG4211|consen  339 GKDGANMGHRYVELFLN  355 (510)
T ss_pred             ccCCcccCcceeeeccc
Confidence            99888888888887664

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.73  E-value=7.4e-17  Score=136.21  Aligned_cols=82  Identities=33%  Similarity=0.564  Sum_probs=77.8

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEccC
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAID  325 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a~~  325 (453)
                      .-++|||++|+|.++.+.|+++|++||+|+.+.|+.|+.||+||||+||+|.+.++|.+|++..|..|+||+..|.+|..
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNLASL   90 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccchhhh
Confidence            44799999999999999999999999999999999999999999999999999999999999999899999999999876


Q ss_pred             CC
Q 012923          326 GP  327 (453)
Q Consensus       326 ~~  327 (453)
                      ..
T Consensus        91 g~   92 (247)
T KOG0149|consen   91 GG   92 (247)
T ss_pred             cC
Confidence            43

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.70  E-value=3.2e-17  Score=138.43  Aligned_cols=83  Identities=45%  Similarity=0.801  Sum_probs=78.5

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEeccc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASI  208 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~~  208 (453)
                      .-++|||++|+|.++.+.|+++|++||+|+++.||.|+.+++||||+||+|++.++|.+|++.-+-.|+||+..|+++..
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNLASL   90 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccchhhh
Confidence            34789999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             CCC
Q 012923          209 GPA  211 (453)
Q Consensus       209 ~~~  211 (453)
                      ..+
T Consensus        91 g~~   93 (247)
T KOG0149|consen   91 GGK   93 (247)
T ss_pred             cCc
Confidence            433

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.69  E-value=4.1e-16  Score=130.06  Aligned_cols=177  Identities=18%  Similarity=0.242  Sum_probs=123.3

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcc-cCCCCCcceEEEEEEccHHHHHHHHHcCCCc-c---CCeEeEEE
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVC-DKVSGKSKGYGFILFKTRSGARKALKEPQKK-I---GNRMTACQ  204 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~-d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~---~gr~~~v~  204 (453)
                      -|||||.+||.++...+|..+|..|--.+.+.|.. ++...-++-+|||+|.+..+|.+|+.+||+. +   .+..|++.
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            48999999999999999999999997777666544 3323346689999999999999999999975 3   67889999


Q ss_pred             ecccCCCCCCCcCcccccc-----------ccccc---cc----------------------------------------
Q 012923          205 LASIGPATTPAVASTATHQ-----------HQHQH---QH----------------------------------------  230 (453)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~-----------~~~~~---~~----------------------------------------  230 (453)
                      ++....+..+......+..           .++..   ++                                        
T Consensus       114 lAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P~a  193 (284)
T KOG1457|consen  114 LAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAPSA  193 (284)
T ss_pred             ehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCCcc
Confidence            9876554422221110000           00000   00                                        


Q ss_pred             ccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC
Q 012923          231 QHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH  310 (453)
Q Consensus       231 ~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~  310 (453)
                      ..+.............+.+|||.||...||+++|+++|+.|-....++|.   ..|. ...|||+|.+.+.|..|+..|.
T Consensus       194 ~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~---~~~g-~~vaf~~~~~~~~at~am~~lq  269 (284)
T KOG1457|consen  194 NAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIR---ARGG-MPVAFADFEEIEQATDAMNHLQ  269 (284)
T ss_pred             cchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEe---cCCC-cceEeecHHHHHHHHHHHHHhh
Confidence            00000001112334556899999999999999999999999877666662   2222 4579999999999999998865

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.69  E-value=5.9e-16  Score=145.87  Aligned_cols=83  Identities=16%  Similarity=0.276  Sum_probs=77.9

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      .....++|||+|||+++|+++|+++|+.||.|+.|+|++|+.+++++|||||+|.+.++|.+||..|+ ..|.+++|+|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            34456899999999999999999999999999999999999999999999999999999999999999 89999999999


Q ss_pred             EccC
Q 012923          322 RAID  325 (453)
Q Consensus       322 ~a~~  325 (453)
                      ++..
T Consensus       183 ~a~p  186 (346)
T TIGR01659       183 YARP  186 (346)
T ss_pred             cccc
Confidence            8864

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).

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.68  E-value=3.2e-16  Score=151.69  Aligned_cols=193  Identities=21%  Similarity=0.245  Sum_probs=137.0

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~~~v~  204 (453)
                      .....+.|+|+|||..+..++|..+|..||.|..|.+.  + .|.   -|+|.|.+..+|.+|+..+... +....+.+.
T Consensus       381 ~~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp--~-~G~---~aiv~fl~p~eAr~Afrklaysr~k~~plyle  454 (725)
T KOG0110|consen  381 AERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLP--P-GGT---GAIVEFLNPLEARKAFRKLAYSRFKSAPLYLE  454 (725)
T ss_pred             hhhhcceeeeccCccccccHHHHHHhhcccccceeecC--c-ccc---eeeeeecCccchHHHHHHhchhhhccCccccc
Confidence            44556889999999999999999999999999998443  2 232   3999999999999999999844 666777777


Q ss_pred             ecccCCCCCCC-----cCccccc----ccccccccccccc--------cccccc-cccccccEEEEecCCCCccHHHHHH
Q 012923          205 LASIGPATTPA-----VASTATH----QHQHQHQHQHQHQ--------HQQHHQ-QSEYTQRKIFVSNVGSELEPQKLLA  266 (453)
Q Consensus       205 ~~~~~~~~~~~-----~~~~~~~----~~~~~~~~~~~~~--------~~~~~~-~~~~~~~~l~V~nLp~~~t~~~l~~  266 (453)
                      |+........+     .......    ..+.......+..        ...... ......++|||.||++.+|.++|..
T Consensus       455 ~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~  534 (725)
T KOG0110|consen  455 WAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLED  534 (725)
T ss_pred             cChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHH
Confidence            76533332110     0000000    0000000000000        000101 1122223499999999999999999


Q ss_pred             HHhccCCcceeeeeccCCC---CCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          267 FFSKYGEIEEGPLGIDKAT---GKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       267 ~F~~~G~i~~v~i~~d~~~---g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      +|...|.|..|.|...+..   -.|.|||||+|.+.++|..|++.|+ ..|+|+.|.|+++.
T Consensus       535 ~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  535 LFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             HHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            9999999999988765422   2356999999999999999999999 99999999999987

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.65  E-value=3.6e-16  Score=133.56  Aligned_cols=164  Identities=18%  Similarity=0.322  Sum_probs=128.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEecccC
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQLASIG  209 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~~~~~  209 (453)
                      .+|||++||+.+.+.+|..||..||.|..|.+..        ||+||+|.+..+|..|+..+++ .|++..+.|.++...
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            4799999999999999999999999999987543        5899999999999999999985 478877888887643


Q ss_pred             CCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCc
Q 012923          210 PATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPK  289 (453)
Q Consensus       210 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~k  289 (453)
                      ..........            ................++|+|.+|+..+.+.+|...|.++|.+....+        .+
T Consensus        74 ~~~~g~~~~g------------~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~  133 (216)
T KOG0106|consen   74 RRGRGRPRGG------------DRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RR  133 (216)
T ss_pred             ccccCCCCCC------------CccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hc
Confidence            2211000000            000011112233455679999999999999999999999999965544        27


Q ss_pred             eEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          290 GFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       290 g~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      +++||+|.+.++|.+||..++ ..|.++.|.+..
T Consensus       134 ~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen  134 NFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             cccceeehhhhhhhhcchhccchhhcCceeeecc
Confidence            799999999999999999999 899999999943

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.63  E-value=7.2e-15  Score=131.19  Aligned_cols=196  Identities=16%  Similarity=0.261  Sum_probs=138.6

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~~  206 (453)
                      ..-.+|||..+.++.+++||+.+|+.||+|..|.+-+++..+.+|||+||+|.+..+...|+..+|- .|.|..|+|..+
T Consensus       208 k~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~  287 (544)
T KOG0124|consen  208 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC  287 (544)
T ss_pred             HhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccc
Confidence            3456899999999999999999999999999999999998889999999999999999999999995 499999999776


Q ss_pred             ccCCCC-----------------------------------------CCCcCccccccccc-----c-------------
Q 012923          207 SIGPAT-----------------------------------------TPAVASTATHQHQH-----Q-------------  227 (453)
Q Consensus       207 ~~~~~~-----------------------------------------~~~~~~~~~~~~~~-----~-------------  227 (453)
                      .-.+..                                         .....+......+.     +             
T Consensus       288 vTPP~aLl~Pat~s~~P~aaaVAaAAaTAKi~A~eAvAg~avlg~~G~~~~vSpA~~aa~p~~~l~qa~~a~~~pgvi~~  367 (544)
T KOG0124|consen  288 VTPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGSAVLGTVGAPGLVSPAPRAAQPLGTLPQAVMAAQAPGVITG  367 (544)
T ss_pred             cCCCchhcCCCCcccCchHHHHHHHHHHHHHHHHHHhccCCcccccCCccccCccccccCCCCCccccchhccCCceecc
Confidence            422211                                         00000000000000     0             


Q ss_pred             ----------------------------------------c-cccccccc----------cc--------cccccccccc
Q 012923          228 ----------------------------------------H-QHQHQHQH----------QQ--------HHQQSEYTQR  248 (453)
Q Consensus       228 ----------------------------------------~-~~~~~~~~----------~~--------~~~~~~~~~~  248 (453)
                                                              . +.+.....          ..        ........++
T Consensus       368 vtP~~P~iP~~i~p~g~v~P~LA~ppT~g~L~kkkeKe~eelqpkl~~~~~L~~QE~msI~G~sARhlvMqkLmR~~~S~  447 (544)
T KOG0124|consen  368 VTPARPPIPVTIPPVGVVNPILASPPTLGLLEKKKEKEEEELQPKLERPEMLSEQEHMSISGSSARHLVMQKLMRKQEST  447 (544)
T ss_pred             CCCCCCCCCccCCCcceechhhcCCCchhhcchhhhhhHhhhcccccCHHHhhhhhCccccCccHHHHHHHHHhccccCc
Confidence                                                    0 00000000          00        0022344567


Q ss_pred             EEEEecC--CCCcc---HHHHHHHHhccCCcceeeeeccCCCCCC----ceEEEEEECCHHHHHHHHHcCC-CccCCeEE
Q 012923          249 KIFVSNV--GSELE---PQKLLAFFSKYGEIEEGPLGIDKATGKP----KGFCLFVYKTVDAAKKALEEPH-KNFEGHIL  318 (453)
Q Consensus       249 ~l~V~nL--p~~~t---~~~l~~~F~~~G~i~~v~i~~d~~~g~~----kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l  318 (453)
                      .|.++|+  |.+++   +.+|++-|.+||.|.+|.|...+.++.-    ---.||+|.....+.+|+.+|+ ++|.||++
T Consensus       448 VivLRNMV~P~DiDe~LegEi~EECgKfG~V~rViI~nekq~e~edaeiiVKIFVefS~~~e~~rak~ALdGRfFgGr~V  527 (544)
T KOG0124|consen  448 VIVLRNMVDPKDIDEDLEGEITEECGKFGAVNRVIIYNEKQGEEEDAEIIVKIFVEFSIASETHRAKQALDGRFFGGRKV  527 (544)
T ss_pred             EEEEeccCChhhhhhHHHHHHHHHHhcccceeEEEEEecccccccchhhhheeeeeechhhHHHHHHHhhccceecCcee
Confidence            8889998  44443   4678999999999999988776544321    1137999999999999999999 88999988


Q ss_pred             EEEEc
Q 012923          319 NCQRA  323 (453)
Q Consensus       319 ~v~~a  323 (453)
                      .....
T Consensus       528 vAE~Y  532 (544)
T KOG0124|consen  528 VAEVY  532 (544)
T ss_pred             ehhhh
Confidence            76543

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

Probab=99.63  E-value=1e-15  Score=129.78  Aligned_cols=81  Identities=23%  Similarity=0.444  Sum_probs=77.4

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ...+|.|.||+.++++++|+++|.+||.|.+|.|.+|+.||.+||||||+|.+.++|.+||..|| +-++.-.|+|.|++
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            55799999999999999999999999999999999999999999999999999999999999999 88999999999996


Q ss_pred             CC
Q 012923          325 DG  326 (453)
Q Consensus       325 ~~  326 (453)
                      ++
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            54

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.63  E-value=9.1e-16  Score=116.61  Aligned_cols=79  Identities=23%  Similarity=0.421  Sum_probs=75.5

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ..+++|||+||++.+++++|.++|+++|.|..|.+-.|+.+..+.|||||+|.+.++|..||+.++ ..|+.++|.|.|.
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            345799999999999999999999999999999999999999999999999999999999999999 8999999999987

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.60  E-value=1.6e-15  Score=136.17  Aligned_cols=193  Identities=16%  Similarity=0.225  Sum_probs=134.2

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcc----CCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEe
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQY----GEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQL  205 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~----G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~  205 (453)
                      .-.|.+++||+++|+.++.+||.+-    |-++.|.+++.+ +|+..|-|||.|..+++|+.||.+....|..|.|.+..
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIElFR  239 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIELFR  239 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHHHH
Confidence            3468899999999999999999632    234456555554 89999999999999999999999988888888887765


Q ss_pred             cccCCCCCCCcCccc-ccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCC-cce--eeeec
Q 012923          206 ASIGPATTPAVASTA-THQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGE-IEE--GPLGI  281 (453)
Q Consensus       206 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~-i~~--v~i~~  281 (453)
                      +.......-...... ......  ............-.......+|.+++||+..+.++|..||..|-. |..  |+++.
T Consensus       240 STaaEvqqvlnr~~s~pLi~~~--~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~  317 (508)
T KOG1365|consen  240 STAAEVQQVLNREVSEPLIPGL--TSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVL  317 (508)
T ss_pred             HhHHHHHHHHHhhccccccCCC--CCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEE
Confidence            532111000000000 000000  000000001111222333569999999999999999999998864 333  66666


Q ss_pred             cCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCC
Q 012923          282 DKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDG  326 (453)
Q Consensus       282 d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~  326 (453)
                      + ..|+..|-|||+|.+.++|..|....+ +....|.|.|..+...
T Consensus       318 N-~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~e  362 (508)
T KOG1365|consen  318 N-GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCSVE  362 (508)
T ss_pred             c-CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeeccHH
Confidence            4 579999999999999999999999988 5556999999887543

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

Probab=99.60  E-value=3.2e-15  Score=126.76  Aligned_cols=81  Identities=23%  Similarity=0.388  Sum_probs=76.5

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCCeEeEEEecc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGNRMTACQLAS  207 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~~~v~~~~  207 (453)
                      +..+|.|.||+.++++++|++||.+||.|..|.|.+|+.||.+||||||.|.+.++|.+||..|++. +..-.|+|.|+.
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            6678999999999999999999999999999999999999999999999999999999999999966 888899999986


Q ss_pred             cC
Q 012923          208 IG  209 (453)
Q Consensus       208 ~~  209 (453)
                      +.
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            43

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.60  E-value=1.2e-14  Score=136.03  Aligned_cols=169  Identities=22%  Similarity=0.344  Sum_probs=123.9

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~  208 (453)
                      .++|||+|||+++|+++|+++|.+||.|..|+|..++.+++++|||||.|.+.++|..|+..++ ..|.|+.|.|.+...
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            5899999999999999999999999999999999998899999999999999999999999999 669999999999753


Q ss_pred             --CCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCC
Q 012923          209 --GPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATG  286 (453)
Q Consensus       209 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g  286 (453)
                        .........          ......................+++.+++..++...+...|..+|.|..+.+.......
T Consensus       195 ~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  264 (306)
T COG0724         195 ASQPRSELSNN----------LDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGK  264 (306)
T ss_pred             ccccccccccc----------cchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCCCCc
Confidence              111111100          00000000012223344455799999999999999999999999999877776554333


Q ss_pred             CCceEEEEEECCHHHHHHHHHc
Q 012923          287 KPKGFCLFVYKTVDAAKKALEE  308 (453)
Q Consensus       287 ~~kg~afV~F~~~~~A~~Al~~  308 (453)
                      ....+.++.+.....+..++..
T Consensus       265 ~~~~~~~~~~~~~~~~~~~~~~  286 (306)
T COG0724         265 IPKSRSFVGNEASKDALESNSR  286 (306)
T ss_pred             ccccccccchhHHHhhhhhhcc
Confidence            3444444444444444444433

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.59  E-value=2.9e-15  Score=113.86  Aligned_cols=80  Identities=19%  Similarity=0.333  Sum_probs=74.6

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~~  206 (453)
                      ..++||||+||++.+||+.|.++|+++|+|..|.+-.|+.+....|||||+|.+.++|..||+-++. .|..+.|++.|-
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            4468999999999999999999999999999999999998999999999999999999999999985 499999999986


Q ss_pred             c
Q 012923          207 S  207 (453)
Q Consensus       207 ~  207 (453)
                      .
T Consensus       114 ~  114 (153)
T KOG0121|consen  114 A  114 (153)
T ss_pred             c
Confidence            4

>PF00076 RRM_1: RNA recognition motif

Probab=99.59  E-value=5.8e-15  Score=106.74  Aligned_cols=69  Identities=43%  Similarity=0.640  Sum_probs=64.3

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeE
Q 012923          133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTA  202 (453)
Q Consensus       133 lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~  202 (453)
                      |||+|||.++|+++|+++|++||.|..++++.+ .++.+++||||+|.+.++|.+|++.++ ..+.|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            899999999999999999999999999999998 488999999999999999999999877 458888875

(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 ....

>PF00076 RRM_1: RNA recognition motif

Probab=99.58  E-value=5e-15  Score=107.08  Aligned_cols=69  Identities=30%  Similarity=0.609  Sum_probs=65.6

Q ss_pred             EEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEE
Q 012923          250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILN  319 (453)
Q Consensus       250 l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~  319 (453)
                      |||+|||..+|+++|+++|+.||.|..+.+..+ .++..++||||+|.+.++|.+|+..++ ..|+|++|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999987 688899999999999999999999988 889999885

(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 ....

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.58  E-value=6.9e-15  Score=121.37  Aligned_cols=82  Identities=24%  Similarity=0.363  Sum_probs=77.4

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ....+|.|-||.+-+|.++|+.+|++||.|-+|.|++|+.|..++|||||.|....+|+.|+.+|+ ..|+|+.|.|++|
T Consensus        11 ~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~a   90 (256)
T KOG4207|consen   11 EGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMA   90 (256)
T ss_pred             ccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhh
Confidence            345699999999999999999999999999999999999999999999999999999999999999 8999999999998


Q ss_pred             cCC
Q 012923          324 IDG  326 (453)
Q Consensus       324 ~~~  326 (453)
                      .=.
T Consensus        91 ryg   93 (256)
T KOG4207|consen   91 RYG   93 (256)
T ss_pred             hcC
Confidence            643

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.56  E-value=1.1e-13  Score=126.61  Aligned_cols=74  Identities=18%  Similarity=0.241  Sum_probs=67.5

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+++|+..|++-|..||.|..+.|+   +.|+++|  .|.|.++++|+.|+..|+ ..|+||.|+|.+.
T Consensus       534 rKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadim---e~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  534 RKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIM---ENGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             ccccEEEEecCCccccHHHHHHHHHhccceehhhhh---ccCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            445789999999999999999999999999999984   4688887  899999999999999999 8999999999873

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.56  E-value=1.4e-13  Score=125.08  Aligned_cols=187  Identities=17%  Similarity=0.207  Sum_probs=140.0

Q ss_pred             cCeEEEcCCC-CCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecc
Q 012923          130 HRKIFVHGLG-WDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLAS  207 (453)
Q Consensus       130 ~~~lfV~nLp-~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~  207 (453)
                      ++.|.|.||. ..+|.+-|..+|.-||.|..|+|+.++.     --|+|+|.+...|+.|++.|+ ..|.|++|+|.++.
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            6789999996 7789999999999999999999998763     359999999999999999999 56999999999987


Q ss_pred             cCCCCCCCcCccc---ccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCC
Q 012923          208 IGPATTPAVASTA---THQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKA  284 (453)
Q Consensus       208 ~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~  284 (453)
                      ......+......   .........++..............++.+|++.|+|.++++++|+.+|...|-..+.....   
T Consensus       372 H~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff---  448 (492)
T KOG1190|consen  372 HTNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFF---  448 (492)
T ss_pred             CccccCCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeec---
Confidence            5544332211111   1111111111111222223334456678999999999999999999999988776554332   


Q ss_pred             CCCCceEEEEEECCHHHHHHHHHcCC-CccCC-eEEEEEEccC
Q 012923          285 TGKPKGFCLFVYKTVDAAKKALEEPH-KNFEG-HILNCQRAID  325 (453)
Q Consensus       285 ~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g-~~l~v~~a~~  325 (453)
                       ++.+-+|++.+.+.+.|..|+..++ +.+.. +.|+|+|.++
T Consensus       449 -~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  449 -QKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             -CCCcceeecccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence             3346799999999999999999998 77765 5899998764

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.56  E-value=2.2e-14  Score=137.26  Aligned_cols=187  Identities=18%  Similarity=0.257  Sum_probs=141.2

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~~~v~~~~~  208 (453)
                      ..++||++||...++..++++...||.+...+++.|..+|.++||||.+|.+......|+..+|++ +.++.|.|..+..
T Consensus       289 ~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~  368 (500)
T KOG0120|consen  289 PNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIV  368 (500)
T ss_pred             cchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhc
Confidence            457999999999999999999999999999999999999999999999999999999999999966 7889999999876


Q ss_pred             CCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCC--Cc-c-------HHHHHHHHhccCCcceee
Q 012923          209 GPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGS--EL-E-------PQKLLAFFSKYGEIEEGP  278 (453)
Q Consensus       209 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~--~~-t-------~~~l~~~F~~~G~i~~v~  278 (453)
                      .............        .................+..|.+.|+=.  .+ .       -++|+.-|.+||.|..|.
T Consensus       369 g~~~~~~~~~~~~--------~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~  440 (500)
T KOG0120|consen  369 GASNANVNFNISQ--------SQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVE  440 (500)
T ss_pred             cchhccccCCccc--------cccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEe
Confidence            6544333222000        0000111111123344445666666511  11 1       145667788999999999


Q ss_pred             eeccC---CCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          279 LGIDK---ATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       279 i~~d~---~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      |.++-   ...-..|..||+|.+.+++++|...|+ .+|.+|.|.+.|..
T Consensus       441 ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  441 IPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYD  490 (500)
T ss_pred             cCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecC
Confidence            98872   223346779999999999999999999 89999999998863

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.55  E-value=2.4e-14  Score=125.77  Aligned_cols=77  Identities=18%  Similarity=0.210  Sum_probs=70.0

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecccC
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASIG  209 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~~~  209 (453)
                      .++|||+|||+.+|+++|++||+.||.|.+|+|+++..   ++|||||+|.+.++|..||...+..|.|+.|.|.++...
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            47999999999999999999999999999999998863   579999999999999999976557899999999998643

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.55  E-value=1.6e-14  Score=104.33  Aligned_cols=69  Identities=28%  Similarity=0.539  Sum_probs=63.4

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeE
Q 012923          133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTA  202 (453)
Q Consensus       133 lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~  202 (453)
                      |||+|||+++++++|+++|+.||.|..|+++.++. +.++|+|||+|.+.++|.+|+..++ ..+.|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999986 8999999999999999999999998 669999874

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 ....

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.55  E-value=2e-14  Score=110.31  Aligned_cols=92  Identities=26%  Similarity=0.395  Sum_probs=84.0

Q ss_pred             cccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEE
Q 012923          242 QSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNC  320 (453)
Q Consensus       242 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v  320 (453)
                      ........|||.++...+|+++|...|..||.|++|.|-.|+.||-.||||+|+|.+...|.+|+..+| ..|.|.+|.|
T Consensus        67 qrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~V  146 (170)
T KOG0130|consen   67 QRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSV  146 (170)
T ss_pred             ccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeE
Confidence            344456799999999999999999999999999999999999999999999999999999999999999 9999999999


Q ss_pred             EEccCCCCCCCCC
Q 012923          321 QRAIDGPKPGKSR  333 (453)
Q Consensus       321 ~~a~~~~~~~~~~  333 (453)
                      .|++.+++....+
T Consensus       147 Dw~Fv~gp~~g~r  159 (170)
T KOG0130|consen  147 DWCFVKGPERGKR  159 (170)
T ss_pred             EEEEecCCccCcc
Confidence            9999887654443

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.54  E-value=1.1e-15  Score=123.53  Aligned_cols=87  Identities=26%  Similarity=0.389  Sum_probs=78.6

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~~~v  203 (453)
                      ..=.++.-|||+|||++.||.||..+|++||+|++|.|++|+.||+|+||||+.|.+..+-..|+..+|+. |.||.|+|
T Consensus        30 ~~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirV  109 (219)
T KOG0126|consen   30 QEYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRV  109 (219)
T ss_pred             hhcccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEe
Confidence            34455678999999999999999999999999999999999999999999999999999999999999965 99999999


Q ss_pred             EecccCCC
Q 012923          204 QLASIGPA  211 (453)
Q Consensus       204 ~~~~~~~~  211 (453)
                      .-......
T Consensus       110 DHv~~Yk~  117 (219)
T KOG0126|consen  110 DHVSNYKK  117 (219)
T ss_pred             eecccccC
Confidence            87654433

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.54  E-value=4.1e-14  Score=123.44  Aligned_cols=83  Identities=25%  Similarity=0.372  Sum_probs=77.7

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ..+-+||||.-|++.+++..|+..|+.||.|+.|+||+|+.||+++|||||+|.+.-+...|.+..+ ..|+|+.|.|.+
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            3456899999999999999999999999999999999999999999999999999999999999998 899999999988


Q ss_pred             ccCC
Q 012923          323 AIDG  326 (453)
Q Consensus       323 a~~~  326 (453)
                      -..+
T Consensus       178 ERgR  181 (335)
T KOG0113|consen  178 ERGR  181 (335)
T ss_pred             cccc
Confidence            7544

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.53  E-value=2.6e-14  Score=103.20  Aligned_cols=69  Identities=30%  Similarity=0.583  Sum_probs=64.0

Q ss_pred             EEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEE
Q 012923          250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILN  319 (453)
Q Consensus       250 l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~  319 (453)
                      |||+|||+.+++++|+++|+.||.|..+++..++. +.++++|||+|.+.++|.+|+..++ ..|+|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999876 8999999999999999999999999 899999885

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 ....

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.53  E-value=4.2e-14  Score=140.31  Aligned_cols=134  Identities=21%  Similarity=0.239  Sum_probs=97.2

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcc--CCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQY--GEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~--G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      .++|||+||++++|+++|+++|++|  |.|..|++++        +||||+|.+.++|.+||+.++ ..|.|+.|.|.++
T Consensus       233 ~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r--------gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~A  304 (578)
T TIGR01648       233 VKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR--------DYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLA  304 (578)
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec--------CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            5789999999999999999999999  9999998764        499999999999999999888 5699999999999


Q ss_pred             ccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcc
Q 012923          207 SIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIE  275 (453)
Q Consensus       207 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~  275 (453)
                      .................  .  ....................++++.||++.++++.|+++|..+|.|.
T Consensus       305 kp~~~~~~~~~~rg~gg--~--~~~~~~~~~~~g~~~sp~s~~~~~g~~~~~~~~~~~~~~f~~~g~~~  369 (578)
T TIGR01648       305 KPVDKKSYVRYTRGTGG--R--GKERQAARQSLGQVYDPASRSLAYEDYYYHPPYAPSLHFPRMPGPIR  369 (578)
T ss_pred             cCCCcccccccccccCC--C--cccccccccccCcccCccccccccccccccccccchhhccccCcccc
Confidence            65433211000000000  0  00000000011122333467999999999999999999999998754

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.

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.53  E-value=5.6e-14  Score=123.47  Aligned_cols=76  Identities=22%  Similarity=0.235  Sum_probs=69.4

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .++|||+||++.+|+++|+++|+.||.|.+|+|+++..   ++|||||+|.+.++|..||. |+ ..|.|+.|.|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            36999999999999999999999999999999998864   47999999999999999996 56 999999999999864


Q ss_pred             C
Q 012923          326 G  326 (453)
Q Consensus       326 ~  326 (453)
                      .
T Consensus        80 ~   80 (260)
T PLN03120         80 Y   80 (260)
T ss_pred             C
Confidence            4

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.53  E-value=2.4e-14  Score=126.39  Aligned_cols=88  Identities=23%  Similarity=0.334  Sum_probs=78.4

Q ss_pred             ccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEE
Q 012923          241 QQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILN  319 (453)
Q Consensus       241 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~  319 (453)
                      .......++|+|.|||+..-+-||+.+|.+||.|.+|.||.+  ...||||+||+|++.+||++|..+|| ..+.||+|+
T Consensus        90 s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--ERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIE  167 (376)
T KOG0125|consen   90 SSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--ERGSKGFGFVTMENPADADRARAELHGTVVEGRKIE  167 (376)
T ss_pred             CCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEec--cCCCCccceEEecChhhHHHHHHHhhcceeeceEEE
Confidence            444555689999999999999999999999999999999875  45679999999999999999999999 899999999


Q ss_pred             EEEccCCCCCC
Q 012923          320 CQRAIDGPKPG  330 (453)
Q Consensus       320 v~~a~~~~~~~  330 (453)
                      |..+..+....
T Consensus       168 Vn~ATarV~n~  178 (376)
T KOG0125|consen  168 VNNATARVHNK  178 (376)
T ss_pred             EeccchhhccC
Confidence            99998774433

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.53  E-value=1.3e-15  Score=123.07  Aligned_cols=83  Identities=29%  Similarity=0.465  Sum_probs=77.6

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      +.-|||+|||+.+|+.+|.-+|++||.|+.|.|+||+.||+|+||||+.|.+..+...|+..+| ..|.||.|+|.-...
T Consensus        35 sA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~~  114 (219)
T KOG0126|consen   35 SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVSN  114 (219)
T ss_pred             ceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeeccc
Confidence            3589999999999999999999999999999999999999999999999999999999999999 899999999988765


Q ss_pred             CCCC
Q 012923          326 GPKP  329 (453)
Q Consensus       326 ~~~~  329 (453)
                      ...+
T Consensus       115 Yk~p  118 (219)
T KOG0126|consen  115 YKKP  118 (219)
T ss_pred             ccCC
Confidence            5444

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.53  E-value=3e-14  Score=124.26  Aligned_cols=83  Identities=33%  Similarity=0.520  Sum_probs=76.6

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ..-+||||.-|+++++|.+|+..|+.||.|..|+|++|+.||+++|||||+|.+..+...|.+... .+|.|+.|.|.+-
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            346899999999999999999999999999999999999999999999999999999999999887 5599999999987


Q ss_pred             ccCC
Q 012923          207 SIGP  210 (453)
Q Consensus       207 ~~~~  210 (453)
                      ....
T Consensus       179 RgRT  182 (335)
T KOG0113|consen  179 RGRT  182 (335)
T ss_pred             cccc
Confidence            5443

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.51  E-value=4.6e-14  Score=113.72  Aligned_cols=78  Identities=22%  Similarity=0.367  Sum_probs=71.3

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEecc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQLAS  207 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~~~  207 (453)
                      ..++|||+||+..+++.+|..+|..||.|..|+|-+++     .|||||+|.++.+|..|+..|++ .|+|..|+|.++.
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            46899999999999999999999999999999998865     58999999999999999999995 5999999999987


Q ss_pred             cCCC
Q 012923          208 IGPA  211 (453)
Q Consensus       208 ~~~~  211 (453)
                      ..+.
T Consensus        84 G~~r   87 (195)
T KOG0107|consen   84 GRPR   87 (195)
T ss_pred             CCcc
Confidence            6554

>PLN03213 repressor of silencing 3; Provisional

Probab=99.50  E-value=2.8e-14  Score=132.34  Aligned_cols=74  Identities=18%  Similarity=0.280  Sum_probs=67.9

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccH--HHHHHHHHcCC-CccCCeEeEEEec
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTR--SGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~--~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ..+||||||++++|+++|+.+|..||.|.+|.|++.  +|  ||||||+|.+.  .++.+||..|+ ..+.||.|+|..+
T Consensus        10 gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE--TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKA   85 (759)
T PLN03213         10 GVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT--KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKA   85 (759)
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc--cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeec
Confidence            468999999999999999999999999999999944  66  99999999987  78999999999 4599999999988


Q ss_pred             c
Q 012923          207 S  207 (453)
Q Consensus       207 ~  207 (453)
                      .
T Consensus        86 K   86 (759)
T PLN03213         86 K   86 (759)
T ss_pred             c
Confidence            5

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.50  E-value=1.3e-13  Score=111.16  Aligned_cols=77  Identities=23%  Similarity=0.408  Sum_probs=71.8

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .++|||+||+..+++.+|..+|..||.|..|.|.+.+     .|||||+|++..+|..|+..|+ ..|+|..|.|++...
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            4699999999999999999999999999999998755     8999999999999999999999 999999999999876


Q ss_pred             CCC
Q 012923          326 GPK  328 (453)
Q Consensus       326 ~~~  328 (453)
                      .+.
T Consensus        85 ~~r   87 (195)
T KOG0107|consen   85 RPR   87 (195)
T ss_pred             Ccc
Confidence            654

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.49  E-value=3.6e-14  Score=118.18  Aligned_cols=81  Identities=20%  Similarity=0.404  Sum_probs=77.5

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||++|...+|+.-|...|-+||.|..|.++.|.+++++|||+||+|.-.++|.+||..|| .+|.||.|+|.+|+
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            44799999999999999999999999999999999999999999999999999999999999999 99999999999996


Q ss_pred             CC
Q 012923          325 DG  326 (453)
Q Consensus       325 ~~  326 (453)
                      +.
T Consensus        89 P~   90 (298)
T KOG0111|consen   89 PE   90 (298)
T ss_pred             Cc
Confidence            54

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.49  E-value=1.6e-13  Score=100.36  Aligned_cols=77  Identities=22%  Similarity=0.408  Sum_probs=70.0

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCCeEeEEEecc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGNRMTACQLAS  207 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~~~v~~~~  207 (453)
                      .++-|||+|||+++|.+++.++|.+||.|..|+|-..+   ..+|.|||.|++..+|.+|+..|.+. +.++.+.|.+..
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k---~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK---ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc---CcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            45789999999999999999999999999999998765   46899999999999999999999965 999999998875


Q ss_pred             c
Q 012923          208 I  208 (453)
Q Consensus       208 ~  208 (453)
                      .
T Consensus        94 ~   94 (124)
T KOG0114|consen   94 P   94 (124)
T ss_pred             H
Confidence            3

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.47  E-value=3e-13  Score=98.97  Aligned_cols=78  Identities=24%  Similarity=0.391  Sum_probs=71.1

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      .-.+.|||+|||+.+|.+++.++|.+||.|..|+|-..+.|   +|.|||.|++..+|.+|+..|+ ..+.++.|.|-+-
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~T---rGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyy   92 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKET---RGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYY   92 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCc---CceEEEEehHhhhHHHHHHHhcccccCCceEEEEec
Confidence            34578999999999999999999999999999999766555   9999999999999999999999 8999999999887


Q ss_pred             cC
Q 012923          324 ID  325 (453)
Q Consensus       324 ~~  325 (453)
                      ..
T Consensus        93 q~   94 (124)
T KOG0114|consen   93 QP   94 (124)
T ss_pred             CH
Confidence            53

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.47  E-value=2.9e-13  Score=116.94  Aligned_cols=77  Identities=14%  Similarity=0.106  Sum_probs=70.0

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEeccc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASI  208 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~~  208 (453)
                      ...+|||+||++.+|+++|++||+.||.|.+|+|++|.   .+++||||+|.++++|..||...+..|.++.|.|.....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCcc
Confidence            45799999999999999999999999999999999984   556899999999999999998777889999999988653

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.47  E-value=3.5e-13  Score=109.33  Aligned_cols=77  Identities=23%  Similarity=0.430  Sum_probs=68.9

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||.++-+.+|..+|-+||.|..|.|   ++.-....||||+|++..+|+.||..-+ ..++|..|+|.++.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieL---K~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIEL---KNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEe---ccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            4579999999999999999999999999999988   3334457899999999999999999999 89999999999985


Q ss_pred             C
Q 012923          325 D  325 (453)
Q Consensus       325 ~  325 (453)
                      .
T Consensus        82 g   82 (241)
T KOG0105|consen   82 G   82 (241)
T ss_pred             C
Confidence            3

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.46  E-value=1.5e-13  Score=121.54  Aligned_cols=80  Identities=19%  Similarity=0.384  Sum_probs=73.2

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~~  206 (453)
                      ..-++|+|.|||+...+.||+.+|.+||.|.+|.||.+.  .-||||+||+|.+.++|++|-++|++ .|.||+|.|..+
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~A  171 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNA  171 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEecc
Confidence            335789999999999999999999999999999999874  45899999999999999999999995 499999999998


Q ss_pred             ccC
Q 012923          207 SIG  209 (453)
Q Consensus       207 ~~~  209 (453)
                      ..+
T Consensus       172 Tar  174 (376)
T KOG0125|consen  172 TAR  174 (376)
T ss_pred             chh
Confidence            765

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.45  E-value=1.1e-13  Score=114.38  Aligned_cols=82  Identities=24%  Similarity=0.436  Sum_probs=77.0

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~~~~  208 (453)
                      ..+|.|-||-+-+|.++|+.+|++||.|-+|.|.+|+.|+.++|||||.|....+|+.||+.|.+ .|.|+.|.|+++.-
T Consensus        13 m~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ary   92 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMARY   92 (256)
T ss_pred             ceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhhc
Confidence            46899999999999999999999999999999999999999999999999999999999999995 59999999999875


Q ss_pred             CCC
Q 012923          209 GPA  211 (453)
Q Consensus       209 ~~~  211 (453)
                      ...
T Consensus        93 gr~   95 (256)
T KOG4207|consen   93 GRP   95 (256)
T ss_pred             CCC
Confidence            544

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=99.45  E-value=1.6e-12  Score=122.25  Aligned_cols=190  Identities=19%  Similarity=0.269  Sum_probs=128.0

Q ss_pred             cCCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCC--Ccce---EEEEEEccHHHHHHHHHcCCCccCC
Q 012923          124 ADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSG--KSKG---YGFILFKTRSGARKALKEPQKKIGN  198 (453)
Q Consensus       124 ~~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g--~~~G---~afV~f~~~~~a~~A~~~~~~~~~g  198 (453)
                      .....-+++|||++||++++|+.|...|..||.|..-+-.+....+  -.+|   |+|+.|.++.+++.-|......-..
T Consensus       253 ~~~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~  332 (520)
T KOG0129|consen  253 YRSPRYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEGN  332 (520)
T ss_pred             CCccccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcccc
Confidence            3445668899999999999999999999999987544332211111  2456   9999999999999888765432222


Q ss_pred             eEeEEEecccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHh-ccCCccee
Q 012923          199 RMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFS-KYGEIEEG  277 (453)
Q Consensus       199 r~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~-~~G~i~~v  277 (453)
                      -.+.|.....+......    .++..       .....-..........+||||++||.-++.++|..+|. -||.|..+
T Consensus       333 ~yf~vss~~~k~k~VQI----rPW~l-------aDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~ya  401 (520)
T KOG0129|consen  333 YYFKVSSPTIKDKEVQI----RPWVL-------ADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYV  401 (520)
T ss_pred             eEEEEecCcccccceeE----EeeEe-------ccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEE
Confidence            22222222111110000    00000       00000001233445668999999999999999999999 79999999


Q ss_pred             eeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCcc----CCeEEEEEEcc
Q 012923          278 PLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNF----EGHILNCQRAI  324 (453)
Q Consensus       278 ~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l----~g~~l~v~~a~  324 (453)
                      -|-.|++-+-++|-|-|+|.+..+-.+||.+--..|    ..++|.|+.-.
T Consensus       402 GIDtD~k~KYPkGaGRVtFsnqqsYi~AIsarFvql~h~d~~KRVEIkPYv  452 (520)
T KOG0129|consen  402 GIDTDPKLKYPKGAGRVTFSNQQAYIKAISARFVQLDHTDIDKRVEIKPYV  452 (520)
T ss_pred             EeccCcccCCCCCcceeeecccHHHHHHHhhheEEEeccccceeeeeccee
Confidence            999998889999999999999999999998744222    23456655443

>PLN03213 repressor of silencing 3; Provisional

Probab=99.45  E-value=2.3e-13  Score=126.27  Aligned_cols=76  Identities=17%  Similarity=0.331  Sum_probs=70.2

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCH--HHHHHHHHcCC-CccCCeEEEEEE
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTV--DAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~--~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ...+|||+||++.+|+++|+.+|+.||.|.+|.|++  .+|  ||||||+|.+.  .++.+||..|| ..+.|+.|+|..
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            446999999999999999999999999999999995  467  99999999987  78999999999 899999999999


Q ss_pred             ccC
Q 012923          323 AID  325 (453)
Q Consensus       323 a~~  325 (453)
                      |++
T Consensus        85 AKP   87 (759)
T PLN03213         85 AKE   87 (759)
T ss_pred             ccH
Confidence            974

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=99.44  E-value=1.7e-13  Score=125.02  Aligned_cols=178  Identities=21%  Similarity=0.210  Sum_probs=143.4

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEecc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQLAS  207 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~~~  207 (453)
                      ..+++|++++...+.+.++..+|..+|.+..+.+.....+..++|+++|.|...+.+..||..... .+.++.+...+..
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            467999999999999999999999999988888888777889999999999999999999998874 4555555554443


Q ss_pred             cCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCC
Q 012923          208 IGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGK  287 (453)
Q Consensus       208 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~  287 (453)
                      .......                     ............+.++|.+|++.+++++|+..|..+|.|..+++..++.++.
T Consensus       167 ~~~~~~~---------------------n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~  225 (285)
T KOG4210|consen  167 RRGLRPK---------------------NKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGD  225 (285)
T ss_pred             ccccccc---------------------chhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccc
Confidence            2221000                     0000111222233455999999999999999999999999999999999999


Q ss_pred             CceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCCC
Q 012923          288 PKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGPK  328 (453)
Q Consensus       288 ~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~~  328 (453)
                      ++||+||.|.+...+..++.. . ..+.++++.|.+...++.
T Consensus       226 ~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  266 (285)
T KOG4210|consen  226 SKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRPK  266 (285)
T ss_pred             hhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCcc
Confidence            999999999999999999998 6 889999999988865543

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.42  E-value=9.3e-13  Score=113.81  Aligned_cols=76  Identities=16%  Similarity=0.105  Sum_probs=68.7

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a~~  325 (453)
                      ..+|||+||++.+|+++|++||+.||.|.+|+|+++.   ..++||||+|.+.++|..||...+..|.+++|.|.....
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCcc
Confidence            4699999999999999999999999999999999884   447899999999999999996655999999999988653

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.42  E-value=1.5e-12  Score=118.37  Aligned_cols=187  Identities=15%  Similarity=0.136  Sum_probs=127.4

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC---CccCCeEeEEE
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ---KKIGNRMTACQ  204 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~---~~~~gr~~~v~  204 (453)
                      ..++.|.+||||++++|.+|..++.+||.|..+.+++.+.      -|||+|.+.++|..-+....   -.+.++.|.|+
T Consensus        26 ~pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGkn------QAflem~d~~sAvtmv~~y~~~~p~lr~~~~yiq   99 (492)
T KOG1190|consen   26 EPSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGKN------QAFLEMADEESAVTMVNYYTSVTPVLRGQPIYIQ   99 (492)
T ss_pred             CCcceeEeccCCccccHHHHHHhcccccceeeeeeeccch------hhhhhhcchhhhhheeecccccCccccCcceeeh
Confidence            3578999999999999999999999999999998776542      59999999999887554433   34789999998


Q ss_pred             ecccCCCCCCCcCccccc----ccccccc---ccccc-ccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcce
Q 012923          205 LASIGPATTPAVASTATH----QHQHQHQ---HQHQH-QHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEE  276 (453)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~----~~~~~~~---~~~~~-~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~  276 (453)
                      ++................    ......+   ..... ............-.+++|.|+-+.+|-+-|.++|++||.|.+
T Consensus       100 ~sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~VlK  179 (492)
T KOG1190|consen  100 YSNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVLK  179 (492)
T ss_pred             hhhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcceeEE
Confidence            875433222111100000    0000000   00000 000011122223458889999999999999999999999998


Q ss_pred             eeeeccCCCCCCceE-EEEEECCHHHHHHHHHcCC-Ccc-CC-eEEEEEEccC
Q 012923          277 GPLGIDKATGKPKGF-CLFVYKTVDAAKKALEEPH-KNF-EG-HILNCQRAID  325 (453)
Q Consensus       277 v~i~~d~~~g~~kg~-afV~F~~~~~A~~Al~~~~-~~l-~g-~~l~v~~a~~  325 (453)
                      |.-+...     .+| |.|+|.+.+.|..|...|. ..| +| +.|++.+...
T Consensus       180 IiTF~Kn-----n~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Skl  227 (492)
T KOG1190|consen  180 IITFTKN-----NGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKL  227 (492)
T ss_pred             EEEEecc-----cchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhc
Confidence            8765432     444 8999999999999999998 555 33 5566666543

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.42  E-value=1.9e-13  Score=130.44  Aligned_cols=81  Identities=25%  Similarity=0.457  Sum_probs=77.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecccC
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASIG  209 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~~  209 (453)
                      +.|||+|||+++++++|..+|+..|.|.+++++.|+.+|+++|||||+|.+.++|..|++.|+ ..+.||+|+|.|+...
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            899999999999999999999999999999999999999999999999999999999999999 5699999999998755


Q ss_pred             CC
Q 012923          210 PA  211 (453)
Q Consensus       210 ~~  211 (453)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            44

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.41  E-value=2.9e-13  Score=112.80  Aligned_cols=84  Identities=26%  Similarity=0.413  Sum_probs=78.1

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ...|||||++|..++|+.-|...|-+||.|.+|.|..|-.++++||||||+|...++|.+||..|+ ..|.||.|+|.++
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            345899999999999999999999999999999999999999999999999999999999999999 5699999999999


Q ss_pred             ccCCC
Q 012923          207 SIGPA  211 (453)
Q Consensus       207 ~~~~~  211 (453)
                      .+...
T Consensus        88 kP~ki   92 (298)
T KOG0111|consen   88 KPEKI   92 (298)
T ss_pred             CCccc
Confidence            75443

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.40  E-value=3.3e-11  Score=118.18  Aligned_cols=109  Identities=21%  Similarity=0.316  Sum_probs=86.4

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ..+|||||++|+.++++.||..+|+.||.|.+|.++.      ++|||||......+|.+||..|+ ..+..+.|+|.|+
T Consensus       419 V~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~------~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa  492 (894)
T KOG0132|consen  419 VCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP------PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWA  492 (894)
T ss_pred             EeeeeeeeccccchhhHHHHHHHHHhcccceeEeecc------CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeee
Confidence            3478999999999999999999999999999998775      46899999999999999999988 5599999999999


Q ss_pred             ccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHh
Q 012923          207 SIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFS  269 (453)
Q Consensus       207 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~  269 (453)
                      ...-...                           .....+...|=|.-||+..-.++|+.+++
T Consensus       493 ~g~G~ks---------------------------e~k~~wD~~lGVt~IP~~kLt~dl~~~~e  528 (894)
T KOG0132|consen  493 VGKGPKS---------------------------EYKDYWDVELGVTYIPWEKLTDDLEAWCE  528 (894)
T ss_pred             ccCCcch---------------------------hhhhhhhcccCeeEeehHhcCHHHHHhhh
Confidence            7554332                           11122333456666788755555777765

>smart00362 RRM_2 RNA recognition motif

Probab=99.40  E-value=1.3e-12  Score=94.46  Aligned_cols=71  Identities=31%  Similarity=0.577  Sum_probs=66.2

Q ss_pred             EEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       249 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      +|||+|||..++.++|+++|..||.|..+.+.++.  +.++++|||+|.+.++|.+|+..++ ..|.|+.|.|+
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            58999999999999999999999999999998875  7789999999999999999999999 88999998873

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.39  E-value=7.3e-13  Score=101.78  Aligned_cols=82  Identities=23%  Similarity=0.383  Sum_probs=77.0

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~  208 (453)
                      .-.|||.++...+|+++|.+.|..||+|.+|+|-.|+.||-.+|||+|+|.+.+.|++|+..+| ..|.+..|.|.|+..
T Consensus        72 GwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv  151 (170)
T KOG0130|consen   72 GWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFV  151 (170)
T ss_pred             eEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEe
Confidence            4579999999999999999999999999999999999999999999999999999999999999 569999999999986


Q ss_pred             CCC
Q 012923          209 GPA  211 (453)
Q Consensus       209 ~~~  211 (453)
                      ...
T Consensus       152 ~gp  154 (170)
T KOG0130|consen  152 KGP  154 (170)
T ss_pred             cCC
Confidence            544

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.39  E-value=6.8e-11  Score=106.47  Aligned_cols=163  Identities=14%  Similarity=0.189  Sum_probs=123.4

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC---CccCCeEeEEE
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ---KKIGNRMTACQ  204 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~---~~~~gr~~~v~  204 (453)
                      ..+-.|.|++|-..+++.||.+.++.||.|..|..+..+      .-|.|+|.+.+.|..|+...-   -.+.|....+.
T Consensus        29 ~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~------r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~N  102 (494)
T KOG1456|consen   29 NPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHK------RQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFN  102 (494)
T ss_pred             CCCceEEEeccccccchhHHHHHHhcCCceEEEEecccc------ceeeeeeccccchhhheehhccCcccccCchhhcc
Confidence            345679999999999999999999999999998776543      369999999999999986432   33677777777


Q ss_pred             ecccCCCCCCCcCcccccccccccccccccccccccccccccccEEE--EecCCCCccHHHHHHHHhccCCcceeeeecc
Q 012923          205 LASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIF--VSNVGSELEPQKLLAFFSKYGEIEEGPLGID  282 (453)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~--V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d  282 (453)
                      ++......+..                         .......+.|.  |-|--+.+|.+-|.+++..+|.|.+|.|++.
T Consensus       103 yStsq~i~R~g-------------------------~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk  157 (494)
T KOG1456|consen  103 YSTSQCIERPG-------------------------DESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK  157 (494)
T ss_pred             cchhhhhccCC-------------------------CCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec
Confidence            76544332211                         11111223333  4566678999999999999999999999875


Q ss_pred             CCCCCCceEEEEEECCHHHHHHHHHcCC-Ccc--CCeEEEEEEccCC
Q 012923          283 KATGKPKGFCLFVYKTVDAAKKALEEPH-KNF--EGHILNCQRAIDG  326 (453)
Q Consensus       283 ~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l--~g~~l~v~~a~~~  326 (453)
                        +|   --|.|+|++.+.|.+|...|| ..|  +-.+|+|.+|++.
T Consensus       158 --ng---VQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~  199 (494)
T KOG1456|consen  158 --NG---VQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPT  199 (494)
T ss_pred             --cc---eeeEEeechhHHHHHHHhhcccccccccceeEEEEecCcc
Confidence              22   259999999999999999999 444  3478999998644

>smart00362 RRM_2 RNA recognition motif

Probab=99.39  E-value=1.9e-12  Score=93.61  Aligned_cols=70  Identities=36%  Similarity=0.579  Sum_probs=64.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       132 ~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      +|||+|||..++.++|+++|.+||.|..++++.++  +.++|+|||+|.+.++|..|+..++ ..+.++.|.|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence            59999999999999999999999999999998876  7789999999999999999999988 5688888876

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.38  E-value=5.9e-13  Score=108.07  Aligned_cols=78  Identities=18%  Similarity=0.330  Sum_probs=75.5

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..+|||+||+..++++.|+++|-+.|.|++++|++|+.+...+|||||+|.+.++|.=|++.|| ..|.||+|+|..+.
T Consensus         9 d~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen    9 DATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             CceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            4599999999999999999999999999999999999999999999999999999999999999 89999999999986

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.38  E-value=1.9e-12  Score=119.18  Aligned_cols=82  Identities=22%  Similarity=0.412  Sum_probs=75.4

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-Ccc-CCeEEEEEE
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNF-EGHILNCQR  322 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l-~g~~l~v~~  322 (453)
                      ...+-|||+.||.++.+++|.-+|++.|.|-.++|++|+.+|.+||||||+|.+.+.|..||+.|| .+| .|+.|.|..
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            456799999999999999999999999999999999999999999999999999999999999999 766 688888877


Q ss_pred             ccCC
Q 012923          323 AIDG  326 (453)
Q Consensus       323 a~~~  326 (453)
                      +..+
T Consensus       161 Svan  164 (506)
T KOG0117|consen  161 SVAN  164 (506)
T ss_pred             eeec
Confidence            6543

>smart00360 RRM RNA recognition motif

Probab=99.36  E-value=2.2e-12  Score=92.97  Aligned_cols=70  Identities=37%  Similarity=0.608  Sum_probs=65.6

Q ss_pred             EecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          252 VSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       252 V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      |+|||..+++++|+++|+.||.|..+.+..++.++.++|+|||+|.+.++|.+|+..++ ..+.|+.|.|.
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            57999999999999999999999999999988789999999999999999999999999 88999998873

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.35  E-value=2.9e-12  Score=122.91  Aligned_cols=187  Identities=19%  Similarity=0.254  Sum_probs=142.5

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhcc-----------C-CeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQY-----------G-EIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ  193 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~-----------G-~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~  193 (453)
                      .....+++||++||+.++++.+..||..-           | .|..|.|-.      .+.||||+|.+.+.|..|+....
T Consensus       171 ~t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~------~~nfa~ie~~s~~~at~~~~~~~  244 (500)
T KOG0120|consen  171 ATRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNL------EKNFAFIEFRSISEATEAMALDG  244 (500)
T ss_pred             hhhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecc------cccceeEEecCCCchhhhhcccc
Confidence            34456789999999999999999999754           2 255555443      34699999999999999998887


Q ss_pred             CccCCeEeEEEecccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCC
Q 012923          194 KKIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGE  273 (453)
Q Consensus       194 ~~~~gr~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~  273 (453)
                      ..+.|+.+.+..................         ...................+||++||..+++++++++...||.
T Consensus       245 ~~f~g~~~~~~r~~d~~~~p~~~~~~~~---------~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~  315 (500)
T KOG0120|consen  245 IIFEGRPLKIRRPHDYQPVPGITLSPSQ---------LGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGP  315 (500)
T ss_pred             hhhCCCCceecccccccCCccchhhhcc---------ccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhccc
Confidence            7788888877654432222111100000         0000011111233444579999999999999999999999999


Q ss_pred             cceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCC
Q 012923          274 IEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGP  327 (453)
Q Consensus       274 i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~  327 (453)
                      +....++.+..+|.++||||.+|.+......|+..|| ..+.+++|.|..|....
T Consensus       316 lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~  370 (500)
T KOG0120|consen  316 LKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGA  370 (500)
T ss_pred             chhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccc
Confidence            9999999999999999999999999999999999999 88999999999997554

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.34  E-value=2e-12  Score=123.50  Aligned_cols=81  Identities=30%  Similarity=0.475  Sum_probs=77.9

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCC
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDG  326 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~  326 (453)
                      +.|||+|+|+.+++++|..+|+..|.|.+++++.|+.||+++||+||+|.+.++|..|++.|| .++.||+|+|.|+...
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            689999999999999999999999999999999999999999999999999999999999999 9999999999999765


Q ss_pred             CC
Q 012923          327 PK  328 (453)
Q Consensus       327 ~~  328 (453)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            44

>smart00360 RRM RNA recognition motif

Probab=99.33  E-value=5.5e-12  Score=90.85  Aligned_cols=69  Identities=36%  Similarity=0.558  Sum_probs=64.1

Q ss_pred             EcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          135 VHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       135 V~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      |+|||..+++++|+.+|.+||.|..+++..++.+++++|||||+|.+.++|..|+..++ ..+.++.|.|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v   70 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV   70 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEe
Confidence            67999999999999999999999999999988788999999999999999999999988 5588888876

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=99.31  E-value=3.3e-13  Score=133.56  Aligned_cols=149  Identities=21%  Similarity=0.186  Sum_probs=130.8

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecc
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLAS  207 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~  207 (453)
                      +...++||.||++.+.+.+|..+|..+|.|..++|......++.+|+|||.|...+++.+||......+.|+        
T Consensus       665 R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~gK--------  736 (881)
T KOG0128|consen  665 RDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFGK--------  736 (881)
T ss_pred             HHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhhh--------
Confidence            445689999999999999999999999999988887677789999999999999999999999877655541        


Q ss_pred             cCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCC
Q 012923          208 IGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGK  287 (453)
Q Consensus       208 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~  287 (453)
                                                              ..|||+|+|+..|.+.|+.+|..+|.+++++++..+ .|+
T Consensus       737 ----------------------------------------~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r-~gk  775 (881)
T KOG0128|consen  737 ----------------------------------------ISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AGK  775 (881)
T ss_pred             ----------------------------------------hhhheeCCCCCCchHHHHhhccccCCccccchhhhh-ccc
Confidence                                                    279999999999999999999999999999988765 799


Q ss_pred             CceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          288 PKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       288 ~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      ++|.|||.|.+..++.+++.... ..+.-+.+.|....+
T Consensus       776 pkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  776 PKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             cccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            99999999999999999999888 666667777766543

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.30  E-value=1.4e-11  Score=89.64  Aligned_cols=73  Identities=33%  Similarity=0.546  Sum_probs=67.0

Q ss_pred             EEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       249 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      +|+|+|||..+++++|+++|+.||.|..+.+..+..+ .++++|||+|.+.++|..|+..++ ..++|+.|.|.+
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 779999999999999999999999 669999999864

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=99.29  E-value=2.2e-11  Score=88.54  Aligned_cols=73  Identities=34%  Similarity=0.569  Sum_probs=66.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCCeEeEEEe
Q 012923          132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGNRMTACQL  205 (453)
Q Consensus       132 ~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~~~v~~  205 (453)
                      +|+|+|||..+++++|+++|..||.|..+.+..++.+ ..+|+|||+|.+.++|..|+..++.. +.++.+.|.+
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            5899999999999999999999999999999988744 77899999999999999999999965 8999888753

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).

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=99.29  E-value=2.7e-11  Score=115.10  Aligned_cols=82  Identities=26%  Similarity=0.447  Sum_probs=71.6

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEccCCC
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAIDGP  327 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a~~~~  327 (453)
                      .+|||+|||.+++..+|+++|..||.|+...|......++..+||||+|.+..++..||.+.-..|++++|.|.......
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            35999999999999999999999999999888765434555599999999999999999998888999999999887655


Q ss_pred             CC
Q 012923          328 KP  329 (453)
Q Consensus       328 ~~  329 (453)
                      ..
T Consensus       369 ~g  370 (419)
T KOG0116|consen  369 RG  370 (419)
T ss_pred             cc
Confidence            44

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.27  E-value=1.4e-11  Score=115.15  Aligned_cols=79  Identities=32%  Similarity=0.573  Sum_probs=76.0

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      ..+|||+|||+.+|+++|+++|..||.|..|.|..++.+++++|||||+|.+.++|..|+..++ ..|.|++|.|.++..
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            5799999999999999999999999999999999999899999999999999999999999999 999999999999753

>smart00361 RRM_1 RNA recognition motif

Probab=99.27  E-value=1.4e-11  Score=88.45  Aligned_cols=60  Identities=18%  Similarity=0.387  Sum_probs=54.3

Q ss_pred             HHHHHHHHh----ccCCcceee-eeccCCC--CCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEE
Q 012923          261 PQKLLAFFS----KYGEIEEGP-LGIDKAT--GKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNC  320 (453)
Q Consensus       261 ~~~l~~~F~----~~G~i~~v~-i~~d~~~--g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v  320 (453)
                      +++|+++|+    .||.|.+|. |+.++.+  +.++||+||+|.+.++|.+|+..|| ..|.|+.|.+
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 7777766  9999999999999999999999999 8999999987

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.25  E-value=1.1e-09  Score=107.68  Aligned_cols=80  Identities=19%  Similarity=0.273  Sum_probs=73.0

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      ....++||||++|+..+++.+|..+|+.||.|.+|.++..      ++||||+..+.++|.+||.+|+ ..+.++.|+|.
T Consensus       417 isV~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~  490 (894)
T KOG0132|consen  417 ISVCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIA  490 (894)
T ss_pred             eeEeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEe
Confidence            3445789999999999999999999999999999999765      8999999999999999999999 89999999999


Q ss_pred             EccCCCC
Q 012923          322 RAIDGPK  328 (453)
Q Consensus       322 ~a~~~~~  328 (453)
                      |+.....
T Consensus       491 Wa~g~G~  497 (894)
T KOG0132|consen  491 WAVGKGP  497 (894)
T ss_pred             eeccCCc
Confidence            9976543

>PF13893 RRM_5: RNA recognition motif

Probab=99.22  E-value=3.1e-11  Score=82.58  Aligned_cols=55  Identities=33%  Similarity=0.606  Sum_probs=49.9

Q ss_pred             HHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          264 LLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       264 l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      |+++|++||.|.+|.+....     +++|||+|.+.++|.+|+..|| ..|+|++|+|.|+
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            68899999999999998763     6899999999999999999999 8899999999986

(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 ....

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=99.18  E-value=5.2e-12  Score=105.53  Aligned_cols=133  Identities=19%  Similarity=0.289  Sum_probs=111.6

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCCeEeEEEecc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGNRMTACQLAS  207 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~~~v~~~~  207 (453)
                      ..+||||.||...++++-|.++|-+.|+|..|.|..++ .++.+ ||||.|.++-++.-|++.+|+. +.++.+.|.+  
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~--   83 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTL--   83 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhccc--
Confidence            34899999999999999999999999999999887776 67777 9999999999999999999954 7777766644  


Q ss_pred             cCCCCCCCcCcccccccccccccccccccccccccccccccEEEEec----CCCCccHHHHHHHHhccCCcceeeeeccC
Q 012923          208 IGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSN----VGSELEPQKLLAFFSKYGEIEEGPLGIDK  283 (453)
Q Consensus       208 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~n----Lp~~~t~~~l~~~F~~~G~i~~v~i~~d~  283 (453)
                                                                 +.++    |...++++.+..+|+..+.|..+++.++.
T Consensus        84 -------------------------------------------r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~  120 (267)
T KOG4454|consen   84 -------------------------------------------RCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDN  120 (267)
T ss_pred             -------------------------------------------ccCCCcchhhhhcchhhheeeecccCCCCCccccccc
Confidence                                                       4444    66678899999999999999999999886


Q ss_pred             CCCCCceEEEEEECCHHHHHHHHHcC
Q 012923          284 ATGKPKGFCLFVYKTVDAAKKALEEP  309 (453)
Q Consensus       284 ~~g~~kg~afV~F~~~~~A~~Al~~~  309 (453)
                      . |+.+.++|+.+....+.-.++...
T Consensus       121 d-~rnrn~~~~~~qr~~~~P~~~~~y  145 (267)
T KOG4454|consen  121 D-GRNRNFGFVTYQRLCAVPFALDLY  145 (267)
T ss_pred             c-CCccCccchhhhhhhcCcHHhhhh
Confidence            4 888999999887666655555543

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.18  E-value=3.4e-11  Score=107.64  Aligned_cols=88  Identities=14%  Similarity=0.242  Sum_probs=80.8

Q ss_pred             ccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEE
Q 012923          241 QQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILN  319 (453)
Q Consensus       241 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~  319 (453)
                      .....+.+.|||..|.+-+|.++|.-+|+.||.|.+|.|++|..||.+-.||||+|.+.+++++|.-+|. ..|+.+.|.
T Consensus       233 Ad~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIH  312 (479)
T KOG0415|consen  233 ADVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIH  312 (479)
T ss_pred             cccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEE
Confidence            3345566899999999999999999999999999999999999999999999999999999999999998 889999999


Q ss_pred             EEEccCCCC
Q 012923          320 CQRAIDGPK  328 (453)
Q Consensus       320 v~~a~~~~~  328 (453)
                      |.|+.+-.+
T Consensus       313 VDFSQSVsk  321 (479)
T KOG0415|consen  313 VDFSQSVSK  321 (479)
T ss_pred             eehhhhhhh
Confidence            999876544

>smart00361 RRM_1 RNA recognition motif

Probab=99.18  E-value=9.1e-11  Score=84.17  Aligned_cols=60  Identities=20%  Similarity=0.384  Sum_probs=53.1

Q ss_pred             HHHHHHHHh----ccCCeeEEE-EcccCCC--CCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          144 AETLIDAFK----QYGEIEDCK-AVCDKVS--GKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       144 e~~l~~~f~----~~G~i~~v~-i~~d~~~--g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      +++|+++|+    +||.|..|. |+.++.+  +.++|||||+|.+.++|.+|+..|+ ..+.||.|.+
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            578999998    999999996 7777666  8999999999999999999999988 4589999876

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.18  E-value=7.7e-11  Score=107.91  Aligned_cols=85  Identities=26%  Similarity=0.451  Sum_probs=79.0

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEeccc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASI  208 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~~  208 (453)
                      ..++|||++||.++++++|+++|.+||.|..+-++.|..+.+++||+||.|.+.+++.+++...-+.|+++.+.|..+..
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~~f~~~~gk~vevkrA~p  175 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQKFHDFNGKKVEVKRAIP  175 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecccceeeecCceeeEeeccc
Confidence            45689999999999999999999999999999999999999999999999999999999999888999999999999986


Q ss_pred             CCCCC
Q 012923          209 GPATT  213 (453)
Q Consensus       209 ~~~~~  213 (453)
                      +....
T Consensus       176 k~~~~  180 (311)
T KOG4205|consen  176 KEVMQ  180 (311)
T ss_pred             hhhcc
Confidence            65543

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.18  E-value=3.2e-11  Score=108.91  Aligned_cols=182  Identities=17%  Similarity=0.243  Sum_probs=130.2

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQ  204 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~  204 (453)
                      ....+...|..++||+..++.+|..||.-.-...-.+.+.....|+..|+|.|.|.+.+.-..|++...+.+.+|.|.|.
T Consensus        55 ~~~~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ryievY  134 (508)
T KOG1365|consen   55 HSADDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKRHKHHMGTRYIEVY  134 (508)
T ss_pred             cccCcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHhhhhhccCCceeee
Confidence            34445567889999999999999999985533333344444447788899999999999999999999999999999998


Q ss_pred             ecccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccC----Ccceeeee
Q 012923          205 LASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYG----EIEEGPLG  280 (453)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G----~i~~v~i~  280 (453)
                      .+.............                .....-......-.|.+++||+++|+.+|.+||.+..    ..+.|-++
T Consensus       135 ka~ge~f~~iagg~s----------------~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV  198 (508)
T KOG1365|consen  135 KATGEEFLKIAGGTS----------------NEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFV  198 (508)
T ss_pred             ccCchhheEecCCcc----------------ccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEE
Confidence            775433221000000                0000000111223678899999999999999997432    34456555


Q ss_pred             ccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEc
Q 012923          281 IDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRA  323 (453)
Q Consensus       281 ~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a  323 (453)
                      +. ..|+..|-|||.|...++|..||.+....|+-|.|.|.++
T Consensus       199 ~r-pdgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIElFRS  240 (508)
T KOG1365|consen  199 TR-PDGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIELFRS  240 (508)
T ss_pred             EC-CCCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence            53 4799999999999999999999998777677777766544

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.17  E-value=3.3e-11  Score=103.63  Aligned_cols=87  Identities=25%  Similarity=0.391  Sum_probs=79.4

Q ss_pred             cCCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCCeEeE
Q 012923          124 ADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGNRMTA  202 (453)
Q Consensus       124 ~~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~~~  202 (453)
                      ....++.|+|||..||.+..+.+|...|-+||.|.+.+++.|+.|..+|.|+||.|.++.+|+.||..+|+. |.=+.|+
T Consensus       279 qreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLK  358 (371)
T KOG0146|consen  279 QREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLK  358 (371)
T ss_pred             hhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhh
Confidence            456788999999999999999999999999999999999999999999999999999999999999999965 7777888


Q ss_pred             EEecccCC
Q 012923          203 CQLASIGP  210 (453)
Q Consensus       203 v~~~~~~~  210 (453)
                      |.+...+.
T Consensus       359 VQLKRPkd  366 (371)
T KOG0146|consen  359 VQLKRPKD  366 (371)
T ss_pred             hhhcCccc
Confidence            88765443

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.14  E-value=1.6e-10  Score=103.34  Aligned_cols=84  Identities=26%  Similarity=0.429  Sum_probs=76.7

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v  203 (453)
                      +..+....|||..|.+-+|.+||.-+|+.||.|.+|.||+|..||.+.-||||+|.+.+++++|.-.|.. .|..|.|.|
T Consensus       234 d~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHV  313 (479)
T KOG0415|consen  234 DVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHV  313 (479)
T ss_pred             ccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEe
Confidence            4445667899999999999999999999999999999999999999999999999999999999987774 589999999


Q ss_pred             Eeccc
Q 012923          204 QLASI  208 (453)
Q Consensus       204 ~~~~~  208 (453)
                      .++.+
T Consensus       314 DFSQS  318 (479)
T KOG0415|consen  314 DFSQS  318 (479)
T ss_pred             ehhhh
Confidence            98753

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.14  E-value=5.5e-11  Score=103.73  Aligned_cols=71  Identities=23%  Similarity=0.386  Sum_probs=67.1

Q ss_pred             EEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCC
Q 012923          249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGP  327 (453)
Q Consensus       249 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~  327 (453)
                      +|||+|||..+++.+|+.+|++||+|+.|.|++        .|+||+.++...|..||..|| .+|+|..|.|+.++++.
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvK--------NYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs   75 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGKVLECDIVK--------NYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS   75 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCceEeeeeec--------ccceEEeecccccHHHHhhcccceecceEEEEEeccccC
Confidence            799999999999999999999999999999984        599999999999999999999 89999999999998773

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=99.13  E-value=6.4e-11  Score=101.42  Aligned_cols=172  Identities=22%  Similarity=0.277  Sum_probs=131.3

Q ss_pred             CCCcCeEEEcCCCCCCCHHH-H--HHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeE
Q 012923          127 DPVHRKIFVHGLGWDTKAET-L--IDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTA  202 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~-l--~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~  202 (453)
                      .+....+|+.++-..+..+- |  ...|+.+-.+...+++++. .+..++++|+.|.....-.++-..-++ ++.-+.|+
T Consensus        93 ~P~vf~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~-p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR  171 (290)
T KOG0226|consen   93 APAVFRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDR-PQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVR  171 (290)
T ss_pred             CcccccccccccccccCCCCCCcchhhhccchhhhhhhhhhcC-CCccCcccccCcchhhhhhhhccccccccccCccee
Confidence            35566788888877776665 3  5777777777777778777 678889999999988777777665553 34444444


Q ss_pred             EEecccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeecc
Q 012923          203 CQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGID  282 (453)
Q Consensus       203 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d  282 (453)
                      +.........                          .........-+||.+.|...++.+.|-..|.+|-.....++++|
T Consensus       172 ~a~gtswedP--------------------------sl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRd  225 (290)
T KOG0226|consen  172 LAAGTSWEDP--------------------------SLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRD  225 (290)
T ss_pred             eccccccCCc--------------------------ccccCccccceeecccccccccHHHHHHHHHhccchhhcccccc
Confidence            4333221111                          01122233459999999999999999999999999999999999


Q ss_pred             CCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          283 KATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       283 ~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      +.||+++||+||.|.+..++..|++.|+ ..++.|+|+++...-
T Consensus       226 kRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~w  269 (290)
T KOG0226|consen  226 KRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSEW  269 (290)
T ss_pred             ccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhhH
Confidence            9999999999999999999999999999 888999998866543

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=99.12  E-value=2.4e-09  Score=95.67  Aligned_cols=76  Identities=20%  Similarity=0.248  Sum_probs=66.2

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccC--CcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYG--EIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G--~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      .++||+||-|.+|+++|.+.+...|  .|..++++.++..|.+||||+|...+..+..+.+..|- ++|.|+.-.|.-.
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            4999999999999999999888776  47788888999999999999999999999999999999 8898876555433

>PF13893 RRM_5: RNA recognition motif

Probab=99.09  E-value=3.6e-10  Score=77.29  Aligned_cols=55  Identities=25%  Similarity=0.516  Sum_probs=48.4

Q ss_pred             HHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          147 LIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       147 l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      |+++|++||.|..|.+..+.     +++|||+|.+.++|.+|++.++ ..+.|+.|.|.++
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            68999999999999987654     6899999999999999999888 4599999999875

(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 Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=99.09  E-value=2.3e-10  Score=95.36  Aligned_cols=81  Identities=19%  Similarity=0.406  Sum_probs=73.2

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhcc-CCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCCeEeEEEec
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQY-GEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGNRMTACQLA  206 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~-G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~~~v~~~  206 (453)
                      ...-+||..||.-+.+..|..+|.+| |.|..+++.+++.||.|+|||||+|.+.+.|.-|.+.||.. |.++.|.|.+.
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vm  127 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVM  127 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEe
Confidence            34579999999999999999999999 88999999999999999999999999999999999999976 78889999887


Q ss_pred             ccC
Q 012923          207 SIG  209 (453)
Q Consensus       207 ~~~  209 (453)
                      ...
T Consensus       128 ppe  130 (214)
T KOG4208|consen  128 PPE  130 (214)
T ss_pred             Cch
Confidence            543

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.04  E-value=1.3e-08  Score=92.12  Aligned_cols=193  Identities=11%  Similarity=0.085  Sum_probs=132.1

Q ss_pred             CCcCeEEEcCCC-CCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEe
Q 012923          128 PVHRKIFVHGLG-WDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQL  205 (453)
Q Consensus       128 ~~~~~lfV~nLp-~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~  205 (453)
                      ...+.+.|.+|. -.++-+.|..+|..||.|..|++++.+     .|.|.|++.+..++++|+..||. .+.|.+|.|.+
T Consensus       285 ~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~  359 (494)
T KOG1456|consen  285 APGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCV  359 (494)
T ss_pred             CCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEEee
Confidence            456889999998 456777899999999999999999876     46899999999999999999985 48999999988


Q ss_pred             cccCCCCCCCcCcccccccc---ccccc--ccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCC-cceeee
Q 012923          206 ASIGPATTPAVASTATHQHQ---HQHQH--QHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGE-IEEGPL  279 (453)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~---~~~~~--~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~-i~~v~i  279 (453)
                      +.......-...........   .....  ...............++++|+.-|.|..+||+.|..+|...+. ..+|+|
T Consensus       360 SkQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~svkv  439 (494)
T KOG1456|consen  360 SKQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTSVKV  439 (494)
T ss_pred             ccccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCCCcceEEe
Confidence            75332221100000000000   00000  0000111111233445679999999999999999999986653 456777


Q ss_pred             eccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCC----eEEEEEEccCCC
Q 012923          280 GIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEG----HILNCQRAIDGP  327 (453)
Q Consensus       280 ~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g----~~l~v~~a~~~~  327 (453)
                      +.-+ +-+ .--+.++|++.++|..||.++| ..|.+    -+..++|+.+.+
T Consensus       440 Fp~k-ser-SssGllEfe~~s~Aveal~~~NH~pi~~p~gs~PfilKlcfsts  490 (494)
T KOG1456|consen  440 FPLK-SER-SSSGLLEFENKSDAVEALMKLNHYPIEGPNGSFPFILKLCFSTS  490 (494)
T ss_pred             eccc-ccc-cccceeeeehHHHHHHHHHHhccccccCCCCCCCeeeeeeeccc
Confidence            6654 333 2347899999999999999999 55544    345666665544

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=99.03  E-value=7.1e-10  Score=92.50  Aligned_cols=81  Identities=21%  Similarity=0.413  Sum_probs=73.4

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhcc-CCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKY-GEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      .....++|..+|..+.+..|..+|.+| |.|+.+++-|.+.||.|||||||+|.+.+.|.-|-+.|| .-|.++.|.|.+
T Consensus        47 ~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~v  126 (214)
T KOG4208|consen   47 EIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHV  126 (214)
T ss_pred             CCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEE
Confidence            334589999999999999999999998 778888888999999999999999999999999999999 778899999988


Q ss_pred             ccC
Q 012923          323 AID  325 (453)
Q Consensus       323 a~~  325 (453)
                      -.+
T Consensus       127 mpp  129 (214)
T KOG4208|consen  127 MPP  129 (214)
T ss_pred             eCc
Confidence            643

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.00  E-value=1.9e-10  Score=114.76  Aligned_cols=163  Identities=17%  Similarity=0.214  Sum_probs=130.4

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~~~v  203 (453)
                      ++...++|||++||+..+++.+|+..|..+|.|.+|.|.+-+ .+.-.-||||.|.+...+-.|+..+... |....+++
T Consensus       367 DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~  445 (975)
T KOG0112|consen  367 DDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRI  445 (975)
T ss_pred             cchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCcccc
Confidence            556778999999999999999999999999999999987654 4455569999999999999998877744 33333333


Q ss_pred             EecccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccC
Q 012923          204 QLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDK  283 (453)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~  283 (453)
                      .+...                                  .....+.|+|++|..++....|...|..||.|..|.+-.. 
T Consensus       446 glG~~----------------------------------kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg-  490 (975)
T KOG0112|consen  446 GLGQP----------------------------------KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG-  490 (975)
T ss_pred             ccccc----------------------------------ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC-
Confidence            33321                                  1223468999999999999999999999999999877332 


Q ss_pred             CCCCCceEEEEEECCHHHHHHHHHcCC-CccCC--eEEEEEEccCCCC
Q 012923          284 ATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEG--HILNCQRAIDGPK  328 (453)
Q Consensus       284 ~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g--~~l~v~~a~~~~~  328 (453)
                           .-|+||.|.+...|..|+..+. .-|++  +.|.|.++.....
T Consensus       491 -----q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~~~~  533 (975)
T KOG0112|consen  491 -----QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASPPGA  533 (975)
T ss_pred             -----CcceeeecccCccchhhHHHHhcCcCCCCCcccccccccCCCC
Confidence                 4599999999999999999988 66765  6788988865443

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.00  E-value=1e-09  Score=93.17  Aligned_cols=78  Identities=24%  Similarity=0.373  Sum_probs=71.6

Q ss_pred             cEEEEecCCCCccHHHHHH----HHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          248 RKIFVSNVGSELEPQKLLA----FFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~----~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      .||||.||+..+..++|+.    +|++||.|..|...+   +.+.+|-|||.|.+.+.|..|+..|+ .-|.|++++|.|
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            3999999999999999998    999999999998864   67889999999999999999999999 889999999999


Q ss_pred             ccCCCC
Q 012923          323 AIDGPK  328 (453)
Q Consensus       323 a~~~~~  328 (453)
                      |.+...
T Consensus        87 A~s~sd   92 (221)
T KOG4206|consen   87 AKSDSD   92 (221)
T ss_pred             ccCccc
Confidence            987644

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.98  E-value=1.2e-09  Score=97.90  Aligned_cols=79  Identities=22%  Similarity=0.341  Sum_probs=69.9

Q ss_pred             ccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC--CccCCeEE
Q 012923          241 QQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH--KNFEGHIL  318 (453)
Q Consensus       241 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~--~~l~g~~l  318 (453)
                      +.....-++|||++|-..+++.+|+.+|.+||.|..|+++..      +++|||+|.+..+|+.|....-  ..|+|++|
T Consensus       222 pPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl  295 (377)
T KOG0153|consen  222 PPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRL  295 (377)
T ss_pred             CCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEE
Confidence            334445579999999999999999999999999999999875      6799999999999999998765  77899999


Q ss_pred             EEEEccC
Q 012923          319 NCQRAID  325 (453)
Q Consensus       319 ~v~~a~~  325 (453)
                      .|.|..+
T Consensus       296 ~i~Wg~~  302 (377)
T KOG0153|consen  296 KIKWGRP  302 (377)
T ss_pred             EEEeCCC
Confidence            9999865

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.96  E-value=2e-09  Score=104.46  Aligned_cols=195  Identities=9%  Similarity=-0.022  Sum_probs=139.8

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecc
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLAS  207 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~  207 (453)
                      .+.+.|-+.+.++++...|+++||... .|..+.|..+...+...|-++|.|....++++|++..+..+..|.+.+....
T Consensus       309 ~d~~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~rn~~~~~~R~~q~~P~g  387 (944)
T KOG4307|consen  309 SDKYYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTRNPSDDVNRPFQTGPPG  387 (944)
T ss_pred             chhheeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHhcCchhhhhcceeecCCC
Confidence            456778889999999999999999754 4666677777756666899999999999999999998888888888887765


Q ss_pred             cCCCCCCCcCc-ccccccccccc------cccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcce-eee
Q 012923          208 IGPATTPAVAS-TATHQHQHQHQ------HQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEE-GPL  279 (453)
Q Consensus       208 ~~~~~~~~~~~-~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~-v~i  279 (453)
                      ........... ........+..      ...................+|||..||..++..++..+|...-.|++ |.|
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            43322111111 00000000000      00011111123345556789999999999999999999998878887 555


Q ss_pred             eccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          280 GIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       280 ~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      .+ .-+++.++.|||.|...+++.+|+...+ +.++.|.|+|.-..
T Consensus       468 t~-~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~  512 (944)
T KOG4307|consen  468 TR-LPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIA  512 (944)
T ss_pred             cc-CCcccccchhhheeccccccchhhhcccccccCceEEEeechh
Confidence            44 4578889999999999999999988887 77888889886543

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.94  E-value=2.5e-09  Score=95.95  Aligned_cols=79  Identities=27%  Similarity=0.390  Sum_probs=69.1

Q ss_pred             cCCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC--CccCCeEe
Q 012923          124 ADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ--KKIGNRMT  201 (453)
Q Consensus       124 ~~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~--~~~~gr~~  201 (453)
                      .-.+...++|||++|-..+++.+|+++|.+||+|+.|+++...      ++|||+|.+..+|+.|.+..-  ..|.|+.|
T Consensus       222 pPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~------~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl  295 (377)
T KOG0153|consen  222 PPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK------GCAFVTFTTREAAEKAAEKSFNKLVINGFRL  295 (377)
T ss_pred             CCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc------ccceeeehhhHHHHHHHHhhcceeeecceEE
Confidence            3455667899999999999999999999999999999988653      599999999999999998755  34899999


Q ss_pred             EEEeccc
Q 012923          202 ACQLASI  208 (453)
Q Consensus       202 ~v~~~~~  208 (453)
                      .|.|...
T Consensus       296 ~i~Wg~~  302 (377)
T KOG0153|consen  296 KIKWGRP  302 (377)
T ss_pred             EEEeCCC
Confidence            9999875

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.93  E-value=2.6e-09  Score=101.36  Aligned_cols=84  Identities=27%  Similarity=0.489  Sum_probs=76.2

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ....++|||.+|...+...||+.+|++||.|+-.+|+.+..+.-.+.|+||++.+.++|.+||..|+ ..|.||.|.|..
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            3457899999999999999999999999999999999998887889999999999999999999999 559999999998


Q ss_pred             cccCC
Q 012923          206 ASIGP  210 (453)
Q Consensus       206 ~~~~~  210 (453)
                      +...+
T Consensus       482 aKNEp  486 (940)
T KOG4661|consen  482 AKNEP  486 (940)
T ss_pred             cccCc
Confidence            86433

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.89  E-value=3.7e-09  Score=100.38  Aligned_cols=83  Identities=20%  Similarity=0.382  Sum_probs=76.1

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ....+.|||.+|...+-..+|+.+|++||.|+-.+|+.+..+-..++|+||++.+.++|.+||..|+ ..|.|+.|.|..
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            4456899999999999999999999999999999999887776779999999999999999999999 899999999999


Q ss_pred             ccCC
Q 012923          323 AIDG  326 (453)
Q Consensus       323 a~~~  326 (453)
                      ++..
T Consensus       482 aKNE  485 (940)
T KOG4661|consen  482 AKNE  485 (940)
T ss_pred             cccC
Confidence            8754

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.80  E-value=2.8e-08  Score=94.94  Aligned_cols=176  Identities=14%  Similarity=0.077  Sum_probs=109.8

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ..+...++|+|-|||..+++++|+.+|+.||+|+.|+.-     -..+|.+||+|.+..+|+.|++.++ ..|.|+.|..
T Consensus        70 ~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t-----~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~  144 (549)
T KOG4660|consen   70 EKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRET-----PNKRGIVFVEFYDVRDAERALKALNRREIAGKRIKR  144 (549)
T ss_pred             cccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcc-----cccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcC
Confidence            345567899999999999999999999999999997643     3457899999999999999999999 5588888772


Q ss_pred             EecccCCCCCCCcCccccccccccccccccccccccccccccc-ccEEEEecCCCCccHHHHHHHHhccCCcceeeeecc
Q 012923          204 QLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYT-QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGID  282 (453)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d  282 (453)
                      .........           .+.......+............+ ...+|+- |++..+...++.+|+-+|.+.. +.   
T Consensus       145 ~~~~~~~~~-----------~~~~~~~~~~~~~p~a~s~pgg~~~~~~~g~-l~P~~s~~~~~~~~~~~~~~~~-~~---  208 (549)
T KOG4660|consen  145 PGGARRAMG-----------LQSGTSFLNHFGSPLANSPPGGWPRGQLFGM-LSPTRSSILLEHISSVDGSSPG-RE---  208 (549)
T ss_pred             CCcccccch-----------hcccchhhhhccchhhcCCCCCCcCCcceee-eccchhhhhhhcchhccCcccc-cc---
Confidence            211111000           00000111111111111111111 2234433 9998888888888888887765 32   


Q ss_pred             CCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEc
Q 012923          283 KATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRA  323 (453)
Q Consensus       283 ~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a  323 (453)
                        ++.-+-.-|+.|.+..++..++..+...+.+....+.+.
T Consensus       209 --~~~~~hq~~~~~~~~~s~a~~~~~~G~~~s~~~~v~t~S  247 (549)
T KOG4660|consen  209 --TPLLNHQRFVEFADNRSYAFSEPRGGFLISNSSGVITFS  247 (549)
T ss_pred             --ccchhhhhhhhhccccchhhcccCCceecCCCCceEEec
Confidence              222233567888888888555553323344444444443

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.80  E-value=4e-09  Score=95.85  Aligned_cols=179  Identities=11%  Similarity=0.048  Sum_probs=124.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCC---CCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecc
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVS---GKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLAS  207 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~---g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~  207 (453)
                      ..|.|-||.+.+|.+.|..||.-.|.|.+++|+.+...   ......|||.|.+...+..|....|..+-++.|.|.+..
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~~   87 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPYG   87 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEecC
Confidence            37999999999999999999999999999999764322   234568999999999999999999988888988887765


Q ss_pred             cCCCCCCCc-----------------Cccccccccccc-cccccccc-ccc-----cccccccccEEEEecCCCCccHHH
Q 012923          208 IGPATTPAV-----------------ASTATHQHQHQH-QHQHQHQH-QQH-----HQQSEYTQRKIFVSNVGSELEPQK  263 (453)
Q Consensus       208 ~~~~~~~~~-----------------~~~~~~~~~~~~-~~~~~~~~-~~~-----~~~~~~~~~~l~V~nLp~~~t~~~  263 (453)
                      ........+                 ............ +...+... +..     ........++|+|.+|+..|...+
T Consensus        88 ~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l~e  167 (479)
T KOG4676|consen   88 DEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAILPE  167 (479)
T ss_pred             CCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcchh
Confidence            443321100                 000000000000 00000000 000     011111237899999999999999


Q ss_pred             HHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCcc
Q 012923          264 LLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNF  313 (453)
Q Consensus       264 l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l  313 (453)
                      +.++|..+|.|...++.-    +...-+|.|.|....+...|+..++..+
T Consensus       168 ~~e~f~r~Gev~ya~~as----k~~s~~c~~sf~~qts~~halr~~gre~  213 (479)
T KOG4676|consen  168 SGESFERKGEVSYAHTAS----KSRSSSCSHSFRKQTSSKHALRSHGRER  213 (479)
T ss_pred             hhhhhhhcchhhhhhhhc----cCCCcchhhhHhhhhhHHHHHHhcchhh
Confidence            999999999999887743    3335678899999999999999888443

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.75  E-value=4e-08  Score=86.53  Aligned_cols=84  Identities=21%  Similarity=0.351  Sum_probs=74.9

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~~~v~  204 (453)
                      .+....+|+|.|||+.++..||+++|..||.+..+-|-.++ +|.+.|.|-|.|...++|..|++.++.. +.|+.+.+.
T Consensus        79 ~~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~  157 (243)
T KOG0533|consen   79 NETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIE  157 (243)
T ss_pred             cCCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeE
Confidence            34455789999999999999999999999999999888888 9999999999999999999999999965 899998888


Q ss_pred             ecccCC
Q 012923          205 LASIGP  210 (453)
Q Consensus       205 ~~~~~~  210 (453)
                      ......
T Consensus       158 ~i~~~~  163 (243)
T KOG0533|consen  158 IISSPS  163 (243)
T ss_pred             EecCcc
Confidence            765443

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.74  E-value=2e-08  Score=95.74  Aligned_cols=78  Identities=26%  Similarity=0.423  Sum_probs=68.6

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLAS  207 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~  207 (453)
                      ..+|||+|||++++..+|+++|..||.|+...|......++...||||+|.+.++++.||.+....|.+++|.|....
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEEKR  365 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEecc
Confidence            446999999999999999999999999999988765434555589999999999999999998778999999998753

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.71  E-value=4.3e-08  Score=86.38  Aligned_cols=80  Identities=19%  Similarity=0.328  Sum_probs=72.9

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ...+|+|.||++.+++++|+++|..||.+..+-|..++ .|++.|.|-|.|...++|.+|++.++ ..|+|+.|.+....
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~  160 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIIS  160 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEec
Confidence            34689999999999999999999999998888887764 89999999999999999999999999 88999999998876


Q ss_pred             CC
Q 012923          325 DG  326 (453)
Q Consensus       325 ~~  326 (453)
                      +.
T Consensus       161 ~~  162 (243)
T KOG0533|consen  161 SP  162 (243)
T ss_pred             Cc
Confidence            44

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.70  E-value=5.6e-08  Score=86.03  Aligned_cols=83  Identities=20%  Similarity=0.324  Sum_probs=76.7

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      .....+.+||+|+.+.+|.++|...|+.||.|..|.|+.|+.++.+|||+||+|.+.+.+..|+. |+ ..|.++.+.|.
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVT  175 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceee
Confidence            33455699999999999999999999999999999999999999999999999999999999999 77 89999999999


Q ss_pred             EccCC
Q 012923          322 RAIDG  326 (453)
Q Consensus       322 ~a~~~  326 (453)
                      +...+
T Consensus       176 ~~r~~  180 (231)
T KOG4209|consen  176 LKRTN  180 (231)
T ss_pred             eeeee
Confidence            98766

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.66  E-value=1.5e-07  Score=70.69  Aligned_cols=77  Identities=17%  Similarity=0.215  Sum_probs=64.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhc--cCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-c----CCeEeEE
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQ--YGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-I----GNRMTAC  203 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~--~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~----~gr~~~v  203 (453)
                      +||.|+|||...|.++|.+++..  .|...-+.+..|..++.+.|||||.|.+++.|.+..+..++. +    ..+.+.|
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            69999999999999999998865  356777889999989999999999999999999999988743 3    3455566


Q ss_pred             Eecc
Q 012923          204 QLAS  207 (453)
Q Consensus       204 ~~~~  207 (453)
                      .+|.
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            6664

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.63  E-value=1.9e-07  Score=78.84  Aligned_cols=89  Identities=19%  Similarity=0.334  Sum_probs=71.0

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeee-ccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccC---CeEEEE
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLG-IDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFE---GHILNC  320 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~-~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~---g~~l~v  320 (453)
                      ..+||||.+||.++...+|..+|..|-..+...|- .++....++-+|||+|.+.++|.+|+.+|| ..|+   +..|+|
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhi  112 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHI  112 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEe
Confidence            35799999999999999999999998766655442 222223346799999999999999999999 6664   688999


Q ss_pred             EEccCCCCCCCCCC
Q 012923          321 QRAIDGPKPGKSRH  334 (453)
Q Consensus       321 ~~a~~~~~~~~~~~  334 (453)
                      .+++++.+..+.+.
T Consensus       113 ElAKSNtK~kr~k~  126 (284)
T KOG1457|consen  113 ELAKSNTKRKRRKG  126 (284)
T ss_pred             eehhcCcccccCCC
Confidence            99998887665543

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.62  E-value=9.6e-07  Score=86.36  Aligned_cols=79  Identities=14%  Similarity=0.101  Sum_probs=65.6

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeE-EEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIED-CKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~-v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ...-.|||..||..+++.++.++|...-.|++ |.|.+-+ +++.++.|||.|..++++.+|+..-. ..+..|.|+|+.
T Consensus       432 ~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~s  510 (944)
T KOG4307|consen  432 GAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDS  510 (944)
T ss_pred             CccceEEeccCCccccccchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEeec
Confidence            33568999999999999999999998888887 6665555 88899999999999888888887666 457888888876


Q ss_pred             cc
Q 012923          206 AS  207 (453)
Q Consensus       206 ~~  207 (453)
                      ..
T Consensus       511 i~  512 (944)
T KOG4307|consen  511 IA  512 (944)
T ss_pred             hh
Confidence            64

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.61  E-value=4.5e-08  Score=84.22  Aligned_cols=82  Identities=32%  Similarity=0.534  Sum_probs=72.8

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~~~v~  204 (453)
                      -+.+..+||++.|..+++.+-|...|.+|-.....++++|+.|++++||+||.|.++.++..|+..+++. +..|.|.+.
T Consensus       186 w~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklR  265 (290)
T KOG0226|consen  186 WDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLR  265 (290)
T ss_pred             CccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhh
Confidence            3445678999999999999999999999999999999999999999999999999999999999999954 777777665


Q ss_pred             ecc
Q 012923          205 LAS  207 (453)
Q Consensus       205 ~~~  207 (453)
                      .+.
T Consensus       266 kS~  268 (290)
T KOG0226|consen  266 KSE  268 (290)
T ss_pred             hhh
Confidence            443

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.60  E-value=1.1e-07  Score=85.50  Aligned_cols=80  Identities=24%  Similarity=0.301  Sum_probs=72.4

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcc--------eeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCe
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIE--------EGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGH  316 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~--------~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~  316 (453)
                      ..+.|||.|||.++|.+++.++|++||.|.        .|+|.++. .|..||-|.|.|...+++..||..|+ ..|.|+
T Consensus       133 ~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~  211 (382)
T KOG1548|consen  133 VNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELRGK  211 (382)
T ss_pred             cCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccccCc
Confidence            345799999999999999999999999886        47888875 59999999999999999999999999 899999


Q ss_pred             EEEEEEccCC
Q 012923          317 ILNCQRAIDG  326 (453)
Q Consensus       317 ~l~v~~a~~~  326 (453)
                      .|+|..|.-.
T Consensus       212 ~~rVerAkfq  221 (382)
T KOG1548|consen  212 KLRVERAKFQ  221 (382)
T ss_pred             EEEEehhhhh
Confidence            9999999643

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.54  E-value=1.2e-07  Score=83.88  Aligned_cols=85  Identities=16%  Similarity=0.248  Sum_probs=76.8

Q ss_pred             cCCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEE
Q 012923          124 ADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTAC  203 (453)
Q Consensus       124 ~~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v  203 (453)
                      .....+.+.|||+|+.+.+|.++|...|+-||.|..+.|..|+.++.++|||||+|.+.+.+..|+......|.++.+.|
T Consensus        95 ~~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~v  174 (231)
T KOG4209|consen   95 RQKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEV  174 (231)
T ss_pred             hhhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhhcCCccccccccee
Confidence            34566778999999999999999999999999999999999999989999999999999999999995447799999999


Q ss_pred             Eeccc
Q 012923          204 QLASI  208 (453)
Q Consensus       204 ~~~~~  208 (453)
                      .+...
T Consensus       175 t~~r~  179 (231)
T KOG4209|consen  175 TLKRT  179 (231)
T ss_pred             eeeee
Confidence            88753

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.52  E-value=1.8e-08  Score=92.48  Aligned_cols=150  Identities=17%  Similarity=0.228  Sum_probs=116.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc--cCCeEeEEEecccC
Q 012923          132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK--IGNRMTACQLASIG  209 (453)
Q Consensus       132 ~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~--~~gr~~~v~~~~~~  209 (453)
                      .|||+||.+.++..+|..+|...-      +.....--...|||||.+.+...|.+|++.+++.  +.|..+.|.....+
T Consensus         3 klyignL~p~~~psdl~svfg~ak------~~~~g~fl~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~k   76 (584)
T KOG2193|consen    3 KLYIGNLSPQVTPSDLESVFGDAK------IPGSGQFLVKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPK   76 (584)
T ss_pred             cccccccCCCCChHHHHHHhcccc------CCCCcceeeecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhH
Confidence            699999999999999999997541      1111000022479999999999999999999954  78888888776533


Q ss_pred             CCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeee-ccCCCCCC
Q 012923          210 PATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLG-IDKATGKP  288 (453)
Q Consensus       210 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~-~d~~~g~~  288 (453)
                      ..                                  ..+.+-|+|+|....++.|..++..||.+..|..+ .+..    
T Consensus        77 kq----------------------------------rsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~e----  118 (584)
T KOG2193|consen   77 KQ----------------------------------RSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSE----  118 (584)
T ss_pred             HH----------------------------------HhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchH----
Confidence            22                                  12468999999999999999999999999988653 3322    


Q ss_pred             ceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          289 KGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       289 kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .-..-|+|.+.+.+..||..++ ..|....++|.|.-.
T Consensus       119 tavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiPd  156 (584)
T KOG2193|consen  119 TAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIPD  156 (584)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCch
Confidence            2234478999999999999999 888888999988643

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.49  E-value=7.4e-06  Score=73.82  Aligned_cols=77  Identities=21%  Similarity=0.392  Sum_probs=65.5

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccC--CeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYG--EIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G--~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      -....+||+||-|.+|.+||.+.+...|  .|.+++++.++.+|.+||||+|...+..++++.++.|- +.|+|..-.|.
T Consensus        78 Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   78 GRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             CceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            3445799999999999999999998777  57888999999999999999999999999999999887 44776654443

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.49  E-value=1e-07  Score=91.13  Aligned_cols=71  Identities=24%  Similarity=0.406  Sum_probs=64.1

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILN  319 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~  319 (453)
                      .....+|+|-|||..++.++|+.+|+.||+|+.|+.-+     ..+|.+||+|-+..+|.+|++.|+ ..|.|+.|.
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~-----~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETP-----NKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccc-----ccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            44567999999999999999999999999999976644     348999999999999999999999 889999887

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.46  E-value=5.3e-07  Score=82.03  Aligned_cols=87  Identities=28%  Similarity=0.303  Sum_probs=78.6

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcc--------eeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccC
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIE--------EGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFE  314 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~--------~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~  314 (453)
                      .....+|||-+||..+++++|..+|.++|.|.        .|.|.++++|+++||-|.|.|.+...|+.||..++ ..|.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            44556999999999999999999999999885        57788999999999999999999999999999999 8899


Q ss_pred             CeEEEEEEccCCCCCC
Q 012923          315 GHILNCQRAIDGPKPG  330 (453)
Q Consensus       315 g~~l~v~~a~~~~~~~  330 (453)
                      +.+|+|.+|..++...
T Consensus       143 gn~ikvs~a~~r~~ve  158 (351)
T KOG1995|consen  143 GNTIKVSLAERRTGVE  158 (351)
T ss_pred             CCCchhhhhhhccCcc
Confidence            9999999998776543

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.43  E-value=3.7e-07  Score=89.41  Aligned_cols=85  Identities=22%  Similarity=0.387  Sum_probs=73.3

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCC---CCcceEEEEEEccHHHHHHHHHcCCCc-cCCeEeE
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVS---GKSKGYGFILFKTRSGARKALKEPQKK-IGNRMTA  202 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~---g~~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~~~  202 (453)
                      ++..++|||+||++.++++.|...|..||+|..|+|+.-+..   .+.+-|+||.|-+..+|++|++.|++. +..+.++
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            677889999999999999999999999999999999876532   345679999999999999999999965 7888999


Q ss_pred             EEecccCCC
Q 012923          203 CQLASIGPA  211 (453)
Q Consensus       203 v~~~~~~~~  211 (453)
                      +.|+..-+.
T Consensus       251 ~gWgk~V~i  259 (877)
T KOG0151|consen  251 LGWGKAVPI  259 (877)
T ss_pred             ecccccccc
Confidence            888854433

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.41  E-value=1.9e-06  Score=64.75  Aligned_cols=78  Identities=14%  Similarity=0.193  Sum_probs=65.5

Q ss_pred             cEEEEecCCCCccHHHHHHHHhcc--CCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccC----CeEEEE
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKY--GEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFE----GHILNC  320 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~----g~~l~v  320 (453)
                      +||.|+|||...|.++|.+++...  |...-+-++.|..++.+.|||||.|.+++.|.+-....+ ..+.    .+.+.|
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            599999999999999999988753  566678888888889999999999999999999998887 4443    466778


Q ss_pred             EEccC
Q 012923          321 QRAID  325 (453)
Q Consensus       321 ~~a~~  325 (453)
                      .||.-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            77754

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.32  E-value=2e-07  Score=78.51  Aligned_cols=76  Identities=14%  Similarity=0.184  Sum_probs=67.9

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      .++|||.||...++++.|.++|-+.|.|..|.|..++ .++.| ||||.|.+.-++.-|+..+| ..|.++.|.|.+-.
T Consensus         9 drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~   85 (267)
T KOG4454|consen    9 DRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRC   85 (267)
T ss_pred             hhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhccccc
Confidence            3699999999999999999999999999999998775 45667 99999999999999999999 88888888877653

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.27  E-value=7.6e-07  Score=76.74  Aligned_cols=70  Identities=19%  Similarity=0.406  Sum_probs=63.6

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      ..|||++||+.+.+.+|..||..||.|..|.+.        .||+||+|.+..+|..|+..++ ..|.+-.+.|.++..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~   72 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            379999999999999999999999999998873        6799999999999999999999 888888888888753

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.25  E-value=5.7e-08  Score=97.17  Aligned_cols=164  Identities=20%  Similarity=0.158  Sum_probs=126.7

Q ss_pred             cCeEEEcCCCCCCCHH-HHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAE-TLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~-~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~~  208 (453)
                      .+.+.+.|+-+..... .++..|..+|.|+.|++......-..-.+.++.+....+++.|.....+.+.++.+.|..+..
T Consensus       571 ~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~pa~~~~a~~~~av~~ad~  650 (881)
T KOG0128|consen  571 RREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATVPAGGALANRSAAVGLADA  650 (881)
T ss_pred             hhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhcccccccccCCccccCCCCCc
Confidence            3567777887776655 678899999999999876633222222389999999999999999888889998888888765


Q ss_pred             CCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCC
Q 012923          209 GPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKP  288 (453)
Q Consensus       209 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~  288 (453)
                      ..........                      +.......++||+||+..+.+.+|...|..+|.|..++|.....+++.
T Consensus       651 ~~~~~~~kvs----------------------~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~  708 (881)
T KOG0128|consen  651 EEKEENFKVS----------------------PNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRF  708 (881)
T ss_pred             hhhhhccCcC----------------------chHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhcccc
Confidence            5432211111                      111123358999999999999999999999999998888766778999


Q ss_pred             ceEEEEEECCHHHHHHHHHcCCCccCC
Q 012923          289 KGFCLFVYKTVDAAKKALEEPHKNFEG  315 (453)
Q Consensus       289 kg~afV~F~~~~~A~~Al~~~~~~l~g  315 (453)
                      +|+|||.|...+++.+||......+.|
T Consensus       709 rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  709 RGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             ccceeeEeecCCchhhhhhhhhhhhhh
Confidence            999999999999999999988854555

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.21  E-value=2.4e-06  Score=83.96  Aligned_cols=84  Identities=13%  Similarity=0.225  Sum_probs=73.9

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccC---CCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDK---ATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILN  319 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~---~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~  319 (453)
                      ...++.|||+||++.++++.|...|..||.|..|+|+..+   +..+.+.|+||-|.+..+|.+|++.|+ ..+....++
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            4556899999999999999999999999999999998655   335568899999999999999999999 888999999


Q ss_pred             EEEccCCC
Q 012923          320 CQRAIDGP  327 (453)
Q Consensus       320 v~~a~~~~  327 (453)
                      +.|.+.-+
T Consensus       251 ~gWgk~V~  258 (877)
T KOG0151|consen  251 LGWGKAVP  258 (877)
T ss_pred             eccccccc
Confidence            99985543

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.17  E-value=1.8e-06  Score=78.66  Aligned_cols=83  Identities=24%  Similarity=0.244  Sum_probs=73.7

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCee--------EEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCC
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIE--------DCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGN  198 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~--------~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~g  198 (453)
                      ...-+|||.+||..+++++|.++|.+||.|.        .|+|.+|+.|++.||-|.|.|.+...|+.|+..+. ..+++
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~g  143 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCG  143 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccC
Confidence            4456899999999999999999999999875        47788999999999999999999999999999988 55999


Q ss_pred             eEeEEEecccCC
Q 012923          199 RMTACQLASIGP  210 (453)
Q Consensus       199 r~~~v~~~~~~~  210 (453)
                      .+|.|.++...+
T Consensus       144 n~ikvs~a~~r~  155 (351)
T KOG1995|consen  144 NTIKVSLAERRT  155 (351)
T ss_pred             CCchhhhhhhcc
Confidence            999988876544

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=98.07  E-value=6.7e-06  Score=63.51  Aligned_cols=69  Identities=22%  Similarity=0.277  Sum_probs=43.9

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-C-----ccCCeEEEEE
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-K-----NFEGHILNCQ  321 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~-----~l~g~~l~v~  321 (453)
                      ..|+|.++...++.++|+++|+.||.|..|.+.+.      -..|||.|.+.++|.+|+..+. .     .|.+..+.+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            47999999999999999999999999999998765      3369999999999999998766 3     4555555544


Q ss_pred             E
Q 012923          322 R  322 (453)
Q Consensus       322 ~  322 (453)
                      .
T Consensus        76 v   76 (105)
T PF08777_consen   76 V   76 (105)
T ss_dssp             -
T ss_pred             E
Confidence            3

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=98.07  E-value=2.1e-06  Score=74.24  Aligned_cols=71  Identities=17%  Similarity=0.257  Sum_probs=58.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCC--------CCcce----EEEEEEccHHHHHHHHHcCCCc-cC
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVS--------GKSKG----YGFILFKTRSGARKALKEPQKK-IG  197 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~--------g~~~G----~afV~f~~~~~a~~A~~~~~~~-~~  197 (453)
                      -.|||.+||+.+...-|+++|+.||.|-.|.|.....+        |.++.    -++|+|.+...|..+...||+. |.
T Consensus        75 GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~Ig  154 (278)
T KOG3152|consen   75 GVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPIG  154 (278)
T ss_pred             eEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCccC
Confidence            47999999999999999999999999999988765544        23322    3789999999999999998855 77


Q ss_pred             CeEe
Q 012923          198 NRMT  201 (453)
Q Consensus       198 gr~~  201 (453)
                      |+.-
T Consensus       155 gkk~  158 (278)
T KOG3152|consen  155 GKKK  158 (278)
T ss_pred             CCCC
Confidence            7653

>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=98.05  E-value=1.8e-05  Score=56.44  Aligned_cols=67  Identities=12%  Similarity=0.198  Sum_probs=46.9

Q ss_pred             CeEEEcCCCCCCCHHHH----HHHHhccC-CeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCCeEeEEE
Q 012923          131 RKIFVHGLGWDTKAETL----IDAFKQYG-EIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGNRMTACQ  204 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l----~~~f~~~G-~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~~~v~  204 (453)
                      ..|||.|||.+.+...|    +.++.-|| .|..|.          .+.|+|.|.+.+.|.+|++.|.+. +.|++|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            46999999999987755    46666786 566652          246999999999999999999865 899999999


Q ss_pred             ecc
Q 012923          205 LAS  207 (453)
Q Consensus       205 ~~~  207 (453)
                      +..
T Consensus        73 ~~~   75 (90)
T PF11608_consen   73 FSP   75 (90)
T ss_dssp             SS-
T ss_pred             EcC
Confidence            874

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_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=98.00  E-value=1.9e-05  Score=56.40  Aligned_cols=67  Identities=15%  Similarity=0.274  Sum_probs=46.4

Q ss_pred             cEEEEecCCCCccHHH----HHHHHhccC-CcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          248 RKIFVSNVGSELEPQK----LLAFFSKYG-EIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~----l~~~F~~~G-~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      ..|+|.|||...+...    |++++..|| .|..|.          .+.|+|.|.+.+.|.+|.+.|+ ..+.|++|.|+
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            4799999999988765    456777776 455541          4579999999999999999999 77899999999


Q ss_pred             Ecc
Q 012923          322 RAI  324 (453)
Q Consensus       322 ~a~  324 (453)
                      +..
T Consensus        73 ~~~   75 (90)
T PF11608_consen   73 FSP   75 (90)
T ss_dssp             SS-
T ss_pred             EcC
Confidence            873

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.86  E-value=1e-05  Score=74.39  Aligned_cols=81  Identities=27%  Similarity=0.455  Sum_probs=71.8

Q ss_pred             CeEE-EcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecccC
Q 012923          131 RKIF-VHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASIG  209 (453)
Q Consensus       131 ~~lf-V~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~~~  209 (453)
                      .++| |++|++.+++++|+.+|..+|.|..+++..+..++.++|||||.|.+...+..++..-...+.++.+.+......
T Consensus       185 ~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  264 (285)
T KOG4210|consen  185 DTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALNDQTRSIGGRPLRLEEDEPR  264 (285)
T ss_pred             ccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhcccCcccCcccccccCCCC
Confidence            3455 999999999999999999999999999999999999999999999999999999998336688888988887654


Q ss_pred             CC
Q 012923          210 PA  211 (453)
Q Consensus       210 ~~  211 (453)
                      +.
T Consensus       265 ~~  266 (285)
T KOG4210|consen  265 PK  266 (285)
T ss_pred             cc
Confidence            43

>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=97.80  E-value=4e-05  Score=59.20  Aligned_cols=57  Identities=32%  Similarity=0.453  Sum_probs=38.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ  193 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~  193 (453)
                      +.|+|.+++..++.++|+++|+.||.|..|.+.+...      .|||.|.+.+.|+.|++.+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~------~g~VRf~~~~~A~~a~~~~~   58 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDT------EGYVRFKTPEAAQKALEKLK   58 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-S------EEEEEESS---HHHHHHHHH
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCC------EEEEEECCcchHHHHHHHHH
Confidence            4689999999999999999999999999998776442      69999999999999998754

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.77  E-value=3.3e-05  Score=71.82  Aligned_cols=66  Identities=27%  Similarity=0.333  Sum_probs=56.5

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeecc---CCC--CCC--------ceEEEEEECCHHHHHHHHHcCC
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGID---KAT--GKP--------KGFCLFVYKTVDAAKKALEEPH  310 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d---~~~--g~~--------kg~afV~F~~~~~A~~Al~~~~  310 (453)
                      ...++|.+-|||.+-.-+.|.++|..||.|..|+|...   +..  +.+        +-+|||+|...+.|.+|.+.+|
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLN  307 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhc
Confidence            45679999999999999999999999999999999875   322  222        4579999999999999999997

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.73  E-value=8.1e-05  Score=49.52  Aligned_cols=52  Identities=29%  Similarity=0.399  Sum_probs=42.8

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHH
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKAL  306 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al  306 (453)
                      +.|.|.+.+....+. |..+|..||.|..+.+...      +.+.||+|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            478999998877755 5558889999999988522      568999999999999986

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.59  E-value=0.00039  Score=60.60  Aligned_cols=87  Identities=22%  Similarity=0.229  Sum_probs=74.3

Q ss_pred             HHHHHHHcCCC-ccCCeEeEEEecccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHH
Q 012923          184 GARKALKEPQK-KIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQ  262 (453)
Q Consensus       184 ~a~~A~~~~~~-~~~gr~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~  262 (453)
                      -|..|-..|.. ...++.++|.++..                                       ..|+|.||...++.+
T Consensus         6 ~ae~ak~eLd~~~~~~~~lr~rfa~~---------------------------------------a~l~V~nl~~~~snd   46 (275)
T KOG0115|consen    6 LAEIAKRELDGRFPKGRSLRVRFAMH---------------------------------------AELYVVNLMQGASND   46 (275)
T ss_pred             HHHHHHHhcCCCCCCCCceEEEeecc---------------------------------------ceEEEEecchhhhhH
Confidence            35556666664 47899999999852                                       379999999999999


Q ss_pred             HHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC
Q 012923          263 KLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH  310 (453)
Q Consensus       263 ~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~  310 (453)
                      .|.+.|+.||.|....++.| ..++..+-++|.|...-.|.+|+..++
T Consensus        47 ll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   47 LLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             HHHHhhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHHHhc
Confidence            99999999999998877776 478889999999999999999999986

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.58  E-value=0.00019  Score=47.76  Aligned_cols=52  Identities=31%  Similarity=0.445  Sum_probs=42.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHH
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL  189 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~  189 (453)
                      +.|-|.+.+.+..+ .|..+|..||+|..+.+-.      ..-+.||.|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~------~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPE------STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCC------CCcEEEEEECCHHHHHhhC
Confidence            57889999988775 5556999999999988662      2338999999999999986

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.44  E-value=0.00031  Score=63.38  Aligned_cols=81  Identities=15%  Similarity=0.353  Sum_probs=63.0

Q ss_pred             cccEEEEecCCCCccHHH----H--HHHHhccCCcceeeeeccCCCCCC-ceE--EEEEECCHHHHHHHHHcCC-CccCC
Q 012923          246 TQRKIFVSNVGSELEPQK----L--LAFFSKYGEIEEGPLGIDKATGKP-KGF--CLFVYKTVDAAKKALEEPH-KNFEG  315 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~----l--~~~F~~~G~i~~v~i~~d~~~g~~-kg~--afV~F~~~~~A~~Al~~~~-~~l~g  315 (453)
                      ...-+||-+|++.+-.++    |  .++|.+||.|..|.|-+...+..+ .+.  .||+|.+.++|.+||...+ ..++|
T Consensus       113 QKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DG  192 (480)
T COG5175         113 QKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDG  192 (480)
T ss_pred             ecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccC
Confidence            345789999998876665    2  379999999999988665422222 222  4999999999999999999 88999


Q ss_pred             eEEEEEEccCC
Q 012923          316 HILNCQRAIDG  326 (453)
Q Consensus       316 ~~l~v~~a~~~  326 (453)
                      |.|++.+...+
T Consensus       193 r~lkatYGTTK  203 (480)
T COG5175         193 RVLKATYGTTK  203 (480)
T ss_pred             ceEeeecCchH
Confidence            99999887643

>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=97.40  E-value=0.00083  Score=51.00  Aligned_cols=77  Identities=17%  Similarity=0.217  Sum_probs=51.2

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceee-eeccC------CCCCCceEEEEEECCHHHHHHHHHcCCCccCCe-EE
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGP-LGIDK------ATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGH-IL  318 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~-i~~d~------~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~-~l  318 (453)
                      .+.|.|-+.|... ...|.+.|++||.|.+.. +.++.      ..-....+..|+|.++.+|.+||......|.|. .+
T Consensus         6 ~~wVtVFGfp~~~-~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~mv   84 (100)
T PF05172_consen    6 ETWVTVFGFPPSA-SNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSGSLMV   84 (100)
T ss_dssp             CCEEEEE---GGG-HHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETTCEEE
T ss_pred             CeEEEEEccCHHH-HHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcCcEEE
Confidence            3579999999884 456777899999998875 11110      001225689999999999999999988778775 55


Q ss_pred             EEEEcc
Q 012923          319 NCQRAI  324 (453)
Q Consensus       319 ~v~~a~  324 (453)
                      -|.++.
T Consensus        85 GV~~~~   90 (100)
T PF05172_consen   85 GVKPCD   90 (100)
T ss_dssp             EEEE-H
T ss_pred             EEEEcH
Confidence            577763

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.

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.36  E-value=0.00044  Score=66.78  Aligned_cols=76  Identities=25%  Similarity=0.308  Sum_probs=61.1

Q ss_pred             ccEEEEecCCCCc------cHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-Ccc-CCeEE
Q 012923          247 QRKIFVSNVGSEL------EPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNF-EGHIL  318 (453)
Q Consensus       247 ~~~l~V~nLp~~~------t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l-~g~~l  318 (453)
                      ..+|+|-|+|.--      -..-|..+|+++|+|+.+.++.+...| ++||.|++|.+..+|..|++.+| +.| ..+++
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            3589999998532      234567899999999999998886554 89999999999999999999999 555 45777


Q ss_pred             EEEEc
Q 012923          319 NCQRA  323 (453)
Q Consensus       319 ~v~~a  323 (453)
                      .|..-
T Consensus       137 ~v~~f  141 (698)
T KOG2314|consen  137 FVRLF  141 (698)
T ss_pred             Eeehh
Confidence            77554

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.33  E-value=0.00022  Score=66.51  Aligned_cols=70  Identities=23%  Similarity=0.279  Sum_probs=58.8

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEccc---CCC--CC--------cceEEEEEEccHHHHHHHHHc
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCD---KVS--GK--------SKGYGFILFKTRSGARKALKE  191 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d---~~~--g~--------~~G~afV~f~~~~~a~~A~~~  191 (453)
                      ..+..+++|.+-|||.+-.-+.|.++|..||.|..|+|+.-   +.+  +.        .+-+|||+|...+.|.+|.+.
T Consensus       226 ~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~  305 (484)
T KOG1855|consen  226 EEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKAREL  305 (484)
T ss_pred             ccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHh
Confidence            44467999999999999999999999999999999998765   222  11        245799999999999999999


Q ss_pred             CCC
Q 012923          192 PQK  194 (453)
Q Consensus       192 ~~~  194 (453)
                      ++.
T Consensus       306 ~~~  308 (484)
T KOG1855|consen  306 LNP  308 (484)
T ss_pred             hch
Confidence            873

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.19  E-value=0.0013  Score=59.52  Aligned_cols=76  Identities=18%  Similarity=0.334  Sum_probs=57.2

Q ss_pred             eEEEcCCCCCCCHHHH------HHHHhccCCeeEEEEcccCCC-CCcceEE--EEEEccHHHHHHHHHcCCCc-cCCeEe
Q 012923          132 KIFVHGLGWDTKAETL------IDAFKQYGEIEDCKAVCDKVS-GKSKGYG--FILFKTRSGARKALKEPQKK-IGNRMT  201 (453)
Q Consensus       132 ~lfV~nLp~~~te~~l------~~~f~~~G~i~~v~i~~d~~~-g~~~G~a--fV~f~~~~~a~~A~~~~~~~-~~gr~~  201 (453)
                      -|||-+||+.+..+++      .++|.+||.|..|.|-+...+ ....+.+  ||+|.+.++|..||....+. +.||.|
T Consensus       116 LvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~l  195 (480)
T COG5175         116 LVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRVL  195 (480)
T ss_pred             eeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCceE
Confidence            5899999988876662      279999999988865443211 1122333  99999999999999999855 899999


Q ss_pred             EEEecc
Q 012923          202 ACQLAS  207 (453)
Q Consensus       202 ~v~~~~  207 (453)
                      +..+..
T Consensus       196 katYGT  201 (480)
T COG5175         196 KATYGT  201 (480)
T ss_pred             eeecCc
Confidence            987764

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.17  E-value=0.0013  Score=63.16  Aligned_cols=79  Identities=20%  Similarity=0.180  Sum_probs=65.5

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHh-ccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC----CccCCeEeE
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFK-QYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ----KKIGNRMTA  202 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~-~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~----~~~~gr~~~  202 (453)
                      ...+|||||+||.-+|.++|..+|. -||-|..+-|=+|+.-+-.+|-|-|+|.+..+-.+||.+--    +.-..++|.
T Consensus       368 DprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsarFvql~h~d~~KRVE  447 (520)
T KOG0129|consen  368 DPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISARFVQLDHTDIDKRVE  447 (520)
T ss_pred             CccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhhheEEEeccccceeee
Confidence            4468999999999999999999999 79999999999997788899999999999999999998632    222233555


Q ss_pred             EEec
Q 012923          203 CQLA  206 (453)
Q Consensus       203 v~~~  206 (453)
                      |+..
T Consensus       448 IkPY  451 (520)
T KOG0129|consen  448 IKPY  451 (520)
T ss_pred             ecce
Confidence            5544

>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=97.13  E-value=0.003  Score=48.00  Aligned_cols=76  Identities=13%  Similarity=0.195  Sum_probs=51.3

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccC-------CCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeE
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDK-------VSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTA  202 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~-------~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~  202 (453)
                      .+.|.|-+.|.. ....|.++|++||.|.+..-+...       ..........|+|.++.+|.+||..+...|.|..+.
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~mv   84 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSGSLMV   84 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETTCEEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcCcEEE
Confidence            467999999998 556788999999999887511110       011233489999999999999999988888776544


Q ss_pred             -EEec
Q 012923          203 -CQLA  206 (453)
Q Consensus       203 -v~~~  206 (453)
                       |.++
T Consensus        85 GV~~~   89 (100)
T PF05172_consen   85 GVKPC   89 (100)
T ss_dssp             EEEE-
T ss_pred             EEEEc
Confidence             5554

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.

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.12  E-value=0.00025  Score=61.72  Aligned_cols=69  Identities=20%  Similarity=0.302  Sum_probs=58.8

Q ss_pred             EEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCC--------CCCceE----EEEEECCHHHHHHHHHcCC-CccCC
Q 012923          249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKAT--------GKPKGF----CLFVYKTVDAAKKALEEPH-KNFEG  315 (453)
Q Consensus       249 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~--------g~~kg~----afV~F~~~~~A~~Al~~~~-~~l~g  315 (453)
                      .|||.+||+.+....|+++|+.||.|-+|.|-....+        |..+.+    ++|+|.+...|..+...|| ..|+|
T Consensus        76 VvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~Igg  155 (278)
T KOG3152|consen   76 VVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPIGG  155 (278)
T ss_pred             EEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCccCC
Confidence            8999999999999999999999999999988765544        333332    7799999999999999999 77888


Q ss_pred             eE
Q 012923          316 HI  317 (453)
Q Consensus       316 ~~  317 (453)
                      ++
T Consensus       156 kk  157 (278)
T KOG3152|consen  156 KK  157 (278)
T ss_pred             CC
Confidence            65

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.08  E-value=0.00096  Score=61.58  Aligned_cols=82  Identities=17%  Similarity=0.160  Sum_probs=67.1

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCC---CCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEcc
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKA---TGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAI  324 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~---~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a~  324 (453)
                      ..|.|.||.+.+|.++++.+|.-.|.|..++|+....   -....-.|||.|.+...+..|-.+.|..|-++.|.|..+.
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~~   87 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPYG   87 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEecC
Confidence            3899999999999999999999999999999876332   1233568999999999999999888877778888887765


Q ss_pred             CCCCC
Q 012923          325 DGPKP  329 (453)
Q Consensus       325 ~~~~~  329 (453)
                      ..+.+
T Consensus        88 ~~~~p   92 (479)
T KOG4676|consen   88 DEVIP   92 (479)
T ss_pred             CCCCc
Confidence            54433

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=97.06  E-value=0.0019  Score=62.99  Aligned_cols=80  Identities=19%  Similarity=0.240  Sum_probs=63.9

Q ss_pred             cccccccccEEEEecCCCCccHHHHHHHHh-ccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-Ccc---C
Q 012923          240 HQQSEYTQRKIFVSNVGSELEPQKLLAFFS-KYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNF---E  314 (453)
Q Consensus       240 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~-~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l---~  314 (453)
                      .+.....++.|+|.||-..+|.-+|+.++. .+|.|+.+.|  |+    -|..|||.|.+.++|...+.+|| ..+   +
T Consensus       437 SPsR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm--Dk----IKShCyV~yss~eEA~atr~AlhnV~WP~sN  510 (718)
T KOG2416|consen  437 SPSRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM--DK----IKSHCYVSYSSVEEAAATREALHNVQWPPSN  510 (718)
T ss_pred             CCCCCCccceEeeecccccchHHHHHHHHhhccCchHHHHH--HH----hhcceeEecccHHHHHHHHHHHhccccCCCC
Confidence            344666778999999999999999999999 6677777733  22    26679999999999999999998 333   6


Q ss_pred             CeEEEEEEccC
Q 012923          315 GHILNCQRAID  325 (453)
Q Consensus       315 g~~l~v~~a~~  325 (453)
                      .+.|.+.|...
T Consensus       511 PK~L~adf~~~  521 (718)
T KOG2416|consen  511 PKHLIADFVRA  521 (718)
T ss_pred             CceeEeeecch
Confidence            68888888753

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.02  E-value=0.0026  Score=61.64  Aligned_cols=74  Identities=27%  Similarity=0.374  Sum_probs=57.9

Q ss_pred             CeEEEcCCCCCC--CHH----HHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-c-CCeEeE
Q 012923          131 RKIFVHGLGWDT--KAE----TLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-I-GNRMTA  202 (453)
Q Consensus       131 ~~lfV~nLp~~~--te~----~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~-~gr~~~  202 (453)
                      ..|+|-|+|.--  ..+    -|..+|+++|+|..+.+..+. .|.++||.|++|.+..+|+.|++.+++. | ......
T Consensus        59 ~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e-~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~  137 (698)
T KOG2314|consen   59 SVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDE-EGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFF  137 (698)
T ss_pred             eEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCc-cCCeeeEEEEEecChhhHHHHHHhcccceecccceEE
Confidence            579999998432  222    455789999999999998888 4559999999999999999999999854 3 444555


Q ss_pred             EEe
Q 012923          203 CQL  205 (453)
Q Consensus       203 v~~  205 (453)
                      |..
T Consensus       138 v~~  140 (698)
T KOG2314|consen  138 VRL  140 (698)
T ss_pred             eeh
Confidence            544

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=97.00  E-value=0.0017  Score=57.73  Aligned_cols=77  Identities=14%  Similarity=0.165  Sum_probs=57.9

Q ss_pred             cEEEEecCC--CCc---cHHHHHHHHhccCCcceeeeeccCCCCCCc-eEEEEEECCHHHHHHHHHcCC-CccCCeEEEE
Q 012923          248 RKIFVSNVG--SEL---EPQKLLAFFSKYGEIEEGPLGIDKATGKPK-GFCLFVYKTVDAAKKALEEPH-KNFEGHILNC  320 (453)
Q Consensus       248 ~~l~V~nLp--~~~---t~~~l~~~F~~~G~i~~v~i~~d~~~g~~k-g~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v  320 (453)
                      +.|.++|+-  -.+   -++++++-+++||.|.+|.|+..+..-... --.||+|...++|.+|+-.|| .+|+||.+..
T Consensus       282 kvlllrnmVg~gevd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A  361 (378)
T KOG1996|consen  282 KVLLLRNMVGAGEVDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSA  361 (378)
T ss_pred             HHHHhhhhcCcccccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeh
Confidence            346666652  223   346788999999999999888765322221 238999999999999999999 8999999887


Q ss_pred             EEcc
Q 012923          321 QRAI  324 (453)
Q Consensus       321 ~~a~  324 (453)
                      .|..
T Consensus       362 ~Fyn  365 (378)
T KOG1996|consen  362 CFYN  365 (378)
T ss_pred             eecc
Confidence            7653

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=96.97  E-value=0.0011  Score=64.50  Aligned_cols=76  Identities=8%  Similarity=0.044  Sum_probs=60.6

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHh-ccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-c---CCeE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFK-QYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-I---GNRM  200 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~-~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~---~gr~  200 (453)
                      ....+..|||.||-.-+|.-.|+.++. .+|.|.+.+|=+-      +-.|||.|.+.++|.+-..+|++. +   +.+.
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDkI------KShCyV~yss~eEA~atr~AlhnV~WP~sNPK~  513 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDKI------KSHCYVSYSSVEEAAATREALHNVQWPPSNPKH  513 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHHHHHHh------hcceeEecccHHHHHHHHHHHhccccCCCCCce
Confidence            345567899999999999999999998 6777887754332      336999999999999999998854 2   5677


Q ss_pred             eEEEecc
Q 012923          201 TACQLAS  207 (453)
Q Consensus       201 ~~v~~~~  207 (453)
                      |.+.|..
T Consensus       514 L~adf~~  520 (718)
T KOG2416|consen  514 LIADFVR  520 (718)
T ss_pred             eEeeecc
Confidence            8777765

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=96.93  E-value=0.003  Score=63.63  Aligned_cols=7  Identities=29%  Similarity=0.306  Sum_probs=2.6

Q ss_pred             HHHHHHH
Q 012923          184 GARKALK  190 (453)
Q Consensus       184 ~a~~A~~  190 (453)
                      .+.+||+
T Consensus       211 eiIrClk  217 (1102)
T KOG1924|consen  211 EIIRCLK  217 (1102)
T ss_pred             HHHHHHH
Confidence            3333333

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.91  E-value=0.0064  Score=49.12  Aligned_cols=74  Identities=19%  Similarity=0.150  Sum_probs=53.0

Q ss_pred             cccEEEEecCC-----CCccH----HHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCe
Q 012923          246 TQRKIFVSNVG-----SELEP----QKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGH  316 (453)
Q Consensus       246 ~~~~l~V~nLp-----~~~t~----~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~  316 (453)
                      +..||.|.-+.     .....    .+|.+.|..||.|.-||++-+        .-+|+|.+-++|.+|+.....+++|+
T Consensus        26 pDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals~dg~~v~g~   97 (146)
T PF08952_consen   26 PDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALSLDGIQVNGR   97 (146)
T ss_dssp             TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHHGCCSEETTE
T ss_pred             CCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHccCCcEECCE
Confidence            33477777555     12223    366788999999998888755        37899999999999999988999999


Q ss_pred             EEEEEEccCCC
Q 012923          317 ILNCQRAIDGP  327 (453)
Q Consensus       317 ~l~v~~a~~~~  327 (453)
                      .|.|+...+..
T Consensus        98 ~l~i~LKtpdW  108 (146)
T PF08952_consen   98 TLKIRLKTPDW  108 (146)
T ss_dssp             EEEEEE-----
T ss_pred             EEEEEeCCccH
Confidence            99999986543

; PDB: 1UFW_A 2DNR_A.

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.74  E-value=0.00072  Score=59.15  Aligned_cols=62  Identities=21%  Similarity=0.337  Sum_probs=49.9

Q ss_pred             HHHHHHHh-ccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          262 QKLLAFFS-KYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       262 ~~l~~~F~-~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ++|...|+ +||.|+.+.|-.+. .-.-+|-+||.|...++|.+|+..|| .+|.|++|.+.+..
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            45555555 89999998765432 22338889999999999999999999 99999999998874

>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]

Probab=96.71  E-value=0.0089  Score=61.95  Aligned_cols=31  Identities=26%  Similarity=0.382  Sum_probs=24.2

Q ss_pred             cceEEEEEEccHHHHHHHHHcCCCccCCeEe
Q 012923          171 SKGYGFILFKTRSGARKALKEPQKKIGNRMT  201 (453)
Q Consensus       171 ~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~  201 (453)
                      -+||-||+=....++..||+-+.....++.+
T Consensus       209 lkGyIYIEA~KqshV~~Ai~gv~niy~~~~~  239 (1024)
T KOG1999|consen  209 LKGYIYIEADKQSHVKEAIEGVRNIYANRIL  239 (1024)
T ss_pred             cceeEEEEechhHHHHHHHhhhhhheeccEE
Confidence            5799999999999999999877654433333

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.71  E-value=0.013  Score=39.88  Aligned_cols=54  Identities=26%  Similarity=0.340  Sum_probs=44.6

Q ss_pred             cEEEEecCCCCccHHHHHHHHhcc---CCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcC
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKY---GEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP  309 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~---G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~  309 (453)
                      ..|+|+++ ..++.++|+.+|..|   ....+|.++-|.       -|-|.|.+.+.|.+||.+|
T Consensus         6 eavhirGv-d~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGV-DELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcC-CCCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            48999999 558888999999998   235578887774       3789999999999999875

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=96.62  E-value=0.012  Score=46.76  Aligned_cols=76  Identities=21%  Similarity=0.331  Sum_probs=60.5

Q ss_pred             CCCCCcCeEEEcCCCCCCC-HHH---HHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeE
Q 012923          125 DEDPVHRKIFVHGLGWDTK-AET---LIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRM  200 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~t-e~~---l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~  200 (453)
                      ..++.-.||.|+-|..++. .+|   |...++.||+|.+|.+.-       +--|.|.|.+..+|-+|+.+++....|..
T Consensus        81 ~kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG-------rqsavVvF~d~~SAC~Av~Af~s~~pgtm  153 (166)
T PF15023_consen   81 TKEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG-------RQSAVVVFKDITSACKAVSAFQSRAPGTM  153 (166)
T ss_pred             CCCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC-------CceEEEEehhhHHHHHHHHhhcCCCCCce
Confidence            4467778999998887774 334   445678899999996542       22599999999999999999999899999


Q ss_pred             eEEEecc
Q 012923          201 TACQLAS  207 (453)
Q Consensus       201 ~~v~~~~  207 (453)
                      +.+.|..
T Consensus       154 ~qCsWqq  160 (166)
T PF15023_consen  154 FQCSWQQ  160 (166)
T ss_pred             EEeeccc
Confidence            9998863

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.58  E-value=0.0068  Score=43.53  Aligned_cols=54  Identities=17%  Similarity=0.327  Sum_probs=40.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC
Q 012923          132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ  193 (453)
Q Consensus       132 ~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~  193 (453)
                      .||--.+|..+...||.++|+.||.|. |..+.|.       -|||.+.+.+.|..++..+.
T Consensus        10 HVFhltFPkeWK~~DI~qlFspfG~I~-VsWi~dT-------SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLTFPKEWKTSDIYQLFSPFGQIY-VSWINDT-------SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE--TT--HHHHHHHCCCCCCEE-EEEECTT-------EEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEeCchHhhhhhHHHHhccCCcEE-EEEEcCC-------cEEEEeecHHHHHHHHHHhc
Confidence            455444999999999999999999984 4445554       59999999999999998765

; 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.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=96.52  E-value=0.014  Score=46.47  Aligned_cols=71  Identities=18%  Similarity=0.307  Sum_probs=56.2

Q ss_pred             cccEEEEecCCCCc----cHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEE
Q 012923          246 TQRKIFVSNVGSEL----EPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQ  321 (453)
Q Consensus       246 ~~~~l~V~nLp~~~----t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~  321 (453)
                      +-.+|.|+=|..++    +...|...++.||.|.+|.+.-       +--|.|.|.+..+|.+|+.++....-|..+.+.
T Consensus        85 PMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG-------rqsavVvF~d~~SAC~Av~Af~s~~pgtm~qCs  157 (166)
T PF15023_consen   85 PMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG-------RQSAVVVFKDITSACKAVSAFQSRAPGTMFQCS  157 (166)
T ss_pred             CceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC-------CceEEEEehhhHHHHHHHHhhcCCCCCceEEee
Confidence            44588887665554    3445666788999999997742       345999999999999999999988889999998


Q ss_pred             Ec
Q 012923          322 RA  323 (453)
Q Consensus       322 ~a  323 (453)
                      |-
T Consensus       158 Wq  159 (166)
T PF15023_consen  158 WQ  159 (166)
T ss_pred             cc
Confidence            85

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.51  E-value=0.013  Score=47.38  Aligned_cols=76  Identities=21%  Similarity=0.278  Sum_probs=54.2

Q ss_pred             CCCCcCeEEEcCCC-----CCCCHH----HHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCcc
Q 012923          126 EDPVHRKIFVHGLG-----WDTKAE----TLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKI  196 (453)
Q Consensus       126 ~~~~~~~lfV~nLp-----~~~te~----~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~  196 (453)
                      -.|..-||.|.=+.     ...-.+    +|.+.|..||+|.-||++-+.        -+|+|.+-++|.+|+......+
T Consensus        23 ~GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~~--------mwVTF~dg~sALaals~dg~~v   94 (146)
T PF08952_consen   23 QGPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGDT--------MWVTFRDGQSALAALSLDGIQV   94 (146)
T ss_dssp             ---TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETTC--------EEEEESSCHHHHHHHHGCCSEE
T ss_pred             cCCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCCe--------EEEEECccHHHHHHHccCCcEE
Confidence            34555677777555     122222    677889999999988887764        8999999999999999999999


Q ss_pred             CCeEeEEEecccC
Q 012923          197 GNRMTACQLASIG  209 (453)
Q Consensus       197 ~gr~~~v~~~~~~  209 (453)
                      +|+.|.|.+....
T Consensus        95 ~g~~l~i~LKtpd  107 (146)
T PF08952_consen   95 NGRTLKIRLKTPD  107 (146)
T ss_dssp             TTEEEEEEE----
T ss_pred             CCEEEEEEeCCcc
Confidence            9999999987644

; PDB: 1UFW_A 2DNR_A.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.38  E-value=0.022  Score=38.82  Aligned_cols=53  Identities=19%  Similarity=0.285  Sum_probs=44.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcc----CCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcC
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQY----GEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP  192 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~----G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~  192 (453)
                      ..|+|++| -+++.++|+.+|..|    + ...|..+-|.       -|-|.|.+.+.|.+||..|
T Consensus         6 eavhirGv-d~lsT~dI~~y~~~y~~~~~-~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGV-DELSTDDIKAYFSEYFDEEG-PFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcC-CCCCHHHHHHHHHHhcccCC-CceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            47999999 457888999999999    4 4467777775       4899999999999999764

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.33  E-value=0.0017  Score=56.91  Aligned_cols=62  Identities=21%  Similarity=0.388  Sum_probs=49.9

Q ss_pred             HHHHHHHh-ccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecc
Q 012923          145 ETLIDAFK-QYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLAS  207 (453)
Q Consensus       145 ~~l~~~f~-~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~  207 (453)
                      ++|...|. +||+|++++|..+. .-.-+|-+||.|...++|++|++.|| ..+.|++|...+..
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            34455555 89999999766554 34567899999999999999999998 55899999998875

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.20  E-value=0.0033  Score=54.98  Aligned_cols=75  Identities=27%  Similarity=0.416  Sum_probs=63.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-----CccCCeEeEEEe
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-----KKIGNRMTACQL  205 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-----~~~~gr~~~v~~  205 (453)
                      ..|||.||+.-+..+.|...|+.||+|....++.|- .++..+-++|.|...-.|.+|+...+     ....++.+.|..
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~-r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP  110 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD-RGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEP  110 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc-cccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCCh
Confidence            579999999999999999999999999988777776 78888999999999999999998774     235666666654


Q ss_pred             c
Q 012923          206 A  206 (453)
Q Consensus       206 ~  206 (453)
                      .
T Consensus       111 ~  111 (275)
T KOG0115|consen  111 M  111 (275)
T ss_pred             h
Confidence            4

>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins

Probab=96.14  E-value=0.00091  Score=63.20  Aligned_cols=7  Identities=29%  Similarity=0.335  Sum_probs=3.6

Q ss_pred             cEEEEec
Q 012923          248 RKIFVSN  254 (453)
Q Consensus       248 ~~l~V~n  254 (453)
                      .|=||.+
T Consensus       192 STDFVCG  198 (458)
T PF10446_consen  192 STDFVCG  198 (458)
T ss_pred             cccccCC
Confidence            4556544

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=95.95  E-value=0.024  Score=40.77  Aligned_cols=54  Identities=17%  Similarity=0.235  Sum_probs=41.4

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH  310 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~  310 (453)
                      ...+|. +|..|-..+|.++|+.||.| .|..+-|.       -|||.+.+.+.|..|+..+.
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I-~VsWi~dT-------SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQI-YVSWINDT-------SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCE-EEEEECTT-------EEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcE-EEEEEcCC-------cEEEEeecHHHHHHHHHHhc
Confidence            356666 99999999999999999988 56666553       59999999999999888776

; 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.

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=95.86  E-value=0.023  Score=50.69  Aligned_cols=65  Identities=14%  Similarity=0.202  Sum_probs=51.3

Q ss_pred             HHHHHHHHhccCCeeEEEEcccCCCCCcc-eEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEeccc
Q 012923          144 AETLIDAFKQYGEIEDCKAVCDKVSGKSK-GYGFILFKTRSGARKALKEPQK-KIGNRMTACQLASI  208 (453)
Q Consensus       144 e~~l~~~f~~~G~i~~v~i~~d~~~g~~~-G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~~~~  208 (453)
                      ++++++-+.+||.|..|.|..++..-... --.||+|...++|.+|+-.||+ .|.||.+...+...
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~  366 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNL  366 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccH
Confidence            45788899999999999887775432222 2379999999999999999995 48899988777653

>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins

Probab=95.46  E-value=0.003  Score=59.78  Aligned_cols=6  Identities=0%  Similarity=0.030  Sum_probs=2.6

Q ss_pred             cCCCCc
Q 012923          254 NVGSEL  259 (453)
Q Consensus       254 nLp~~~  259 (453)
                      +||.+|
T Consensus       188 ~LPDST  193 (458)
T PF10446_consen  188 ELPDST  193 (458)
T ss_pred             CCCCcc
Confidence            344443

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=95.38  E-value=0.015  Score=54.40  Aligned_cols=74  Identities=16%  Similarity=0.324  Sum_probs=58.9

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC--CccCCeEEEEEEccC
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH--KNFEGHILNCQRAID  325 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~--~~l~g~~l~v~~a~~  325 (453)
                      ..||++||.+.++..+|..+|...-.-.+-.++..      .||+||.+.+...|.+|++.++  ..+.|.++.|.....
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 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            37999999999999999999986521112222222      7899999999999999999999  678999999988755


Q ss_pred             CC
Q 012923          326 GP  327 (453)
Q Consensus       326 ~~  327 (453)
                      +.
T Consensus        76 kk   77 (584)
T KOG2193|consen   76 KK   77 (584)
T ss_pred             HH
Confidence            43

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=94.80  E-value=0.76  Score=41.58  Aligned_cols=179  Identities=11%  Similarity=0.141  Sum_probs=105.1

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccC-------CCCCcceEEEEEEccHHHHHHHHH-------
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDK-------VSGKSKGYGFILFKTRSGARKALK-------  190 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~-------~~g~~~G~afV~f~~~~~a~~A~~-------  190 (453)
                      +++=..|.|.+.||..+++-..+...|-+||+|++|.++.+.       ..-+..-...+-|-+.+.|-....       
T Consensus        10 dD~YrTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLs   89 (309)
T PF10567_consen   10 DDEYRTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLS   89 (309)
T ss_pred             CccceeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHH
Confidence            344456889999999999999999999999999999998765       112334568999999988766542       


Q ss_pred             cCCCccCCeEeEEEecccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHH-HHHHH-
Q 012923          191 EPQKKIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQK-LLAFF-  268 (453)
Q Consensus       191 ~~~~~~~gr~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~-l~~~F-  268 (453)
                      ++...+.-..|.+.+....-...........+.   +...   ...-.-.-.....+++|.|- +...+..++ |.+.+ 
T Consensus        90 EfK~~L~S~~L~lsFV~l~y~~~~~~~~~~~~~---~~~~---~~~L~~~i~~~gATRSl~Ie-F~~~~~~~dl~~~kL~  162 (309)
T PF10567_consen   90 EFKTKLKSESLTLSFVSLNYQKKTDPNDEEADF---SDYL---VASLQYNIINRGATRSLAIE-FKDPVDKDDLIEKKLP  162 (309)
T ss_pred             HHHHhcCCcceeEEEEEEeccccccccccccch---hhHH---hhhhhheeecCCcceEEEEE-ecCccchhHHHHHhhh
Confidence            223446677777766543211110000000000   0000   00000011223345677775 334443333 33322 


Q ss_pred             --hccC----CcceeeeeccCCC--CCCceEEEEEECCHHHHHHHHHcCC
Q 012923          269 --SKYG----EIEEGPLGIDKAT--GKPKGFCLFVYKTVDAAKKALEEPH  310 (453)
Q Consensus       269 --~~~G----~i~~v~i~~d~~~--g~~kg~afV~F~~~~~A~~Al~~~~  310 (453)
                        ..-+    .|++|.|+.-...  .-++.||.++|-+..-|...+..+.
T Consensus       163 fL~~~~n~RYVlEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk  212 (309)
T PF10567_consen  163 FLKNSNNKRYVLESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLK  212 (309)
T ss_pred             hhccCCCceEEEEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHH
Confidence              2222    3667777653322  3357899999999999998888766

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>KOG4483 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.79  E-value=0.063  Score=50.09  Aligned_cols=65  Identities=23%  Similarity=0.226  Sum_probs=49.9

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCe-eEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeE
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEI-EDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRM  200 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i-~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~  200 (453)
                      -...|-|.++|.....+||...|+.|+.- -.|+.+-|.       .||-.|.+...|..||..-+.++.-|.
T Consensus       390 lpHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDdt-------halaVFss~~~AaeaLt~kh~~lKiRp  455 (528)
T KOG4483|consen  390 LPHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDDT-------HALAVFSSVNRAAEALTLKHDWLKIRP  455 (528)
T ss_pred             ccceeEeccCchhhccHHHHHHHHHhhcCCceeEEeecc-------eeEEeecchHHHHHHhhccCceEEeee
Confidence            45689999999999999999999999742 244444454       699999999999999987554443333

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=94.78  E-value=0.076  Score=51.80  Aligned_cols=95  Identities=15%  Similarity=0.219  Sum_probs=65.6

Q ss_pred             HHHHHHHHhcchhhhhhhc-ccCCCCCcCeEEEcCCCCCCCHHHHHHHHhc--cCCeeEEEEcccCCCCCcceEEEEEEc
Q 012923          104 NLLREAAENHRDVASRVRQ-VADEDPVHRKIFVHGLGWDTKAETLIDAFKQ--YGEIEDCKAVCDKVSGKSKGYGFILFK  180 (453)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~lfV~nLp~~~te~~l~~~f~~--~G~i~~v~i~~d~~~g~~~G~afV~f~  180 (453)
                      +++.+.......+....+- .-....+.|.|.|+-||.++..++|+.||+-  |-.+.+|.+-.+.       -=||+|.
T Consensus       148 dLI~Evlresp~VqvDekgekVrp~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfe  220 (684)
T KOG2591|consen  148 DLIVEVLRESPNVQVDEKGEKVRPNHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFE  220 (684)
T ss_pred             HHHHHHHhcCCCceeccCccccccCcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEee
Confidence            4455555444433322221 1122344577899999999999999999974  6678888766553       2699999


Q ss_pred             cHHHHHHHHHcCC---CccCCeEeEEEe
Q 012923          181 TRSGARKALKEPQ---KKIGNRMTACQL  205 (453)
Q Consensus       181 ~~~~a~~A~~~~~---~~~~gr~~~v~~  205 (453)
                      +..+|+.|.+.|.   ++|.|+.|...+
T Consensus       221 sd~DAQqAykylreevk~fqgKpImARI  248 (684)
T KOG2591|consen  221 SDTDAQQAYKYLREEVKTFQGKPIMARI  248 (684)
T ss_pred             cchhHHHHHHHHHHHHHhhcCcchhhhh
Confidence            9999999999877   457777765443

>KOG2236 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.72  E-value=0.81  Score=44.06  Aligned_cols=13  Identities=15%  Similarity=0.332  Sum_probs=7.9

Q ss_pred             EEEEEEccHHHHH
Q 012923          174 YGFILFKTRSGAR  186 (453)
Q Consensus       174 ~afV~f~~~~~a~  186 (453)
                      |-.|.|.+.+.+.
T Consensus       261 ~YvvRFnS~~e~~  273 (483)
T KOG2236|consen  261 YYVVRFNSEEEIS  273 (483)
T ss_pred             eEEEecCchhhhh
Confidence            5566666666554

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=94.50  E-value=0.03  Score=53.42  Aligned_cols=81  Identities=22%  Similarity=0.245  Sum_probs=65.8

Q ss_pred             CCCcCeEEEcCCCCCC-CHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDT-KAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~-te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~  205 (453)
                      ..+++.|-+.-+|+.. |-.+|...|.+||.|..|.|-...      -.|.|+|.+..+|-.|.....-.|.+|.|+|.|
T Consensus       369 ~~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~------~~a~vTF~t~aeag~a~~s~~avlnnr~iKl~w  442 (526)
T KOG2135|consen  369 VVDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSS------LHAVVTFKTRAEAGEAYASHGAVLNNRFIKLFW  442 (526)
T ss_pred             hcccchhhhhccCCCCchHhhhhhhhhhcCccccccccCch------hhheeeeeccccccchhccccceecCceeEEEE
Confidence            3556778888888776 567899999999999999765442      259999999999988888777889999999999


Q ss_pred             cccCCCCC
Q 012923          206 ASIGPATT  213 (453)
Q Consensus       206 ~~~~~~~~  213 (453)
                      ....+...
T Consensus       443 hnps~~tn  450 (526)
T KOG2135|consen  443 HNPSPVTN  450 (526)
T ss_pred             ecCCcccC
Confidence            88766443

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=94.37  E-value=0.055  Score=46.18  Aligned_cols=67  Identities=10%  Similarity=0.034  Sum_probs=42.3

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhc-cCCe---eEEEEccc-CCCC-CcceEEEEEEccHHHHHHHHHcCCCc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQ-YGEI---EDCKAVCD-KVSG-KSKGYGFILFKTRSGARKALKEPQKK  195 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~-~G~i---~~v~i~~d-~~~g-~~~G~afV~f~~~~~a~~A~~~~~~~  195 (453)
                      ...+|.||+||+++|++++.+.+.. ++..   ..+.-... .... ..-.-|||.|.+.+++...+..+++.
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~   78 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGH   78 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTE
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCc
Confidence            3468999999999999999987776 5554   23321111 1111 12245999999999999999888753

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.

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=94.18  E-value=0.016  Score=59.63  Aligned_cols=82  Identities=15%  Similarity=0.175  Sum_probs=63.9

Q ss_pred             ccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEE
Q 012923          241 QQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILN  319 (453)
Q Consensus       241 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~  319 (453)
                      ......+.+||++||+..+++.+|+..|..||.|..|.|-+-+ -+.-.-|+||.|.+.+.+-.|+..+. ..|..-.+.
T Consensus       366 ~DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r  444 (975)
T KOG0112|consen  366 LDDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHR  444 (975)
T ss_pred             ccchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCccc
Confidence            3445567899999999999999999999999999999885532 34445689999999999999998887 445433444


Q ss_pred             EEEc
Q 012923          320 CQRA  323 (453)
Q Consensus       320 v~~a  323 (453)
                      +.+.
T Consensus       445 ~glG  448 (975)
T KOG0112|consen  445 IGLG  448 (975)
T ss_pred             cccc
Confidence            4444

>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=94.09  E-value=0.1  Score=38.51  Aligned_cols=72  Identities=15%  Similarity=0.265  Sum_probs=47.7

Q ss_pred             EEEEEccHHHHHHHHHcCCCc--cCCeEeEEEecccCCCCCCCcCcccccccccccccccccccccccccccccccEEEE
Q 012923          175 GFILFKTRSGARKALKEPQKK--IGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFV  252 (453)
Q Consensus       175 afV~f~~~~~a~~A~~~~~~~--~~gr~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V  252 (453)
                      |+|+|.+..-|+..+++-.+.  +.+..+.|...........                       .-.-......++|.|
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~-----------------------k~qv~~~vs~rtVlv   57 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQ-----------------------KFQVFSGVSKRTVLV   57 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCce-----------------------EEEEEEcccCCEEEE
Confidence            789999999999999876643  5666666655421111100                       000123344579999


Q ss_pred             ecCCCCccHHHHHHHHh
Q 012923          253 SNVGSELEPQKLLAFFS  269 (453)
Q Consensus       253 ~nLp~~~t~~~l~~~F~  269 (453)
                      .|||....+++|++.++
T Consensus        58 sgip~~l~ee~l~D~Le   74 (88)
T PF07292_consen   58 SGIPDVLDEEELRDKLE   74 (88)
T ss_pred             eCCCCCCChhhheeeEE
Confidence            99999999999987543

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=93.96  E-value=0.043  Score=54.74  Aligned_cols=70  Identities=13%  Similarity=0.070  Sum_probs=61.3

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ....++||+|+.+.+..+-++.+...||.|.++..+.         |+|+.|..+..+..|+..++ ..++|..+.+...
T Consensus        38 ~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~d  108 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENVD  108 (668)
T ss_pred             CCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhccch
Confidence            3446999999999999999999999999998876543         89999999999999999999 8899988877653

>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=93.95  E-value=0.06  Score=45.97  Aligned_cols=79  Identities=9%  Similarity=-0.037  Sum_probs=46.8

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhc-cCCc---ceeeeeccCC-CC-CCceEEEEEECCHHHHHHHHHcCC-Ccc-CC---
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSK-YGEI---EEGPLGIDKA-TG-KPKGFCLFVYKTVDAAKKALEEPH-KNF-EG---  315 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~-~G~i---~~v~i~~d~~-~g-~~kg~afV~F~~~~~A~~Al~~~~-~~l-~g---  315 (453)
                      ..+|.||+||+.+|++++++.++. ++..   ..+.-..... .. .....|||.|.+.+++..-+..++ +.| +.   
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg~   86 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKGN   86 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS-
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCCC
Confidence            358999999999999999987776 5554   2333111111 11 124469999999999888888876 333 21   


Q ss_pred             -eEEEEEEccC
Q 012923          316 -HILNCQRAID  325 (453)
Q Consensus       316 -~~l~v~~a~~  325 (453)
                       .+..|.+|.-
T Consensus        87 ~~~~~VE~Apy   97 (176)
T PF03467_consen   87 EYPAVVEFAPY   97 (176)
T ss_dssp             EEEEEEEE-SS
T ss_pred             CcceeEEEcch
Confidence             3456666643

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 Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=93.67  E-value=0.24  Score=44.72  Aligned_cols=74  Identities=18%  Similarity=0.230  Sum_probs=56.1

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCC-eEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEG-HILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g-~~l~v~~a~~  325 (453)
                      ...|.|-++|..... .|..+|++||.|++....      ..-.|-+|.|.+.-+|.+||.+....|+| ..|-|..+.+
T Consensus       197 D~WVTVfGFppg~~s-~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALskng~ii~g~vmiGVkpCtD  269 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQVS-IVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALSKNGTIIDGDVMIGVKPCTD  269 (350)
T ss_pred             cceEEEeccCccchh-HHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhhhcCeeeccceEEeeeecCC
Confidence            456788888876554 466789999999887553      22458999999999999999998877777 4466777665


Q ss_pred             CC
Q 012923          326 GP  327 (453)
Q Consensus       326 ~~  327 (453)
                      +.
T Consensus       270 ks  271 (350)
T KOG4285|consen  270 KS  271 (350)
T ss_pred             HH
Confidence            53

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=93.67  E-value=0.092  Score=51.24  Aligned_cols=69  Identities=10%  Similarity=0.160  Sum_probs=57.3

Q ss_pred             cEEEEecCCCCccHHHHHHHHhc--cCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC---CccCCeEEEEEE
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSK--YGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH---KNFEGHILNCQR  322 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~--~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~---~~l~g~~l~v~~  322 (453)
                      +.|+|+-||..+-.++|+.+|..  |-.+.+|.+....       -=||+|.+..||.+|.+.|.   .+|.|++|..++
T Consensus       176 cIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpImARI  248 (684)
T KOG2591|consen  176 CIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPIMARI  248 (684)
T ss_pred             eEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcchhhhh
Confidence            57788999999999999999974  6778888775542       25899999999999999987   689999887665


Q ss_pred             c
Q 012923          323 A  323 (453)
Q Consensus       323 a  323 (453)
                      .
T Consensus       249 K  249 (684)
T KOG2591|consen  249 K  249 (684)
T ss_pred             h
Confidence            4

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=93.41  E-value=0.028  Score=51.60  Aligned_cols=79  Identities=15%  Similarity=0.305  Sum_probs=59.4

Q ss_pred             cEEEEecCCCCccHHHHH---HHHhccCCcceeeeeccCC--CCC-CceEEEEEECCHHHHHHHHHcCC-CccCCeEEEE
Q 012923          248 RKIFVSNVGSELEPQKLL---AFFSKYGEIEEGPLGIDKA--TGK-PKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNC  320 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~---~~F~~~G~i~~v~i~~d~~--~g~-~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v  320 (453)
                      +-+||-+|+..+..+.+.   +.|.+||.|..|.+.++..  .+. ...-++|+|...++|..||...+ ..++|+.|++
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            467888888776555543   5899999999999988762  111 11128999999999999999999 7788888777


Q ss_pred             EEccCC
Q 012923          321 QRAIDG  326 (453)
Q Consensus       321 ~~a~~~  326 (453)
                      .+...+
T Consensus       158 ~~gttk  163 (327)
T KOG2068|consen  158 SLGTTK  163 (327)
T ss_pred             hhCCCc
Confidence            766543

>COG5180 PBP1 Protein interacting with poly(A)-binding protein [RNA processing and modification]

Probab=93.01  E-value=0.22  Score=47.61  Aligned_cols=13  Identities=15%  Similarity=0.286  Sum_probs=6.3

Q ss_pred             EEccHHHHHHHHH
Q 012923          178 LFKTRSGARKALK  190 (453)
Q Consensus       178 ~f~~~~~a~~A~~  190 (453)
                      .|.+..+....|.
T Consensus       329 ~~Ds~K~~lEv~k  341 (654)
T COG5180         329 KFDSSKNLLEVIK  341 (654)
T ss_pred             cccchhHHHHHHH
Confidence            3555544444444

>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]

Probab=92.66  E-value=0.55  Score=49.36  Aligned_cols=22  Identities=23%  Similarity=0.317  Sum_probs=11.6

Q ss_pred             ceEEEEEECCHHHHHHHHHcCC
Q 012923          289 KGFCLFVYKTVDAAKKALEEPH  310 (453)
Q Consensus       289 kg~afV~F~~~~~A~~Al~~~~  310 (453)
                      +||.||+=....++..||+.+.
T Consensus       210 kGyIYIEA~KqshV~~Ai~gv~  231 (1024)
T KOG1999|consen  210 KGYIYIEADKQSHVKEAIEGVR  231 (1024)
T ss_pred             ceeEEEEechhHHHHHHHhhhh
Confidence            5555555555555555555443

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=92.60  E-value=0.079  Score=50.71  Aligned_cols=74  Identities=16%  Similarity=0.193  Sum_probs=58.0

Q ss_pred             cEEEEecCCCCc-cHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEccCC
Q 012923          248 RKIFVSNVGSEL-EPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAIDG  326 (453)
Q Consensus       248 ~~l~V~nLp~~~-t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a~~~  326 (453)
                      +.|-+.-.|+.+ |-.+|-..|.+||.|..|.|-..      .--|.|+|.+..+|-.|-......|++|.|+|.|....
T Consensus       373 s~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~s~~avlnnr~iKl~whnps  446 (526)
T KOG2135|consen  373 SPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYASHGAVLNNRFIKLFWHNPS  446 (526)
T ss_pred             chhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhccccceecCceeEEEEecCC
Confidence            444455455553 66889999999999999987432      23589999999999888877778899999999999764


Q ss_pred             C
Q 012923          327 P  327 (453)
Q Consensus       327 ~  327 (453)
                      +
T Consensus       447 ~  447 (526)
T KOG2135|consen  447 P  447 (526)
T ss_pred             c
Confidence            4

>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production []

Probab=92.43  E-value=0.065  Score=57.47  Aligned_cols=13  Identities=23%  Similarity=0.534  Sum_probs=9.4

Q ss_pred             CHHHHHHHHhccC
Q 012923          143 KAETLIDAFKQYG  155 (453)
Q Consensus       143 te~~l~~~f~~~G  155 (453)
                      |-++|..++..+-
T Consensus       427 s~eel~~lL~~~~  439 (840)
T PF04147_consen  427 SHEELLELLDGYS  439 (840)
T ss_pred             CHHHHHHHHhcCC
Confidence            5678888887654

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=92.41  E-value=0.46  Score=42.96  Aligned_cols=71  Identities=17%  Similarity=0.260  Sum_probs=52.3

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEe-EEEecc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMT-ACQLAS  207 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~-~v~~~~  207 (453)
                      ..=|-|-++|+..+- -|..+|++||.|......      .+-.+-+|.|.+.-+|++||......|.+..+ -|..+.
T Consensus       197 D~WVTVfGFppg~~s-~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALskng~ii~g~vmiGVkpCt  268 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQVS-IVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALSKNGTIIDGDVMIGVKPCT  268 (350)
T ss_pred             cceEEEeccCccchh-HHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhhhcCeeeccceEEeeeecC
Confidence            456888888877654 567899999999876422      23348999999999999999998777766543 344443

>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]

Probab=92.33  E-value=1.6  Score=40.33  Aligned_cols=13  Identities=0%  Similarity=-0.291  Sum_probs=5.4

Q ss_pred             EEEcCCCCCCCHH
Q 012923          133 IFVHGLGWDTKAE  145 (453)
Q Consensus       133 lfV~nLp~~~te~  145 (453)
                      |-+...|.++++-
T Consensus       152 L~~~k~p~Nin~~  164 (465)
T KOG3973|consen  152 LNFPKQPGNINEW  164 (465)
T ss_pred             cCCCCCCCCchHH
Confidence            3333344444443

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=91.65  E-value=1.5  Score=34.16  Aligned_cols=62  Identities=16%  Similarity=0.135  Sum_probs=44.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccC-CeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc
Q 012923          132 KIFVHGLGWDTKAETLIDAFKQYG-EIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK  195 (453)
Q Consensus       132 ~lfV~nLp~~~te~~l~~~f~~~G-~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~  195 (453)
                      .+-+...|+.++-++|..+.+.+- .|..++|++|..  .++=.++|.|.+.++|.......|++
T Consensus        15 ~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~fNGk   77 (110)
T PF07576_consen   15 LCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEEFNGK   77 (110)
T ss_pred             EEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHHhCCC
Confidence            344444455555666766666554 477889998753  35557999999999999999998854

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=91.22  E-value=0.21  Score=46.04  Aligned_cols=77  Identities=21%  Similarity=0.330  Sum_probs=56.2

Q ss_pred             CeEEEcCCCCCCCHHHHH---HHHhccCCeeEEEEcccCC--CCC-cceEEEEEEccHHHHHHHHHcCCCc-cCCeEeEE
Q 012923          131 RKIFVHGLGWDTKAETLI---DAFKQYGEIEDCKAVCDKV--SGK-SKGYGFILFKTRSGARKALKEPQKK-IGNRMTAC  203 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~---~~f~~~G~i~~v~i~~d~~--~g~-~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~~~v  203 (453)
                      .-+||-+|+...-.+.+.   ++|.+||.|..|.+..++.  .+. ..--++|+|...++|..||...++. +.|+.++.
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            457888898777655544   6899999999998887762  110 1113899999999999999998865 67777665


Q ss_pred             Eecc
Q 012923          204 QLAS  207 (453)
Q Consensus       204 ~~~~  207 (453)
                      .+..
T Consensus       158 ~~gt  161 (327)
T KOG2068|consen  158 SLGT  161 (327)
T ss_pred             hhCC
Confidence            5543

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=91.21  E-value=0.13  Score=51.49  Aligned_cols=160  Identities=14%  Similarity=0.085  Sum_probs=94.1

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v  203 (453)
                      ...+...+|||+||...+..+-++.+...||.|.+++.+.         |+|+.|..+.....|+..+.. .+.+..+.+
T Consensus        35 ~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~  105 (668)
T KOG2253|consen   35 QPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIE  105 (668)
T ss_pred             cCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhc
Confidence            3445567999999999999999999999999998876543         999999999999999998884 466777666


Q ss_pred             EecccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccC
Q 012923          204 QLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDK  283 (453)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~  283 (453)
                      ..-...-..........              ......-......+-++|.|++..+.+......|.-.+.+.....+.+.
T Consensus       106 ~~d~q~~~n~~k~~~~~--------------~~~~~~f~p~~srr~e~i~~k~~~l~~~~~~~~~~is~s~~s~~~~~e~  171 (668)
T KOG2253|consen  106 NVDEQTIENADKEKSIA--------------NKESHKFVPSSSRRQESIQNKPLSLDEQIHKKSLQISSSAASRRQIAEA  171 (668)
T ss_pred             cchhhhhcCccccccch--------------hhhhcccCCchhHHHHHhhccccchhHHHHHHHHhccchhhhhhhhHHH
Confidence            55211000000000000              0000000011114567888888887777777666654444433332221


Q ss_pred             CCCCCceEEEEEECCHHHHHHHHHc
Q 012923          284 ATGKPKGFCLFVYKTVDAAKKALEE  308 (453)
Q Consensus       284 ~~g~~kg~afV~F~~~~~A~~Al~~  308 (453)
                       ....+-++|-+|.+......++..
T Consensus       172 -d~h~~e~~~~~~~s~~~~~~~~~~  195 (668)
T KOG2253|consen  172 -DDHCLELEKTETESNSALSKEAES  195 (668)
T ss_pred             -HHHHHHHHHhhcccccccCccccc
Confidence             122233445455444444333333

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=90.76  E-value=0.76  Score=39.41  Aligned_cols=60  Identities=18%  Similarity=0.149  Sum_probs=43.6

Q ss_pred             cHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC---CccCCeEEEEEEccC
Q 012923          260 EPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH---KNFEGHILNCQRAID  325 (453)
Q Consensus       260 t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~---~~l~g~~l~v~~a~~  325 (453)
                      ....|+.+|..|+.+..+.+++.      =+-..|.|.+.++|.+|...++   ..|.|..|+|.++..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            45789999999999998887764      2347899999999999999988   468999999998843

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=90.10  E-value=0.19  Score=51.67  Aligned_cols=74  Identities=23%  Similarity=0.239  Sum_probs=60.7

Q ss_pred             EEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-C--ccCCeEEEEEEccC
Q 012923          249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-K--NFEGHILNCQRAID  325 (453)
Q Consensus       249 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~--~l~g~~l~v~~a~~  325 (453)
                      +..+-|.+-..+-..|..+|+.||.|.+++.+++      -..|.|+|.+.+.|..|+.++. +  ..-|-+.+|.+++.
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~------~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~  373 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRD------LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheeccc------ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            3444555667788889999999999999999887      4469999999999999999998 3  45788899999876


Q ss_pred             CCC
Q 012923          326 GPK  328 (453)
Q Consensus       326 ~~~  328 (453)
                      -+.
T Consensus       374 ~~~  376 (1007)
T KOG4574|consen  374 LPM  376 (1007)
T ss_pred             ccc
Confidence            654

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=89.96  E-value=0.94  Score=43.43  Aligned_cols=64  Identities=16%  Similarity=0.183  Sum_probs=55.0

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccC-CeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYG-EIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK  195 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G-~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~  195 (453)
                      ++.|+|-.+|..+|-.||..|+..|- .|..++|++|...  ++=.++|.|.+.++|....+.+|+.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~p--nrymvLIkFr~q~da~~Fy~efNGk  138 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMP--NRYMVLIKFRDQADADTFYEEFNGK  138 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCC--ceEEEEEEeccchhHHHHHHHcCCC
Confidence            78999999999999999999998765 5889999997532  3446899999999999999999854

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=89.53  E-value=3.1  Score=32.37  Aligned_cols=65  Identities=18%  Similarity=0.156  Sum_probs=47.6

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccC-CcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccC
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYG-EIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFE  314 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G-~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~  314 (453)
                      ..+.+...|+.++-+.|..+.+.+- .|..++|++|.  ..++-.+.++|.+.++|..=....| ..|+
T Consensus        14 ~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   14 TLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             eEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            4555566667777778877777664 46678888863  2346668999999999999999988 5443

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=88.82  E-value=2.3  Score=42.29  Aligned_cols=77  Identities=19%  Similarity=0.303  Sum_probs=53.3

Q ss_pred             CcCeEEEcCCCCC-CCHHHHHHHHhcc----CCeeEEEEcccC----------CCCC-----------------------
Q 012923          129 VHRKIFVHGLGWD-TKAETLIDAFKQY----GEIEDCKAVCDK----------VSGK-----------------------  170 (453)
Q Consensus       129 ~~~~lfV~nLp~~-~te~~l~~~f~~~----G~i~~v~i~~d~----------~~g~-----------------------  170 (453)
                      .+++|-|.||.|+ +...||.-+|..|    |.|.+|.|+...          .+|.                       
T Consensus       173 ~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~~~  252 (650)
T KOG2318|consen  173 ETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEEED  252 (650)
T ss_pred             ccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhhhh
Confidence            4579999999975 5678999888765    478888874210          0111                       


Q ss_pred             --------------cceEEEEEEccHHHHHHHHHcCCCc-cC--CeEeEEEe
Q 012923          171 --------------SKGYGFILFKTRSGARKALKEPQKK-IG--NRMTACQL  205 (453)
Q Consensus       171 --------------~~G~afV~f~~~~~a~~A~~~~~~~-~~--gr~~~v~~  205 (453)
                                    ..=||.|+|.+++.|.+..+.+.+. +.  +..|.+.+
T Consensus       253 ~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRF  304 (650)
T KOG2318|consen  253 VDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRF  304 (650)
T ss_pred             HHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeee
Confidence                          1127999999999999999988754 43  33444443

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=88.32  E-value=0.42  Score=49.29  Aligned_cols=82  Identities=18%  Similarity=0.238  Sum_probs=67.2

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc---cCCeEeEEE
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK---IGNRMTACQ  204 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~---~~gr~~~v~  204 (453)
                      +..-+.++-|.+-..+-.-|..+|.+||.|.++|.+++-.      .|.|.|.+.+.|..|+.+++++   +.|-+.+|.
T Consensus       296 plqp~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N------~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~  369 (1007)
T KOG4574|consen  296 PLQPKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLN------MALVSFSSVESAILALDALQGKEVSVTGAPSRVS  369 (1007)
T ss_pred             cCcchhhhhcccccchHHHHHHHHHhhcchhhheeccccc------chhhhhHHHHHHHHhhhhhcCCcccccCCceeEE
Confidence            3445677778888889999999999999999999888763      6999999999999999999854   678888888


Q ss_pred             ecccCCCCCCC
Q 012923          205 LASIGPATTPA  215 (453)
Q Consensus       205 ~~~~~~~~~~~  215 (453)
                      ++..-+....+
T Consensus       370 ~ak~~~~~ep~  380 (1007)
T KOG4574|consen  370 FAKTLPMYEPP  380 (1007)
T ss_pred             eccccccccCC
Confidence            88755554433

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=85.87  E-value=2.9  Score=35.91  Aligned_cols=59  Identities=10%  Similarity=0.104  Sum_probs=43.0

Q ss_pred             CHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC--Cc-cCCeEeEEEecc
Q 012923          143 KAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ--KK-IGNRMTACQLAS  207 (453)
Q Consensus       143 te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~--~~-~~gr~~~v~~~~  207 (453)
                      ....|+++|..|+.+..+.+++.-      +-..|.|.+.+.|.+|...++  .. +.|..++|.++.
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sF------rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~   69 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSF------RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQ   69 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTT------TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE---
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCC------CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcc
Confidence            357899999999998888766543      248999999999999999988  44 899999998884

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=85.54  E-value=2.7  Score=30.07  Aligned_cols=58  Identities=21%  Similarity=0.322  Sum_probs=33.7

Q ss_pred             CCccHHHHHHHHhccCCc-----ceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          257 SELEPQKLLAFFSKYGEI-----EEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       257 ~~~t~~~l~~~F~~~G~i-----~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ..++..+|..++...+.|     -.|+|.        ..|+||+-.. +.|..++..++ ..+.|++|.|+.|
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~--------~~~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIF--------DNFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE---------SS-EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEe--------eeEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            457788888888766544     456664        3389998764 47888999988 8899999999875

; PDB: 2G0C_A 3MOJ_B.

>COG5180 PBP1 Protein interacting with poly(A)-binding protein [RNA processing and modification]

Probab=85.50  E-value=6.3  Score=38.13  Aligned_cols=21  Identities=14%  Similarity=0.097  Sum_probs=8.5

Q ss_pred             CCCCCCCcccccccCchhhhh
Q 012923          367 PSGPAIPPAAAQALNPALGQA  387 (453)
Q Consensus       367 p~~~~~~p~~~~~~~p~~~~~  387 (453)
                      |.++.++......|+|.+.|+
T Consensus       537 P~M~~~~~G~~~~Y~P~~PQ~  557 (654)
T COG5180         537 PMMNGFAAGSMGMYMPFQPQP  557 (654)
T ss_pred             CCcCCcccCCcccccCCCCCc
Confidence            333333333334444444443

>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]

Probab=85.42  E-value=0.4  Score=48.68  Aligned_cols=25  Identities=12%  Similarity=0.115  Sum_probs=13.0

Q ss_pred             EEEEEECCHHHHHHHHHcCC-CccCC
Q 012923          291 FCLFVYKTVDAAKKALEEPH-KNFEG  315 (453)
Q Consensus       291 ~afV~F~~~~~A~~Al~~~~-~~l~g  315 (453)
                      -.||...+.++-..|++.+- ..|.|
T Consensus       623 ~IFcsImsaeDyiDAFEklLkL~LK~  648 (822)
T KOG2141|consen  623 AIFCSIMSAEDYIDAFEKLLKLSLKG  648 (822)
T ss_pred             hheeeeecchHHHHHHHHHHhccCCC
Confidence            34555555666555555543 33444

>KOG4594 consensus Sequence-specific single-stranded-DNA-binding protein [Replication, recombination and repair; Transcription; General function prediction only]

Probab=85.21  E-value=17  Score=32.92  Aligned_cols=8  Identities=50%  Similarity=0.904  Sum_probs=3.9

Q ss_pred             CCCCCCCC
Q 012923          444 GQYGAPYM  451 (453)
Q Consensus       444 g~~g~p~~  451 (453)
                      +..+.|+|
T Consensus       241 ~~pgtpim  248 (354)
T KOG4594|consen  241 GPPGTPIM  248 (354)
T ss_pred             CCCCCCcC
Confidence            44445555

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=83.90  E-value=5.1  Score=27.88  Aligned_cols=53  Identities=15%  Similarity=0.255  Sum_probs=39.1

Q ss_pred             CccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEE
Q 012923          258 ELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILN  319 (453)
Q Consensus       258 ~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~  319 (453)
                      .++-++|+..+..|.   ..+|..|+     .|| ||.|.+..+|.++....+ ..+....|.
T Consensus        11 ~~~v~d~K~~Lr~y~---~~~I~~d~-----tGf-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~   64 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYR---WDRIRDDR-----TGF-YIVFNDSKEAERCFRAEDGTLFFTYRMQ   64 (66)
T ss_pred             CccHHHHHHHHhcCC---cceEEecC-----CEE-EEEECChHHHHHHHHhcCCCEEEEEEEE
Confidence            467889999999985   33344443     453 789999999999999988 555555543

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=82.97  E-value=4.4  Score=39.11  Aligned_cols=67  Identities=18%  Similarity=0.251  Sum_probs=54.4

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccC-CcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYG-EIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEG  315 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G-~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g  315 (453)
                      .+.|+|-.+|..+|-.+|..|+..|- .|..|+|+||..  ..+=.+.|+|.+..+|..-...+| ..|+.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~--pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGM--PNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCC--CceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            56899999999999999999988764 488999999632  224448899999999999999988 55543

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=80.58  E-value=6.7  Score=27.27  Aligned_cols=47  Identities=15%  Similarity=0.309  Sum_probs=36.3

Q ss_pred             CCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc
Q 012923          140 WDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK  195 (453)
Q Consensus       140 ~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~  195 (453)
                      ..++-.+|+..+..|.-   .+|+.|+ +    | =||.|.+..+|++|....++.
T Consensus        10 ~~~~v~d~K~~Lr~y~~---~~I~~d~-t----G-fYIvF~~~~Ea~rC~~~~~~~   56 (66)
T PF11767_consen   10 HGVTVEDFKKRLRKYRW---DRIRDDR-T----G-FYIVFNDSKEAERCFRAEDGT   56 (66)
T ss_pred             CCccHHHHHHHHhcCCc---ceEEecC-C----E-EEEEECChHHHHHHHHhcCCC
Confidence            45677899999999953   3445555 3    3 489999999999999988854

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG0262 consensus RNA polymerase I, large subunit [Transcription]

Probab=80.16  E-value=5.2  Score=43.65  Aligned_cols=23  Identities=9%  Similarity=0.096  Sum_probs=13.4

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQ  153 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~  153 (453)
                      -++|-+. ||.....-+|..+..+
T Consensus      1442 wcev~~~-lp~~~~k~~mssiVe~ 1464 (1640)
T KOG0262|consen 1442 WCEVELK-LPLDKEKLDMSSIVES 1464 (1640)
T ss_pred             EEEEEEE-ecCCCcchHHHHHHHH
Confidence            3445544 7777666666665543

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=80.12  E-value=6.8  Score=27.93  Aligned_cols=58  Identities=17%  Similarity=0.198  Sum_probs=34.0

Q ss_pred             CCCCHHHHHHHHhccC-----CeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          140 WDTKAETLIDAFKQYG-----EIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       140 ~~~te~~l~~~f~~~G-----~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ..++..+|..++...+     .|-.|+|..+        |+||+-... .|..++..++ ..+.|+.+.|..+
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            5677889999888765     3556766554        799987765 6778888777 5699999999764

; PDB: 2G0C_A 3MOJ_B.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	453
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		2e-14
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		1e-13
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		8e-04
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-13
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		7e-04
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		1e-13
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		7e-04
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		1e-13
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		7e-04
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		1e-13
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		8e-04
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		2e-13
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		6e-10
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		2e-04
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		7e-10
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		9e-04
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		1e-09
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		2e-04
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		3e-08
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		3e-08
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		8e-08
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		2e-06
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		3e-06
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		3e-06
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		4e-06
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		5e-06
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		5e-06
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		8e-06
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		1e-05
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		2e-05
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		2e-05
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		2e-05
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		2e-05
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		2e-05
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		5e-05
1wtb_A	79	Complex Structure Of The C-Terminal Rna-Binding Dom		8e-05
1x4e_A	85	Solution Structure Of Rrm Domain In Rna Binding Mot		1e-04
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		2e-04
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		2e-04
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		2e-04
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		2e-04
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		3e-04
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		3e-04
1iqt_A	75	Solution Structure Of The C-Terminal Rna-Binding Do		4e-04

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 77.4 bits (189), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 48/192 (25%), Positives = 86/192 (44%), Gaps = 33/192 (17%)
Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K+F+ GL WDT  + L + F +YG + D K + D  +G+S+G+GF+ F+  S   + +K 
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK- 63
Query: 192 PQKKIGNRMTACQLASIGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSEYTQRKIF 251
            Q  +  ++   + A                                     +    KIF
Sbjct: 64  TQHILDGKVIDPKRA--------------------------------IPRDEQDKTGKIF 91
Query: 252 VSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHK 311
           V  +G ++ P++   FFS++G I +  L +DK TG+ +GF    Y + DA  +  +    
Sbjct: 92  VGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFI 151
Query: 312 NFEGHILNCQRA 323
           +F+   +  +RA
Sbjct: 152 DFKDRKIEIKRA 163

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 74.3 bits (181), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 46/191 (24%), Positives = 82/191 (42%), Gaps = 28/191 (14%)
Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           RK+F+ GL ++T  E+L   F+Q+G + DC  + D  + +S+G+GF+ + T      A+ 
Sbjct: 14  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 191 EPQKKIGNRMTACQLASIGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSEYTQRKI 250
               K+  R+   + A                                    +  T +KI
Sbjct: 74  ARPHKVDGRVVEPKRA--------------------------VSREDSQRPGAHLTVKKI 107
Query: 251 FVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH 310
           FV  +  + E   L  +F +YG+IE   +  D+ +GK +GF    +   D+  K + + +
Sbjct: 108 FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKY 167
Query: 311 KNFEGHILNCQ 321
               GH  NC+
Sbjct: 168 HTVNGH--NCE 176

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 41.6 bits (96), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/87 (27%), Positives = 44/87 (50%), Gaps = 5/87 (5%)
Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           RK+F+  +  E   + L + F ++G + +  +  D  T + +GF    Y TV+    A+ 
Sbjct: 14  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 308 -EPHKNFEGHILNCQRAI---DGPKPG 330
             PHK  +G ++  +RA+   D  +PG
Sbjct: 74  ARPHK-VDGRVVEPKRAVSREDSQRPG 99

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 74.3 bits (181), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 46/191 (24%), Positives = 82/191 (42%), Gaps = 28/191 (14%)
Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           RK+F+ GL ++T  E+L   F+Q+G + DC  + D  + +S+G+GF+ + T      A+ 
Sbjct: 14  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 191 EPQKKIGNRMTACQLASIGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSEYTQRKI 250
               K+  R+   + A                                    +  T +KI
Sbjct: 74  ARPHKVDGRVVEPKRA--------------------------VSREDSQRPGAHLTVKKI 107
Query: 251 FVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH 310
           FV  +  + E   L  +F +YG+IE   +  D+ +GK +GF    +   D+  K + + +
Sbjct: 108 FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKY 167
Query: 311 KNFEGHILNCQ 321
               GH  NC+
Sbjct: 168 HTVNGH--NCE 176

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 42.0 bits (97), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 24/87 (27%), Positives = 44/87 (50%), Gaps = 5/87 (5%)
Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           RK+F+  +  E   + L + F ++G + +  +  D  T + +GF    Y TV+    A+ 
Sbjct: 14  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 308 -EPHKNFEGHILNCQRAI---DGPKPG 330
             PHK  +G ++  +RA+   D  +PG
Sbjct: 74  ARPHK-VDGRVVEPKRAVSREDSQRPG 99

>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 = 74.3 bits (181), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 46/191 (24%), Positives = 82/191 (42%), Gaps = 28/191 (14%)
Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           RK+F+ GL ++T  E+L   F+Q+G + DC  + D  + +S+G+GF+ + T      A+ 
Sbjct: 13  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
Query: 191 EPQKKIGNRMTACQLASIGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSEYTQRKI 250
               K+  R+   + A                                    +  T +KI
Sbjct: 73  ARPHKVDGRVVEPKRA--------------------------VSREDSQRPGAHLTVKKI 106
Query: 251 FVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH 310
           FV  +  + E   L  +F +YG+IE   +  D+ +GK +GF    +   D+  K + + +
Sbjct: 107 FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKY 166
Query: 311 KNFEGHILNCQ 321
               GH  NC+
Sbjct: 167 HTVNGH--NCE 175

>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 = 42.0 bits (97), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 24/87 (27%), Positives = 44/87 (50%), Gaps = 5/87 (5%)
Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           RK+F+  +  E   + L + F ++G + +  +  D  T + +GF    Y TV+    A+ 
Sbjct: 13  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
Query: 308 -EPHKNFEGHILNCQRAI---DGPKPG 330
             PHK  +G ++  +RA+   D  +PG
Sbjct: 73  ARPHK-VDGRVVEPKRAVSREDSQRPG 98

>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 = 74.3 bits (181), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 46/191 (24%), Positives = 82/191 (42%), Gaps = 28/191 (14%)
Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           RK+F+ GL ++T  E+L   F+Q+G + DC  + D  + +S+G+GF+ + T      A+ 
Sbjct: 15  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
Query: 191 EPQKKIGNRMTACQLASIGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSEYTQRKI 250
               K+  R+   + A                                    +  T +KI
Sbjct: 75  ARPHKVDGRVVEPKRA--------------------------VSREDSQRPGAHLTVKKI 108
Query: 251 FVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH 310
           FV  +  + E   L  +F +YG+IE   +  D+ +GK +GF    +   D+  K + + +
Sbjct: 109 FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKY 168
Query: 311 KNFEGHILNCQ 321
               GH  NC+
Sbjct: 169 HTVNGH--NCE 177

>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 = 42.0 bits (97), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 24/87 (27%), Positives = 44/87 (50%), Gaps = 5/87 (5%)
Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           RK+F+  +  E   + L + F ++G + +  +  D  T + +GF    Y TV+    A+ 
Sbjct: 15  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
Query: 308 -EPHKNFEGHILNCQRAI---DGPKPG 330
             PHK  +G ++  +RA+   D  +PG
Sbjct: 75  ARPHK-VDGRVVEPKRAVSREDSQRPG 100

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 73.9 bits (180), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 46/191 (24%), Positives = 82/191 (42%), Gaps = 28/191 (14%)
Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           RK+F+ GL ++T  E+L   F+Q+G + DC  + D  + +S+G+GF+ + T      A+ 
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 191 EPQKKIGNRMTACQLASIGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSEYTQRKI 250
               K+  R+   + A                                    +  T +KI
Sbjct: 67  ARPHKVDGRVVEPKRA--------------------------VSREDSQRPGAHLTVKKI 100
Query: 251 FVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH 310
           FV  +  + E   L  +F +YG+IE   +  D+ +GK +GF    +   D+  K + + +
Sbjct: 101 FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKY 160
Query: 311 KNFEGHILNCQ 321
               GH  NC+
Sbjct: 161 HTVNGH--NCE 169

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/87 (27%), Positives = 44/87 (50%), Gaps = 5/87 (5%)
Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           RK+F+  +  E   + L + F ++G + +  +  D  T + +GF    Y TV+    A+ 
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 308 -EPHKNFEGHILNCQRAI---DGPKPG 330
             PHK  +G ++  +RA+   D  +PG
Sbjct: 67  ARPHK-VDGRVVEPKRAVSREDSQRPG 92

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 73.9 bits (180), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 46/191 (24%), Positives = 82/191 (42%), Gaps = 28/191 (14%)
Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           RK+F+ GL ++T  E+L   F+Q+G + DC  + D  + +S+G+GF+ + T      A+ 
Sbjct: 12  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
Query: 191 EPQKKIGNRMTACQLASIGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSEYTQRKI 250
               K+  R+   + A                                    +  T +KI
Sbjct: 72  ARPHKVDGRVVEPKRA--------------------------VSREDSQRPGAHLTVKKI 105
Query: 251 FVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH 310
           FV  +  + E   L  +F +YG+IE   +  D+ +GK +GF    +   D+  K + + +
Sbjct: 106 FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKY 165
Query: 311 KNFEGHILNCQ 321
               GH  NC+
Sbjct: 166 HTVNGH--NCE 174

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 62.0 bits (149), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 24/68 (35%), Positives = 42/68 (61%)
Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           +F+ GL WDT  + L D F ++GE+ DC    D ++G+S+G+GF+LFK      K + + 
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 193 QKKIGNRM 200
           + K+  ++
Sbjct: 62  EHKLNGKV 69

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 18/74 (24%), Positives = 41/74 (55%)
Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP 309
           +F+  +  +   + L  +FSK+GE+ +  L +D  TG+ +GF   ++K  ++  K +++ 
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 310 HKNFEGHILNCQRA 323
                G +++ +RA
Sbjct: 62  EHKLNGKVIDPKRA 75

>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 = 62.0 bits (149), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 28/69 (40%), Positives = 42/69 (60%)
Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K FV GL WDT  + L D F ++GE+ DC    D  +G+S+G+GFILFK  +   K L +
Sbjct: 13  KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 192 PQKKIGNRM 200
            + ++  R+
Sbjct: 73  KEHRLDGRV 81

>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 = 41.6 bits (96), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 18/75 (24%), Positives = 41/75 (54%)
Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           K FV  +  +   + L  +F+K+GE+ +  +  D  TG+ +GF   ++K   + +K L++
Sbjct: 13  KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 309 PHKNFEGHILNCQRA 323
                +G +++ ++A
Sbjct: 73  KEHRLDGRVIDPKKA 87

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 61.2 bits (147), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 31/84 (36%), Positives = 47/84 (55%)
Query: 126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGA 185
           +D    KIFV GL + T   +L   F+ +G+IE+   + D+ +GKS+GYGF+    R+ A
Sbjct: 13  KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
Query: 186 RKALKEPQKKIGNRMTACQLASIG 209
            +A K+P   I  R     LA +G
Sbjct: 73  ERACKDPNPIIDGRKANVNLAYLG 96

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 26/84 (30%), Positives = 40/84 (47%)
Query: 246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKA 305
           T  KIFV  +        L  +F  +G+IEE  +  D+ TGK +G+         AA++A
Sbjct: 16  TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75
Query: 306 LEEPHKNFEGHILNCQRAIDGPKP 329
            ++P+   +G   N   A  G KP
Sbjct: 76  CKDPNPIIDGRKANVNLAYLGAKP 99

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 56.6 bits (135), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 25/49 (51%), Positives = 33/49 (67%)
Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFK 180
           K+FV GL W T  ETL   F QYGE+ DC  + DK + +S+G+GF+ FK
Sbjct: 18  KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFK 66

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 56.6 bits (135), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 23/75 (30%), Positives = 47/75 (62%)
Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K+F+ GL W T  E L + F Q+GE+++C  + D ++ +S+G+GF+ F  ++G  K L +
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 192 PQKKIGNRMTACQLA 206
            + ++ ++    ++A
Sbjct: 62  SRHELDSKTIDPKVA 76

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 55.1 bits (131), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 23/75 (30%), Positives = 47/75 (62%)
Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K+F+ GL W T  E L + F Q+GE+++C  + D ++ +S+G+GF+ F  ++G  K L +
Sbjct: 27  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 192 PQKKIGNRMTACQLA 206
            + ++ ++    ++A
Sbjct: 87  SRHELDSKTIDPKVA 101

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 23/74 (31%), Positives = 42/74 (56%)
Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           IFV GL  +T  E +   F+Q+G+++D   + DK + + +G+GF+ F++     K  +  
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 193 QKKIGNRMTACQLA 206
             +I N+M  C+ A
Sbjct: 62  FHEINNKMVECKKA 75

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/70 (38%), Positives = 38/70 (54%), Gaps = 7/70 (10%)
Query: 127 DPVHRK-----IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKT 181
           DP  RK     IF+  L      + L D F  +G I  CK VCD+    SKGYGF+ F+T
Sbjct: 90  DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFET 147
Query: 182 RSGARKALKE 191
           +  A +A+++
Sbjct: 148 QEAAERAIEK 157

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/70 (38%), Positives = 38/70 (54%), Gaps = 7/70 (10%)
Query: 127 DPVHRK-----IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKT 181
           DP  RK     IF+  L      + L D F  +G I  CK VCD+    SKGYGF+ F+T
Sbjct: 95  DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFET 152
Query: 182 RSGARKALKE 191
           +  A +A+++
Sbjct: 153 QEAAERAIEK 162

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 24/68 (35%), Positives = 40/68 (58%)
Query: 122 QVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKT 181
           Q+  E  V R + V+ +        L   F++YG IE  K VCD+ + +S+GYGF+ F++
Sbjct: 34  QMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQS 93
Query: 182 RSGARKAL 189
            S A++A+
Sbjct: 94  GSSAQQAI 101

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 22/70 (31%), Positives = 42/70 (60%)
Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           RK+F+ GL ++T  E+L + ++Q+G++ DC  + D  S +S+G+GF+ F + +    A+ 
Sbjct: 28  RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 191 EPQKKIGNRM 200
                I  R+
Sbjct: 88  ARPHSIDGRV 97

>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 = 49.3 bits (116), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 39/204 (19%), Positives = 83/204 (40%), Gaps = 25/204 (12%)
Query: 129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKA 188
           +  +++V  + ++   +T+  AF  +G I+      D V+ K KG+ F+ ++    A+ A
Sbjct: 27  IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLA 86
Query: 189 LKEPQKKI--GNRMTACQLASIGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSEYT 246
           L++    +  G  +   + ++IG                                     
Sbjct: 87  LEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF--------------------- 125
Query: 247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKAL 306
             +I+V++V  +L    + + F  +G+I+   L  D  TGK KG+    Y+   +++ A+
Sbjct: 126 -NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAV 184
Query: 307 EEPHK-NFEGHILNCQRAIDGPKP 329
              +  +  G  L   +A+  P P
Sbjct: 185 SSMNLFDLGGQYLRVGKAVTPPMP 208

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 48.5 bits (114), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 27/70 (38%), Positives = 38/70 (54%), Gaps = 7/70 (10%)
Query: 127 DPVHRK-----IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKT 181
           DP  RK     IF+  L      + L D F  +G I  CK VCD+    SKGYGF+ F+T
Sbjct: 3   DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFET 60
Query: 182 RSGARKALKE 191
           +  A +A+++
Sbjct: 61  QEAAERAIEK 70

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 21/58 (36%), Positives = 37/58 (63%)
Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           K+FV GL +DT  ++L   F +YG+I +   V D+ + +S+G+GF+ F+    A+ A+
Sbjct: 14  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 71

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 43/217 (19%), Positives = 89/217 (41%), Gaps = 29/217 (13%)
Query: 116 VASRVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYG 175
           +A R R +A    +  +++V  + ++   +T+  AF  +G I+      D V+ K KG+ 
Sbjct: 3   MAQRQRALA----IMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFA 58
Query: 176 FILFKTRSGARKALKEPQKKI--GNRMTACQLASIGXXXXXXXXXXXXXXXXXXXXXXXX 233
           F+ ++    A+ AL++    +  G  +   + ++IG                        
Sbjct: 59  FVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF-------- 110
Query: 234 XXXXXXXXXSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCL 293
                          +I+V++V  +L    + + F  +G+I+   L  D  TGK KG+  
Sbjct: 111 --------------NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGF 156
Query: 294 FVYKTVDAAKKALEEPHK-NFEGHILNCQRAIDGPKP 329
             Y+   +++ A+   +  +  G  L   +A+  P P
Sbjct: 157 IEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMP 193

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/60 (38%), Positives = 33/60 (55%)
Query: 130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           H  +FV  L  +   E +  AF  +G+I D + V D  +GKSKGYGF+ F  +  A  A+
Sbjct: 15  HFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAI 74

>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 = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 44/216 (20%), Positives = 89/216 (41%), Gaps = 29/216 (13%)
Query: 117 ASRVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGF 176
           A R R +A    +  +++V  + ++   +T+  AF  +G I+      D V+ K KG+ F
Sbjct: 3   AQRQRALA----IXCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAF 58
Query: 177 ILFKTRSGARKALKEPQK-KIGNR-MTACQLASIGXXXXXXXXXXXXXXXXXXXXXXXXX 234
           + ++    A+ AL++     +G R +   + ++IG                         
Sbjct: 59  VEYEVPEAAQLALEQXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF--------- 109
Query: 235 XXXXXXXXSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLF 294
                         +I+V++V  +L    + + F  +G+I+   L  D  TGK KG+   
Sbjct: 110 -------------NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFI 156
Query: 295 VYKTVDAAKKALEEPHK-NFEGHILNCQRAIDGPKP 329
            Y+   +++ A+   +  +  G  L   +A+  P P
Sbjct: 157 EYEKAQSSQDAVSSXNLFDLGGQYLRVGKAVTPPXP 192

>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 = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/62 (37%), Positives = 34/62 (54%)
Query: 130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           H  +FV  L  +   E +  AF  +G I D + V D  +GKSKGYGF+ F  +  A  A+
Sbjct: 15  HFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 74
Query: 190 KE 191
           ++
Sbjct: 75  QQ 76

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/59 (38%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           IF+  L      + L D F  +G I  CK VCD+    SKGYGF+ F+T+  A +A+++
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 64

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 36/60 (60%)
Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           +++V  L ++   + L   F+ +G IE  + + D  +G+SKGYGFI F     A+KAL++
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87

>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 = 45.1 bits (105), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 21/65 (32%), Positives = 36/65 (55%)
Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           +KIFV  +  +   +K+  +F  +GE+E   L +D  T K +GFC   +K  +  KK +E
Sbjct: 2   KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
Query: 308 EPHKN 312
           + + N
Sbjct: 62  KKYHN 66

>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 2 Length = 85

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 22/57 (38%), Positives = 35/57 (61%)
Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           +++ GL   T  + L+   + YG+I   KA+ DK + K KGYGF+ F + S A+KA+
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 38/175 (21%), Positives = 67/175 (38%), Gaps = 31/175 (17%)
Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           + V+ L  +   E     F   GEIE CK V DK++G+S GYGF+ +     A KA+   
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI--- 61
Query: 193 QKKIGNRMTACQLASIGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSEYTQRKIFV 252
                N +   +L +                                   +      ++V
Sbjct: 62  -----NTLNGLRLQT-----------------------KTIKVSYARPSSASIRDANLYV 93
Query: 253 SNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           S +   +  ++L   FS+YG I    + +D+ TG  +G     +     A++A++
Sbjct: 94  SGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 37/175 (21%), Positives = 64/175 (36%), Gaps = 33/175 (18%)
Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           + V+ L  D     L   F+  G I  C+   D  +G S GY F+ F +   +++A+K  
Sbjct: 17  LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 193 QK-KIGNRMTACQLASIGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSEYTQRKIF 251
               + N+      A  G                                        ++
Sbjct: 77  NGITVRNKRLKVSYARPGGESIKDT--------------------------------NLY 104
Query: 252 VSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKAL 306
           V+N+   +   +L   F KYG I +  +  DK TG+P+G     Y   + A++A+
Sbjct: 105 VTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 159

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 37/175 (21%), Positives = 65/175 (37%), Gaps = 33/175 (18%)
Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           + V+ L  D     L   F+  G I  C+ + D  +G S GY F+ F +   +++A+K  
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 193 QK-KIGNRMTACQLASIGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSEYTQRKIF 251
               + N+      A  G                                        ++
Sbjct: 66  NGITVRNKRLKVSYARPGGESIKDT--------------------------------NLY 93
Query: 252 VSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKAL 306
           V+N+   +   +L   F KYG I +  +  DK TG+P+G     Y   + A++A+
Sbjct: 94  VTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 34/157 (21%), Positives = 63/157 (40%), Gaps = 31/157 (19%)
Query: 151 FKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASIGX 210
           F   G+IE CK V DK++G+S GYGF+ +   + A KA+        N +   +L +   
Sbjct: 25  FGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI--------NTLNGLKLQT--- 73
Query: 211 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSEYTQRKIFVSNVGSELEPQKLLAFFSK 270
                                           +      ++VS +   +  +++   FS+
Sbjct: 74  --------------------KTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQ 113
Query: 271 YGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           YG I    + +D+ATG  +G     +     A++A++
Sbjct: 114 YGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 150

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 39/185 (21%), Positives = 71/185 (38%), Gaps = 37/185 (20%)
Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           + V+ L  +   + L   F   GE+E  K + DKV+G S GYGF+ + T   A +A+   
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI--- 61
Query: 193 QKKIGNRMTACQLASIGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSEYTQ-RKIF 251
                N +   +L S                                   SE  +   ++
Sbjct: 62  -----NTLNGLRLQS------------------------KTIKVSYARPSSEVIKDANLY 92
Query: 252 VSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHK 311
           +S +   +  + +   FS++G I    + +D+ TG  +G     +     A++A+     
Sbjct: 93  ISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI----T 148
Query: 312 NFEGH 316
           +F GH
Sbjct: 149 SFNGH 153

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 39/185 (21%), Positives = 71/185 (38%), Gaps = 37/185 (20%)
Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           + V+ L  +   + L   F   GE+E  K + DKV+G S GYGF+ + T   A +A+   
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI--- 61
Query: 193 QKKIGNRMTACQLASIGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSEYTQ-RKIF 251
                N +   +L S                                   SE  +   ++
Sbjct: 62  -----NTLNGLRLQS------------------------KTIKVSYARPSSEVIKDANLY 92
Query: 252 VSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHK 311
           +S +   +  + +   FS++G I    + +D+ TG  +G     +     A++A+     
Sbjct: 93  ISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI----T 148
Query: 312 NFEGH 316
           +F GH
Sbjct: 149 SFNGH 153

>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 = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 34/63 (53%)
Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP 309
           IFV  +  +   +K+  +F  +GE+E   L +D  T K +GFC   +K  +  KK +E+ 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 310 HKN 312
           + N
Sbjct: 62  YHN 64

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	453
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	100.0
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	100.0
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	100.0
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	100.0
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	100.0
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.98
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.98
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.97
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.97
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.97
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.97
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.97
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.97
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.97
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.97
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.91
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.88
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.85
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.84
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.84
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.84
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.84
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.82
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.82
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.82
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.82
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.82
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.81
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.81
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.81
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.81
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.8
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.8
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.8
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.8
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.8
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.79
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.79
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.79
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.79
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.79
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.79
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.79
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.79
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.79
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.79
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.79
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.79
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.78
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.78
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.78
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.78
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.78
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.78
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.78
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.78
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.78
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.78
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.78
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.78
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.78
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.78
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.78
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.78
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.78
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.77
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.77
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.77
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.77
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.77
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.77
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.77
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.77
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.77
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.77
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.77
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.77
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.77
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.77
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.77
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.77
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.77
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.77
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.77
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.77
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.77
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.77
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.77
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.77
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.77
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.77
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.77
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.76
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.76
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.76
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.76
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.76
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.76
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.76
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.76
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.76
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.76
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.76
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.76
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.76
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.76
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.76
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.76
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.76
2div_A	99	TRNA selenocysteine associated protein; structural	99.76
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.76
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.76
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.76
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.76
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.76
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.76
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.76
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.76
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.75
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.75
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.75
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.75
2div_A	99	TRNA selenocysteine associated protein; structural	99.75
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.75
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.75
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.75
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.75
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.75
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.75
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.75
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.75
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.75
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.75
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.75
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.75
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.75
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.75
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.75
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.75
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.75
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.75
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.75
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.75
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.75
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.75
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.75
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.75
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.75
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.75
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.75
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.75
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.75
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.75
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.75
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.74
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.74
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.74
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.74
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.74
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.74
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.74
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.74
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.74
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.74
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.74
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.74
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.74
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.74
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.74
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.74
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.74
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.74
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.73
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.73
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.73
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.73
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.73
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.73
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.73
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.73
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.73
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.73
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.73
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.73
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.73
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.73
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.73
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.73
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.73
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.73
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.73
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.73
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.73
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.73
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.73
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.73
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.72
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.72
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.72
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.72
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.72
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.72
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.72
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.72
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.72
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.72
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.72
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.72
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.72
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.72
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.72
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.72
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.72
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.72
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.71
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.71
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.71
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.71
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.71
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.71
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.71
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.71
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.71
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.71
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.71
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.71
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.71
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.71
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.71
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.71
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.71
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.71
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.71
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.71
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.71
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.7
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.7
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.7
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.7
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.7
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.7
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.7
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.53
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.69
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.69
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.69
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.69
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.69
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.69
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.69
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.69
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.69
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.69
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.69
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.69
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.69
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.68
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.68
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.68
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.68
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.68
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.68
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.68
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.68
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.67
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.67
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.67
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.67
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.67
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.67
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.67
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.67
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.67
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.67
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.67
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.48
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.66
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.66
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.66
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.66
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.66
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.66
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.66
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.66
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.66
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.66
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.66
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.65
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.65
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.65
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.65
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.65
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.65
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.65
1x5p_A	97	Negative elongation factor E; structure genomics,	99.65
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.65
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.65
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.65
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.65
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.64
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.64
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.64
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.64
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.64
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.63
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.63
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.63
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.63
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.63
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.63
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.63
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.63
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.63
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.62
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.62
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.62
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.62
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.62
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.62
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.62
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.61
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.61
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.61
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.61
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.61
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.61
1x5p_A	97	Negative elongation factor E; structure genomics,	99.6
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.6
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.59
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.59
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.59
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.59
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.59
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.59
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.59
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.58
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.58
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.58
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.58
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.57
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.56
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.56
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.56
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.56
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.55
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.54
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.53
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.52
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.51
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.51
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.5
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.48
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.47
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.45
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.45
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.44
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.44
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.43
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.42
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.41
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.4
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.4
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.39
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.33
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.26
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.25
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.17
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.15
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.13
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.11
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.0
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.97
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.83
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.82
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.6
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.5
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.46
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.09
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.01
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.68
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.54
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.32
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.24
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.23
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.17
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.11
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.97
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.83
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.75
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.6
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.54
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.21
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.13
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.92
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.68
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	86.84
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	86.83

>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=100.00  E-value=1.6e-36  Score=267.02  Aligned_cols=179  Identities=26%  Similarity=0.495  Sum_probs=153.2

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEe
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQL  205 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~  205 (453)
                      +....++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||+.++..|.|+.|.|.+
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~   88 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKR   88 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeec
Confidence            44567899999999999999999999999999999999999899999999999999999999999977889999999999


Q ss_pred             cccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCC
Q 012923          206 ASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKAT  285 (453)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~  285 (453)
                      +........                          .......++|||+|||+.+|+++|+++|+.||.|..|+|++++.+
T Consensus        89 ~~~~~~~~~--------------------------~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~  142 (196)
T 1l3k_A           89 AVSREDSQR--------------------------PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGS  142 (196)
T ss_dssp             CCC-------------------------------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTT
T ss_pred             ccCcccccc--------------------------cccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCC
Confidence            864432211                          112234479999999999999999999999999999999999999


Q ss_pred             CCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEccCCCCCC
Q 012923          286 GKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAIDGPKPG  330 (453)
Q Consensus       286 g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a~~~~~~~  330 (453)
                      +.++|||||+|.+.++|.+||..++..|+|+.|.|.++.++....
T Consensus       143 g~~~g~afV~F~~~~~A~~A~~~~~~~~~G~~i~v~~a~~k~~~~  187 (196)
T 1l3k_A          143 GKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMA  187 (196)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEECC------
T ss_pred             CCccceEEEEECCHHHHHHHHHhCCcEECCEEEEEEecCChhHhc
Confidence            999999999999999999999986689999999999998765443

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

Probab=100.00  E-value=9.5e-37  Score=271.48  Aligned_cols=166  Identities=20%  Similarity=0.320  Sum_probs=148.6

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEecc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQLAS  207 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~~~  207 (453)
                      ..+||||+|||+++|+++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|.+||+.++. .+.|+.|++.++.
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            458999999999999999999999999999999999999999999999999999999999998884 5899999998875


Q ss_pred             cCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCC
Q 012923          208 IGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGK  287 (453)
Q Consensus       208 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~  287 (453)
                      .....                              .....++|||+|||+.+|+++|+++|+.||.|..|+|+++.  +.
T Consensus        94 ~~~~~------------------------------~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~  141 (213)
T 4f02_A           94 RDPSL------------------------------RKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NG  141 (213)
T ss_dssp             CCTHH------------------------------HHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TE
T ss_pred             ccccc------------------------------cccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CC
Confidence            32211                              11123589999999999999999999999999999999984  55


Q ss_pred             CceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCC
Q 012923          288 PKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDG  326 (453)
Q Consensus       288 ~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~  326 (453)
                      ++|||||+|.+.++|.+||..|| ..|+|++|.|.++.++
T Consensus       142 ~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~  181 (213)
T 4f02_A          142 SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR  181 (213)
T ss_dssp             EEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCH
T ss_pred             CceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            79999999999999999999999 8999999999999754

>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=100.00  E-value=1.1e-35  Score=254.61  Aligned_cols=164  Identities=29%  Similarity=0.580  Sum_probs=149.0

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEeccc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASI  208 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~~  208 (453)
                      .+++|||+|||+++|+++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|.+|+.. ...+.|+.|.|.++..
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~g~~i~v~~~~~   80 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT-QHILDGKVIDPKRAIP   80 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS-CCEETTEECCCEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc-ccccCCeEcccccccc
Confidence            468999999999999999999999999999999999998999999999999999999999996 4679999999888642


Q ss_pred             CCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCC
Q 012923          209 GPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKP  288 (453)
Q Consensus       209 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~  288 (453)
                      ..                                .....++|||+|||+.+|+++|+++|++||.|..|+|++++.+|.+
T Consensus        81 ~~--------------------------------~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~  128 (167)
T 2cjk_A           81 RD--------------------------------EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQS  128 (167)
T ss_dssp             HH--------------------------------HHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTT
T ss_pred             hh--------------------------------hccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCcc
Confidence            11                                1112458999999999999999999999999999999999889999


Q ss_pred             ceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCC
Q 012923          289 KGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDG  326 (453)
Q Consensus       289 kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~  326 (453)
                      +|||||+|.+.++|.+|+. ++ ..|+|++|.|.|+.++
T Consensus       129 ~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          129 RGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             SEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             ceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            9999999999999999999 67 8999999999999654

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

Probab=100.00  E-value=1.2e-34  Score=247.90  Aligned_cols=163  Identities=22%  Similarity=0.364  Sum_probs=148.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecccC
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASIG  209 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~~  209 (453)
                      |+|||+|||+++|+++|+++|++||.|.+|+|++++ +++++|||||+|.+.++|.+|+..++ ..+.|+.|.|.++...
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            689999999999999999999999999999999998 68899999999999999999998777 5599999999998644


Q ss_pred             CCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCc
Q 012923          210 PATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPK  289 (453)
Q Consensus       210 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~k  289 (453)
                      ...                              .....++|||+|||+.+|+++|+++|++||.|..+.+++++.++.++
T Consensus        80 ~~~------------------------------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~  129 (166)
T 3md3_A           80 QQS------------------------------SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSR  129 (166)
T ss_dssp             CCC------------------------------CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEE
T ss_pred             CCC------------------------------CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcc
Confidence            321                              12234699999999999999999999999999999999999999999


Q ss_pred             eEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          290 GFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       290 g~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      |||||+|.+.++|.+|+..|| ..|+|++|.|.|+.
T Consensus       130 g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  165 (166)
T 3md3_A          130 GYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA  165 (166)
T ss_dssp             EEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESC
T ss_pred             eEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecC
Confidence            999999999999999999998 89999999999984

>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=100.00  E-value=1.9e-34  Score=247.20  Aligned_cols=162  Identities=25%  Similarity=0.430  Sum_probs=149.4

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~  208 (453)
                      +++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+|++.++ ..+.|+.|.|.++..
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            5899999999999999999999999999999999999899999999999999999999999777 559999999999864


Q ss_pred             CCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCC
Q 012923          209 GPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKP  288 (453)
Q Consensus       209 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~  288 (453)
                      ....                                ...++|||+|||..+|+++|+++|++||.|..++|+++..++++
T Consensus        83 ~~~~--------------------------------~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~  130 (168)
T 1b7f_A           83 GGES--------------------------------IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRP  130 (168)
T ss_dssp             CSST--------------------------------TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCE
T ss_pred             Cccc--------------------------------CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCc
Confidence            3221                                23469999999999999999999999999999999999889999


Q ss_pred             ceEEEEEECCHHHHHHHHHcCC-CccCC--eEEEEEEc
Q 012923          289 KGFCLFVYKTVDAAKKALEEPH-KNFEG--HILNCQRA  323 (453)
Q Consensus       289 kg~afV~F~~~~~A~~Al~~~~-~~l~g--~~l~v~~a  323 (453)
                      +|||||+|.+.++|.+|+..|| ..|.|  ++|+|.||
T Consensus       131 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          131 RGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             ceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            9999999999999999999999 88877  99999986

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

Probab=100.00  E-value=4e-35  Score=262.22  Aligned_cols=179  Identities=22%  Similarity=0.427  Sum_probs=152.2

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~  208 (453)
                      .++|||+|||+++|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+||+.++ ..|.|+.|.|.++..
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~  107 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN  107 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCC
Confidence            4799999999999999999999999999999999999899999999999999999999999777 569999999987653


Q ss_pred             CCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCC
Q 012923          209 GPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKP  288 (453)
Q Consensus       209 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~  288 (453)
                      .......                     ...........++|||+|||+.+|+++|+++|+.||.|..|+|++++.++++
T Consensus       108 ~~~~~~~---------------------~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~  166 (216)
T 2qfj_A          108 IGQAQPI---------------------IDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKH  166 (216)
T ss_dssp             CGGGHHH---------------------HHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCE
T ss_pred             ccccchh---------------------hhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCc
Confidence            2211000                     0000112234579999999999999999999999999999999999999999


Q ss_pred             ceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCCCC
Q 012923          289 KGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGPKP  329 (453)
Q Consensus       289 kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~~~  329 (453)
                      +|||||+|.+.++|.+||..|| ..|+|+.|.|.++...+.+
T Consensus       167 ~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~~~  208 (216)
T 2qfj_A          167 KGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMP  208 (216)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCSST
T ss_pred             CceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCCCC
Confidence            9999999999999999999999 8999999999999876544

>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=100.00  E-value=3.8e-34  Score=245.00  Aligned_cols=162  Identities=25%  Similarity=0.425  Sum_probs=148.0

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~  208 (453)
                      +++|||+|||+++|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+|++.++ ..+.|+.|.|.++..
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            5899999999999999999999999999999999999899999999999999999999999777 569999999999863


Q ss_pred             CCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCC
Q 012923          209 GPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKP  288 (453)
Q Consensus       209 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~  288 (453)
                      ...                                ....++|||+|||..+|+++|+++|++||.|..++++++..+|.+
T Consensus        82 ~~~--------------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~  129 (167)
T 1fxl_A           82 SSA--------------------------------SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVS  129 (167)
T ss_dssp             CCG--------------------------------GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCE
T ss_pred             Ccc--------------------------------cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCc
Confidence            321                                123468999999999999999999999999999999999889999


Q ss_pred             ceEEEEEECCHHHHHHHHHcCC-CccCCeE--EEEEEc
Q 012923          289 KGFCLFVYKTVDAAKKALEEPH-KNFEGHI--LNCQRA  323 (453)
Q Consensus       289 kg~afV~F~~~~~A~~Al~~~~-~~l~g~~--l~v~~a  323 (453)
                      +|||||+|.+.++|.+|+..|| ..|.|+.  |.|.||
T Consensus       130 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          130 RGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             EEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             cceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            9999999999999999999999 8899965  888775

>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=100.00  E-value=3.6e-33  Score=240.86  Aligned_cols=163  Identities=21%  Similarity=0.314  Sum_probs=142.6

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCC--CcceEEEEEEccHHHHHHHHHcCCCc-cC---CeEeE
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSG--KSKGYGFILFKTRSGARKALKEPQKK-IG---NRMTA  202 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g--~~~G~afV~f~~~~~a~~A~~~~~~~-~~---gr~~~  202 (453)
                      ++++|||+|||+++|+++|+++|++||.|.+|+|++++.++  +++|||||+|.+.++|.+|++.+++. +.   ++.+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            46899999999999999999999999999999999999776  89999999999999999999988753 43   56677


Q ss_pred             EEecccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeecc
Q 012923          203 CQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGID  282 (453)
Q Consensus       203 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d  282 (453)
                      +.++.....                               .....++|||+|||+.+|+++|+++|++||.|..|+|+++
T Consensus        82 ~~~~~~~~~-------------------------------~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~  130 (175)
T 3nmr_A           82 MKPADSEKN-------------------------------NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG  130 (175)
T ss_dssp             EEECGGGCC-------------------------------SCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC
T ss_pred             Ecccccccc-------------------------------ccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEEC
Confidence            766543221                               1123468999999999999999999999999999999998


Q ss_pred             CCCCCCceEEEEEECCHHHHHHHHHcCC-CccC---CeEEEEEEc
Q 012923          283 KATGKPKGFCLFVYKTVDAAKKALEEPH-KNFE---GHILNCQRA  323 (453)
Q Consensus       283 ~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~---g~~l~v~~a  323 (453)
                      . +|+++|||||+|.+.++|.+||..|| ..+.   +++|.|.||
T Consensus       131 ~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~a  174 (175)
T 3nmr_A          131 P-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA  174 (175)
T ss_dssp             T-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEEC
T ss_pred             C-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEec
Confidence            6 69999999999999999999999999 5555   499999997

>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=100.00  E-value=3e-32  Score=234.41  Aligned_cols=157  Identities=17%  Similarity=0.307  Sum_probs=139.3

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhcc----C-------CeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-Ccc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQY----G-------EIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKI  196 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~----G-------~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~  196 (453)
                      .+++|||+|||+++|+++|+++|++|    |       .|..+++.      +++|||||+|.+.++|.+|+ .++ ..+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            46899999999999999999999999    6       66777654      45799999999999999999 555 669


Q ss_pred             CCeEeEEEecccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcce
Q 012923          197 GNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEE  276 (453)
Q Consensus       197 ~gr~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~  276 (453)
                      .|+.|.|.++......                                ...++|||+|||+.+|+++|+++|++||.|..
T Consensus        76 ~g~~i~v~~~~~~~~~--------------------------------~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~  123 (172)
T 2g4b_A           76 QGQSLKIRRPHDYQPL--------------------------------PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKA  123 (172)
T ss_dssp             TTEECEEECCSSCCCC--------------------------------TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEE
T ss_pred             cCceeeecCCcccCCC--------------------------------CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceE
Confidence            9999999986533211                                12469999999999999999999999999999


Q ss_pred             eeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          277 GPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       277 v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      |+|++++.+|+++|||||+|.+.++|.+|+..|| ..|+|++|.|.||.
T Consensus       124 v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          124 FNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             EEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             EEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            9999998899999999999999999999999998 89999999999973

>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=100.00  E-value=8.4e-33  Score=238.58  Aligned_cols=165  Identities=20%  Similarity=0.255  Sum_probs=142.4

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEe
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQL  205 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~  205 (453)
                      .....++|||+|||+++|+++|+++|..||.|.. .++++..+++++|||||+|.+.++|.+||+..+..|.|+.|.|.+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~   87 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEK   87 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEec
Confidence            4556789999999999999999999999998877 345565688999999999999999999996333669999999999


Q ss_pred             cccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCC
Q 012923          206 ASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKAT  285 (453)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~  285 (453)
                      +......                              .....++|||+|||+.+|+++|+++|++||.|..+     ..+
T Consensus        88 ~~~~~~~------------------------------~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~  132 (175)
T 1fje_B           88 PKGRDSK------------------------------KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQD  132 (175)
T ss_dssp             CCCSSCS------------------------------TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSS
T ss_pred             CCCcccc------------------------------ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCC
Confidence            8643221                              11234699999999999999999999999988765     458


Q ss_pred             CCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCC
Q 012923          286 GKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDG  326 (453)
Q Consensus       286 g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~  326 (453)
                      +.++|||||+|.+.++|.+||..|| ..|+|+.|.|.|+.++
T Consensus       133 ~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          133 GKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             SSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             CCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            8999999999999999999999999 8999999999999765

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

Probab=99.98  E-value=1e-31  Score=236.68  Aligned_cols=181  Identities=15%  Similarity=0.248  Sum_probs=145.2

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccC-----------CeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-Ccc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYG-----------EIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKI  196 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G-----------~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~  196 (453)
                      .+++|||+|||+++|+++|+++|++||           .|..+++      ++++|||||+|.+.++|.+|| .++ ..|
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            468999999999999999999999994           4555553      456899999999999999999 566 569


Q ss_pred             CCeEeEEEecccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcce
Q 012923          197 GNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEE  276 (453)
Q Consensus       197 ~gr~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~  276 (453)
                      .|+.|.|.++..............            ...............++|||+|||+.+|+++|+++|++||.|..
T Consensus        76 ~g~~i~v~~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~  143 (198)
T 2yh0_A           76 QGQSLKIRRPHDYQPLPGMSENPS------------VYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKA  143 (198)
T ss_dssp             TTEEEEEECCCCCCCCCCSSSCSS------------CCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEE
T ss_pred             cCceEEEeCCCCCCCCCCCcCCCc------------CCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccE
Confidence            999999998765432211100000            00000011222345689999999999999999999999999999


Q ss_pred             eeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCCC
Q 012923          277 GPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGPK  328 (453)
Q Consensus       277 v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~~  328 (453)
                      |+|++++.++.++|||||+|.+.++|.+||..|| ..|+|+.|.|.++.++.+
T Consensus       144 ~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          144 FNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             EEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             EEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            9999998899999999999999999999999998 899999999999976543

>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=99.98  E-value=1.5e-31  Score=235.24  Aligned_cols=188  Identities=10%  Similarity=0.092  Sum_probs=141.0

Q ss_pred             CcCeEEEcCCC-CCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          129 VHRKIFVHGLG-WDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       129 ~~~~lfV~nLp-~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      .+++|||+||| +.+|+++|+++|++||.|.+|+|+++     ++|||||+|.+.++|.+||+.|+ ..|.|+.|.|.++
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            46899999999 89999999999999999999999876     37999999999999999999888 5599999999998


Q ss_pred             ccCCCCCCCcCccccccc--cccccccccccc---ccccccccccccEEEEecCCCCccHHHHHHHHhccCCc--ceeee
Q 012923          207 SIGPATTPAVASTATHQH--QHQHQHQHQHQH---QQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEI--EEGPL  279 (453)
Q Consensus       207 ~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~---~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i--~~v~i  279 (453)
                      ..................  ............   .........+.++|||+|||+.+|+++|+++|++||.|  ..|+|
T Consensus        78 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~  157 (205)
T 3tyt_A           78 KQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKV  157 (205)
T ss_dssp             SCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEE
T ss_pred             cCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEE
Confidence            644321110000000000  000000000000   00001112346799999999999999999999999999  89999


Q ss_pred             eccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCe----EEEEEEc
Q 012923          280 GIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGH----ILNCQRA  323 (453)
Q Consensus       280 ~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~----~l~v~~a  323 (453)
                      +.+.  +.++|||||+|.+.++|.+||..|| ..|.|+    ++.|+++
T Consensus       158 ~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          158 FSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             CSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             EcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            8774  5667999999999999999999999 788776    6777776

>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=99.97  E-value=6.4e-31  Score=244.68  Aligned_cols=191  Identities=19%  Similarity=0.223  Sum_probs=145.8

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHH----HHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLI----DAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRM  200 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~----~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~  200 (453)
                      +...+++|||+|||+++|+++|+    ++|++||.|..|+|++   +++++|||||+|.+.++|.+||+.+++ .|.|+.
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   81 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcE
Confidence            44567999999999999999977    8999999999999886   778999999999999999999988884 589999


Q ss_pred             eEEEecccCCCCCCCcCccccccc----------cccc------------------------------------------
Q 012923          201 TACQLASIGPATTPAVASTATHQH----------QHQH------------------------------------------  228 (453)
Q Consensus       201 ~~v~~~~~~~~~~~~~~~~~~~~~----------~~~~------------------------------------------  228 (453)
                      |.|.++..................          ....                                          
T Consensus        82 l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~  161 (282)
T 3pgw_A           82 MRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQP  161 (282)
T ss_pred             EEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCC
Confidence            999998654421000000000000          0000                                          


Q ss_pred             ---------------------------ccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeec
Q 012923          229 ---------------------------QHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGI  281 (453)
Q Consensus       229 ---------------------------~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~  281 (453)
                                                 ...................++|||+|||..+|+++|+++|+.||.|..|+|+.
T Consensus       162 ~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~  241 (282)
T 3pgw_A          162 PYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP  241 (282)
T ss_pred             CCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEec
Confidence                                       00000000000112334568999999999999999999999999999999987


Q ss_pred             cCCCCCCceEEEEEECCHHHHHHHHHcCC-CccC-CeEEEEEEcc
Q 012923          282 DKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFE-GHILNCQRAI  324 (453)
Q Consensus       282 d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~-g~~l~v~~a~  324 (453)
                      ++     +|||||+|.+.++|.+||..|| ..|. |+.|+|.|++
T Consensus       242 ~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          242 GR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            64     6899999999999999999999 8888 9999999985

>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=99.97  E-value=3.6e-31  Score=246.64  Aligned_cols=172  Identities=22%  Similarity=0.358  Sum_probs=154.0

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      .+..++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+|+..++ ..+.|+.|.|.+
T Consensus        92 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~  171 (284)
T 3smz_A           92 QPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHW  171 (284)
T ss_dssp             CCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            4456899999999999999999999999999999999999899999999999999999999998777 569999999999


Q ss_pred             cccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCc-cHHHHHHHHhccCCcceeeeeccCC
Q 012923          206 ASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSEL-EPQKLLAFFSKYGEIEEGPLGIDKA  284 (453)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~-t~~~l~~~F~~~G~i~~v~i~~d~~  284 (453)
                      +......                             ......++|||+|||+.+ |+++|+++|+.||.|..|+|+++. 
T Consensus       172 a~~~~~~-----------------------------~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-  221 (284)
T 3smz_A          172 TDAGQLT-----------------------------PALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-  221 (284)
T ss_dssp             CCGGGCC-----------------------------TTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-
T ss_pred             CCCCCCC-----------------------------cccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-
Confidence            8643221                             112345799999999995 999999999999999999999986 


Q ss_pred             CCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCCC
Q 012923          285 TGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGPK  328 (453)
Q Consensus       285 ~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~~  328 (453)
                      +|+++|||||+|.+.++|.+|+..|| ..|+|++|.|.|+.++..
T Consensus       222 ~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  266 (284)
T 3smz_A          222 DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP  266 (284)
T ss_dssp             SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSSC
T ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCc
Confidence            89999999999999999999999999 899999999999976543

>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=99.97  E-value=3.2e-31  Score=247.97  Aligned_cols=172  Identities=14%  Similarity=0.212  Sum_probs=143.1

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccC-CeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYG-EIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G-~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ..++|||+|||+++|+++|+++|..|| .|..|+|++++ .+.++|||||+|.+.++|.+|+..++ ..|.|+.|.|.++
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  194 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            578999999999999999999999999 99999999988 48899999999999999999999777 5699999999998


Q ss_pred             ccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCC-ccHHHHHHHHhccCCcceeeeeccCC-
Q 012923          207 SIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSE-LEPQKLLAFFSKYGEIEEGPLGIDKA-  284 (453)
Q Consensus       207 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~-~t~~~l~~~F~~~G~i~~v~i~~d~~-  284 (453)
                      .........                         .......++|||+|||+. +|+++|+++|+.||.|..|+|+++.. 
T Consensus       195 ~~~~~~~~~-------------------------~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~  249 (292)
T 2ghp_A          195 NPLEKSKRT-------------------------DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKE  249 (292)
T ss_dssp             CCC----------------------------------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC-
T ss_pred             CCCcccccc-------------------------cccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCc
Confidence            644322111                         112334579999999999 99999999999999999999999876 


Q ss_pred             CCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCC
Q 012923          285 TGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGP  327 (453)
Q Consensus       285 ~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~  327 (453)
                      |+.++|||||+|.+.++|.+|| .|| ..|+|++|.|.|+.+++
T Consensus       250 tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k~  292 (292)
T 2ghp_A          250 HSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKKP  292 (292)
T ss_dssp             --CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCCC
T ss_pred             CCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCCC
Confidence            6999999999999999999999 888 88999999999997653

>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=99.97  E-value=1.1e-30  Score=235.07  Aligned_cols=191  Identities=16%  Similarity=0.212  Sum_probs=146.0

Q ss_pred             CCCCCcCeEEEcCCCC-CCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeE
Q 012923          125 DEDPVHRKIFVHGLGW-DTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTA  202 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~-~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~  202 (453)
                      ...+.+++|||+|||+ ++|+++|+++|++||.|..|+|++++     +|||||+|.+.++|.+|++.++ ..|.|+.|.
T Consensus        29 ~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~  103 (229)
T 2adc_A           29 LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIR  103 (229)
T ss_dssp             GGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            3446679999999999 99999999999999999999999875     7899999999999999999777 569999999


Q ss_pred             EEecccCCCCCCCcCcccccccc---cccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccC-Ccceee
Q 012923          203 CQLASIGPATTPAVASTATHQHQ---HQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYG-EIEEGP  278 (453)
Q Consensus       203 v~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-~i~~v~  278 (453)
                      |.++...................   ......................++|||+|||+.+|+++|+++|+.|| .|..|+
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            99987543221111000000000   00000000000001112233468999999999999999999999999 999999


Q ss_pred             eeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccC-CeEEEEEEccC
Q 012923          279 LGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFE-GHILNCQRAID  325 (453)
Q Consensus       279 i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~-g~~l~v~~a~~  325 (453)
                      |+.+     .+|||||+|.+.++|.+||..|| ..|. |++|+|.|+.+
T Consensus       184 i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~  227 (229)
T 2adc_A          184 FFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  227 (229)
T ss_dssp             ECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             EEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecC
Confidence            9763     27999999999999999999999 8898 99999999865

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

Probab=99.97  E-value=1.3e-30  Score=229.43  Aligned_cols=186  Identities=16%  Similarity=0.230  Sum_probs=143.5

Q ss_pred             cCeEEEcCCCC-CCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecc
Q 012923          130 HRKIFVHGLGW-DTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLAS  207 (453)
Q Consensus       130 ~~~lfV~nLp~-~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~  207 (453)
                      +++|||+|||+ ++|+++|+++|++||.|..|+|++++     +|||||+|.+.++|.+|+..++ ..|.|+.|.|.++.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            58999999999 99999999999999999999999875     7899999999999999999777 56999999999987


Q ss_pred             cCCCCCCCcCccccccccc---ccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccC-CcceeeeeccC
Q 012923          208 IGPATTPAVASTATHQHQH---QHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYG-EIEEGPLGIDK  283 (453)
Q Consensus       208 ~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-~i~~v~i~~d~  283 (453)
                      ...................   .....................++|||+|||..+|+++|+++|+.|| .|..|+|+++.
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~  157 (198)
T 1qm9_A           78 HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD  157 (198)
T ss_dssp             CCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT
T ss_pred             CCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC
Confidence            5532221111000000000   0000000000001112233478999999999999999999999999 99999997642


Q ss_pred             CCCCCceEEEEEECCHHHHHHHHHcCC-CccC-CeEEEEEEccC
Q 012923          284 ATGKPKGFCLFVYKTVDAAKKALEEPH-KNFE-GHILNCQRAID  325 (453)
Q Consensus       284 ~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~-g~~l~v~~a~~  325 (453)
                           +|||||+|.+.++|.+|+..|| ..|+ |++|.|.|+.+
T Consensus       158 -----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~  196 (198)
T 1qm9_A          158 -----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  196 (198)
T ss_dssp             -----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECC
T ss_pred             -----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeecc
Confidence                 8999999999999999999999 8888 99999999864

>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=99.97  E-value=3e-30  Score=236.85  Aligned_cols=155  Identities=22%  Similarity=0.289  Sum_probs=140.0

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ....++|||+|||+++|+++|+++|++||.|..|+|.+      ++|||||+|.+.++|.+|+..++ ..|.|+.|.|.+
T Consensus        19 ~~~~~~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           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR------DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            35568999999999999999999999999999999864      46899999999999999999777 569999999999


Q ss_pred             cccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCC
Q 012923          206 ASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKAT  285 (453)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~  285 (453)
                      +..                                      .++|||+|||+.+|+++|+++|+.||.|..|.|+++ .+
T Consensus        93 a~~--------------------------------------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~  133 (261)
T 3sde_A           93 ATH--------------------------------------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DR  133 (261)
T ss_dssp             CCC--------------------------------------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TT
T ss_pred             ccc--------------------------------------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CC
Confidence            752                                      248999999999999999999999999999999999 58


Q ss_pred             CCCceEEEEEECCHHHHHHHHHcCC-Cc-cC---CeEEEEEEccCC
Q 012923          286 GKPKGFCLFVYKTVDAAKKALEEPH-KN-FE---GHILNCQRAIDG  326 (453)
Q Consensus       286 g~~kg~afV~F~~~~~A~~Al~~~~-~~-l~---g~~l~v~~a~~~  326 (453)
                      |+++|||||+|.+.++|.+||..+| .. +.   +++|.|.++...
T Consensus       134 g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~  179 (261)
T 3sde_A          134 GRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQF  179 (261)
T ss_dssp             SCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCE
T ss_pred             CCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeecccc
Confidence            9999999999999999999999995 43 33   999999998654

>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=99.97  E-value=4.4e-30  Score=240.28  Aligned_cols=160  Identities=13%  Similarity=0.145  Sum_probs=136.1

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEe
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQL  205 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~  205 (453)
                      .....++|||+|||+++|+++|+++|+.||.|..|+|++++. + ++|||||+|.+.++|.+||+..+..|.|+.|.|.+
T Consensus        37 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-~-~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~  114 (292)
T 2ghp_A           37 RNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK-K-NFRFARIEFARYDGALAAITKTHKVVGQNEIIVSH  114 (292)
T ss_dssp             -----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT-S-SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC-C-CcEEEEEEECCHHHHHHHHHhCCcEeCCcEEEEEE
Confidence            345578999999999999999999999999999999999873 3 58999999999999999997444679999999988


Q ss_pred             cccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccC-CcceeeeeccCC
Q 012923          206 ASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYG-EIEEGPLGIDKA  284 (453)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-~i~~v~i~~d~~  284 (453)
                      +.                                       .++|||+|||+.+|+++|+++|+.|| .|..|+|+++..
T Consensus       115 ~~---------------------------------------~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~  155 (292)
T 2ghp_A          115 LT---------------------------------------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF  155 (292)
T ss_dssp             CC---------------------------------------SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC----
T ss_pred             CC---------------------------------------CCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC
Confidence            62                                       25999999999999999999999999 999999998864


Q ss_pred             CCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCC
Q 012923          285 TGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGP  327 (453)
Q Consensus       285 ~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~  327 (453)
                       +.++|||||+|.+.++|.+||..|+ ..|.|+.|.|.++....
T Consensus       156 -~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  198 (292)
T 2ghp_A          156 -NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLE  198 (292)
T ss_dssp             ----CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC-
T ss_pred             -CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCc
Confidence             8899999999999999999999888 89999999999986543

>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=99.97  E-value=6.9e-30  Score=237.96  Aligned_cols=154  Identities=24%  Similarity=0.358  Sum_probs=141.5

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLAS  207 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~  207 (453)
                      .+++|||+|||+++|+++|+++|+.|| |..|++      ++++|||||+|.+.++|.+|+..++ ..|.|+.|.|.++.
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~------~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~   93 (284)
T 3smz_A           21 NRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP   93 (284)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE------ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC
Confidence            358999999999999999999999999 999987      4678999999999999999999877 55999999998853


Q ss_pred             cCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCC
Q 012923          208 IGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGK  287 (453)
Q Consensus       208 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~  287 (453)
                                                            ..++|||+|||+.+|+++|+++|+.||.|..|+|++++.+|.
T Consensus        94 --------------------------------------~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~  135 (284)
T 3smz_A           94 --------------------------------------TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQ  135 (284)
T ss_dssp             --------------------------------------CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCC
T ss_pred             --------------------------------------CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCc
Confidence                                                  125899999999999999999999999999999999999999


Q ss_pred             CceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCC
Q 012923          288 PKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGP  327 (453)
Q Consensus       288 ~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~  327 (453)
                      ++|||||+|.+.++|.+|+..++ ..|+|+.|.|.++....
T Consensus       136 ~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~  176 (284)
T 3smz_A          136 SKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQ  176 (284)
T ss_dssp             EEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGG
T ss_pred             cceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCC
Confidence            99999999999999999999888 89999999999996543

>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=99.91  E-value=4.1e-24  Score=180.55  Aligned_cols=147  Identities=20%  Similarity=0.260  Sum_probs=111.5

Q ss_pred             EEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc--cCCeEeEEEecccCCCCCCCcCccccccccccccccccccc
Q 012923          159 DCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK--IGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQH  236 (453)
Q Consensus       159 ~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~--~~gr~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  236 (453)
                      .++|+++..  +++|||||+|.+.++|++|++.++..  +.+.. .+..........                   ....
T Consensus         2 ~~kl~ln~~--~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~-~~~~~~~~~~~~-------------------~~~~   59 (158)
T 2kn4_A            2 QYKLILNGK--TLKGETTTEAVDAATAEKVFKQYANDNGVDGEW-TYDDATKTFTVT-------------------EGSH   59 (158)
T ss_dssp             EEEEEEECS--SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEE-EEETTTTEEEEE-------------------CCCC
T ss_pred             cEEEEecCc--cccchhHHHHHHHHhHHHHHHhhcccCCCCCcc-cccCcccccccc-------------------cccc
Confidence            567788753  69999999999999999999877632  22222 221111000000                   0000


Q ss_pred             ccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCC
Q 012923          237 QQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEG  315 (453)
Q Consensus       237 ~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g  315 (453)
                      ...........++|||+|||+.+|+++|+++|+.||.|..|+|++++.+|+++|||||+|.+.++|.+||..|| ..|.|
T Consensus        60 ~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g  139 (158)
T 2kn4_A           60 HHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG  139 (158)
T ss_dssp             CSSCCCCCCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSS
T ss_pred             ccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            00112223345799999999999999999999999999999999999999999999999999999999999998 88999


Q ss_pred             eEEEEEEccCCC
Q 012923          316 HILNCQRAIDGP  327 (453)
Q Consensus       316 ~~l~v~~a~~~~  327 (453)
                      ++|.|.++....
T Consensus       140 ~~l~v~~a~~~~  151 (158)
T 2kn4_A          140 RELRVQMARYGR  151 (158)
T ss_dssp             SEEEEEEECCSS
T ss_pred             eEEEEEECCCCC
Confidence            999999997653

>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=99.88  E-value=1.6e-22  Score=160.54  Aligned_cols=108  Identities=24%  Similarity=0.461  Sum_probs=72.2

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~  208 (453)
                      +++|||+|||+++|+++|+++|++||.|.+|+|++++  +.++|||||+|.+.++|.+||+.++ ..|.|+.|.|.++..
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            4689999999999999999999999999999999985  4589999999999999999999877 569999999999864


Q ss_pred             CCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHH
Q 012923          209 GPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQK  263 (453)
Q Consensus       209 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~  263 (453)
                      ........                        .......++|||+|||+.+|++.
T Consensus        83 ~~~~~~~~------------------------~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           83 RKEREAEL------------------------GARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             CCC----------------------------------------------------
T ss_pred             cccccccc------------------------ccccCCCCceEeCCCCCCccccc
Confidence            43221110                        11122335799999999999864

>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=99.85  E-value=3e-21  Score=161.24  Aligned_cols=137  Identities=19%  Similarity=0.231  Sum_probs=108.4

Q ss_pred             CCCcceEEEEEEccHHHHHHHHHcC-C-CccCCeEeEEEecccCCCCCCCcCcccccccccccccccccccccccccccc
Q 012923          168 SGKSKGYGFILFKTRSGARKALKEP-Q-KKIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEY  245 (453)
Q Consensus       168 ~g~~~G~afV~f~~~~~a~~A~~~~-~-~~~~gr~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  245 (453)
                      ..+.+|+++|+|.+.++|++|++.+ + ..+.| .+.+.++..........                .............
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~----------------~~~~~~~~~~~~~   71 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGS----------------HHHHHHMHRDSCP   71 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSS----------------SSCCCCSCSSSST
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCcccccccc----------------ccccccccccCCC
Confidence            3467899999999999999999988 6 55888 88888765321100000                0000011123344


Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+|+++|+++|++||.|..|+|+++     ++|||||+|.+.++|.+||..|| ..|+|++|+|.|+.
T Consensus        72 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  146 (150)
T 2i2y_A           72 LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSN  146 (150)
T ss_dssp             TSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcC
Confidence            5679999999999999999999999999999999876     48999999999999999999988 88999999999996


Q ss_pred             CC
Q 012923          325 DG  326 (453)
Q Consensus       325 ~~  326 (453)
                      ++
T Consensus       147 ~~  148 (150)
T 2i2y_A          147 GE  148 (150)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.84  E-value=5.1e-21  Score=147.18  Aligned_cols=80  Identities=21%  Similarity=0.365  Sum_probs=76.3

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+|+++|+++|++||.|..|+|++++.+|+++|||||+|.+.++|.+||..|| ..|+|++|+|.||+
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            35689999999999999999999999999999999999999999999999999999999999998 89999999999985


Q ss_pred             C
Q 012923          325 D  325 (453)
Q Consensus       325 ~  325 (453)
                      +
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            3

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.84  E-value=5.5e-21  Score=144.69  Aligned_cols=81  Identities=16%  Similarity=0.283  Sum_probs=75.8

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccC-CcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC--CccCCeEEEEEEcc
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYG-EIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH--KNFEGHILNCQRAI  324 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G-~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~--~~l~g~~l~v~~a~  324 (453)
                      ++|||+|||+.+|+++|+++|++|| .|.+|+|++++.+++++|||||+|.+.++|.+||..++  ..|+|++|.|.++.
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            5899999999999999999999999 89999999999999999999999999999999999874  57999999999997


Q ss_pred             CCCC
Q 012923          325 DGPK  328 (453)
Q Consensus       325 ~~~~  328 (453)
                      ++++
T Consensus        82 ~~~~   85 (91)
T 2lxi_A           82 PKPK   85 (91)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            6654

>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=99.84  E-value=1.3e-20  Score=144.82  Aligned_cols=79  Identities=27%  Similarity=0.440  Sum_probs=74.8

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLAS  207 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~  207 (453)
                      ..++|||+|||+++|+++|+++|++||.|..|+|++|+.+++++|||||+|.+.++|.+|++.++ ..|.|+.|.|.++.
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            45799999999999999999999999999999999999999999999999999999999999877 56999999999984

>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=99.84  E-value=4.9e-21  Score=186.68  Aligned_cols=82  Identities=22%  Similarity=0.379  Sum_probs=77.8

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+|+++|+++|+.||.|+.|.|+.++.+++++|||||+|.+.++|.+||..|| ..|+|+.|.|.|+.
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~  180 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  180 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            45799999999999999999999999999999999999999999999999999999999999999 89999999999997


Q ss_pred             CCC
Q 012923          325 DGP  327 (453)
Q Consensus       325 ~~~  327 (453)
                      ...
T Consensus       181 ~~~  183 (437)
T 3pgw_S          181 GRT  183 (437)
T ss_pred             CCC
Confidence            554

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.82  E-value=1.5e-20  Score=142.35  Aligned_cols=82  Identities=16%  Similarity=0.312  Sum_probs=75.3

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccC-CeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-C-ccCCeEeEEEec
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYG-EIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-K-KIGNRMTACQLA  206 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G-~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~-~~~gr~~~v~~~  206 (453)
                      +++|||+|||+++|+++|+++|++|| .|.+|+|++|+.+++++|||||+|.+.++|.+||+.++ . .|.||.|.|.++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            46899999999999999999999999 89999999999999999999999999999999999875 3 489999999998


Q ss_pred             ccCCC
Q 012923          207 SIGPA  211 (453)
Q Consensus       207 ~~~~~  211 (453)
                      ..++.
T Consensus        81 ~~~~~   85 (91)
T 2lxi_A           81 DPKPK   85 (91)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            75543

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

Probab=99.82  E-value=1.4e-20  Score=153.47  Aligned_cols=123  Identities=17%  Similarity=0.180  Sum_probs=80.6

Q ss_pred             EEEEEEccHHHHHHHHHcCCCc-cCCeEeEEEecccCCCCCCCcCcccccccccccccccccccccccccccccccEEEE
Q 012923          174 YGFILFKTRSGARKALKEPQKK-IGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFV  252 (453)
Q Consensus       174 ~afV~f~~~~~a~~A~~~~~~~-~~gr~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V  252 (453)
                      ++|++|.+...+..|+..++.. ..++. .+.+.  .                              ........++|||
T Consensus         6 ~~~~~~~~~~~~~~a~~~~~g~~~~g~~-~~~~~--~------------------------------~~~~~~~~~~l~V   52 (135)
T 2lea_A            6 HHHHHSSGLVPRGSHMASMTGGQQMGRG-SMSYG--R------------------------------PPPDVEGMTSLKV   52 (135)
T ss_dssp             ------------------------------CCSC--C------------------------------SCSSGGGCCCEEE
T ss_pred             cccccccCCCchhhhhhhccCCCCCCCC-CCCcC--C------------------------------CCCCCCCCCEEEE
Confidence            6788888888888888887733 22222 11000  0                              0122334579999


Q ss_pred             ecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCCCC
Q 012923          253 SNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGPKP  329 (453)
Q Consensus       253 ~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~~~  329 (453)
                      +|||+.+|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+||..|| ..|.|++|.|.|+.....+
T Consensus        53 ~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~~  130 (135)
T 2lea_A           53 DNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  130 (135)
T ss_dssp             ECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCCC
T ss_pred             eCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence            9999999999999999999999999999999899999999999999999999999999 8899999999999765543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.82  E-value=1.5e-20  Score=142.79  Aligned_cols=79  Identities=18%  Similarity=0.270  Sum_probs=73.7

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCC--cceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-C----ccCCeEEE
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGE--IEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-K----NFEGHILN  319 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~--i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~----~l~g~~l~  319 (453)
                      -.+|||+|||+.+|+++|+++|++||.  |.+|+|++|+.+|++||||||+|.+.++|.+||+.|| .    .|+||+|.
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            359999999999999999999999995  7799999999999999999999999999999999988 3    48999999


Q ss_pred             EEEccC
Q 012923          320 CQRAID  325 (453)
Q Consensus       320 v~~a~~  325 (453)
                      |.||++
T Consensus        89 V~~Aks   94 (95)
T 2lkz_A           89 VDFAKS   94 (95)
T ss_dssp             EEECCC
T ss_pred             EEEccC
Confidence            999964

>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=99.82  E-value=8e-21  Score=169.35  Aligned_cols=79  Identities=18%  Similarity=0.222  Sum_probs=75.4

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccC--CcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYG--EIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G--~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      .++|||+||++.+|+++|+++|+.||  .|+.|+|++++.++++||||||+|.+.++|.+||..|| ..|+|+.|+|.++
T Consensus        68 ~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~a  147 (229)
T 3q2s_C           68 RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPV  147 (229)
T ss_dssp             -CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEEC
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEEC
Confidence            35999999999999999999999999  99999999999999999999999999999999999999 8999999999998


Q ss_pred             cC
Q 012923          324 ID  325 (453)
Q Consensus       324 ~~  325 (453)
                      ..
T Consensus       148 ~~  149 (229)
T 3q2s_C          148 NK  149 (229)
T ss_dssp             CH
T ss_pred             CC
Confidence            64

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

Probab=99.82  E-value=2.5e-19  Score=142.55  Aligned_cols=87  Identities=30%  Similarity=0.479  Sum_probs=80.4

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEE
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQR  322 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~  322 (453)
                      .....++|||+|||+.+|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||..++..|.|+.|.|.+
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~   92 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNL   92 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCCcCCCEEEEEEE
Confidence            34456899999999999999999999999999999999999999999999999999999999999999889999999999


Q ss_pred             ccCCCCC
Q 012923          323 AIDGPKP  329 (453)
Q Consensus       323 a~~~~~~  329 (453)
                      +.....+
T Consensus        93 a~~~~~~   99 (116)
T 2cqd_A           93 AYLGAKP   99 (116)
T ss_dssp             STTTCCC
T ss_pred             cccCCCc
Confidence            9765444

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.81  E-value=3.2e-20  Score=140.88  Aligned_cols=80  Identities=18%  Similarity=0.365  Sum_probs=73.9

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCC--eeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-----ccCCeE
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGE--IEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-----KIGNRM  200 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~--i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-----~~~gr~  200 (453)
                      ..-.||||+|||+++|+++|+++|++||.  |.+|+|++|+.++++||||||+|.+.++|.+||+.+++     .|.||.
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~   86 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKT   86 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEE
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEE
Confidence            34569999999999999999999999995  77999999999999999999999999999999998875     389999


Q ss_pred             eEEEecc
Q 012923          201 TACQLAS  207 (453)
Q Consensus       201 ~~v~~~~  207 (453)
                      |.|.++.
T Consensus        87 i~V~~Ak   93 (95)
T 2lkz_A           87 IGVDFAK   93 (95)
T ss_dssp             EEEEECC
T ss_pred             EEEEEcc
Confidence            9999985

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

Probab=99.81  E-value=9.4e-20  Score=142.80  Aligned_cols=80  Identities=21%  Similarity=0.374  Sum_probs=76.4

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+|+++|+++|++||.|..|+|++|+.|++++|||||+|.+.++|.+||..|| ..|.|+.|.|.++.
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~   84 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDI   84 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            34699999999999999999999999999999999999999999999999999999999999999 89999999999985


Q ss_pred             C
Q 012923          325 D  325 (453)
Q Consensus       325 ~  325 (453)
                      .
T Consensus        85 ~   85 (110)
T 3s8s_A           85 K   85 (110)
T ss_dssp             T
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=99.81  E-value=1.2e-19  Score=142.19  Aligned_cols=80  Identities=20%  Similarity=0.332  Sum_probs=75.8

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      +..++|||+|||+++|+++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|.+||+.+| ..|.|+.|.|.++
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            456899999999999999999999999999999999999999999999999999999999999888 5599999999998


Q ss_pred             c
Q 012923          207 S  207 (453)
Q Consensus       207 ~  207 (453)
                      .
T Consensus        84 ~   84 (110)
T 3s8s_A           84 I   84 (110)
T ss_dssp             S
T ss_pred             C
Confidence            5

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

Probab=99.81  E-value=4.8e-19  Score=140.73  Aligned_cols=87  Identities=22%  Similarity=0.379  Sum_probs=80.5

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      .....++|||+|||+.+|+++|+++|+.||.|..|+|++++.++.++|||||+|.+.++|.+||..|| ..|+|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   90 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            33456799999999999999999999999999999999998899999999999999999999999999 88999999999


Q ss_pred             EccCCCCC
Q 012923          322 RAIDGPKP  329 (453)
Q Consensus       322 ~a~~~~~~  329 (453)
                      |+..+...
T Consensus        91 ~a~~~~~~   98 (115)
T 2dgo_A           91 WATRKPPA   98 (115)
T ss_dssp             ESSCCCCC
T ss_pred             EccCCCCC
Confidence            99876544

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

Probab=99.80  E-value=5.5e-19  Score=145.48  Aligned_cols=86  Identities=20%  Similarity=0.352  Sum_probs=80.0

Q ss_pred             cccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEE
Q 012923          242 QSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNC  320 (453)
Q Consensus       242 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v  320 (453)
                      ......++|||+|||+.+|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+||..|| ..|.|+.|+|
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  116 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV  116 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            344556899999999999999999999999999999999999999999999999999999999999999 8899999999


Q ss_pred             EEccCCC
Q 012923          321 QRAIDGP  327 (453)
Q Consensus       321 ~~a~~~~  327 (453)
                      .++....
T Consensus       117 ~~a~~~~  123 (139)
T 1u6f_A          117 ALAASGH  123 (139)
T ss_dssp             EESSCCC
T ss_pred             EECCCCC
Confidence            9997654

>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=99.80  E-value=3.4e-19  Score=137.57  Aligned_cols=84  Identities=29%  Similarity=0.424  Sum_probs=78.5

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+||..|| ..|.|++|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   85 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            345799999999999999999999999999999999999899999999999999999999999999 8899999999999


Q ss_pred             cCCCC
Q 012923          324 IDGPK  328 (453)
Q Consensus       324 ~~~~~  328 (453)
                      ..+..
T Consensus        86 ~~~~~   90 (99)
T 1whw_A           86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCcc
Confidence            76553

>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=99.80  E-value=2.5e-19  Score=134.73  Aligned_cols=81  Identities=36%  Similarity=0.710  Sum_probs=76.2

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEe
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQL  205 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~  205 (453)
                      .....++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+|++.++..|.|+.|.|.+
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEEEEe
Confidence            45567899999999999999999999999999999999999899999999999999999999999888889999999987


Q ss_pred             c
Q 012923          206 A  206 (453)
Q Consensus       206 ~  206 (453)
                      +
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.80  E-value=2.4e-19  Score=150.73  Aligned_cols=83  Identities=20%  Similarity=0.364  Sum_probs=78.3

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|+.||.|..|.|++++.++.++|||||+|.+.++|.+||..|| ..|+|+.|.|.|+
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            345799999999999999999999999999999999999999999999999999999999999999 8999999999999


Q ss_pred             cCCC
Q 012923          324 IDGP  327 (453)
Q Consensus       324 ~~~~  327 (453)
                      ....
T Consensus       117 ~~~~  120 (156)
T 1h2v_Z          117 AGFK  120 (156)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7644

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

Probab=99.80  E-value=4.1e-19  Score=136.26  Aligned_cols=83  Identities=23%  Similarity=0.397  Sum_probs=77.9

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCccee-eeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEG-PLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v-~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ..++|||+|||+.+|+++|+++|+.||.|..| +|++++.++.++|||||+|.+.++|.+||..|| ..|.|++|.|.++
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            34699999999999999999999999999999 999998999999999999999999999999999 8899999999999


Q ss_pred             cCCCC
Q 012923          324 IDGPK  328 (453)
Q Consensus       324 ~~~~~  328 (453)
                      ..+..
T Consensus        84 ~~~~~   88 (96)
T 1x5t_A           84 FKKDS   88 (96)
T ss_dssp             CCCCC
T ss_pred             cccCC
Confidence            76553

>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=99.79  E-value=2.3e-19  Score=134.99  Aligned_cols=82  Identities=23%  Similarity=0.406  Sum_probs=75.4

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||..|| ..|+|+.|+|.|+.
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            34699999999999999999999999999999999998899999999999999999999999988 88999999999997


Q ss_pred             CCC
Q 012923          325 DGP  327 (453)
Q Consensus       325 ~~~  327 (453)
                      .+|
T Consensus        85 ~kp   87 (87)
T 3bs9_A           85 RKP   87 (87)
T ss_dssp             ---
T ss_pred             CCC
Confidence            653

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

Probab=99.79  E-value=4.8e-19  Score=135.63  Aligned_cols=82  Identities=20%  Similarity=0.397  Sum_probs=77.5

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||..|| ..|.|++|+|.++.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   83 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVT   83 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcc
Confidence            34699999999999999999999999999999999999999999999999999999999999988 89999999999997


Q ss_pred             CCC
Q 012923          325 DGP  327 (453)
Q Consensus       325 ~~~  327 (453)
                      .+.
T Consensus        84 ~~~   86 (95)
T 2dnz_A           84 ERL   86 (95)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            654

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

Probab=99.79  E-value=5.8e-19  Score=136.21  Aligned_cols=82  Identities=22%  Similarity=0.428  Sum_probs=76.9

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+||. ++ ..|+|+.|.|.++
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a   86 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRA   86 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEEC
Confidence            355799999999999999999999999999999999999999999999999999999999999 77 8999999999999


Q ss_pred             cCCC
Q 012923          324 IDGP  327 (453)
Q Consensus       324 ~~~~  327 (453)
                      ..+.
T Consensus        87 ~~~~   90 (99)
T 2dgs_A           87 EPRD   90 (99)
T ss_dssp             CCCC
T ss_pred             CCCc
Confidence            7654

>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=99.79  E-value=9e-19  Score=138.96  Aligned_cols=81  Identities=27%  Similarity=0.439  Sum_probs=76.4

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+|+++|+++|+.||.|..|.|+++. +++++|||||+|.+.++|.+||..|| ..|+|+.|.|.++.
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   84 (116)
T 2fy1_A            6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAK   84 (116)
T ss_dssp             SCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            34699999999999999999999999999999999998 99999999999999999999999999 88999999999997


Q ss_pred             CCC
Q 012923          325 DGP  327 (453)
Q Consensus       325 ~~~  327 (453)
                      ...
T Consensus        85 ~~~   87 (116)
T 2fy1_A           85 KPS   87 (116)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            654

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

Probab=99.79  E-value=8.9e-19  Score=139.38  Aligned_cols=87  Identities=36%  Similarity=0.664  Sum_probs=80.8

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQ  204 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~  204 (453)
                      ..+...++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||+.+++.|.|+.|.|.
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~   91 (116)
T 2cqd_A           12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVN   91 (116)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCCcCCCEEEEEE
Confidence            44566799999999999999999999999999999999999989999999999999999999999999999999999999


Q ss_pred             ecccCCC
Q 012923          205 LASIGPA  211 (453)
Q Consensus       205 ~~~~~~~  211 (453)
                      ++.....
T Consensus        92 ~a~~~~~   98 (116)
T 2cqd_A           92 LAYLGAK   98 (116)
T ss_dssp             ESTTTCC
T ss_pred             EcccCCC
Confidence            9975443

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

Probab=99.79  E-value=5.4e-19  Score=138.64  Aligned_cols=87  Identities=28%  Similarity=0.584  Sum_probs=76.9

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQ  204 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~  204 (453)
                      +.....++|||+|||+++|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+||..++..|.|+.|.|.
T Consensus        20 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~   99 (109)
T 2rs2_A           20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPK   99 (109)
T ss_dssp             ------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEE
Confidence            44556789999999999999999999999999999999999989999999999999999999999999888999999999


Q ss_pred             ecccCCC
Q 012923          205 LASIGPA  211 (453)
Q Consensus       205 ~~~~~~~  211 (453)
                      ++..+..
T Consensus       100 ~a~~~~~  106 (109)
T 2rs2_A          100 VAFPRRA  106 (109)
T ss_dssp             ECCCCCC
T ss_pred             EccCCCC
Confidence            9875543

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

Probab=99.79  E-value=5.1e-19  Score=137.61  Aligned_cols=85  Identities=25%  Similarity=0.390  Sum_probs=79.1

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ....++|||+|||+.+|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||..|| ..|+|+.|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            3456799999999999999999999999999999999999999999999999999999999999999 889999999999


Q ss_pred             ccCCCC
Q 012923          323 AIDGPK  328 (453)
Q Consensus       323 a~~~~~  328 (453)
                      +..+..
T Consensus        92 a~~~~~   97 (103)
T 2cq0_A           92 AKPSTN   97 (103)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            976543

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

Probab=99.79  E-value=5.5e-19  Score=137.20  Aligned_cols=84  Identities=27%  Similarity=0.465  Sum_probs=78.7

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+||..|| ..|+|++|+|.++
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            345799999999999999999999999999999999999999999999999999999999999998 8899999999999


Q ss_pred             cCCCC
Q 012923          324 IDGPK  328 (453)
Q Consensus       324 ~~~~~  328 (453)
                      ..+..
T Consensus        90 ~~~~~   94 (102)
T 1x5s_A           90 GKSSD   94 (102)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            76654

>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=99.79  E-value=5.2e-19  Score=131.76  Aligned_cols=80  Identities=19%  Similarity=0.370  Sum_probs=76.3

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCC
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDG  326 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~  326 (453)
                      .+|||+|||+.+|+++|+++|+.||.|..|.|++++.+++++|||||+|.+.++|.+|+..|| ..|+|++|+|.++..+
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            589999999999999999999999999999999999999999999999999999999999988 8899999999999765


Q ss_pred             C
Q 012923          327 P  327 (453)
Q Consensus       327 ~  327 (453)
                      .
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.79  E-value=8.2e-19  Score=136.99  Aligned_cols=85  Identities=15%  Similarity=0.296  Sum_probs=79.2

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ....++|||+|||+.+|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||..|| ..|+|++|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   91 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   91 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            3456799999999999999999999999999999999999999999999999999999999999999 889999999999


Q ss_pred             ccCCCC
Q 012923          323 AIDGPK  328 (453)
Q Consensus       323 a~~~~~  328 (453)
                      +.....
T Consensus        92 a~~~~~   97 (105)
T 1x5u_A           92 ASAHNK   97 (105)
T ss_dssp             TTTTSC
T ss_pred             CCCCCc
Confidence            976543

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

Probab=99.79  E-value=4.9e-19  Score=137.50  Aligned_cols=83  Identities=22%  Similarity=0.389  Sum_probs=78.1

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+||..|| ..|+|++|.|.++
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            345799999999999999999999999999999999999999999999999999999999999988 8899999999999


Q ss_pred             cCCC
Q 012923          324 IDGP  327 (453)
Q Consensus       324 ~~~~  327 (453)
                      ....
T Consensus        90 ~~~~   93 (102)
T 2cqb_A           90 KPMR   93 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.79  E-value=6.4e-19  Score=140.00  Aligned_cols=86  Identities=21%  Similarity=0.268  Sum_probs=79.3

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      .....++|||+|||+.+|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+||..|| ..|+|++|+|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  100 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ  100 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            33455799999999999999999999999999999999999999999999999999999999999998 89999999999


Q ss_pred             EccCCCC
Q 012923          322 RAIDGPK  328 (453)
Q Consensus       322 ~a~~~~~  328 (453)
                      |+..+..
T Consensus       101 ~a~~~~~  107 (115)
T 2cpz_A          101 LKRSKND  107 (115)
T ss_dssp             CCCCSCC
T ss_pred             EcCCCCc
Confidence            9976543

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

Probab=99.78  E-value=4.9e-19  Score=137.71  Aligned_cols=84  Identities=23%  Similarity=0.312  Sum_probs=78.5

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ....++|||+|||+.+|+++|+++|+.||.|..|.|++++.+++++|||||+|.+.++|.+||..|| ..|+|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV   89 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            3445799999999999999999999999999999999999999999999999999999999999988 889999999999


Q ss_pred             ccCCC
Q 012923          323 AIDGP  327 (453)
Q Consensus       323 a~~~~  327 (453)
                      +....
T Consensus        90 a~~~~   94 (103)
T 2dnm_A           90 ARYGR   94 (103)
T ss_dssp             CSSCC
T ss_pred             CCcCC
Confidence            97654

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

Probab=99.78  E-value=4.7e-19  Score=136.95  Aligned_cols=81  Identities=16%  Similarity=0.272  Sum_probs=74.3

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEe
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQL  205 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~  205 (453)
                      .+...++|||+|||+++|+++|+++|++||.|.+|+|++++. ++++|||||+|.+.++|.+||...+..|.|+.|.|.+
T Consensus         7 ~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~~   85 (103)
T 1s79_A            7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILF   85 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEEE
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345568999999999999999999999999999999999986 9999999999999999999999544779999999998


Q ss_pred             cc
Q 012923          206 AS  207 (453)
Q Consensus       206 ~~  207 (453)
                      +.
T Consensus        86 ~~   87 (103)
T 1s79_A           86 KD   87 (103)
T ss_dssp             HH
T ss_pred             ch
Confidence            75

>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=99.78  E-value=7.9e-19  Score=131.98  Aligned_cols=79  Identities=23%  Similarity=0.576  Sum_probs=74.6

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||..++..|+|+.|.|.+|
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            3557999999999999999999999999999999999999999999999999999999999988778899999999886

>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=99.78  E-value=4.8e-19  Score=150.16  Aligned_cols=142  Identities=18%  Similarity=0.237  Sum_probs=79.9

Q ss_pred             EEEccHHHHHHHHHcCCCc---cCCeEeEEEecccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEe
Q 012923          177 ILFKTRSGARKALKEPQKK---IGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVS  253 (453)
Q Consensus       177 V~f~~~~~a~~A~~~~~~~---~~gr~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~  253 (453)
                      .+|.+.++|..|+..++..   -.|+.+.+.+.......     ....       ............+......++|||+
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~-----~~~~-------~~~s~~~~~~~~~~~~~~~~~l~V~   78 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIH-----SYER-------VRNEDDDELEPGPQRSVEGWILFVT   78 (165)
T ss_dssp             -------------------------------------------------------------------CCCCC-CEEEEEE
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCcccccccc-----Cccc-------cccCCCCCCCCCCCCCCCCCEEEEe
Confidence            7889999999999888743   23444444432111000     0000       0000000011122334456799999


Q ss_pred             cCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCCCCC
Q 012923          254 NVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGPKPG  330 (453)
Q Consensus       254 nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~~~~  330 (453)
                      |||+.+|+++|+++|+.||.|..|.|++++.+|.++|||||+|.+.++|.+||..|| ..|.|++|.|.|+..++...
T Consensus        79 nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~~  156 (165)
T 1rk8_A           79 SIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR  156 (165)
T ss_dssp             SCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC---
T ss_pred             CCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCCCC
Confidence            999999999999999999999999999999999999999999999999999999999 88999999999998766543

>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=99.78  E-value=1.6e-18  Score=133.73  Aligned_cols=85  Identities=25%  Similarity=0.396  Sum_probs=78.4

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ....++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||..++ ..|.|+.|.|.+
T Consensus         5 ~~~~~~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            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            4567899999999999999999999999999999999999899999999999999999999998888 459999999999


Q ss_pred             cccCCC
Q 012923          206 ASIGPA  211 (453)
Q Consensus       206 ~~~~~~  211 (453)
                      +.....
T Consensus        85 a~~~~~   90 (99)
T 1whw_A           85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             cCCCcc
Confidence            976544

>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=99.78  E-value=4.9e-19  Score=143.16  Aligned_cols=87  Identities=26%  Similarity=0.430  Sum_probs=80.5

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      .....++|||+|||+.+|+++|+++|+.||.|..|.|++++.++.++|||||+|.+.++|.+||..|| ..|+|+.|.|.
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            34456799999999999999999999999999999999999999999999999999999999999988 89999999999


Q ss_pred             EccCCCCC
Q 012923          322 RAIDGPKP  329 (453)
Q Consensus       322 ~a~~~~~~  329 (453)
                      |+..+...
T Consensus        98 ~a~~~~~~  105 (126)
T 3ex7_B           98 WCFVRGPP  105 (126)
T ss_dssp             ESEESSSC
T ss_pred             EecCCCCC
Confidence            99876544

>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=99.78  E-value=1.4e-19  Score=136.87  Aligned_cols=81  Identities=17%  Similarity=0.197  Sum_probs=71.6

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccC--CcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYG--EIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G--~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      .+|||+|||+.+|+++|+++|++||  .|..|+|++++.+|+++|||||+|.+.++|.+||..|| ..|+|+.|+|.++.
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            4899999999999999999999999  99999999999999999999999999999999999999 89999999999997


Q ss_pred             CCCC
Q 012923          325 DGPK  328 (453)
Q Consensus       325 ~~~~  328 (453)
                      +.+.
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            6543

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

Probab=99.78  E-value=8e-19  Score=137.65  Aligned_cols=85  Identities=16%  Similarity=0.345  Sum_probs=77.2

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEc
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRA  323 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a  323 (453)
                      ....++|||+|||+.+|+++|+++|+.||.|..|+|++++.+|+++|||||+|.+.++|.+||..++..|+|+.|.|.++
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~~a  101 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA  101 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEc
Confidence            34457999999999999999999999999999999999999999999999999999999999999988899999999999


Q ss_pred             cCCCC
Q 012923          324 IDGPK  328 (453)
Q Consensus       324 ~~~~~  328 (453)
                      ..+..
T Consensus       102 ~~~~~  106 (109)
T 2rs2_A          102 FPRRA  106 (109)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            76543

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

Probab=99.78  E-value=1.9e-18  Score=133.29  Aligned_cols=87  Identities=21%  Similarity=0.382  Sum_probs=78.5

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEe
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQL  205 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~  205 (453)
                      .....++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||+..+..|.|+.|.|.+
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l~V~~   85 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKR   85 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34567899999999999999999999999999999999999899999999999999999999999434679999999999


Q ss_pred             cccCCCC
Q 012923          206 ASIGPAT  212 (453)
Q Consensus       206 ~~~~~~~  212 (453)
                      +......
T Consensus        86 a~~~~~~   92 (99)
T 2dgs_A           86 AEPRDSK   92 (99)
T ss_dssp             CCCCCCC
T ss_pred             CCCCccc
Confidence            9755443

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

Probab=99.78  E-value=7.4e-19  Score=137.49  Aligned_cols=86  Identities=26%  Similarity=0.406  Sum_probs=79.8

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      .....++|||+|||+.+|+++|+++|+.||.|..|.|++++.+++++|||||+|.+.++|.+||..|| ..|+|+.|.|.
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   98 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   98 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEE
Confidence            34456799999999999999999999999999999999999999999999999999999999999988 89999999999


Q ss_pred             EccCCCC
Q 012923          322 RAIDGPK  328 (453)
Q Consensus       322 ~a~~~~~  328 (453)
                      ++..++.
T Consensus        99 ~a~~~~~  105 (106)
T 1p27_B           99 WCFVRGP  105 (106)
T ss_dssp             ESEESSC
T ss_pred             eecCCCC
Confidence            9987653

>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=99.78  E-value=7.6e-19  Score=132.14  Aligned_cols=81  Identities=31%  Similarity=0.513  Sum_probs=74.5

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLAS  207 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~  207 (453)
                      ..++|||+|||.++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+|++.++ ..+.|+.|.|.++.
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            46899999999999999999999999999999999998899999999999999999999999877 56999999999986


Q ss_pred             cC
Q 012923          208 IG  209 (453)
Q Consensus       208 ~~  209 (453)
                      .+
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            43

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

Probab=99.78  E-value=1.4e-18  Score=136.21  Aligned_cols=86  Identities=27%  Similarity=0.368  Sum_probs=79.2

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeecc-CCCCCCceEEEEEECCHHHHHHHHHcC-C-CccCCeEEE
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGID-KATGKPKGFCLFVYKTVDAAKKALEEP-H-KNFEGHILN  319 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d-~~~g~~kg~afV~F~~~~~A~~Al~~~-~-~~l~g~~l~  319 (453)
                      .....++|||+|||+.+|+++|+++|+.||.|..|+|+++ +.+++++|||||+|.+.++|.+||..| | ..|.|+.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            3445679999999999999999999999999999999999 789999999999999999999999999 7 899999999


Q ss_pred             EEEccCCCC
Q 012923          320 CQRAIDGPK  328 (453)
Q Consensus       320 v~~a~~~~~  328 (453)
                      |.|+..+..
T Consensus        91 v~~a~~~~~   99 (107)
T 2cph_A           91 LEWADSEVT   99 (107)
T ss_dssp             EEECCCCCC
T ss_pred             EEeCCCCCC
Confidence            999976543

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

Probab=99.78  E-value=1.7e-18  Score=134.56  Aligned_cols=82  Identities=26%  Similarity=0.270  Sum_probs=76.0

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ....++|||+|||+.+|+++|+++|+.|| |..|+|++++.+++++|||||+|.+.++|.+|| .|| ..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   89 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDI   89 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEE
Confidence            34467999999999999999999999997 999999999999999999999999999999999 788 899999999999


Q ss_pred             ccCCC
Q 012923          323 AIDGP  327 (453)
Q Consensus       323 a~~~~  327 (453)
                      +..+.
T Consensus        90 a~~~~   94 (103)
T 2dng_A           90 AEGRK   94 (103)
T ss_dssp             CCCCC
T ss_pred             ecCCC
Confidence            97654

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

Probab=99.78  E-value=1.3e-18  Score=134.58  Aligned_cols=83  Identities=20%  Similarity=0.374  Sum_probs=77.4

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ....++|||+|||+.+|+++|+++|+.||.|..|+|++++ +++++|||||+|.+.++|.+||..|| ..|+|++|+|.+
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   92 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAI   92 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456799999999999999999999999999999999998 99999999999999999999999988 889999999999


Q ss_pred             ccCCC
Q 012923          323 AIDGP  327 (453)
Q Consensus       323 a~~~~  327 (453)
                      +.+++
T Consensus        93 a~~~~   97 (100)
T 2do4_A           93 SNSGP   97 (100)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            97654

>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=99.78  E-value=1.2e-18  Score=136.20  Aligned_cols=84  Identities=23%  Similarity=0.344  Sum_probs=77.6

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-Ccc---CCeEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNF---EGHILN  319 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l---~g~~l~  319 (453)
                      ....++|||+|||+.+|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||..|| ..+   .|++|.
T Consensus        10 ~~~~~~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           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEE
Confidence            3455799999999999999999999999999999999999999999999999999999999999998 666   889999


Q ss_pred             EEEccCCC
Q 012923          320 CQRAIDGP  327 (453)
Q Consensus       320 v~~a~~~~  327 (453)
                      |.++....
T Consensus        90 v~~a~~~~   97 (106)
T 2dgp_A           90 VKPADSES   97 (106)
T ss_dssp             EEECCCCS
T ss_pred             EEECCccc
Confidence            99997654

>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=99.78  E-value=1.6e-18  Score=135.07  Aligned_cols=81  Identities=16%  Similarity=0.249  Sum_probs=75.6

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCC-CCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKAT-GKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~-g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ...++|||+|||+.+|+++|+++|+.|| |..|+|++++.+ ++++|||||+|.+.++|.+|| .|| ..|.|+.|.|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   90 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEE
Confidence            3457999999999999999999999999 999999999888 999999999999999999999 888 889999999999


Q ss_pred             ccCCC
Q 012923          323 AIDGP  327 (453)
Q Consensus       323 a~~~~  327 (453)
                      +..+.
T Consensus        91 a~~~~   95 (104)
T 1wi8_A           91 ADQAQ   95 (104)
T ss_dssp             CCCCC
T ss_pred             ccCCC
Confidence            97654

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

Probab=99.78  E-value=8.4e-19  Score=135.05  Aligned_cols=83  Identities=25%  Similarity=0.380  Sum_probs=76.7

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCC---CCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKA---TGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~---~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      ..++|||+|||+.+|+++|+++|+.||.|..|+|++++.   +++++|||||+|.+.++|.+||..|| ..|+|+.|.|.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR   83 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            346999999999999999999999999999999999876   66899999999999999999999999 89999999999


Q ss_pred             EccCCCC
Q 012923          322 RAIDGPK  328 (453)
Q Consensus       322 ~a~~~~~  328 (453)
                      ++..+..
T Consensus        84 ~a~~~~~   90 (98)
T 2cpf_A           84 ISERATK   90 (98)
T ss_dssp             CSSCSSC
T ss_pred             EccCCCC
Confidence            9976543

>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=99.77  E-value=1e-18  Score=134.00  Aligned_cols=81  Identities=15%  Similarity=0.404  Sum_probs=77.0

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .++|||+|||+.+++++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||..+| ..|+|+.|.|.++..
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            4699999999999999999999999999999999999999999999999999999999999998 889999999999976


Q ss_pred             CC
Q 012923          326 GP  327 (453)
Q Consensus       326 ~~  327 (453)
                      +.
T Consensus        82 ~~   83 (96)
T 2x1f_A           82 SD   83 (96)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

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

Probab=99.77  E-value=3.2e-18  Score=135.99  Aligned_cols=88  Identities=31%  Similarity=0.520  Sum_probs=80.3

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ......++|||+|||+++|+++|+++|.+||.|..|+|++++.+++++|||||+|.+.++|.+||+.++ ..|.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   89 (115)
T 2dgo_A           10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRT   89 (115)
T ss_dssp             CCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            345567899999999999999999999999999999999998899999999999999999999999887 5599999999


Q ss_pred             EecccCCCC
Q 012923          204 QLASIGPAT  212 (453)
Q Consensus       204 ~~~~~~~~~  212 (453)
                      .++......
T Consensus        90 ~~a~~~~~~   98 (115)
T 2dgo_A           90 NWATRKPPA   98 (115)
T ss_dssp             EESSCCCCC
T ss_pred             EEccCCCCC
Confidence            999766544

>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=99.77  E-value=1.4e-18  Score=137.96  Aligned_cols=88  Identities=23%  Similarity=0.380  Sum_probs=79.8

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ...+..++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||+.++ ..|.|+.|.|
T Consensus        20 ~~~~~~~~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           20 KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKV   99 (115)
T ss_dssp             CCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            445567899999999999999999999999999999999999899999999999999999999998877 5699999999


Q ss_pred             EecccCCCC
Q 012923          204 QLASIGPAT  212 (453)
Q Consensus       204 ~~~~~~~~~  212 (453)
                      .++......
T Consensus       100 ~~a~~~~~~  108 (115)
T 2cpz_A          100 QLKRSKNDS  108 (115)
T ss_dssp             ECCCCSCCC
T ss_pred             EEcCCCCcC
Confidence            998755443

>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=99.77  E-value=7.8e-19  Score=131.44  Aligned_cols=79  Identities=23%  Similarity=0.438  Sum_probs=75.3

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+++++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+|+..|| ..|+|++|+|.|++
T Consensus         6 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~ak   85 (85)
T 3mdf_A            6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   85 (85)
T ss_dssp             CSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            45799999999999999999999999999999999998999999999999999999999999988 89999999999974

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

Probab=99.77  E-value=2.6e-19  Score=138.15  Aligned_cols=80  Identities=30%  Similarity=0.374  Sum_probs=76.2

Q ss_pred             ccEEEEecCCC------CccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCC-eEE
Q 012923          247 QRKIFVSNVGS------ELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEG-HIL  318 (453)
Q Consensus       247 ~~~l~V~nLp~------~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g-~~l  318 (453)
                      .++|||+|||+      .+++++|+++|++||.|..|+|++++.||+++|||||+|.+.++|.+||..|| ..|.| +.|
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            46999999999      99999999999999999999999999999999999999999999999999999 89999 999


Q ss_pred             EEEEccCC
Q 012923          319 NCQRAIDG  326 (453)
Q Consensus       319 ~v~~a~~~  326 (453)
                      .|.++.++
T Consensus        86 ~V~~a~~~   93 (100)
T 3ns6_A           86 FLYTMKDV   93 (100)
T ss_dssp             EEEESHHH
T ss_pred             EEEECchh
Confidence            99998653

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

Probab=99.77  E-value=1.2e-18  Score=135.77  Aligned_cols=82  Identities=23%  Similarity=0.386  Sum_probs=76.6

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhc-cCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-Cc-cCCeEEEEEE
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSK-YGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KN-FEGHILNCQR  322 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~-~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~-l~g~~l~v~~  322 (453)
                      ..++|||+|||+.+|+++|+++|+. ||.|..|+|++++ +++++|||||+|.+.++|.+||..|+ .. |+|++|.|.+
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~   86 (104)
T 2dhg_A            8 PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSV   86 (104)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCB
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEE
Confidence            4579999999999999999999999 9999999999998 99999999999999999999999999 77 9999999999


Q ss_pred             ccCCCC
Q 012923          323 AIDGPK  328 (453)
Q Consensus       323 a~~~~~  328 (453)
                      +..+..
T Consensus        87 a~~~~~   92 (104)
T 2dhg_A           87 AIPKAS   92 (104)
T ss_dssp             CCCCCS
T ss_pred             ccCCCc
Confidence            965543

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

Probab=99.77  E-value=1.5e-18  Score=134.98  Aligned_cols=86  Identities=26%  Similarity=0.360  Sum_probs=79.1

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      .....++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||..++ ..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            44567899999999999999999999999999999999998899999999999999999999999888 56999999999


Q ss_pred             ecccCCC
Q 012923          205 LASIGPA  211 (453)
Q Consensus       205 ~~~~~~~  211 (453)
                      ++.....
T Consensus        91 ~a~~~~~   97 (103)
T 2cq0_A           91 WAKPSTN   97 (103)
T ss_dssp             ESSCCCC
T ss_pred             ECCCCCC
Confidence            9875544

>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=99.77  E-value=1.7e-18  Score=128.98  Aligned_cols=79  Identities=28%  Similarity=0.442  Sum_probs=74.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecccC
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASIG  209 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~~  209 (453)
                      ++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+|+..++ ..|.|+.|.|.++..+
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            689999999999999999999999999999999998899999999999999999999999877 5699999999998644

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

Probab=99.77  E-value=1.6e-18  Score=137.22  Aligned_cols=86  Identities=29%  Similarity=0.427  Sum_probs=79.0

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcc--------eeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-Ccc
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIE--------EGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNF  313 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~--------~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l  313 (453)
                      .....++|||+|||+.+|+++|+++|+.||.|.        .|+|++++.+++++|||||+|.+.++|.+||..|| ..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            334567999999999999999999999999999        69999998999999999999999999999999988 889


Q ss_pred             CCeEEEEEEccCCCC
Q 012923          314 EGHILNCQRAIDGPK  328 (453)
Q Consensus       314 ~g~~l~v~~a~~~~~  328 (453)
                      .|+.|+|.++..+..
T Consensus        91 ~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           91 QGSKLKVSLARKKPP  105 (113)
T ss_dssp             TTEECEEECSSCCCC
T ss_pred             CCCEEEEEECCCCCC
Confidence            999999999976543

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

Probab=99.77  E-value=2.1e-18  Score=132.25  Aligned_cols=84  Identities=26%  Similarity=0.365  Sum_probs=77.6

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEE-EEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDC-KAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v-~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ...++|||+|||+++|+++|+++|++||.|..| +|++++.+++++|||||+|.+.++|.+||..++ ..|.|+.|.|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            356899999999999999999999999999999 999998899999999999999999999999888 559999999999


Q ss_pred             cccCCC
Q 012923          206 ASIGPA  211 (453)
Q Consensus       206 ~~~~~~  211 (453)
                      +.....
T Consensus        83 a~~~~~   88 (96)
T 1x5t_A           83 AFKKDS   88 (96)
T ss_dssp             SCCCCC
T ss_pred             ecccCC
Confidence            875544

>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=99.77  E-value=9.3e-19  Score=138.78  Aligned_cols=79  Identities=22%  Similarity=0.360  Sum_probs=73.1

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .++|||+|||+.+|+++|+++|+.||.|.+|+|++++  +.++|||||+|.+.++|.+||..|+ ..|+|++|.|.++..
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            3589999999999999999999999999999999985  4589999999999999999999998 899999999999875


Q ss_pred             CC
Q 012923          326 GP  327 (453)
Q Consensus       326 ~~  327 (453)
                      +.
T Consensus        83 ~~   84 (115)
T 4f25_A           83 RK   84 (115)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

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

Probab=99.77  E-value=1.1e-18  Score=133.55  Aligned_cols=82  Identities=22%  Similarity=0.344  Sum_probs=77.2

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ....++|||+|||+.+|+++|+++|++||.|..|.|++++.+++++|||||+|.+.++|.+||..|| ..|+|++|+|.+
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            3456799999999999999999999999999999999999999999999999999999999999998 889999999999


Q ss_pred             ccC
Q 012923          323 AID  325 (453)
Q Consensus       323 a~~  325 (453)
                      +.+
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            864

>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=99.77  E-value=2.7e-18  Score=134.04  Aligned_cols=87  Identities=25%  Similarity=0.348  Sum_probs=79.7

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ......++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||..++ ..|.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            345567899999999999999999999999999999999999899999999999999999999999887 5699999999


Q ss_pred             EecccCCC
Q 012923          204 QLASIGPA  211 (453)
Q Consensus       204 ~~~~~~~~  211 (453)
                      .++.....
T Consensus        90 ~~a~~~~~   97 (105)
T 1x5u_A           90 NKASAHNK   97 (105)
T ss_dssp             EETTTTSC
T ss_pred             EECCCCCc
Confidence            99876544

>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=99.77  E-value=1.5e-18  Score=129.87  Aligned_cols=80  Identities=25%  Similarity=0.422  Sum_probs=74.9

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ....++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+|++.++ ..|.|+.|.|.+
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            3467899999999999999999999999999999999998899999999999999999999998877 569999999998


Q ss_pred             c
Q 012923          206 A  206 (453)
Q Consensus       206 ~  206 (453)
                      +
T Consensus        84 a   84 (85)
T 3mdf_A           84 A   84 (85)
T ss_dssp             C
T ss_pred             c
Confidence            6

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

Probab=99.77  E-value=1.6e-18  Score=134.84  Aligned_cols=84  Identities=21%  Similarity=0.406  Sum_probs=77.4

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      .....++|||+|||+.+|+++|+++|+.||.|..|+|+++  ++.++|||||+|.+.++|.+||..|| ..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVA   88 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            3345679999999999999999999999999999999998  89999999999999999999999988 88999999999


Q ss_pred             EccCCCC
Q 012923          322 RAIDGPK  328 (453)
Q Consensus       322 ~a~~~~~  328 (453)
                      ++..+..
T Consensus        89 ~a~~~~~   95 (103)
T 2d9p_A           89 LAQRKEE   95 (103)
T ss_dssp             ECSSCCC
T ss_pred             Eeccccc
Confidence            9976553

>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=99.77  E-value=1.6e-18  Score=136.59  Aligned_cols=86  Identities=24%  Similarity=0.375  Sum_probs=79.7

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      .....++|||+|||+.+|+++|+++|+.||.|..|.|++++.+++++|||||+|.+.++|.+||..|| ..|+|+.|.|.
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  101 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  101 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34456799999999999999999999999999999999999999999999999999999999999988 88999999999


Q ss_pred             EccCCCC
Q 012923          322 RAIDGPK  328 (453)
Q Consensus       322 ~a~~~~~  328 (453)
                      |+..+..
T Consensus       102 ~a~~~~~  108 (110)
T 1oo0_B          102 WCFVKGP  108 (110)
T ss_dssp             ESEESSC
T ss_pred             EcccCCC
Confidence            9976653

>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=99.77  E-value=2.4e-18  Score=134.28  Aligned_cols=83  Identities=20%  Similarity=0.298  Sum_probs=76.6

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCC---eEEEE
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEG---HILNC  320 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g---~~l~v  320 (453)
                      ...++|||+|||+.+|+++|+++|+.||.|..|+|++++ +++++|||||+|.+.++|.+||..|| ..|.|   ++|.|
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            346799999999999999999999999999999999987 89999999999999999999999998 77887   99999


Q ss_pred             EEccCCCC
Q 012923          321 QRAIDGPK  328 (453)
Q Consensus       321 ~~a~~~~~  328 (453)
                      .++.....
T Consensus        92 ~~a~~~~~   99 (105)
T 2dnh_A           92 KFADTDKE   99 (105)
T ss_dssp             EESCSSCC
T ss_pred             EECccCcc
Confidence            99976553

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

Probab=99.77  E-value=1.5e-18  Score=132.58  Aligned_cols=81  Identities=27%  Similarity=0.439  Sum_probs=76.4

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ....++|||+|||+.+|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||..|| ..|+|++|+|.|
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            3455799999999999999999999999999999999999999999999999999999999999999 889999999999


Q ss_pred             cc
Q 012923          323 AI  324 (453)
Q Consensus       323 a~  324 (453)
                      ++
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>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=99.77  E-value=2.5e-18  Score=135.68  Aligned_cols=88  Identities=24%  Similarity=0.423  Sum_probs=79.7

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC------C-ccC
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ------K-KIG  197 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~------~-~~~  197 (453)
                      ......++|||+|||+++|+++|+++|.+||.|..|+|++++.+++++|||||+|.+.++|.+||..++      . .|.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~   89 (111)
T 1x4h_A           10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   89 (111)
T ss_dssp             CCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             CcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEc
Confidence            445567899999999999999999999999999999999999899999999999999999999999886      4 599


Q ss_pred             CeEeEEEecccCCCC
Q 012923          198 NRMTACQLASIGPAT  212 (453)
Q Consensus       198 gr~~~v~~~~~~~~~  212 (453)
                      |+.|.|.++......
T Consensus        90 g~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           90 GRQLKVDLAVTRDEA  104 (111)
T ss_dssp             SCEEEEECCCCCCCC
T ss_pred             CEEEEEEECCCCccC
Confidence            999999998765443

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

Probab=99.77  E-value=1.9e-18  Score=132.21  Aligned_cols=84  Identities=25%  Similarity=0.429  Sum_probs=77.6

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ..+++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||+.++ ..|.|+.|.|.++
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            456899999999999999999999999999999999999899999999999999999999999777 5699999999999


Q ss_pred             ccCCC
Q 012923          207 SIGPA  211 (453)
Q Consensus       207 ~~~~~  211 (453)
                      .....
T Consensus        83 ~~~~~   87 (95)
T 2dnz_A           83 TERLD   87 (95)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            75544

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

Probab=99.77  E-value=1e-18  Score=135.06  Aligned_cols=78  Identities=14%  Similarity=0.234  Sum_probs=73.4

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+|+++|+++|++||.|..|+|++++. ++++|||||+|.+.++|.+||. ++ ..|+|+.|.|.++.
T Consensus        10 ~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A           10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   87 (103)
T ss_dssp             GGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEch
Confidence            447999999999999999999999999999999999987 9999999999999999999999 66 89999999999976


Q ss_pred             C
Q 012923          325 D  325 (453)
Q Consensus       325 ~  325 (453)
                      .
T Consensus        88 ~   88 (103)
T 1s79_A           88 D   88 (103)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=99.77  E-value=7.7e-19  Score=156.50  Aligned_cols=79  Identities=18%  Similarity=0.363  Sum_probs=74.1

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccC--CeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYG--EIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G--~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ..++|||+|||+++|+++|+++|++||  .|..|+|++|+.+++++|||||+|.+.++|.+||+.|+ ..|.|+.|.|.+
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            467999999999999999999999999  99999999999999999999999999999999999888 569999999999


Q ss_pred             cc
Q 012923          206 AS  207 (453)
Q Consensus       206 ~~  207 (453)
                      +.
T Consensus       147 a~  148 (229)
T 3q2s_C          147 VN  148 (229)
T ss_dssp             CC
T ss_pred             CC
Confidence            85

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

Probab=99.77  E-value=5.1e-18  Score=134.59  Aligned_cols=81  Identities=19%  Similarity=0.211  Sum_probs=75.6

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|+.||.|..|+|++++ +++++|||||+|.+.++|.+||..|| ..|+|+.|.|.++
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            345799999999999999999999999999999999987 69999999999999999999999988 8899999999998


Q ss_pred             cCC
Q 012923          324 IDG  326 (453)
Q Consensus       324 ~~~  326 (453)
                      ...
T Consensus        92 ~~~   94 (114)
T 2do0_A           92 ERA   94 (114)
T ss_dssp             SCC
T ss_pred             ccC
Confidence            654

>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=99.77  E-value=2.6e-18  Score=135.63  Aligned_cols=85  Identities=19%  Similarity=0.330  Sum_probs=78.2

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-------CccCCe
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-------KNFEGH  316 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-------~~l~g~  316 (453)
                      ....++|||+|||+.+|+++|+++|+.||.|..|+|++++.++.++|||||+|.+.++|.+||..+|       ..|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~   91 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   91 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCE
Confidence            3456799999999999999999999999999999999999999999999999999999999999885       578999


Q ss_pred             EEEEEEccCCCC
Q 012923          317 ILNCQRAIDGPK  328 (453)
Q Consensus       317 ~l~v~~a~~~~~  328 (453)
                      .|.|.++..+..
T Consensus        92 ~l~v~~a~~~~~  103 (111)
T 1x4h_A           92 QLKVDLAVTRDE  103 (111)
T ss_dssp             EEEEECCCCCCC
T ss_pred             EEEEEECCCCcc
Confidence            999999976543

>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=99.77  E-value=3.7e-19  Score=134.60  Aligned_cols=80  Identities=18%  Similarity=0.339  Sum_probs=70.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccC--CeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecc
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYG--EIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLAS  207 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G--~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~  207 (453)
                      .+|||+|||+++|+++|+++|++||  .|.+|+|++++.+|+++|||||+|.+.++|.+|++.++ ..|.|+.|.|.++.
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  99999999999999999999999999999999999888 56999999999987


Q ss_pred             cCC
Q 012923          208 IGP  210 (453)
Q Consensus       208 ~~~  210 (453)
                      ..+
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            543

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

Probab=99.77  E-value=2.6e-18  Score=132.76  Aligned_cols=85  Identities=24%  Similarity=0.468  Sum_probs=77.6

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ......++|||+|||+++|+++|+++|++||.|..|+|+.++ +++++|||||+|.+.++|.+||+.++ ..|.|+.|.|
T Consensus        12 ~~~~~~~~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           12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKV   90 (100)
T ss_dssp             SSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            344567899999999999999999999999999999999998 99999999999999999999998877 5599999999


Q ss_pred             EecccCC
Q 012923          204 QLASIGP  210 (453)
Q Consensus       204 ~~~~~~~  210 (453)
                      .++....
T Consensus        91 ~~a~~~~   97 (100)
T 2do4_A           91 AISNSGP   97 (100)
T ss_dssp             EECCCCS
T ss_pred             EECCCCC
Confidence            9986543

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

Probab=99.77  E-value=1.7e-18  Score=133.52  Aligned_cols=82  Identities=27%  Similarity=0.382  Sum_probs=76.8

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcce--------eeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-Ccc
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEE--------GPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNF  313 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~--------v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l  313 (453)
                      .....++|||+|||+.+|+++|+++|++||.|..        |+|++++.+++++|||||+|.+.++|.+||..|| ..|
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            3445679999999999999999999999999999        9999999999999999999999999999999988 899


Q ss_pred             CCeEEEEEEcc
Q 012923          314 EGHILNCQRAI  324 (453)
Q Consensus       314 ~g~~l~v~~a~  324 (453)
                      .|+.|+|.+|.
T Consensus        89 ~g~~l~V~~A~   99 (99)
T 2la6_A           89 SGNPIKVSFAT   99 (99)
T ss_dssp             SSSBCEEEECC
T ss_pred             CCcEEEEEecC
Confidence            99999999973

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

Probab=99.76  E-value=4.9e-19  Score=136.62  Aligned_cols=80  Identities=20%  Similarity=0.267  Sum_probs=75.0

Q ss_pred             CCcCeEEEcCCCC------CCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCC-e
Q 012923          128 PVHRKIFVHGLGW------DTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGN-R  199 (453)
Q Consensus       128 ~~~~~lfV~nLp~------~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~g-r  199 (453)
                      ..+++|||+|||+      ++++++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||+.++ ..|.| +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            3468999999999      99999999999999999999999999899999999999999999999999887 55898 9


Q ss_pred             EeEEEecc
Q 012923          200 MTACQLAS  207 (453)
Q Consensus       200 ~~~v~~~~  207 (453)
                      .|.|.++.
T Consensus        84 ~l~V~~a~   91 (100)
T 3ns6_A           84 RLFLYTMK   91 (100)
T ss_dssp             BCEEEESH
T ss_pred             EEEEEECc
Confidence            99999985

>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=99.76  E-value=4.5e-18  Score=132.20  Aligned_cols=85  Identities=19%  Similarity=0.329  Sum_probs=77.6

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEc
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRA  323 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a  323 (453)
                      ....++|||+|||+.+|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+||.. .+.|+|+.|.|.++
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            34457999999999999999999999999999999999999999999999999999999999995 46799999999999


Q ss_pred             cCCCCC
Q 012923          324 IDGPKP  329 (453)
Q Consensus       324 ~~~~~~  329 (453)
                      ..+...
T Consensus        91 ~~~~~~   96 (103)
T 2cqg_A           91 NSKQSQ   96 (103)
T ss_dssp             CTTCCC
T ss_pred             CCCCcC
Confidence            776543

>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=99.76  E-value=2.3e-19  Score=145.92  Aligned_cols=79  Identities=14%  Similarity=0.147  Sum_probs=72.1

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+|+++|+++|++|| |+.|+|++++. ++++|||||+|.+.++|.+|| .+| ..|+||.|.|.++.
T Consensus        45 ~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~  121 (139)
T 2hgn_A           45 TGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNS  121 (139)
T ss_dssp             CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECC
Confidence            446999999999999999999999999 77999999975 999999999999999999999 667 89999999999986


Q ss_pred             CCC
Q 012923          325 DGP  327 (453)
Q Consensus       325 ~~~  327 (453)
                      ...
T Consensus       122 ~~~  124 (139)
T 2hgn_A          122 TTG  124 (139)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            543

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

Probab=99.76  E-value=2.2e-18  Score=133.75  Aligned_cols=87  Identities=23%  Similarity=0.351  Sum_probs=79.0

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      .....++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||+.++ ..|.|+.|.|.
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   87 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999877 55999999999


Q ss_pred             ecccCCCC
Q 012923          205 LASIGPAT  212 (453)
Q Consensus       205 ~~~~~~~~  212 (453)
                      ++......
T Consensus        88 ~a~~~~~~   95 (102)
T 2cqb_A           88 LAKPMRIK   95 (102)
T ss_dssp             ECCCCCCC
T ss_pred             eCCCCCCC
Confidence            98755443

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

Probab=99.76  E-value=2.4e-18  Score=131.66  Aligned_cols=83  Identities=25%  Similarity=0.396  Sum_probs=77.0

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ......++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+|+..++ ..|.|+.|.|
T Consensus        10 ~~~~~~~~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           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   89 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            345567899999999999999999999999999999999999899999999999999999999999877 5599999999


Q ss_pred             Eecc
Q 012923          204 QLAS  207 (453)
Q Consensus       204 ~~~~  207 (453)
                      .++.
T Consensus        90 ~~a~   93 (95)
T 2cqc_A           90 SGPS   93 (95)
T ss_dssp             ECCS
T ss_pred             EecC
Confidence            9975

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

Probab=99.76  E-value=2.8e-18  Score=136.44  Aligned_cols=83  Identities=17%  Similarity=0.437  Sum_probs=77.5

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+||.. + ..|+|+.|.|.++
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a  103 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRA  103 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEEC
Confidence            3457999999999999999999999999999999999999999999999999999999999999 6 8899999999999


Q ss_pred             cCCCC
Q 012923          324 IDGPK  328 (453)
Q Consensus       324 ~~~~~  328 (453)
                      ..+..
T Consensus       104 ~~~~~  108 (116)
T 1x4b_A          104 VAREE  108 (116)
T ss_dssp             SSCCC
T ss_pred             CCCcc
Confidence            76543

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

Probab=99.76  E-value=2e-18  Score=134.27  Aligned_cols=86  Identities=21%  Similarity=0.347  Sum_probs=78.6

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      .....++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||+.++ ..|.|+.|.|.
T Consensus         9 ~~~~~~~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            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQ   88 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34557899999999999999999999999999999999999899999999999999999999999777 56999999999


Q ss_pred             ecccCCC
Q 012923          205 LASIGPA  211 (453)
Q Consensus       205 ~~~~~~~  211 (453)
                      ++.....
T Consensus        89 ~a~~~~~   95 (103)
T 2dnm_A           89 VARYGRR   95 (103)
T ss_dssp             ECSSCCS
T ss_pred             ECCcCCC
Confidence            9975443

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

Probab=99.76  E-value=2.3e-18  Score=133.60  Aligned_cols=86  Identities=28%  Similarity=0.518  Sum_probs=78.8

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      .....++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||+.++ ..|.|+.|.|.
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   87 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD   87 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34567899999999999999999999999999999999999899999999999999999999998877 56999999999


Q ss_pred             ecccCCC
Q 012923          205 LASIGPA  211 (453)
Q Consensus       205 ~~~~~~~  211 (453)
                      ++.....
T Consensus        88 ~a~~~~~   94 (102)
T 1x5s_A           88 QAGKSSD   94 (102)
T ss_dssp             EEECCCC
T ss_pred             ECCCCCC
Confidence            9876544

>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=99.76  E-value=5.4e-18  Score=131.77  Aligned_cols=87  Identities=25%  Similarity=0.472  Sum_probs=78.7

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQ  204 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~  204 (453)
                      ......++|||+|||+++|+++|+++|.+||.|..|+|++++.+++++|||||+|.+.++|.+||.. ...|.|+.|.|.
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~g~~l~v~   88 (103)
T 2cqg_A           10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ-RHMIDGRWCDCK   88 (103)
T ss_dssp             CCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS-CEEETTEEEEEE
T ss_pred             CccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc-CCeeCCeEEEEE
Confidence            3445678999999999999999999999999999999999998999999999999999999999995 457999999999


Q ss_pred             ecccCCCC
Q 012923          205 LASIGPAT  212 (453)
Q Consensus       205 ~~~~~~~~  212 (453)
                      ++......
T Consensus        89 ~a~~~~~~   96 (103)
T 2cqg_A           89 LPNSKQSQ   96 (103)
T ss_dssp             CCCTTCCC
T ss_pred             ecCCCCcC
Confidence            99765443

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

Probab=99.76  E-value=2.5e-18  Score=132.37  Aligned_cols=84  Identities=26%  Similarity=0.426  Sum_probs=76.4

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCC---CCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKV---SGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~---~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ...++|||+|||+++|+++|+++|++||.|..|+|++++.   +++++|||||+|.+.++|.+||..|+ ..|.|+.|.|
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            4568999999999999999999999999999999999886   56899999999999999999999887 5699999999


Q ss_pred             EecccCCC
Q 012923          204 QLASIGPA  211 (453)
Q Consensus       204 ~~~~~~~~  211 (453)
                      .++.....
T Consensus        83 ~~a~~~~~   90 (98)
T 2cpf_A           83 RISERATK   90 (98)
T ss_dssp             ECSSCSSC
T ss_pred             EEccCCCC
Confidence            99875544

>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=99.76  E-value=2.6e-18  Score=131.68  Aligned_cols=81  Identities=25%  Similarity=0.518  Sum_probs=75.9

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~  208 (453)
                      +++|||+|||.++|+++|+++|++||.|..|+|+.++.+++++|||||+|.+.++|.+|++.++ ..|.|+.|.|.++..
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            5799999999999999999999999999999999999899999999999999999999999877 559999999999875


Q ss_pred             CC
Q 012923          209 GP  210 (453)
Q Consensus       209 ~~  210 (453)
                      ..
T Consensus        82 ~~   83 (96)
T 2x1f_A           82 SD   83 (96)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

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

Probab=99.76  E-value=2.7e-18  Score=131.08  Aligned_cols=81  Identities=26%  Similarity=0.454  Sum_probs=75.7

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      ..+..++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+|++.++ ..|.|+.|.|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   91 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKAS   91 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            44567899999999999999999999999999999999999889999999999999999999999888 45999999999


Q ss_pred             ec
Q 012923          205 LA  206 (453)
Q Consensus       205 ~~  206 (453)
                      ++
T Consensus        92 ~a   93 (94)
T 2e5h_A           92 IA   93 (94)
T ss_dssp             EC
T ss_pred             ec
Confidence            86

>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=99.76  E-value=1.9e-18  Score=135.24  Aligned_cols=84  Identities=23%  Similarity=0.427  Sum_probs=78.4

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      .....++|||+|||+.+|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||..+| ..|+|++|+|.
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG  101 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34456799999999999999999999999999999999999999999999999999999999999988 89999999999


Q ss_pred             EccCC
Q 012923          322 RAIDG  326 (453)
Q Consensus       322 ~a~~~  326 (453)
                      ++..+
T Consensus       102 ~a~~k  106 (108)
T 2jrs_A          102 HVTER  106 (108)
T ss_dssp             CSCSS
T ss_pred             EcccC
Confidence            99654

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.4e-18  Score=133.02  Aligned_cols=81  Identities=15%  Similarity=0.140  Sum_probs=71.9

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC---CccCCeEeE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ---KKIGNRMTA  202 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~---~~~~gr~~~  202 (453)
                      .....++|||+|||+++|+++|+++|++||.|.+|+|+++      ||||||+|.+.++|.+|++.++   ..|.||.|.
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~   85 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY   85 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            4556789999999999999999999999999999999875      6899999999999999999664   459999999


Q ss_pred             EEecccCCCC
Q 012923          203 CQLASIGPAT  212 (453)
Q Consensus       203 v~~~~~~~~~  212 (453)
                      |.++..+...
T Consensus        86 V~~A~~~~~~   95 (105)
T 1sjq_A           86 IQFSNHKELK   95 (105)
T ss_dssp             BCCCSSSSCC
T ss_pred             EEEcCCCCCC
Confidence            9998765444

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

Probab=99.76  E-value=7.6e-19  Score=128.80  Aligned_cols=76  Identities=30%  Similarity=0.705  Sum_probs=73.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEec
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLA  206 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~  206 (453)
                      ++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+|++.++..+.|+.|.|.++
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            5899999999999999999999999999999999998999999999999999999999999997799999999886

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

Probab=99.76  E-value=9.9e-19  Score=142.15  Aligned_cols=83  Identities=20%  Similarity=0.292  Sum_probs=76.9

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcce--eeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-C----ccCC
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEE--GPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-K----NFEG  315 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~--v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~----~l~g  315 (453)
                      .....++|||+|||+.+|+++|+++|++||.|..  |+|++|+.+|+++|||||+|.+. +|.+||..|| .    .|+|
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g   97 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG   97 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC
Confidence            3455679999999999999999999999999976  99999999999999999999999 9999999999 7    8999


Q ss_pred             eEEEEEEccCC
Q 012923          316 HILNCQRAIDG  326 (453)
Q Consensus       316 ~~l~v~~a~~~  326 (453)
                      +.|.|.++...
T Consensus        98 r~l~V~~a~~~  108 (131)
T 2m2b_A           98 KTINVEFAKGS  108 (131)
T ss_dssp             CCCCCEECCCS
T ss_pred             EEEEEEECCCC
Confidence            99999999654

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.1e-18  Score=133.67  Aligned_cols=79  Identities=11%  Similarity=0.111  Sum_probs=71.1

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC---CccCCeEEEEE
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH---KNFEGHILNCQ  321 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~---~~l~g~~l~v~  321 (453)
                      ...++|||+|||+.+|+++|+++|++||.|.+|+|+++      ||||||+|.+.++|.+||..++   ..|.|++|+|.
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   87 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ   87 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            34579999999999999999999999999999999976      8999999999999999999764   57999999999


Q ss_pred             EccCCCCC
Q 012923          322 RAIDGPKP  329 (453)
Q Consensus       322 ~a~~~~~~  329 (453)
                      |+..+...
T Consensus        88 ~A~~~~~~   95 (105)
T 1sjq_A           88 FSNHKELK   95 (105)
T ss_dssp             CCSSSSCC
T ss_pred             EcCCCCCC
Confidence            99766543

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

Probab=99.76  E-value=2.3e-18  Score=132.88  Aligned_cols=81  Identities=17%  Similarity=0.348  Sum_probs=76.6

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcc-eeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeE----EE
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIE-EGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHI----LN  319 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~-~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~----l~  319 (453)
                      ..++|||+|||+.+|+++|+++|++||.|. .|+|++++.+++++|||||+|.+.++|.+||..|| ..|.|+.    |+
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~   87 (99)
T 2div_A            8 MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFK   87 (99)
T ss_dssp             SSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEE
Confidence            457999999999999999999999999999 99999999999999999999999999999999999 8899999    99


Q ss_pred             EEEccCC
Q 012923          320 CQRAIDG  326 (453)
Q Consensus       320 v~~a~~~  326 (453)
                      |.|+...
T Consensus        88 v~~a~~~   94 (99)
T 2div_A           88 LNYATYS   94 (99)
T ss_dssp             EEETTCC
T ss_pred             EeecCCC
Confidence            9998654

>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=99.76  E-value=2.3e-18  Score=132.64  Aligned_cols=82  Identities=17%  Similarity=0.181  Sum_probs=76.9

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|+.||.|..+.+++++.+++++|||||+|.+.++|.+||..|| ..|.|++|+|.++
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            345799999999999999999999999999999999999999999999999999999999999999 8999999999998


Q ss_pred             cCC
Q 012923          324 IDG  326 (453)
Q Consensus       324 ~~~  326 (453)
                      ..+
T Consensus        93 ~~~   95 (98)
T 2cqp_A           93 SGP   95 (98)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            643

>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=99.76  E-value=2.1e-18  Score=134.89  Aligned_cols=86  Identities=26%  Similarity=0.447  Sum_probs=78.8

Q ss_pred             cCCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeE
Q 012923          124 ADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTA  202 (453)
Q Consensus       124 ~~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~  202 (453)
                      .......++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+|++.++ ..|.|+.|.
T Consensus        20 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~   99 (108)
T 2jrs_A           20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMK   99 (108)
T ss_dssp             CCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            4456677999999999999999999999999999999999999899999999999999999999999877 569999999


Q ss_pred             EEecccC
Q 012923          203 CQLASIG  209 (453)
Q Consensus       203 v~~~~~~  209 (453)
                      |.++..+
T Consensus       100 V~~a~~k  106 (108)
T 2jrs_A          100 VGHVTER  106 (108)
T ss_dssp             EECSCSS
T ss_pred             EEEcccC
Confidence            9998643

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=1.3e-18  Score=135.75  Aligned_cols=85  Identities=20%  Similarity=0.370  Sum_probs=78.4

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      .....++|||+|||+.+|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+||.. + ..|+|+.|.|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~   90 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPK   90 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEE
Confidence            344567999999999999999999999999999999999999999999999999999999999999 7 88999999999


Q ss_pred             EccCCCC
Q 012923          322 RAIDGPK  328 (453)
Q Consensus       322 ~a~~~~~  328 (453)
                      ++..+..
T Consensus        91 ~a~~~~~   97 (105)
T 2dh8_A           91 PCTPRGM   97 (105)
T ss_dssp             CSCCSSC
T ss_pred             EccCCCC
Confidence            9976543

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

Probab=99.76  E-value=4.4e-18  Score=133.31  Aligned_cols=87  Identities=20%  Similarity=0.389  Sum_probs=79.3

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEccc-CCCCCcceEEEEEEccHHHHHHHHHcC-C-CccCCeEe
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCD-KVSGKSKGYGFILFKTRSGARKALKEP-Q-KKIGNRMT  201 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d-~~~g~~~G~afV~f~~~~~a~~A~~~~-~-~~~~gr~~  201 (453)
                      ......++|||+|||+++|+++|+++|++||.|..|+|+++ +.+++++|||||+|.+.++|.+||..+ + ..|.|+.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l   89 (107)
T 2cph_A           10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRL   89 (107)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBC
T ss_pred             ccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEE
Confidence            34556789999999999999999999999999999999999 789999999999999999999999998 5 66999999


Q ss_pred             EEEecccCCC
Q 012923          202 ACQLASIGPA  211 (453)
Q Consensus       202 ~v~~~~~~~~  211 (453)
                      .|.++.....
T Consensus        90 ~v~~a~~~~~   99 (107)
T 2cph_A           90 VLEWADSEVT   99 (107)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEeCCCCCC
Confidence            9999976544

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

Probab=99.76  E-value=2.9e-18  Score=134.06  Aligned_cols=83  Identities=22%  Similarity=0.366  Sum_probs=77.0

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ....++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||..++ ..|.|+.|.|.+
T Consensus        20 ~~~~~~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           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   99 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEe
Confidence            3456899999999999999999999999999999999999899999999999999999999999877 569999999999


Q ss_pred             cccC
Q 012923          206 ASIG  209 (453)
Q Consensus       206 ~~~~  209 (453)
                      +...
T Consensus       100 a~~~  103 (106)
T 1p27_B          100 CFVR  103 (106)
T ss_dssp             SEES
T ss_pred             ecCC
Confidence            8754

>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=99.76  E-value=7.4e-18  Score=130.99  Aligned_cols=85  Identities=22%  Similarity=0.370  Sum_probs=76.5

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      .....++|||+|||+.+|+++|+++|+.||.|..|+|++++.  .++|||||+|.+.++|.+||..|| ..|+|+.|.|.
T Consensus        11 ~~~~~~~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           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   88 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            344567999999999999999999999999999999998853  489999999999999999999988 88999999999


Q ss_pred             EccCCCCC
Q 012923          322 RAIDGPKP  329 (453)
Q Consensus       322 ~a~~~~~~  329 (453)
                      ++..+...
T Consensus        89 ~a~~~~~~   96 (103)
T 2cq3_A           89 NATARVMT   96 (103)
T ss_dssp             ECCSSCCC
T ss_pred             EcccCCCC
Confidence            99776543

>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=99.76  E-value=3.3e-18  Score=129.17  Aligned_cols=78  Identities=24%  Similarity=0.418  Sum_probs=74.4

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .++|||+|||+.+|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+|| .+| ..|.|+.|.|.++.+
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            469999999999999999999999999999999999999999999999999999999999 788 889999999999865

>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=99.76  E-value=6.2e-18  Score=131.42  Aligned_cols=83  Identities=16%  Similarity=0.306  Sum_probs=75.0

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ....++|||+|||+.+|+++|+++|++||.|..|+|++++.  .++|||||+|.+.++|.+||..|| ..|.|+.|+|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEE
Confidence            34567999999999999999999999999999999999854  368999999999999999999988 889999999999


Q ss_pred             ccCCCC
Q 012923          323 AIDGPK  328 (453)
Q Consensus       323 a~~~~~  328 (453)
                      +.....
T Consensus        90 a~~~~~   95 (103)
T 2cqi_A           90 ATTPSS   95 (103)
T ss_dssp             CCCTTC
T ss_pred             CCCCcc
Confidence            976543

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

Probab=99.75  E-value=9.8e-19  Score=128.22  Aligned_cols=77  Identities=18%  Similarity=0.403  Sum_probs=73.9

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEcc
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAI  324 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a~  324 (453)
                      ++|||+|||+.+|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+|+..++..|+|++|.|.+|.
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~a~   77 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAF   77 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEECC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCCCccCCEEEEEEecC
Confidence            37999999999999999999999999999999999999999999999999999999999999988999999999873

>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=99.75  E-value=6e-18  Score=134.19  Aligned_cols=84  Identities=25%  Similarity=0.419  Sum_probs=77.0

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ....++|||+|||+++|+++|+++|++||.|..|+|+.++ +++++|||||+|.+.++|.+|++.++ ..|.|+.|.|.+
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~   82 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456899999999999999999999999999999999998 99999999999999999999999887 569999999999


Q ss_pred             cccCCC
Q 012923          206 ASIGPA  211 (453)
Q Consensus       206 ~~~~~~  211 (453)
                      +.....
T Consensus        83 a~~~~~   88 (116)
T 2fy1_A           83 AKKPSF   88 (116)
T ss_dssp             CCCSSC
T ss_pred             CCCCCC
Confidence            875543

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

Probab=99.75  E-value=1.8e-18  Score=126.11  Aligned_cols=74  Identities=24%  Similarity=0.587  Sum_probs=70.7

Q ss_pred             EEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       249 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      +|||+|||+.+|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+|+. ++ ..|+|++|.|.+|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            59999999999999999999999999999999999899999999999999999999998 66 8999999999875

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

Probab=99.75  E-value=1.7e-18  Score=134.14  Aligned_cols=76  Identities=24%  Similarity=0.363  Sum_probs=70.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecccC
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASIG  209 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~~  209 (453)
                      ++|||+|||+++|+++|+++|++||.|..|+|+.+     ++|||||+|.+.++|.+|++.++ ..+.|+.|.|.++...
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            58999999999999999999999999999999887     78999999999999999999877 6699999999999765


Q ss_pred             CC
Q 012923          210 PA  211 (453)
Q Consensus       210 ~~  211 (453)
                      ..
T Consensus        76 ~~   77 (101)
T 2hvz_A           76 PR   77 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

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

Probab=99.75  E-value=3.7e-18  Score=131.69  Aligned_cols=83  Identities=19%  Similarity=0.288  Sum_probs=76.6

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCee-EEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeE----
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIE-DCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRM----  200 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~-~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~----  200 (453)
                      ....++|||+|||+++|+++|+++|++||.|. .|+|++++.+++++|||||+|.+.++|.+|++.++ ..|.|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            44578999999999999999999999999999 99999999999999999999999999999999888 4589998    


Q ss_pred             eEEEecccC
Q 012923          201 TACQLASIG  209 (453)
Q Consensus       201 ~~v~~~~~~  209 (453)
                      |+|.++...
T Consensus        86 l~v~~a~~~   94 (99)
T 2div_A           86 FKLNYATYS   94 (99)
T ss_dssp             CCEEETTCC
T ss_pred             EEEeecCCC
Confidence            999998644

>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=99.75  E-value=4.9e-18  Score=132.55  Aligned_cols=86  Identities=22%  Similarity=0.409  Sum_probs=77.4

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCC---eEe
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGN---RMT  201 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~g---r~~  201 (453)
                      .....++|||+|||+++|+++|+++|++||.|..|+|++++ +++++|||||+|.+.++|.+||+.+++ .+.+   +.|
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l   89 (105)
T 2dnh_A           11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSL   89 (105)
T ss_dssp             SCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccE
Confidence            34567999999999999999999999999999999999998 899999999999999999999998885 4777   999


Q ss_pred             EEEecccCCCC
Q 012923          202 ACQLASIGPAT  212 (453)
Q Consensus       202 ~v~~~~~~~~~  212 (453)
                      .|.++......
T Consensus        90 ~V~~a~~~~~~  100 (105)
T 2dnh_A           90 VVKFADTDKES  100 (105)
T ss_dssp             EEEESCSSCCC
T ss_pred             EEEECccCccc
Confidence            99999765443

>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=99.75  E-value=8.4e-18  Score=132.15  Aligned_cols=84  Identities=17%  Similarity=0.179  Sum_probs=77.2

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCC-cceeeee-ccCCCCCCceEEEEEECCHHHHHHHHHcCC---CccCCeEEEE
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGE-IEEGPLG-IDKATGKPKGFCLFVYKTVDAAKKALEEPH---KNFEGHILNC  320 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~-i~~v~i~-~d~~~g~~kg~afV~F~~~~~A~~Al~~~~---~~l~g~~l~v  320 (453)
                      ..++|||+|||+.+|+++|+++|+.||. |..|.|+ +++.+++++|||||+|.+.++|.+||..|+   ..|+|+.|.|
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            3469999999999999999999999998 9999998 888899999999999999999999999985   6899999999


Q ss_pred             EEccCCCCC
Q 012923          321 QRAIDGPKP  329 (453)
Q Consensus       321 ~~a~~~~~~  329 (453)
                      .|+..+..+
T Consensus        87 ~~a~~~~~~   95 (109)
T 2dis_A           87 DWAEPEIDV   95 (109)
T ss_dssp             EESCSSCST
T ss_pred             EEcCCCCCc
Confidence            999776543

>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=99.75  E-value=4e-18  Score=133.31  Aligned_cols=87  Identities=23%  Similarity=0.323  Sum_probs=78.6

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-cc---CCeE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KI---GNRM  200 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~---~gr~  200 (453)
                      ......++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||+.++. .+   .++.
T Consensus         8 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~   87 (106)
T 2dgp_A            8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRP   87 (106)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCce
Confidence            3455678999999999999999999999999999999999998999999999999999999999998885 45   8899


Q ss_pred             eEEEecccCCC
Q 012923          201 TACQLASIGPA  211 (453)
Q Consensus       201 ~~v~~~~~~~~  211 (453)
                      |.|.++.....
T Consensus        88 l~v~~a~~~~~   98 (106)
T 2dgp_A           88 IQVKPADSESR   98 (106)
T ss_dssp             CEEEECCCCSC
T ss_pred             EEEEECCcccc
Confidence            99999875543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=7.4e-18  Score=127.76  Aligned_cols=80  Identities=15%  Similarity=0.280  Sum_probs=74.9

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|+.| .|..|+|+++ .+|+++|||||+|.+.++|.+||. +| ..|+|+.|.|.++
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a   84 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFRE   84 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEE
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEEC
Confidence            345799999999999999999999999 9999999998 789999999999999999999999 88 8899999999999


Q ss_pred             cCCC
Q 012923          324 IDGP  327 (453)
Q Consensus       324 ~~~~  327 (453)
                      ..++
T Consensus        85 ~~~~   88 (91)
T 2dgw_A           85 KSGP   88 (91)
T ss_dssp             SSCC
T ss_pred             CcCC
Confidence            7664

>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=99.75  E-value=3.2e-18  Score=132.26  Aligned_cols=79  Identities=14%  Similarity=0.144  Sum_probs=71.9

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|+.|| |+.|+|++++ +++++|||||+|.+.++|.+||. +| ..|+||.|.|.++
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-ceEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            3457999999999999999999999999 5599999997 89999999999999999999996 56 8999999999988


Q ss_pred             cCC
Q 012923          324 IDG  326 (453)
Q Consensus       324 ~~~  326 (453)
                      ...
T Consensus        90 ~~~   92 (102)
T 1wez_A           90 STA   92 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

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

Probab=99.75  E-value=2.1e-18  Score=125.69  Aligned_cols=75  Identities=32%  Similarity=0.621  Sum_probs=70.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEec
Q 012923          132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLA  206 (453)
Q Consensus       132 ~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~  206 (453)
                      +|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|++|++..+..|.|+.|.|.++
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            599999999999999999999999999999999998999999999999999999999995457799999999875

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

Probab=99.75  E-value=5.2e-18  Score=134.27  Aligned_cols=86  Identities=28%  Similarity=0.356  Sum_probs=78.6

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCee--------EEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-Ccc
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIE--------DCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKI  196 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~--------~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~  196 (453)
                      +....++|||+|||+++|+++|+++|++||.|.        .|+|++++.+++++|||||+|.+.++|.+||+.++ ..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            455679999999999999999999999999999        69999998899999999999999999999999877 569


Q ss_pred             CCeEeEEEecccCCC
Q 012923          197 GNRMTACQLASIGPA  211 (453)
Q Consensus       197 ~gr~~~v~~~~~~~~  211 (453)
                      .|+.|.|.++.....
T Consensus        91 ~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           91 QGSKLKVSLARKKPP  105 (113)
T ss_dssp             TTEECEEECSSCCCC
T ss_pred             CCCEEEEEECCCCCC
Confidence            999999999875544

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

Probab=99.75  E-value=3.5e-18  Score=142.61  Aligned_cols=80  Identities=20%  Similarity=0.321  Sum_probs=75.6

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccC--CcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYG--EIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G--~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ..++|||+|||+.+|+++|+++|+.||  .|..|+|++|+.+|+++|||||+|.+.++|.+||..|| ..|+|+.|.|.+
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            347999999999999999999999999  99999999999999999999999999999999999999 899999999999


Q ss_pred             ccC
Q 012923          323 AID  325 (453)
Q Consensus       323 a~~  325 (453)
                      +..
T Consensus       134 a~~  136 (156)
T 3n9u_C          134 ATR  136 (156)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            854

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

Probab=99.75  E-value=4.3e-18  Score=142.05  Aligned_cols=79  Identities=20%  Similarity=0.394  Sum_probs=74.2

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccC--CeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYG--EIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G--~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ..++|||+|||+++|+++|+++|++||  .|..|+|++|+.+|+++|||||+|.+.++|.+||+.++ ..|.|+.|.|.+
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            468999999999999999999999999  99999999999999999999999999999999999988 569999999999


Q ss_pred             cc
Q 012923          206 AS  207 (453)
Q Consensus       206 ~~  207 (453)
                      +.
T Consensus       134 a~  135 (156)
T 3n9u_C          134 AT  135 (156)
T ss_dssp             CC
T ss_pred             cC
Confidence            85

>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=99.75  E-value=6.8e-18  Score=131.21  Aligned_cols=82  Identities=23%  Similarity=0.356  Sum_probs=74.6

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeE-EEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIED-CKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~-v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~  205 (453)
                      ....++|||+|||+++|+++|+++|.+||.|.. |+|+.+ .+++++|||||+|.+.++|.+||......|.+|.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v~~   90 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEEEE
Confidence            345689999999999999999999999999988 889888 599999999999999999999999955779999999998


Q ss_pred             cccC
Q 012923          206 ASIG  209 (453)
Q Consensus       206 ~~~~  209 (453)
                      +...
T Consensus        91 ~~~~   94 (104)
T 1wg5_A           91 SSRA   94 (104)
T ss_dssp             ECTT
T ss_pred             CCHH
Confidence            8644

>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=99.75  E-value=2.5e-18  Score=132.86  Aligned_cols=81  Identities=15%  Similarity=0.226  Sum_probs=72.8

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEec
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLA  206 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~  206 (453)
                      ....++|||+|||+++|+++|+++|++||. ..|+|++++ +++++|||||+|.+.++|.+||+.....|.+|.|.|.++
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEEC
Confidence            345689999999999999999999999995 499999998 899999999999999999999976446799999999987


Q ss_pred             ccC
Q 012923          207 SIG  209 (453)
Q Consensus       207 ~~~  209 (453)
                      ...
T Consensus        90 ~~~   92 (102)
T 1wez_A           90 STA   92 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            644

>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=99.75  E-value=4.6e-18  Score=130.10  Aligned_cols=81  Identities=25%  Similarity=0.379  Sum_probs=74.7

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      .....++|||+|||+++|+++|+++|++||.|..|+|++++ +++++|||||+|.+.++|.+|++.++ ..|.|+.|.|.
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVS   90 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEE
Confidence            34556899999999999999999999999999999999998 49999999999999999999999777 56999999999


Q ss_pred             ecc
Q 012923          205 LAS  207 (453)
Q Consensus       205 ~~~  207 (453)
                      ++.
T Consensus        91 ~a~   93 (95)
T 2ywk_A           91 GPS   93 (95)
T ss_dssp             CCC
T ss_pred             EcC
Confidence            875

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

Probab=99.75  E-value=6.2e-18  Score=136.24  Aligned_cols=81  Identities=25%  Similarity=0.390  Sum_probs=76.0

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+|+++|+++|++||.|..|+|++++.++.++|||||+|.+.++|.+|| .+| ..|+|+.|.|.++.
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            3579999999999999999999999999999999999999999999999999999999999 788 88999999999997


Q ss_pred             CCC
Q 012923          325 DGP  327 (453)
Q Consensus       325 ~~~  327 (453)
                      ...
T Consensus       114 ~~~  116 (124)
T 2jwn_A          114 TNM  116 (124)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.75  E-value=1.6e-18  Score=137.77  Aligned_cols=104  Identities=19%  Similarity=0.368  Sum_probs=90.1

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ...+++|||+|||+++|+++|+++|++||.|..|+|+++   +.++|||||+|.+.++|.+|+..++ ..|.|+.|.|.+
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            345689999999999999999999999999999999875   4569999999999999999999777 569999999999


Q ss_pred             cccCCCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCC
Q 012923          206 ASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGE  273 (453)
Q Consensus       206 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~  273 (453)
                      +......                                        .+++...++++|.++|++||.
T Consensus        82 a~~~~~~----------------------------------------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           82 YNANRAF----------------------------------------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             CCHHHHT----------------------------------------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             ecCChhh----------------------------------------hhhhHhHhHHHHHHHHHHhCC
Confidence            8532110                                        567888999999999999985

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

Probab=99.75  E-value=4.5e-18  Score=131.16  Aligned_cols=82  Identities=28%  Similarity=0.393  Sum_probs=76.0

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeE--------EEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-Cc
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIED--------CKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KK  195 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~--------v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~  195 (453)
                      ......++|||+|||+++|+++|+++|++||.|..        |+|++++.+++++|||||+|.+.++|.+|++.++ ..
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~   87 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   87 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            34556789999999999999999999999999999        9999998899999999999999999999999777 56


Q ss_pred             cCCeEeEEEec
Q 012923          196 IGNRMTACQLA  206 (453)
Q Consensus       196 ~~gr~~~v~~~  206 (453)
                      |.|+.|+|.++
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            99999999986

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

Probab=99.75  E-value=1e-17  Score=130.15  Aligned_cols=84  Identities=21%  Similarity=0.299  Sum_probs=76.0

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      .....++|||+|||+++|+++|+++|++|| |..|+|++++.+++++|||||+|.+.++|.+|| .++ ..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   88 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVD   88 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEE
Confidence            344578999999999999999999999997 999999999989999999999999999999999 666 66999999999


Q ss_pred             ecccCCC
Q 012923          205 LASIGPA  211 (453)
Q Consensus       205 ~~~~~~~  211 (453)
                      ++.....
T Consensus        89 ~a~~~~~   95 (103)
T 2dng_A           89 IAEGRKQ   95 (103)
T ss_dssp             ECCCCCC
T ss_pred             EecCCCC
Confidence            9875544

>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=99.75  E-value=3.5e-18  Score=130.75  Aligned_cols=81  Identities=22%  Similarity=0.397  Sum_probs=75.2

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ....++|||+|||+.+++++|+++|++||.|..|+|++++. ++++|||||+|.+.++|.+||..|| ..|+|++|.|.+
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            33457999999999999999999999999999999999875 9999999999999999999999988 889999999999


Q ss_pred             ccC
Q 012923          323 AID  325 (453)
Q Consensus       323 a~~  325 (453)
                      +..
T Consensus        92 a~~   94 (95)
T 2ywk_A           92 PSS   94 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            854

>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=99.75  E-value=3.9e-18  Score=138.22  Aligned_cols=78  Identities=10%  Similarity=0.094  Sum_probs=73.3

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCC---cceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGE---IEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~---i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      ..++|||+|||+.+|+++|+++|+.||.   |..|+|++++. |+++|||||+|.+.++|.+||. +| ..|+||.|.|.
T Consensus        43 ~~~~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           43 EGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVF  120 (136)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEE
Confidence            4579999999999999999999999999   89999999986 9999999999999999999999 88 89999999999


Q ss_pred             EccC
Q 012923          322 RAID  325 (453)
Q Consensus       322 ~a~~  325 (453)
                      ++..
T Consensus       121 ~a~~  124 (136)
T 2hgl_A          121 KSHR  124 (136)
T ss_dssp             ECCH
T ss_pred             ECCh
Confidence            9854

>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=99.75  E-value=2.2e-18  Score=139.25  Aligned_cols=85  Identities=22%  Similarity=0.346  Sum_probs=78.9

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      .....++|||+|||+.+|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||..|| ..|+|++|.|.
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~  121 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD  121 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEES
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34456799999999999999999999999999999999999999999999999999999999999998 88999999999


Q ss_pred             EccCCC
Q 012923          322 RAIDGP  327 (453)
Q Consensus       322 ~a~~~~  327 (453)
                      |+..+.
T Consensus       122 ~a~~~~  127 (129)
T 2kxn_B          122 FSITKR  127 (129)
T ss_dssp             CCSSSS
T ss_pred             EecCCC
Confidence            997543

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

Probab=99.75  E-value=4.9e-18  Score=128.58  Aligned_cols=79  Identities=13%  Similarity=0.111  Sum_probs=70.3

Q ss_pred             cccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-C--ccCCeEE
Q 012923          242 QSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-K--NFEGHIL  318 (453)
Q Consensus       242 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~--~l~g~~l  318 (453)
                      ....+.++|||+|||+.+|+++|+++|++||.|.+|+|++.      ||||||+|.+.++|.+|+..++ .  .|.|++|
T Consensus        16 ~~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i   89 (100)
T 3r27_A           16 HKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPA   89 (100)
T ss_dssp             -CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEE
T ss_pred             ccCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEE
Confidence            33445679999999999999999999999999999999864      8999999999999999999988 4  4889999


Q ss_pred             EEEEccCC
Q 012923          319 NCQRAIDG  326 (453)
Q Consensus       319 ~v~~a~~~  326 (453)
                      .|.+++.+
T Consensus        90 ~V~~S~~k   97 (100)
T 3r27_A           90 FVNYSTSQ   97 (100)
T ss_dssp             EEEECSCS
T ss_pred             EEEecccc
Confidence            99999654

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=2.9e-18  Score=133.81  Aligned_cols=86  Identities=31%  Similarity=0.520  Sum_probs=78.3

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEe
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQL  205 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~  205 (453)
                      .....++|||+|||+++|+++|+++|.+||.|..|+|++++.+++++|||||+|.+.++|.+||......|.|+.|.|.+
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKP   91 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEBCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEEEEE
Confidence            45667999999999999999999999999999999999999899999999999999999999999933669999999999


Q ss_pred             cccCCC
Q 012923          206 ASIGPA  211 (453)
Q Consensus       206 ~~~~~~  211 (453)
                      +.....
T Consensus        92 a~~~~~   97 (105)
T 2dh8_A           92 CTPRGM   97 (105)
T ss_dssp             SCCSSC
T ss_pred             ccCCCC
Confidence            875543

>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=99.75  E-value=2.1e-18  Score=132.01  Aligned_cols=80  Identities=18%  Similarity=0.220  Sum_probs=74.8

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+|+++|+++|++||.|..+.+++++.+++++|||||+|.+.++|.+||..|| ..|.|++|+|.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            34799999999999999999999999999999999999999999999999999999999999988 89999999999885


Q ss_pred             C
Q 012923          325 D  325 (453)
Q Consensus       325 ~  325 (453)
                      +
T Consensus        94 s   94 (95)
T 2ek1_A           94 S   94 (95)
T ss_dssp             -
T ss_pred             C
Confidence            3

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

Probab=99.75  E-value=6.3e-18  Score=131.36  Aligned_cols=86  Identities=26%  Similarity=0.394  Sum_probs=77.6

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ......++|||+|||+++|+++|+++|++||.|..|+|+.+  +++++|||||+|.+.++|.+||..++ ..|.|+.|.|
T Consensus        10 ~~~~~~~~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           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYV   87 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            34456789999999999999999999999999999999998  89999999999999999999999877 5699999999


Q ss_pred             EecccCCCC
Q 012923          204 QLASIGPAT  212 (453)
Q Consensus       204 ~~~~~~~~~  212 (453)
                      .++......
T Consensus        88 ~~a~~~~~~   96 (103)
T 2d9p_A           88 ALAQRKEER   96 (103)
T ss_dssp             EECSSCCCC
T ss_pred             EEecccccC
Confidence            999765443

>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=99.75  E-value=6.3e-18  Score=133.11  Aligned_cols=85  Identities=20%  Similarity=0.313  Sum_probs=77.9

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      .....++|||+|||+++|+++|+++|++||.|..|+|+.++.+++++|||||+|.+.++|.+||..++ ..|.|+.|.|.
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  101 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  101 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34556899999999999999999999999999999999999899999999999999999999999877 56999999999


Q ss_pred             ecccCC
Q 012923          205 LASIGP  210 (453)
Q Consensus       205 ~~~~~~  210 (453)
                      ++....
T Consensus       102 ~a~~~~  107 (110)
T 1oo0_B          102 WCFVKG  107 (110)
T ss_dssp             ESEESS
T ss_pred             EcccCC
Confidence            987543

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

Probab=99.75  E-value=4.3e-18  Score=135.85  Aligned_cols=82  Identities=26%  Similarity=0.398  Sum_probs=76.3

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ......++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||+.++ ..|.|+.|+|
T Consensus        35 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V  114 (118)
T 2khc_A           35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV  114 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            345667899999999999999999999999999999999998899999999999999999999999887 5599999999


Q ss_pred             Eec
Q 012923          204 QLA  206 (453)
Q Consensus       204 ~~~  206 (453)
                      .++
T Consensus       115 ~~a  117 (118)
T 2khc_A          115 QLK  117 (118)
T ss_dssp             EEC
T ss_pred             Eec
Confidence            986

>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=99.75  E-value=6e-18  Score=132.94  Aligned_cols=81  Identities=11%  Similarity=0.100  Sum_probs=72.6

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC---CccCCeEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH---KNFEGHILNC  320 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~---~~l~g~~l~v  320 (453)
                      ....++|||+|||+.+|+++|+++|++||.|.+|+|+++      ||||||+|.+.++|.+||..++   ..|.|++|+|
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V  101 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI  101 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEE
Confidence            345679999999999999999999999999999999986      8999999999999999999886   4799999999


Q ss_pred             EEccCCCCCC
Q 012923          321 QRAIDGPKPG  330 (453)
Q Consensus       321 ~~a~~~~~~~  330 (453)
                      .|+..+....
T Consensus       102 ~~a~~k~~~~  111 (119)
T 2ad9_A          102 QFSNHKELKT  111 (119)
T ss_dssp             EECSSSSCCC
T ss_pred             EEccCCCCCc
Confidence            9997665443

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

Probab=99.75  E-value=4.9e-18  Score=135.56  Aligned_cols=82  Identities=20%  Similarity=0.252  Sum_probs=76.6

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      .....++|||+|||+.+|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||..|| ..|+|++|+|.
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34456899999999999999999999999999999999999999999999999999999999999998 88999999999


Q ss_pred             Ecc
Q 012923          322 RAI  324 (453)
Q Consensus       322 ~a~  324 (453)
                      |++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            973

>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=99.75  E-value=3.6e-18  Score=130.81  Aligned_cols=76  Identities=13%  Similarity=0.101  Sum_probs=69.4

Q ss_pred             cccEEEEecCCC-CccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-C--ccCCeEEEEE
Q 012923          246 TQRKIFVSNVGS-ELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-K--NFEGHILNCQ  321 (453)
Q Consensus       246 ~~~~l~V~nLp~-~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~--~l~g~~l~v~  321 (453)
                      ..++|||+|||+ .+|+++|+++|++||.|.+|+|+++      +|||||+|.+.++|.+||..|+ .  .|.|++|.|.
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            467999999999 9999999999999999999999876      6899999999999999999887 3  4999999999


Q ss_pred             EccCCC
Q 012923          322 RAIDGP  327 (453)
Q Consensus       322 ~a~~~~  327 (453)
                      ++....
T Consensus        88 ~a~~~~   93 (102)
T 1x4d_A           88 LSQKYK   93 (102)
T ss_dssp             EECCCT
T ss_pred             ECCCCC
Confidence            997543

>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=99.75  E-value=2.2e-18  Score=134.34  Aligned_cols=82  Identities=29%  Similarity=0.489  Sum_probs=77.4

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+||..+| ..|+|+.|.|.++.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            34799999999999999999999999999999999999999999999999999999999999999 88999999999997


Q ss_pred             CCC
Q 012923          325 DGP  327 (453)
Q Consensus       325 ~~~  327 (453)
                      ...
T Consensus        87 ~~~   89 (104)
T 1p1t_A           87 SEK   89 (104)
T ss_dssp             CTT
T ss_pred             Ccc
Confidence            654

>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=99.75  E-value=1.7e-18  Score=126.16  Aligned_cols=75  Identities=31%  Similarity=0.515  Sum_probs=71.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEec
Q 012923          132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLA  206 (453)
Q Consensus       132 ~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~  206 (453)
                      ||||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+|++..+..+.|+.|.|.++
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            699999999999999999999999999999999998999999999999999999999998778899999999875

>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=99.75  E-value=7.7e-18  Score=127.15  Aligned_cols=78  Identities=26%  Similarity=0.479  Sum_probs=73.3

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~  208 (453)
                      .++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+|+ .++ ..|.|+.|.|.++..
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            479999999999999999999999999999999999989999999999999999999999 666 669999999999854

>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=99.74  E-value=1.1e-18  Score=138.18  Aligned_cols=81  Identities=17%  Similarity=0.189  Sum_probs=75.3

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCc-ceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEI-EEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i-~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ...++|||+|||+.+|+++|+++|+.||.| ..|+|++++ +++++|||||+|.+.++|.+||.. | ..|+|+.|.|.+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHV   90 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEE
Confidence            345799999999999999999999999999 899999998 999999999999999999999999 6 889999999999


Q ss_pred             ccCCC
Q 012923          323 AIDGP  327 (453)
Q Consensus       323 a~~~~  327 (453)
                      +....
T Consensus        91 a~~~~   95 (114)
T 2cpy_A           91 VTLED   95 (114)
T ss_dssp             ECHHH
T ss_pred             CCHHH
Confidence            97543

>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=99.74  E-value=1.2e-17  Score=129.99  Aligned_cols=83  Identities=18%  Similarity=0.334  Sum_probs=75.6

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCC-CCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVS-GKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~-g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      ....++|||+|||+++|+++|+++|.+|| |..|+|++++.+ ++++|||||+|.+.++|.+|| .++ ..|.|+.|.|.
T Consensus        12 ~~~~~~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           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEE
Confidence            34568999999999999999999999999 999999999987 999999999999999999999 666 66999999999


Q ss_pred             ecccCCC
Q 012923          205 LASIGPA  211 (453)
Q Consensus       205 ~~~~~~~  211 (453)
                      ++.....
T Consensus        90 ~a~~~~~   96 (104)
T 1wi8_A           90 VADQAQD   96 (104)
T ss_dssp             ECCCCCC
T ss_pred             EccCCCC
Confidence            9876544

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

Probab=99.74  E-value=6.5e-18  Score=131.59  Aligned_cols=85  Identities=28%  Similarity=0.400  Sum_probs=77.5

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhc-cCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-Cc-cCCeEeEE
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQ-YGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KK-IGNRMTAC  203 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~-~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~-~~gr~~~v  203 (453)
                      ....++|||+|||+++|+++|+++|++ ||.|..|+|++++ +++++|||||+|.+.++|.+||+.++ .. |.|+.|.|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            455689999999999999999999999 9999999999999 99999999999999999999999888 56 89999999


Q ss_pred             EecccCCCC
Q 012923          204 QLASIGPAT  212 (453)
Q Consensus       204 ~~~~~~~~~  212 (453)
                      .++......
T Consensus        85 ~~a~~~~~~   93 (104)
T 2dhg_A           85 SVAIPKASR   93 (104)
T ss_dssp             CBCCCCCSC
T ss_pred             EEccCCCcC
Confidence            998655443

>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=99.74  E-value=3.2e-18  Score=135.47  Aligned_cols=82  Identities=13%  Similarity=0.256  Sum_probs=75.4

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCe-eEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEI-EDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i-~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~  204 (453)
                      .....++|||+|||+++|+++|+++|+.||.| ..|+|++++ +++++|||||+|.+.++|.+||+.....|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~v~   89 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVH   89 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEEEE
Confidence            34557899999999999999999999999999 899999999 9999999999999999999999994467999999999


Q ss_pred             eccc
Q 012923          205 LASI  208 (453)
Q Consensus       205 ~~~~  208 (453)
                      ++..
T Consensus        90 ~a~~   93 (114)
T 2cpy_A           90 VVTL   93 (114)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            9863

>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=99.74  E-value=1e-17  Score=130.20  Aligned_cols=81  Identities=14%  Similarity=0.233  Sum_probs=73.9

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcce-eeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEE-GPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~-v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|+.||.|.. |+|+++ .+|+++|||||+|.+.++|.+||...+..|+||.|.|.++
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            34579999999999999999999999999997 889888 7999999999999999999999999338999999999998


Q ss_pred             cCC
Q 012923          324 IDG  326 (453)
Q Consensus       324 ~~~  326 (453)
                      ...
T Consensus        92 ~~~   94 (104)
T 1wg5_A           92 SRA   94 (104)
T ss_dssp             CTT
T ss_pred             CHH
Confidence            644

>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=99.74  E-value=7.3e-18  Score=129.03  Aligned_cols=79  Identities=15%  Similarity=0.169  Sum_probs=73.2

Q ss_pred             cccEEEEecCCCCccHHHHH----HHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEE
Q 012923          246 TQRKIFVSNVGSELEPQKLL----AFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNC  320 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~----~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v  320 (453)
                      ..++|||+|||+.+++++|+    ++|++||.|..|+|++++.+   +|||||+|.+.++|.+||..|| ..|+|++|+|
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            45699999999999999999    99999999999999998766   8999999999999999999999 8899999999


Q ss_pred             EEccCCC
Q 012923          321 QRAIDGP  327 (453)
Q Consensus       321 ~~a~~~~  327 (453)
                      .++...+
T Consensus        85 ~~a~~~~   91 (96)
T 2dgx_A           85 SLATGAS   91 (96)
T ss_dssp             EECCCSS
T ss_pred             EEcCCCC
Confidence            9996554

>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=99.74  E-value=6.2e-18  Score=132.45  Aligned_cols=80  Identities=20%  Similarity=0.352  Sum_probs=75.7

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ....++|||+|||+.+|+++|+++|+.||.|..|.|++++ +++++|||||+|.+.++|.+||..|| ..|.|+.|.|.+
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  104 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3456799999999999999999999999999999999998 99999999999999999999999988 899999999999


Q ss_pred             cc
Q 012923          323 AI  324 (453)
Q Consensus       323 a~  324 (453)
                      +.
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            85

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

Probab=99.74  E-value=7.9e-18  Score=133.86  Aligned_cols=83  Identities=28%  Similarity=0.571  Sum_probs=76.7

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecccC
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASIG  209 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~~~  209 (453)
                      .++|||+|||+++|+++|+++|.+||.|..|+|++++.+++++|||||+|.+.++|.+||......|.|+.|.|.++..+
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            47999999999999999999999999999999999998999999999999999999999999446799999999998765


Q ss_pred             CCC
Q 012923          210 PAT  212 (453)
Q Consensus       210 ~~~  212 (453)
                      ...
T Consensus       107 ~~~  109 (116)
T 1x4b_A          107 EES  109 (116)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            443

>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=99.74  E-value=1.1e-17  Score=128.44  Aligned_cols=80  Identities=11%  Similarity=0.101  Sum_probs=71.3

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC---CccCCeEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH---KNFEGHILNC  320 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~---~~l~g~~l~v  320 (453)
                      ....++|||+|||+.+|+++|+++|++||.|..|+|+++      ||||||+|.+.++|.+||..++   ..|.|++|.|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   85 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   85 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEE
Confidence            345679999999999999999999999999999999875      8999999999999999999764   5799999999


Q ss_pred             EEccCCCCC
Q 012923          321 QRAIDGPKP  329 (453)
Q Consensus       321 ~~a~~~~~~  329 (453)
                      .|+..+...
T Consensus        86 ~~a~~~~~~   94 (101)
T 2cq1_A           86 QYSNHKELK   94 (101)
T ss_dssp             EECSCSSCC
T ss_pred             EEcCcccCc
Confidence            999765443

>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=99.74  E-value=4.2e-18  Score=128.32  Aligned_cols=80  Identities=18%  Similarity=0.417  Sum_probs=74.6

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCC-CceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGK-PKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~-~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      .++|||+|||+.+|+++|+++|++||.|..|.|+++..++. ++|||||+|.+.++|.+|+..|| ..|+|+.|.|.++.
T Consensus         4 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   83 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVL   83 (88)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECC
Confidence            46999999999999999999999999999999999987766 89999999999999999999988 89999999999995


Q ss_pred             CC
Q 012923          325 DG  326 (453)
Q Consensus       325 ~~  326 (453)
                      ..
T Consensus        84 ~~   85 (88)
T 4a8x_A           84 AP   85 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

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

Probab=99.74  E-value=1.2e-17  Score=137.41  Aligned_cols=88  Identities=32%  Similarity=0.508  Sum_probs=80.0

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v  203 (453)
                      ......++|||+|||+++|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+||+.+++ .|.|+.|.|
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  116 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV  116 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            3455678999999999999999999999999999999999998999999999999999999999998884 599999999


Q ss_pred             EecccCCCC
Q 012923          204 QLASIGPAT  212 (453)
Q Consensus       204 ~~~~~~~~~  212 (453)
                      .++......
T Consensus       117 ~~a~~~~~~  125 (139)
T 1u6f_A          117 ALAASGHQR  125 (139)
T ss_dssp             EESSCCCCC
T ss_pred             EECCCCCCC
Confidence            999765443

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

Probab=99.74  E-value=6.8e-18  Score=128.31  Aligned_cols=80  Identities=18%  Similarity=0.306  Sum_probs=74.6

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+|+++|+++|++||.|..|+|+++  +++++|||||+|.+.++|.+||..|| ..|+|+.|+|.++.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   84 (92)
T 2dgv_A            7 GACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDR   84 (92)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            4579999999999999999999999999999999984  88999999999999999999999988 88999999999997


Q ss_pred             CCC
Q 012923          325 DGP  327 (453)
Q Consensus       325 ~~~  327 (453)
                      ...
T Consensus        85 ~~~   87 (92)
T 2dgv_A           85 NAS   87 (92)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            654

>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=99.74  E-value=1.6e-17  Score=129.01  Aligned_cols=78  Identities=24%  Similarity=0.346  Sum_probs=70.4

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|++||.|..|+|+        ++||||+|.+.++|.+||..|| ..|.|+.|.|.++
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   80 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA   80 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEc
Confidence            345799999999999999999999999999999986        4599999999999999999988 8899999999999


Q ss_pred             cCCCCCC
Q 012923          324 IDGPKPG  330 (453)
Q Consensus       324 ~~~~~~~  330 (453)
                      .......
T Consensus        81 ~~~~~~~   87 (103)
T 2dgu_A           81 KPPDQKR   87 (103)
T ss_dssp             CCCCCCC
T ss_pred             CCCcccc
Confidence            7665443

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

Probab=99.74  E-value=8.8e-18  Score=127.18  Aligned_cols=77  Identities=17%  Similarity=0.242  Sum_probs=69.2

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC---ccCCeEeEE
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK---KIGNRMTAC  203 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~---~~~gr~~~v  203 (453)
                      .+.+++|||+|||+++|+++|+++|++||.|.+|+|++      .||||||+|.+.++|.+|++.++.   .|.||.|.|
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V   91 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV   91 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEE
Confidence            35678999999999999999999999999999999885      468999999999999999998873   378999999


Q ss_pred             EecccC
Q 012923          204 QLASIG  209 (453)
Q Consensus       204 ~~~~~~  209 (453)
                      .++..+
T Consensus        92 ~~S~~k   97 (100)
T 3r27_A           92 NYSTSQ   97 (100)
T ss_dssp             EECSCS
T ss_pred             Eecccc
Confidence            998654

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

Probab=99.74  E-value=3.9e-18  Score=124.05  Aligned_cols=72  Identities=14%  Similarity=0.165  Sum_probs=68.2

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ...|||+||++.+|+++|+++|.+||.|.+++++.      +||||||+|.+.++|.+|++.|| ..|.|++|+|.+|.
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            45899999999999999999999999999999976      49999999999999999999999 89999999999984

>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=99.74  E-value=1.6e-17  Score=130.52  Aligned_cols=85  Identities=15%  Similarity=0.228  Sum_probs=77.2

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCC-eeEEEEc-ccCCCCCcceEEEEEEccHHHHHHHHHcCC---CccCCeEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGE-IEDCKAV-CDKVSGKSKGYGFILFKTRSGARKALKEPQ---KKIGNRMT  201 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~-i~~v~i~-~d~~~g~~~G~afV~f~~~~~a~~A~~~~~---~~~~gr~~  201 (453)
                      ....++|||+|||+++|+++|+++|.+||. |..|+|+ .++.+++++|||||+|.+.++|.+|+..++   ..|.|+.|
T Consensus         5 s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l   84 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   84 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeE
Confidence            345689999999999999999999999998 9999998 888889999999999999999999999885   46999999


Q ss_pred             EEEecccCCC
Q 012923          202 ACQLASIGPA  211 (453)
Q Consensus       202 ~v~~~~~~~~  211 (453)
                      .|.++.....
T Consensus        85 ~V~~a~~~~~   94 (109)
T 2dis_A           85 AVDWAEPEID   94 (109)
T ss_dssp             EEEESCSSCS
T ss_pred             EEEEcCCCCC
Confidence            9999976544

>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=99.74  E-value=4.6e-18  Score=137.37  Aligned_cols=85  Identities=24%  Similarity=0.395  Sum_probs=78.2

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ......++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||+.++ ..|.|+.|.|
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V  120 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV  120 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            445667899999999999999999999999999999999999899999999999999999999999877 5699999999


Q ss_pred             EecccC
Q 012923          204 QLASIG  209 (453)
Q Consensus       204 ~~~~~~  209 (453)
                      .++...
T Consensus       121 ~~a~~~  126 (129)
T 2kxn_B          121 DFSITK  126 (129)
T ss_dssp             SCCSSS
T ss_pred             EEecCC
Confidence            998643

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=2e-17  Score=125.36  Aligned_cols=82  Identities=17%  Similarity=0.338  Sum_probs=74.6

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      .....++|||+|||+++|+++|+++|+.| .|..|+|+++ .+++++|||||+|.+.++|.+||. ++ ..|.|+.|.|.
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~   82 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVF   82 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEE
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEE
Confidence            34557899999999999999999999999 9999999999 589999999999999999999999 77 55999999999


Q ss_pred             ecccCC
Q 012923          205 LASIGP  210 (453)
Q Consensus       205 ~~~~~~  210 (453)
                      ++...+
T Consensus        83 ~a~~~~   88 (91)
T 2dgw_A           83 REKSGP   88 (91)
T ss_dssp             EESSCC
T ss_pred             ECCcCC
Confidence            987553

>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=99.73  E-value=1.8e-18  Score=130.87  Aligned_cols=80  Identities=24%  Similarity=0.404  Sum_probs=73.0

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCC
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDG  326 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~  326 (453)
                      ++|||+|||+.+++++|+++|++||.|..|+|++++.+++++|||||+|.+.+ |.+|+..+| ..|+|++|+|.++...
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            48999999999999999999999999999999999999999999999999999 999999999 8899999999999765


Q ss_pred             CC
Q 012923          327 PK  328 (453)
Q Consensus       327 ~~  328 (453)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>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=99.73  E-value=5.3e-18  Score=130.53  Aligned_cols=82  Identities=22%  Similarity=0.313  Sum_probs=75.8

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ....++|||+|||+++|+++|+++|.+||.|..++++.++.+++++|||||+|.+.++|.+||+.++ ..|.|+.|.|.+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            3456899999999999999999999999999999999998899999999999999999999999888 569999999999


Q ss_pred             ccc
Q 012923          206 ASI  208 (453)
Q Consensus       206 ~~~  208 (453)
                      +..
T Consensus        92 a~~   94 (98)
T 2cqp_A           92 GSG   94 (98)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            863

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

Probab=99.73  E-value=2.1e-17  Score=130.97  Aligned_cols=83  Identities=20%  Similarity=0.307  Sum_probs=76.1

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      .....++|||+|||+++|+++|+++|.+||.|..|+|++++ +++++|||||+|.+.++|.+||..++ ..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   89 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK   89 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEE
Confidence            34557899999999999999999999999999999999998 69999999999999999999999877 56999999999


Q ss_pred             ecccC
Q 012923          205 LASIG  209 (453)
Q Consensus       205 ~~~~~  209 (453)
                      ++...
T Consensus        90 ~a~~~   94 (114)
T 2do0_A           90 MDERA   94 (114)
T ss_dssp             ECSCC
T ss_pred             EcccC
Confidence            98643

>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=99.73  E-value=2e-17  Score=129.93  Aligned_cols=81  Identities=19%  Similarity=0.315  Sum_probs=73.2

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ....++|||+|||+.+|+++|+++|++||.|..|+|+.   ++.++|||||+|.+.++|.+||..|| ..|+|+.|.|.|
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   95 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   95 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE---CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            34567999999999999999999999999999999965   45689999999999999999999998 889999999999


Q ss_pred             ccCCC
Q 012923          323 AIDGP  327 (453)
Q Consensus       323 a~~~~  327 (453)
                      +....
T Consensus        96 a~~~~  100 (109)
T 1x4a_A           96 PRSGR  100 (109)
T ss_dssp             CCCCC
T ss_pred             cccCC
Confidence            96543

>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=99.73  E-value=8.7e-18  Score=126.59  Aligned_cols=80  Identities=21%  Similarity=0.388  Sum_probs=73.7

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCC-cceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGK-SKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~-~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ..++|||+|||+++|+++|+++|++||.|..|+|+.++.++. ++|||||+|.+.++|.+|++.++ ..|.|+.|.|.++
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            468999999999999999999999999999999999987665 89999999999999999999877 5699999999998


Q ss_pred             cc
Q 012923          207 SI  208 (453)
Q Consensus       207 ~~  208 (453)
                      ..
T Consensus        83 ~~   84 (88)
T 4a8x_A           83 LA   84 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.73  E-value=1.2e-17  Score=130.80  Aligned_cols=81  Identities=22%  Similarity=0.374  Sum_probs=75.4

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      .....++|||+|||+.+|+++|+++|.+||.|..|+|++++ +++++|||||+|.+.++|.+||+.|+ ..|.|+.|.|.
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  103 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ  103 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34567899999999999999999999999999999999999 99999999999999999999999877 56999999999


Q ss_pred             ecc
Q 012923          205 LAS  207 (453)
Q Consensus       205 ~~~  207 (453)
                      ++.
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            874

>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=99.73  E-value=2.6e-17  Score=127.83  Aligned_cols=86  Identities=21%  Similarity=0.400  Sum_probs=76.6

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ......++|||+|||+++|+++|+++|++||.|..|+|++++.  .++|||||+|.+.++|.+||..++ ..|.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   87 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            4456679999999999999999999999999999999999863  389999999999999999999877 5699999999


Q ss_pred             EecccCCCC
Q 012923          204 QLASIGPAT  212 (453)
Q Consensus       204 ~~~~~~~~~  212 (453)
                      .++......
T Consensus        88 ~~a~~~~~~   96 (103)
T 2cq3_A           88 NNATARVMT   96 (103)
T ss_dssp             EECCSSCCC
T ss_pred             EEcccCCCC
Confidence            999765543

>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=99.73  E-value=1e-17  Score=141.93  Aligned_cols=86  Identities=20%  Similarity=0.310  Sum_probs=77.7

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      .....++|||+|||+.+|+++|+.+|.+||.|..|+|+.++.++.++|||||+|.+.++|.+||..|+ ..|.|+.|.|.
T Consensus        68 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  147 (165)
T 1rk8_A           68 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  147 (165)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34556899999999999999999999999999999999999899999999999999999999999887 45999999999


Q ss_pred             ecccCCC
Q 012923          205 LASIGPA  211 (453)
Q Consensus       205 ~~~~~~~  211 (453)
                      ++.....
T Consensus       148 ~a~~~~~  154 (165)
T 1rk8_A          148 WCFVKGP  154 (165)
T ss_dssp             ESEECC-
T ss_pred             EecCCCC
Confidence            9976544

>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=99.73  E-value=2.3e-17  Score=128.22  Aligned_cols=85  Identities=22%  Similarity=0.393  Sum_probs=75.4

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ......++|||+|||+++|+++|+++|++||.|..|+|++++.  .++|||||+|.+.++|.+||..++ ..|.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   87 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEE
Confidence            3455678999999999999999999999999999999999863  378999999999999999999777 5599999999


Q ss_pred             EecccCCC
Q 012923          204 QLASIGPA  211 (453)
Q Consensus       204 ~~~~~~~~  211 (453)
                      .++.....
T Consensus        88 ~~a~~~~~   95 (103)
T 2cqi_A           88 NWATTPSS   95 (103)
T ss_dssp             EECCCTTC
T ss_pred             EECCCCcc
Confidence            99876443

>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=99.73  E-value=3.2e-18  Score=130.98  Aligned_cols=80  Identities=21%  Similarity=0.311  Sum_probs=73.6

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      +..++|||+|||+++|+++|+++|.+||.|..++++.++.+++++|||||+|.+.++|.+||+.++ ..|.|+.|.|.++
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            345899999999999999999999999999999999998899999999999999999999999877 5699999999987


Q ss_pred             c
Q 012923          207 S  207 (453)
Q Consensus       207 ~  207 (453)
                      .
T Consensus        93 ~   93 (95)
T 2ek1_A           93 S   93 (95)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.73  E-value=5.7e-18  Score=134.97  Aligned_cols=79  Identities=25%  Similarity=0.358  Sum_probs=72.6

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCee--EEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEE
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIE--DCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQ  204 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~--~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~  204 (453)
                      ....++|||+|||+++|+++|+++|++| .|.  .|+|++|+. |+++|||||+|.+.++|.+||+.++..|.||.|.|.
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~V~  116 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGKHKERIGHRYIEVF  116 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHCCCEECCEEEEEE
Confidence            3456899999999999999999999999 677  999999985 999999999999999999999987788999999998


Q ss_pred             ecc
Q 012923          205 LAS  207 (453)
Q Consensus       205 ~~~  207 (453)
                      ++.
T Consensus       117 ~a~  119 (126)
T 2hgm_A          117 KSS  119 (126)
T ss_dssp             EEC
T ss_pred             ECC
Confidence            875

>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=99.73  E-value=2.5e-18  Score=132.77  Aligned_cols=83  Identities=16%  Similarity=0.242  Sum_probs=73.6

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccC-CCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEE
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDK-ATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNC  320 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~-~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v  320 (453)
                      .....++|||+|||+.+|+++|+++|+.|| |..|+|++++ .+|+++|||||+|.+.++|.+|| .++ ..|+|+.|.|
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V   92 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRV   92 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEE
Confidence            344567999999999999999999999999 9999999998 68999999999999999999999 788 8999999999


Q ss_pred             EEccCCC
Q 012923          321 QRAIDGP  327 (453)
Q Consensus       321 ~~a~~~~  327 (453)
                      .++..+.
T Consensus        93 ~~a~~~~   99 (100)
T 2j76_E           93 DVADQAQ   99 (100)
T ss_dssp             EECCCSC
T ss_pred             EeccCCC
Confidence            9996543

>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=99.73  E-value=6.7e-18  Score=131.54  Aligned_cols=80  Identities=26%  Similarity=0.494  Sum_probs=75.1

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~  208 (453)
                      .++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+|++.++ ..|.|+.|.|.++..
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            5899999999999999999999999999999999999899999999999999999999999877 559999999999864


Q ss_pred             C
Q 012923          209 G  209 (453)
Q Consensus       209 ~  209 (453)
                      .
T Consensus        88 ~   88 (104)
T 1p1t_A           88 E   88 (104)
T ss_dssp             T
T ss_pred             c
Confidence            3

>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=99.73  E-value=3e-17  Score=128.56  Aligned_cols=76  Identities=12%  Similarity=0.125  Sum_probs=70.5

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCC-----eEE
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEG-----HIL  318 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g-----~~l  318 (453)
                      ...++|||+|||+.+|+++|+++|++||.|..|.|+++       |||||+|.+.++|.+||..|| ..|.|     ++|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i   85 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   85 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEE
Confidence            34579999999999999999999999999999999875       899999999999999999999 88999     999


Q ss_pred             EEEEccCCC
Q 012923          319 NCQRAIDGP  327 (453)
Q Consensus       319 ~v~~a~~~~  327 (453)
                      .|.++..+.
T Consensus        86 ~V~~a~~~~   94 (108)
T 1x4c_A           86 RVKVDGPRS   94 (108)
T ss_dssp             EEEESSCCS
T ss_pred             EEEeCCCCC
Confidence            999997654

>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=99.73  E-value=1.1e-17  Score=135.29  Aligned_cols=88  Identities=20%  Similarity=0.345  Sum_probs=79.6

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ......++|||+|||+++|+++|+++|++||.|..|+|+.++.+++++|||||+|.+.++|.+||+.|+ ..|.|+.|.|
T Consensus        17 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   96 (126)
T 3ex7_B           17 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV   96 (126)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            344557899999999999999999999999999999999999899999999999999999999999877 5699999999


Q ss_pred             EecccCCCC
Q 012923          204 QLASIGPAT  212 (453)
Q Consensus       204 ~~~~~~~~~  212 (453)
                      .++......
T Consensus        97 ~~a~~~~~~  105 (126)
T 3ex7_B           97 DWCFVRGPP  105 (126)
T ss_dssp             EESEESSSC
T ss_pred             EEecCCCCC
Confidence            999755443

>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=99.73  E-value=1.9e-17  Score=127.83  Aligned_cols=77  Identities=14%  Similarity=0.118  Sum_probs=69.7

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC---CccCCeEEEEE
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH---KNFEGHILNCQ  321 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~---~~l~g~~l~v~  321 (453)
                      ...++|||+|||+.+|+++|+++|++||.|..|.|+++      ||||||+|.+.++|.+||..|+   ..|.|++|.|.
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            34579999999999999999999999999999999864      8999999999999999999876   35999999999


Q ss_pred             EccCCC
Q 012923          322 RAIDGP  327 (453)
Q Consensus       322 ~a~~~~  327 (453)
                      |+..+.
T Consensus        87 ~a~~~~   92 (104)
T 1wex_A           87 YSTSKR   92 (104)
T ss_dssp             ECSSSS
T ss_pred             EccCcc
Confidence            997654

>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=99.73  E-value=3.1e-18  Score=124.84  Aligned_cols=75  Identities=29%  Similarity=0.527  Sum_probs=71.5

Q ss_pred             EEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEc
Q 012923          249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRA  323 (453)
Q Consensus       249 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a  323 (453)
                      +|||+|||+.+|+++|+++|++||.|..|.+++++.+++++|||||+|.+.++|.+||...+..|+|+.|.|.+|
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            599999999999999999999999999999999999999999999999999999999998558899999999875

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

Probab=99.73  E-value=1.8e-18  Score=129.37  Aligned_cols=80  Identities=30%  Similarity=0.481  Sum_probs=73.2

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ...++|||+|||+++|+++|+++|++||.|..|+|+.++.+++++|||||+|.+.++|.+|++.++ ..|.|+.|++.+.
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            456899999999999999999999999999999999999899999999999999999999999888 4588888877654


Q ss_pred             c
Q 012923          207 S  207 (453)
Q Consensus       207 ~  207 (453)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.73  E-value=4.7e-18  Score=134.70  Aligned_cols=82  Identities=17%  Similarity=0.327  Sum_probs=76.6

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+|| .|| ..|+|+.|.|.++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  101 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQAS  101 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEec
Confidence            34579999999999999999999999999999999999999999999999999999999999 777 8899999999999


Q ss_pred             cCCC
Q 012923          324 IDGP  327 (453)
Q Consensus       324 ~~~~  327 (453)
                      ..+.
T Consensus       102 ~~~~  105 (114)
T 2cq4_A          102 QAEK  105 (114)
T ss_dssp             HHHH
T ss_pred             CCCc
Confidence            7643

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

Probab=99.73  E-value=1.2e-17  Score=130.10  Aligned_cols=76  Identities=20%  Similarity=0.340  Sum_probs=70.2

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLAS  207 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~  207 (453)
                      .++|||+|||+++|+++|+++|+.| .|..|+|++|+ +|+++|||||+|.+.++|.+||......|.||.|.|..+.
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT-TCCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC-CCCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECC
Confidence            4689999999999999999999999 89999999998 5999999999999999999999655577999999998875

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

Probab=99.73  E-value=7.7e-18  Score=122.50  Aligned_cols=73  Identities=18%  Similarity=0.145  Sum_probs=67.9

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLAS  207 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~  207 (453)
                      .+..|||+||++.+|+++|+++|.+||+|.+++|+.      ++|||||+|.+.++|.+|++.|| ..+.||.|+|.++.
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            467899999999999999999999999999999865      68999999999999999999998 55999999999984

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

Probab=99.73  E-value=3.1e-18  Score=139.17  Aligned_cols=83  Identities=18%  Similarity=0.333  Sum_probs=76.4

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeE--EEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-----ccCC
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIED--CKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-----KIGN  198 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~--v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-----~~~g  198 (453)
                      .....++|||+|||+++|+++|+++|++||.|..  |+|++|+.+++++|||||+|.+. +|.+||..+++     .|.|
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g   97 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG   97 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC
Confidence            3455789999999999999999999999999977  99999999999999999999999 99999999884     7999


Q ss_pred             eEeEEEecccC
Q 012923          199 RMTACQLASIG  209 (453)
Q Consensus       199 r~~~v~~~~~~  209 (453)
                      |.|.|.++...
T Consensus        98 r~l~V~~a~~~  108 (131)
T 2m2b_A           98 KTINVEFAKGS  108 (131)
T ss_dssp             CCCCCEECCCS
T ss_pred             EEEEEEECCCC
Confidence            99999998654

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

Probab=99.73  E-value=1.5e-18  Score=129.85  Aligned_cols=79  Identities=19%  Similarity=0.308  Sum_probs=73.9

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+++++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||..|| ..|.|+.|+|.++.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCCC
Confidence            34699999999999999999999999999999999999999999999999999999999999999 88999998887653

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.73  E-value=8.9e-18  Score=133.62  Aligned_cols=80  Identities=15%  Similarity=0.312  Sum_probs=73.2

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCC---eeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEE
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGE---IEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTAC  203 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~---i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v  203 (453)
                      ....++|||+|||+++|+++|+++|+.||.   |..|+|++++. ++++|||||+|.+.++|.+||+.....|.||.|.|
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V   92 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALKKDRESMGHRYIEV   92 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEE
Confidence            345689999999999999999999999999   89999999985 99999999999999999999994446699999999


Q ss_pred             Eecc
Q 012923          204 QLAS  207 (453)
Q Consensus       204 ~~~~  207 (453)
                      .++.
T Consensus        93 ~~a~   96 (118)
T 2db1_A           93 FKSH   96 (118)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            9875

>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=99.72  E-value=1e-17  Score=131.94  Aligned_cols=83  Identities=17%  Similarity=0.310  Sum_probs=75.7

Q ss_pred             ccccEEEEecCCCCccHHHHH---HHHhccCCcceeeeeccCCCC---CCceEEEEEECCHHHHHHHHHcCC-CccCCeE
Q 012923          245 YTQRKIFVSNVGSELEPQKLL---AFFSKYGEIEEGPLGIDKATG---KPKGFCLFVYKTVDAAKKALEEPH-KNFEGHI  317 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~---~~F~~~G~i~~v~i~~d~~~g---~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~  317 (453)
                      ...++|||+|||+.+++++|+   ++|++||.|..|.|++++.++   +++|||||+|.+.++|.+||..|| ..|+|++
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~   92 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   92 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEE
Confidence            345799999999999999999   999999999999999988754   556999999999999999999999 8899999


Q ss_pred             EEEEEccCCC
Q 012923          318 LNCQRAIDGP  327 (453)
Q Consensus       318 l~v~~a~~~~  327 (453)
                      |+|.++.+++
T Consensus        93 l~V~~a~~k~  102 (111)
T 2cpi_A           93 LKASLGTTKY  102 (111)
T ss_dssp             EEEESCCCCS
T ss_pred             EEEEeccccc
Confidence            9999997665

>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=99.72  E-value=2.2e-17  Score=126.33  Aligned_cols=80  Identities=15%  Similarity=0.189  Sum_probs=72.6

Q ss_pred             CCcCeEEEcCCCCCCCHHHHH----HHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeE
Q 012923          128 PVHRKIFVHGLGWDTKAETLI----DAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTA  202 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~----~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~  202 (453)
                      ...++|||+|||+++|+++|+    ++|++||.|..|+|++++.+   +|||||+|.+.++|.+||+.+++ .|.|+.|+
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~   83 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKIL   83 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            456799999999999999999    99999999999999998854   89999999999999999998885 59999999


Q ss_pred             EEecccCC
Q 012923          203 CQLASIGP  210 (453)
Q Consensus       203 v~~~~~~~  210 (453)
                      |.++....
T Consensus        84 V~~a~~~~   91 (96)
T 2dgx_A           84 VSLATGAS   91 (96)
T ss_dssp             EEECCCSS
T ss_pred             EEEcCCCC
Confidence            99986543

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=2.3e-17  Score=127.69  Aligned_cols=80  Identities=20%  Similarity=0.317  Sum_probs=71.9

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ....++|||+|||+.+|+++|+++|++||.|   +|+++ .+++++|||||+|.+.++|.+||..|| ..|.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   87 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL   87 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            3456799999999999999999999999977   56665 689999999999999999999999999 889999999999


Q ss_pred             ccCCC
Q 012923          323 AIDGP  327 (453)
Q Consensus       323 a~~~~  327 (453)
                      +..+.
T Consensus        88 a~~~~   92 (101)
T 2fc9_A           88 QGPRG   92 (101)
T ss_dssp             CSSCC
T ss_pred             cCCCC
Confidence            97654

>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=99.72  E-value=8.7e-18  Score=132.04  Aligned_cols=81  Identities=15%  Similarity=0.139  Sum_probs=72.1

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC---CccCCeEeE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ---KKIGNRMTA  202 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~---~~~~gr~~~  202 (453)
                      ..+.+++|||+|||+++|+++|+++|++||.|.+|+|+++      ||||||+|.+.++|.+|++.++   ..|.|+.|.
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~  100 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY  100 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEE
Confidence            3455789999999999999999999999999999999875      6899999999999999999876   359999999


Q ss_pred             EEecccCCCC
Q 012923          203 CQLASIGPAT  212 (453)
Q Consensus       203 v~~~~~~~~~  212 (453)
                      |.++......
T Consensus       101 V~~a~~k~~~  110 (119)
T 2ad9_A          101 IQFSNHKELK  110 (119)
T ss_dssp             EEECSSSSCC
T ss_pred             EEEccCCCCC
Confidence            9999765544

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.72  E-value=1.2e-17  Score=132.81  Aligned_cols=80  Identities=10%  Similarity=0.096  Sum_probs=73.9

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCC---cceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEE
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGE---IEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNC  320 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~---i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v  320 (453)
                      ...++|||+|||+.+|+++|+++|+.||.   |..|+|++++. |+++|||||+|.+.++|.+||. +| ..|+||.|+|
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   92 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEV   92 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEE
Confidence            34579999999999999999999999999   89999999976 9999999999999999999999 67 8899999999


Q ss_pred             EEccCC
Q 012923          321 QRAIDG  326 (453)
Q Consensus       321 ~~a~~~  326 (453)
                      .++...
T Consensus        93 ~~a~~~   98 (118)
T 2db1_A           93 FKSHRT   98 (118)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            998543

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=5.9e-18  Score=134.65  Aligned_cols=79  Identities=24%  Similarity=0.336  Sum_probs=72.0

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCe----eEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEE
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEI----EDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTAC  203 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i----~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v  203 (453)
                      ...++|||+|||+++|+++|++||++||.|    ..|+|+++. +|+++|||||+|.+.++|.+||+..+..|.+|.|.|
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            346899999999999999999999999975    689999996 899999999999999999999998557799999999


Q ss_pred             Eecc
Q 012923          204 QLAS  207 (453)
Q Consensus       204 ~~~~  207 (453)
                      ..+.
T Consensus       100 ~~a~  103 (123)
T 2dha_A          100 FRST  103 (123)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            8874

>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=99.72  E-value=8.1e-18  Score=136.39  Aligned_cols=81  Identities=16%  Similarity=0.288  Sum_probs=74.3

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCC---eeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGE---IEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRM  200 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~---i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~  200 (453)
                      ......++|||+|||+++|+++|+++|++||.   |..|+|++|+. |+++|||||+|.+.++|.+||+ ++ ..|.||.
T Consensus        39 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~  116 (136)
T 2hgl_A           39 PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRY  116 (136)
T ss_dssp             SSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEE
Confidence            34456789999999999999999999999999   89999999995 9999999999999999999999 66 6699999


Q ss_pred             eEEEecc
Q 012923          201 TACQLAS  207 (453)
Q Consensus       201 ~~v~~~~  207 (453)
                      |.|.++.
T Consensus       117 i~V~~a~  123 (136)
T 2hgl_A          117 IEVFKSH  123 (136)
T ss_dssp             EEEEECC
T ss_pred             EEEEECC
Confidence            9999875

>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=99.72  E-value=3.3e-17  Score=137.60  Aligned_cols=85  Identities=18%  Similarity=0.285  Sum_probs=78.3

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      .....++|||+|||+++|+++|+++|++||.|..|+|+.++.+++++|||||+|.+.++|.+||+.|+ ..|.|+.|.|.
T Consensus        35 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  114 (156)
T 1h2v_Z           35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD  114 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34567899999999999999999999999999999999999899999999999999999999999877 56999999999


Q ss_pred             ecccCC
Q 012923          205 LASIGP  210 (453)
Q Consensus       205 ~~~~~~  210 (453)
                      ++....
T Consensus       115 ~a~~~~  120 (156)
T 1h2v_Z          115 WDAGFK  120 (156)
T ss_dssp             EESCCC
T ss_pred             ECCCCC
Confidence            997543

>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=99.72  E-value=7.9e-18  Score=129.91  Aligned_cols=81  Identities=20%  Similarity=0.345  Sum_probs=71.8

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccC-CCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDK-VSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~-~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      ....++|||+|||+++|+++|+++|++|| |..|+|++++ .+++++|||||+|.+.++|.+|| .++ ..|.|+.|.|.
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~   93 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVD   93 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEE
Confidence            34568999999999999999999999999 9999999998 58999999999999999999999 566 66999999999


Q ss_pred             ecccC
Q 012923          205 LASIG  209 (453)
Q Consensus       205 ~~~~~  209 (453)
                      ++...
T Consensus        94 ~a~~~   98 (100)
T 2j76_E           94 VADQA   98 (100)
T ss_dssp             ECCCS
T ss_pred             eccCC
Confidence            98643

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

Probab=99.72  E-value=2.1e-17  Score=125.53  Aligned_cols=82  Identities=24%  Similarity=0.356  Sum_probs=74.5

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ....++|||+|||+++|+++|+++|++||.|..|+|+++  +++++|||||+|.+.++|.+|++.++ ..|.|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   82 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI   82 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            345789999999999999999999999999999999984  78999999999999999999999877 569999999999


Q ss_pred             cccCC
Q 012923          206 ASIGP  210 (453)
Q Consensus       206 ~~~~~  210 (453)
                      +....
T Consensus        83 a~~~~   87 (92)
T 2dgv_A           83 DRNAS   87 (92)
T ss_dssp             CSCCS
T ss_pred             cCCCC
Confidence            86543

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

Probab=99.72  E-value=2.7e-17  Score=127.29  Aligned_cols=76  Identities=22%  Similarity=0.371  Sum_probs=71.3

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCC
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDG  326 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~  326 (453)
                      ++|||+|||+.+|+++|+++|++||.|..|.|+++     ++|||||+|.+.++|.+||..|+ ..|+|+.|.|.++...
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            48999999999999999999999999999999886     69999999999999999999998 8999999999999776


Q ss_pred             CC
Q 012923          327 PK  328 (453)
Q Consensus       327 ~~  328 (453)
                      +.
T Consensus        76 ~~   77 (101)
T 2hvz_A           76 PR   77 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.72  E-value=2.2e-17  Score=126.68  Aligned_cols=81  Identities=12%  Similarity=0.134  Sum_probs=71.3

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC---CccCCeEeE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ---KKIGNRMTA  202 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~---~~~~gr~~~  202 (453)
                      ..+.+++|||+|||+++|+++|+++|++||.|..|+|+++      ||||||+|.+.++|.+|++.++   ..|.|+.|.
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   84 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   84 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEE
Confidence            3456789999999999999999999999999999998864      7899999999999999999764   459999999


Q ss_pred             EEecccCCCC
Q 012923          203 CQLASIGPAT  212 (453)
Q Consensus       203 v~~~~~~~~~  212 (453)
                      |.++......
T Consensus        85 V~~a~~~~~~   94 (101)
T 2cq1_A           85 IQYSNHKELK   94 (101)
T ss_dssp             EEECSCSSCC
T ss_pred             EEEcCcccCc
Confidence            9999755443

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

Probab=99.72  E-value=4.9e-17  Score=130.88  Aligned_cols=84  Identities=18%  Similarity=0.322  Sum_probs=77.9

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      .....++|||+|||+.+++++|+++|+.||.|..|+|++++ +++++|||||+|.+.++|.+||..+| ..|+|+.|+|.
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  109 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  109 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34456799999999999999999999999999999999998 99999999999999999999999988 88999999999


Q ss_pred             EccCCC
Q 012923          322 RAIDGP  327 (453)
Q Consensus       322 ~a~~~~  327 (453)
                      ++....
T Consensus       110 ~a~~~~  115 (124)
T 2kt5_A          110 LVASQI  115 (124)
T ss_dssp             EECCTT
T ss_pred             EeCCCC
Confidence            997654

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

Probab=99.72  E-value=1.3e-17  Score=129.77  Aligned_cols=76  Identities=14%  Similarity=0.155  Sum_probs=70.5

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      ..+|||+|||+.+|+++|+++|+.| .|..|+|++++. |+++|||||+|.+.++|.+||. +| ..|+||.|.|..+..
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEALK-RNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHHH-TTTEEETTEEEEEEECCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEEECCc
Confidence            4699999999999999999999999 899999999975 9999999999999999999995 66 889999999988854

>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=99.72  E-value=1.1e-17  Score=132.49  Aligned_cols=79  Identities=20%  Similarity=0.296  Sum_probs=73.7

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLAS  207 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~  207 (453)
                      ..++|||+|||+++|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+|| .++ ..|.|+.|.|.++.
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~  102 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQ  102 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecC
Confidence            3579999999999999999999999999999999999988999999999999999999999 666 56999999999986


Q ss_pred             c
Q 012923          208 I  208 (453)
Q Consensus       208 ~  208 (453)
                      .
T Consensus       103 ~  103 (114)
T 2cq4_A          103 A  103 (114)
T ss_dssp             H
T ss_pred             C
Confidence            3

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

Probab=99.72  E-value=2.8e-17  Score=135.51  Aligned_cols=81  Identities=23%  Similarity=0.437  Sum_probs=75.8

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      .....++|||+|||+.+|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||..|| ..|+|++|+|.
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34456899999999999999999999999999999999999999999999999999999999999999 88999999998


Q ss_pred             Ec
Q 012923          322 RA  323 (453)
Q Consensus       322 ~a  323 (453)
                      +|
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            85

>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=99.72  E-value=1.1e-17  Score=134.66  Aligned_cols=82  Identities=16%  Similarity=0.225  Sum_probs=75.2

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ....++|||+|||+.+|+++|+++|+.||.|..+.++.+..+|+++|||||+|.+.++|.+||. +| ..|+|+.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            3445799999999999999999999999999998788888899999999999999999999999 78 899999999999


Q ss_pred             ccCC
Q 012923          323 AIDG  326 (453)
Q Consensus       323 a~~~  326 (453)
                      +...
T Consensus       101 a~~~  104 (124)
T 1wel_A          101 ITKK  104 (124)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8643

>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=99.72  E-value=1.3e-17  Score=132.40  Aligned_cols=84  Identities=17%  Similarity=0.352  Sum_probs=73.9

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|+.||.|..+.+..+..+++++|||||+|.+.++|.+||..|| ..|+|+.|.|.|+
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a  102 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG  102 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEc
Confidence            356799999999999999999999999999665554444488999999999999999999999999 8899999999999


Q ss_pred             cCCCC
Q 012923          324 IDGPK  328 (453)
Q Consensus       324 ~~~~~  328 (453)
                      ..+..
T Consensus       103 ~~~~~  107 (115)
T 2cpx_A          103 KNKKQ  107 (115)
T ss_dssp             CCCSC
T ss_pred             cCCCC
Confidence            76543

>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=99.71  E-value=1.3e-17  Score=127.65  Aligned_cols=77  Identities=13%  Similarity=0.127  Sum_probs=69.2

Q ss_pred             CCcCeEEEcCCCC-CCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC---CccCCeEeEE
Q 012923          128 PVHRKIFVHGLGW-DTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ---KKIGNRMTAC  203 (453)
Q Consensus       128 ~~~~~lfV~nLp~-~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~---~~~~gr~~~v  203 (453)
                      ..+++|||+|||+ ++|+++|+++|++||.|.+|+|+++      +|||||+|.+.++|.+||+.++   ..|.||.|.|
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   86 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   86 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEE
Confidence            4578999999999 9999999999999999999999875      4799999999999999999876   2489999999


Q ss_pred             EecccCC
Q 012923          204 QLASIGP  210 (453)
Q Consensus       204 ~~~~~~~  210 (453)
                      .++....
T Consensus        87 ~~a~~~~   93 (102)
T 1x4d_A           87 HLSQKYK   93 (102)
T ss_dssp             EEECCCT
T ss_pred             EECCCCC
Confidence            9997543

>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=99.71  E-value=5e-18  Score=128.46  Aligned_cols=79  Identities=24%  Similarity=0.443  Sum_probs=72.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecccC
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASIG  209 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~~  209 (453)
                      ++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.+ |.+|+..++ ..+.|+.|.|.++...
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            68999999999999999999999999999999999989999999999999999 999999988 4599999999998754


Q ss_pred             C
Q 012923          210 P  210 (453)
Q Consensus       210 ~  210 (453)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            3

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

Probab=99.71  E-value=1.9e-17  Score=129.00  Aligned_cols=80  Identities=21%  Similarity=0.287  Sum_probs=73.4

Q ss_pred             cccEEEEecCCCCc------cHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCe-E
Q 012923          246 TQRKIFVSNVGSEL------EPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGH-I  317 (453)
Q Consensus       246 ~~~~l~V~nLp~~~------t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~-~  317 (453)
                      ..++|||+|||+.+      |+++|+++|++||.|..|+|+  +.+|+++|||||+|.+.++|.+||..|| ..|+|+ +
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~   91 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT   91 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCE
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCce
Confidence            35799999999999      889999999999999999998  3689999999999999999999999999 889998 9


Q ss_pred             EEEEEccCCC
Q 012923          318 LNCQRAIDGP  327 (453)
Q Consensus       318 l~v~~a~~~~  327 (453)
                      |.|.++....
T Consensus        92 l~V~~a~~~~  101 (105)
T 2nlw_A           92 FRVNLFTDFD  101 (105)
T ss_dssp             EEEECSCCCC
T ss_pred             EEEEEcchHh
Confidence            9999996543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.71  E-value=6.2e-18  Score=130.92  Aligned_cols=80  Identities=18%  Similarity=0.223  Sum_probs=73.9

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+|+++|+++|+.||.|.. .++++..+++++|||||+|.+.++|.+||. || ..|.|+.|.|.++.
T Consensus        16 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a~   93 (101)
T 1fj7_A           16 TPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   93 (101)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcC
Confidence            4579999999999999999999999999998 777888889999999999999999999999 88 89999999999997


Q ss_pred             CCC
Q 012923          325 DGP  327 (453)
Q Consensus       325 ~~~  327 (453)
                      .+.
T Consensus        94 ~~~   96 (101)
T 1fj7_A           94 GRD   96 (101)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            554

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.71  E-value=2e-17  Score=129.00  Aligned_cols=78  Identities=17%  Similarity=0.217  Sum_probs=69.7

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccC-CcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYG-EIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G-~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ..++|||+|||+.+|+++|+++|+.|| .|..+.|+.+    +++|||||+|.+.++|.+||..|| ..|+|++|.|.++
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            346999999999999999999999999 8999988642    479999999999999999999999 8899999999999


Q ss_pred             cCCC
Q 012923          324 IDGP  327 (453)
Q Consensus       324 ~~~~  327 (453)
                      ...+
T Consensus       103 ~~~p  106 (111)
T 2jvr_A          103 DNPP  106 (111)
T ss_dssp             CC--
T ss_pred             CCCC
Confidence            6544

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

Probab=99.71  E-value=3.8e-17  Score=131.48  Aligned_cols=84  Identities=23%  Similarity=0.351  Sum_probs=77.0

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~  205 (453)
                      ....++|||+|||+++|+++|+++|++||.|..|+|++++ +++++|||||+|.+.++|.+|+..+++ .|.|+.|.|.+
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            3456899999999999999999999999999999999999 999999999999999999999998774 59999999999


Q ss_pred             cccCCC
Q 012923          206 ASIGPA  211 (453)
Q Consensus       206 ~~~~~~  211 (453)
                      +.....
T Consensus       111 a~~~~~  116 (124)
T 2kt5_A          111 VASQID  116 (124)
T ss_dssp             ECCTTC
T ss_pred             eCCCCC
Confidence            875444

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

Probab=99.71  E-value=2.8e-17  Score=128.89  Aligned_cols=84  Identities=20%  Similarity=0.413  Sum_probs=75.6

Q ss_pred             cCCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeE
Q 012923          124 ADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTA  202 (453)
Q Consensus       124 ~~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~  202 (453)
                      .......++|||+|||.++|+++|+++|++||.|..|+|++++  +.++|||||+|.+.++|.+|++.++ ..|.|+.|.
T Consensus        23 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~  100 (109)
T 2err_A           23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE  100 (109)
T ss_dssp             CSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECE
T ss_pred             ccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            4455677999999999999999999999999999999999985  3589999999999999999999877 569999999


Q ss_pred             EEecccC
Q 012923          203 CQLASIG  209 (453)
Q Consensus       203 v~~~~~~  209 (453)
                      |.++..+
T Consensus       101 V~~a~~~  107 (109)
T 2err_A          101 VNNATAR  107 (109)
T ss_dssp             EEECCCS
T ss_pred             EEECCCC
Confidence            9998644

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

Probab=99.71  E-value=1.5e-17  Score=135.61  Aligned_cols=87  Identities=23%  Similarity=0.400  Sum_probs=78.9

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ......++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||+.++ ..|.|+.|.|
T Consensus        42 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V  121 (135)
T 2lea_A           42 PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV  121 (135)
T ss_dssp             SSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            344557899999999999999999999999999999999999899999999999999999999999888 5599999999


Q ss_pred             EecccCCC
Q 012923          204 QLASIGPA  211 (453)
Q Consensus       204 ~~~~~~~~  211 (453)
                      .++.....
T Consensus       122 ~~a~~~~~  129 (135)
T 2lea_A          122 QMARYGRP  129 (135)
T ss_dssp             EECCCCCC
T ss_pred             EECCCCCC
Confidence            99875433

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

Probab=99.71  E-value=3.8e-17  Score=134.72  Aligned_cols=82  Identities=24%  Similarity=0.413  Sum_probs=75.5

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ......++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||+.++ ..|.|+.|+|
T Consensus        58 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  137 (140)
T 2ku7_A           58 GSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV  137 (140)
T ss_dssp             SSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEE
T ss_pred             CCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            345567899999999999999999999999999999999998899999999999999999999999888 4599999999


Q ss_pred             Eec
Q 012923          204 QLA  206 (453)
Q Consensus       204 ~~~  206 (453)
                      .++
T Consensus       138 ~~A  140 (140)
T 2ku7_A          138 NLA  140 (140)
T ss_dssp             EC-
T ss_pred             EeC
Confidence            875

>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=99.71  E-value=2.7e-17  Score=127.00  Aligned_cols=80  Identities=16%  Similarity=0.179  Sum_probs=70.6

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC---CccCCeEeEE
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ---KKIGNRMTAC  203 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~---~~~~gr~~~v  203 (453)
                      .+.+++|||+|||+++|+++|+++|++||.|..|+|+++      ||||||+|.+.++|.+|++.++   ..|.|+.|.|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V   85 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            455789999999999999999999999999999998764      6899999999999999999765   3489999999


Q ss_pred             EecccCCCC
Q 012923          204 QLASIGPAT  212 (453)
Q Consensus       204 ~~~~~~~~~  212 (453)
                      .++......
T Consensus        86 ~~a~~~~~~   94 (104)
T 1wex_A           86 NYSTSKRIT   94 (104)
T ss_dssp             EECSSSSCC
T ss_pred             EEccCcccc
Confidence            999765443

>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=99.71  E-value=3.7e-17  Score=128.36  Aligned_cols=80  Identities=23%  Similarity=0.417  Sum_probs=73.5

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ....++|||+|||+.+|+++|+++|+.||.|..|+|+++      +|||||+|.+.++|.+||..|+ ..|+|+.|.|.|
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            345679999999999999999999999999999999876      8999999999999999999998 899999999999


Q ss_pred             ccCCCCC
Q 012923          323 AIDGPKP  329 (453)
Q Consensus       323 a~~~~~~  329 (453)
                      +..++..
T Consensus        96 a~~~~~~  102 (109)
T 1x4g_A           96 GKESPDM  102 (109)
T ss_dssp             CCCCCSS
T ss_pred             cCCCCCC
Confidence            9776544

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

Probab=99.71  E-value=3.8e-17  Score=126.72  Aligned_cols=81  Identities=20%  Similarity=0.302  Sum_probs=73.4

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ....++|||+|||+.+|+++|+++|+.|   ..|++++++.+++++|||||+|.+.++|.+||..|| ..|.|+.|.|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDW   88 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            3456799999999999999999999977   478888888899999999999999999999999988 899999999999


Q ss_pred             ccCCC
Q 012923          323 AIDGP  327 (453)
Q Consensus       323 a~~~~  327 (453)
                      +..+.
T Consensus        89 a~~~~   93 (102)
T 2fc8_A           89 AKPKG   93 (102)
T ss_dssp             CCCCC
T ss_pred             ecCCC
Confidence            97654

>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=99.71  E-value=5.6e-17  Score=127.38  Aligned_cols=84  Identities=18%  Similarity=0.262  Sum_probs=74.1

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ......++|||+|||+++|+++|+++|++||.|..|+|+.+   +.++|||||+|.+.++|.+||+.++ ..|.|+.|.|
T Consensus        17 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   93 (109)
T 1x4a_A           17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV   93 (109)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            34556789999999999999999999999999999999664   4689999999999999999998877 5699999999


Q ss_pred             EecccCCC
Q 012923          204 QLASIGPA  211 (453)
Q Consensus       204 ~~~~~~~~  211 (453)
                      .++.....
T Consensus        94 ~~a~~~~~  101 (109)
T 1x4a_A           94 EFPRSGRG  101 (109)
T ss_dssp             ECCCCCCC
T ss_pred             EEcccCCC
Confidence            99875543

>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=99.71  E-value=1.1e-17  Score=130.83  Aligned_cols=81  Identities=20%  Similarity=0.287  Sum_probs=73.6

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCC---eeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGE---IEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTA  202 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~---i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~  202 (453)
                      .....++|||+|||+++|+++|+++|+.||.   |..|+|++++. |+++|||||+|.+.++|.+||...+..|.||.|.
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~   85 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALEKHRMYMGQRYVE   85 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHTTTTCCSSSSCCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHHhCcceeCCeEEE
Confidence            4456789999999999999999999999998   89999999986 9999999999999999999999444669999999


Q ss_pred             EEecc
Q 012923          203 CQLAS  207 (453)
Q Consensus       203 v~~~~  207 (453)
                      |.++.
T Consensus        86 V~~a~   90 (107)
T 2lmi_A           86 VYEIN   90 (107)
T ss_dssp             CEECC
T ss_pred             EEECC
Confidence            99875

>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=99.71  E-value=1.4e-17  Score=132.69  Aligned_cols=79  Identities=18%  Similarity=0.248  Sum_probs=72.3

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcc--eeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEE
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIE--EGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQR  322 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~--~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~  322 (453)
                      ...++|||+|||+.+|+++|+++|+.| .|+  .|+|++++. |+++|||||+|.+.++|.+||..++..|+||.|.|.+
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~V~~  117 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFK  117 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHCCCEECCEEEEEEE
Confidence            345799999999999999999999999 677  999999986 9999999999999999999999866899999999988


Q ss_pred             ccC
Q 012923          323 AID  325 (453)
Q Consensus       323 a~~  325 (453)
                      +..
T Consensus       118 a~~  120 (126)
T 2hgm_A          118 SSQ  120 (126)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            753

>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=99.71  E-value=2.1e-17  Score=128.36  Aligned_cols=78  Identities=18%  Similarity=0.159  Sum_probs=69.8

Q ss_pred             cccccEEEEecCCCC-ccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC---CccCCeEEE
Q 012923          244 EYTQRKIFVSNVGSE-LEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH---KNFEGHILN  319 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~-~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~---~~l~g~~l~  319 (453)
                      ....++|||+|||+. +|+++|+++|++||.|.+|+|++.      ||||||+|.+.++|.+||..|+   ..|.|++|+
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 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            345679999999998 999999999999999999999754      8999999999999999999875   469999999


Q ss_pred             EEEccCCC
Q 012923          320 CQRAIDGP  327 (453)
Q Consensus       320 v~~a~~~~  327 (453)
                      |.++..+.
T Consensus        96 V~~a~~~~  103 (112)
T 1x4f_A           96 VDLSEKYK  103 (112)
T ss_dssp             EEEECSCS
T ss_pred             EEECcccc
Confidence            99996543

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

Probab=99.71  E-value=5e-17  Score=122.84  Aligned_cols=75  Identities=23%  Similarity=0.383  Sum_probs=69.5

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+|+++|+++|++||.|..|+|+        +|||||+|.+.++|.+||..+| ..|+|++|+|.++.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   78 (90)
T 2dnq_A            7 GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASK   78 (90)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSS
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECC
Confidence            45799999999999999999999999999999996        6899999999999999999999 88999999999997


Q ss_pred             CCCC
Q 012923          325 DGPK  328 (453)
Q Consensus       325 ~~~~  328 (453)
                      .+..
T Consensus        79 ~~~~   82 (90)
T 2dnq_A           79 NKSK   82 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6553

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

Probab=99.71  E-value=2.5e-17  Score=129.17  Aligned_cols=82  Identities=21%  Similarity=0.379  Sum_probs=74.9

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      .....++|||+|||+.+|+++|+++|++||.|..|+|++++  +.++|||||+|.+.++|.+|+..|| ..|+|+.|.|.
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  102 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN  102 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34456799999999999999999999999999999999885  4589999999999999999999988 88999999999


Q ss_pred             EccCC
Q 012923          322 RAIDG  326 (453)
Q Consensus       322 ~a~~~  326 (453)
                      ++..+
T Consensus       103 ~a~~~  107 (109)
T 2err_A          103 NATAR  107 (109)
T ss_dssp             ECCCS
T ss_pred             ECCCC
Confidence            99764

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

Probab=99.71  E-value=3.5e-17  Score=127.40  Aligned_cols=82  Identities=21%  Similarity=0.277  Sum_probs=73.0

Q ss_pred             CCCCcCeEEEcCCCCCC------CHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCC
Q 012923          126 EDPVHRKIFVHGLGWDT------KAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGN  198 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~------te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~g  198 (453)
                      .....++|||+|||+.+      |+++|+++|++||.|..|+|+  +.+|+++|||||+|.+.++|.+||..+++ .|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g   88 (105)
T 2nlw_A           11 ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK   88 (105)
T ss_dssp             CCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECST
T ss_pred             CCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCC
Confidence            34456899999999999      789999999999999999988  34899999999999999999999998885 5999


Q ss_pred             e-EeEEEecccC
Q 012923          199 R-MTACQLASIG  209 (453)
Q Consensus       199 r-~~~v~~~~~~  209 (453)
                      + .|.|.++...
T Consensus        89 ~~~l~V~~a~~~  100 (105)
T 2nlw_A           89 QHTFRVNLFTDF  100 (105)
T ss_dssp             TCEEEEECSCCC
T ss_pred             CceEEEEEcchH
Confidence            8 9999998643

>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=99.71  E-value=5.7e-17  Score=136.54  Aligned_cols=84  Identities=24%  Similarity=0.416  Sum_probs=77.7

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~  204 (453)
                      .....++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||..+++ .|.|+.|.|.
T Consensus        66 ~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  145 (158)
T 2kn4_A           66 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ  145 (158)
T ss_dssp             CCCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            345578999999999999999999999999999999999998999999999999999999999998884 5999999999


Q ss_pred             ecccC
Q 012923          205 LASIG  209 (453)
Q Consensus       205 ~~~~~  209 (453)
                      ++...
T Consensus       146 ~a~~~  150 (158)
T 2kn4_A          146 MARYG  150 (158)
T ss_dssp             EECCS
T ss_pred             ECCCC
Confidence            98754

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

Probab=99.71  E-value=5.7e-17  Score=130.54  Aligned_cols=79  Identities=25%  Similarity=0.472  Sum_probs=73.7

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~  208 (453)
                      .++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+|| .++ ..|.|+.|.|.++..
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCC
Confidence            479999999999999999999999999999999999889999999999999999999999 566 569999999999864


Q ss_pred             C
Q 012923          209 G  209 (453)
Q Consensus       209 ~  209 (453)
                      .
T Consensus       115 ~  115 (124)
T 2jwn_A          115 N  115 (124)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.70  E-value=1.6e-17  Score=129.89  Aligned_cols=80  Identities=18%  Similarity=0.155  Sum_probs=73.9

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCC---cceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEE
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGE---IEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNC  320 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~---i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v  320 (453)
                      ...++|||+|||+.+|+++|+++|+.||.   |..|+|++++. |+++|||||+|.+.++|.+||. +| ..|+|+.|.|
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V   86 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEV   86 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEE
Confidence            34579999999999999999999999998   89999999987 9999999999999999999999 77 8899999999


Q ss_pred             EEccCC
Q 012923          321 QRAIDG  326 (453)
Q Consensus       321 ~~a~~~  326 (453)
                      .++..+
T Consensus        87 ~~a~~~   92 (107)
T 2lmi_A           87 YEINNE   92 (107)
T ss_dssp             EECCHH
T ss_pred             EECCHH
Confidence            998643

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.70  E-value=1.6e-17  Score=122.91  Aligned_cols=71  Identities=23%  Similarity=0.348  Sum_probs=66.4

Q ss_pred             cEEEEecCCCCc------cHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCe-EEE
Q 012923          248 RKIFVSNVGSEL------EPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGH-ILN  319 (453)
Q Consensus       248 ~~l~V~nLp~~~------t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~-~l~  319 (453)
                      ++|||+|||+.+      |+++|+++|++||.|..|+|+  +.+|+++|||||+|.+.++|.+||..|| ..|+|+ +|+
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            589999999999      789999999999999999987  3589999999999999999999999999 889999 887


Q ss_pred             E
Q 012923          320 C  320 (453)
Q Consensus       320 v  320 (453)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.70  E-value=2.1e-17  Score=122.25  Aligned_cols=72  Identities=21%  Similarity=0.290  Sum_probs=65.3

Q ss_pred             cCeEEEcCCCCCC------CHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCe-Ee
Q 012923          130 HRKIFVHGLGWDT------KAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNR-MT  201 (453)
Q Consensus       130 ~~~lfV~nLp~~~------te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr-~~  201 (453)
                      +++|||+|||+.+      |+++|+++|++||.|..|+|++  .+++++|||||+|.+.++|.+|++.+++ .|.|+ .|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~--~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC--BTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC--CCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            3799999999999      7899999999999999999873  4899999999999999999999999884 58898 77


Q ss_pred             EE
Q 012923          202 AC  203 (453)
Q Consensus       202 ~v  203 (453)
                      +|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            65

>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=99.70  E-value=4.5e-17  Score=129.08  Aligned_cols=79  Identities=14%  Similarity=0.272  Sum_probs=73.9

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-Ccc--------CC
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNF--------EG  315 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l--------~g  315 (453)
                      ...++|||+|||+.+|+++|+++|+.||.|..|+|++++ ++.++|||||+|.+.++|.+||..|| ..|        .+
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            455799999999999999999999999999999999998 99999999999999999999999998 777        57


Q ss_pred             eEEEEEEcc
Q 012923          316 HILNCQRAI  324 (453)
Q Consensus       316 ~~l~v~~a~  324 (453)
                      ++|.|.|+.
T Consensus       102 ~~l~v~~a~  110 (114)
T 1x5o_A          102 EPLLCKFSG  110 (114)
T ss_dssp             SCBEEEECC
T ss_pred             CceeEEccC
Confidence            889999986

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

Probab=99.70  E-value=4.5e-17  Score=130.45  Aligned_cols=80  Identities=20%  Similarity=0.288  Sum_probs=71.9

Q ss_pred             ccccEEEEecCCCCccHHHHH----HHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEE
Q 012923          245 YTQRKIFVSNVGSELEPQKLL----AFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILN  319 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~----~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~  319 (453)
                      ...++|||+|||+.+++++|+    ++|++||.|..|.+.+   +++++|||||+|.+.++|.+||..|| ..|.|++|+
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    6999999999988753   68899999999999999999999999 899999999


Q ss_pred             EEEccCCC
Q 012923          320 CQRAIDGP  327 (453)
Q Consensus       320 v~~a~~~~  327 (453)
                      |.|+..+.
T Consensus       104 V~~a~~~~  111 (127)
T 2a3j_A          104 ITFSETPQ  111 (127)
T ss_dssp             EEECCCCC
T ss_pred             EEEccCcc
Confidence            99997654

>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=99.70  E-value=1.3e-17  Score=134.11  Aligned_cols=81  Identities=23%  Similarity=0.429  Sum_probs=73.2

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ....++|||+|||+++|+++|+++|..||.|..+.++.+..+++++|||||+|.+.++|.+||. ++ ..|.|+.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            4456899999999999999999999999999987777777799999999999999999999999 66 669999999999


Q ss_pred             ccc
Q 012923          206 ASI  208 (453)
Q Consensus       206 ~~~  208 (453)
                      +..
T Consensus       101 a~~  103 (124)
T 1wel_A          101 ITK  103 (124)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            853

>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=99.70  E-value=1.1e-17  Score=136.02  Aligned_cols=83  Identities=14%  Similarity=0.193  Sum_probs=72.0

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEe
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQL  205 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~  205 (453)
                      .....++|||+|||+++|+++|+++|++|| |..|+|++|+. ++++|||||+|.+.++|.+||...+..|.+|.|.|.+
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~~  119 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFL  119 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEEE
Confidence            334568999999999999999999999999 77999999984 9999999999999999999995544679999999998


Q ss_pred             cccCC
Q 012923          206 ASIGP  210 (453)
Q Consensus       206 ~~~~~  210 (453)
                      +....
T Consensus       120 a~~~~  124 (139)
T 2hgn_A          120 NSTTG  124 (139)
T ss_dssp             CCCSC
T ss_pred             CCCCC
Confidence            86543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.53  E-value=1.2e-18  Score=138.60  Aligned_cols=82  Identities=26%  Similarity=0.375  Sum_probs=77.0

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcce--------eeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCe
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEE--------GPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGH  316 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~--------v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~  316 (453)
                      ..++|||+|||+.+|+++|+++|++||.|..        |+|++++.+++++|||||+|.+.++|.+||..|| ..|.|+
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   85 (116)
T 2lcw_A            6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGN   85 (116)
Confidence            4579999999999999999999999999999        9999998899999999999999999999999999 889999


Q ss_pred             EEEEEEccCCC
Q 012923          317 ILNCQRAIDGP  327 (453)
Q Consensus       317 ~l~v~~a~~~~  327 (453)
                      +|.|.++..++
T Consensus        86 ~l~V~~a~~~~   96 (116)
T 2lcw_A           86 PIKVSFATRRA   96 (116)
Confidence            99999997654

>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=99.69  E-value=3.1e-17  Score=129.14  Aligned_cols=83  Identities=13%  Similarity=0.213  Sum_probs=74.6

Q ss_pred             CCcCeEEEcCCCCCCCHHHHH---HHHhccCCeeEEEEcccCCCC---CcceEEEEEEccHHHHHHHHHcCC-CccCCeE
Q 012923          128 PVHRKIFVHGLGWDTKAETLI---DAFKQYGEIEDCKAVCDKVSG---KSKGYGFILFKTRSGARKALKEPQ-KKIGNRM  200 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~---~~f~~~G~i~~v~i~~d~~~g---~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~  200 (453)
                      ...++|||+|||+++|+++|+   ++|.+||.|..|+|++++.++   +++|||||+|.+.++|.+||+.|+ ..|.|+.
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~   92 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   92 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEE
Confidence            346799999999999999999   999999999999999988654   566999999999999999999977 4599999


Q ss_pred             eEEEecccCC
Q 012923          201 TACQLASIGP  210 (453)
Q Consensus       201 ~~v~~~~~~~  210 (453)
                      |.|.++..++
T Consensus        93 l~V~~a~~k~  102 (111)
T 2cpi_A           93 LKASLGTTKY  102 (111)
T ss_dssp             EEEESCCCCS
T ss_pred             EEEEeccccc
Confidence            9999987654

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=2.8e-17  Score=130.69  Aligned_cols=79  Identities=16%  Similarity=0.227  Sum_probs=71.7

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCc----ceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEE
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEI----EEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQ  321 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i----~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~  321 (453)
                      ...+|||+|||+.+|+++|+++|++||.|    ..|+|+++ .+|+++|||||+|.+.++|.+||...+..|.||.|.|.
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~i~V~  100 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELF  100 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEECCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEEEE
Confidence            45699999999999999999999999875    68999998 48999999999999999999999984488999999998


Q ss_pred             EccC
Q 012923          322 RAID  325 (453)
Q Consensus       322 ~a~~  325 (453)
                      .+..
T Consensus       101 ~a~~  104 (123)
T 2dha_A          101 RSTA  104 (123)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            8853

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.69  E-value=5.9e-17  Score=126.33  Aligned_cols=79  Identities=13%  Similarity=0.072  Sum_probs=70.0

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccC-CeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEE
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYG-EIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQ  204 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G-~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~  204 (453)
                      .+..++|||+|||+++|+++|+++|++|| .|..|+|+.+    +++|||||+|.+.++|.+||+.+++ .|.||.|.|.
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~  100 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVE  100 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            34567999999999999999999999999 9999988643    4889999999999999999998885 5999999999


Q ss_pred             ecccC
Q 012923          205 LASIG  209 (453)
Q Consensus       205 ~~~~~  209 (453)
                      ++...
T Consensus       101 ~a~~~  105 (111)
T 2jvr_A          101 RDDNP  105 (111)
T ss_dssp             ESCC-
T ss_pred             ECCCC
Confidence            98643

>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=99.69  E-value=6.1e-17  Score=124.25  Aligned_cols=77  Identities=21%  Similarity=0.318  Sum_probs=70.5

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccC--CeEEEEE
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFE--GHILNCQ  321 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~--g~~l~v~  321 (453)
                      ...++|||+|||+.+|+++|+++|++||.|..|.|+++      +|||||+|.+.++|.+||..|| ..|.  |++|.|.
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~   88 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEE
Confidence            34579999999999999999999999999999999764      7899999999999999999998 8899  9999999


Q ss_pred             EccCCC
Q 012923          322 RAIDGP  327 (453)
Q Consensus       322 ~a~~~~  327 (453)
                      |+.+++
T Consensus        89 ~a~~~~   94 (97)
T 1why_A           89 FAKSGP   94 (97)
T ss_dssp             ECCCCC
T ss_pred             ECCCCC
Confidence            997654

>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=99.69  E-value=9e-17  Score=120.08  Aligned_cols=75  Identities=21%  Similarity=0.315  Sum_probs=69.3

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcC-C-CccCCeEEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP-H-KNFEGHILNCQ  321 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~-~-~~l~g~~l~v~  321 (453)
                      ....++|||+|||+.+|+++|+++|++||.|..|+++++      +|||||+|.+.++|.+|+..| + ..|+|++|+|.
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~   82 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVK   82 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEE
Confidence            345579999999999999999999999999999999875      899999999999999999988 7 88999999999


Q ss_pred             Ecc
Q 012923          322 RAI  324 (453)
Q Consensus       322 ~a~  324 (453)
                      |++
T Consensus        83 ~ak   85 (85)
T 2ytc_A           83 WGR   85 (85)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            973

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

Probab=99.69  E-value=1.5e-16  Score=120.66  Aligned_cols=76  Identities=21%  Similarity=0.342  Sum_probs=69.3

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|++||.|..|+|+        ++||||+|.+.++|.+||..|| ..|.|+.|+|.++
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            345799999999999999999999999999999997        3499999999999999999998 8899999999999


Q ss_pred             cCCCC
Q 012923          324 IDGPK  328 (453)
Q Consensus       324 ~~~~~  328 (453)
                      ..+..
T Consensus        80 ~~~~~   84 (92)
T 2dgt_A           80 TSRLR   84 (92)
T ss_dssp             SCCCS
T ss_pred             cCCCC
Confidence            76543

>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=99.69  E-value=6.5e-17  Score=128.13  Aligned_cols=82  Identities=17%  Similarity=0.384  Sum_probs=74.3

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-c-------
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-I-------  196 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~-------  196 (453)
                      ..+...++|||+|||+++|+++|+++|.+||.|..|+|++++ +++++|||||+|.+.++|.+||..+++. |       
T Consensus        20 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~   98 (114)
T 1x5o_A           20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVS   98 (114)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCcccc
Confidence            344567899999999999999999999999999999999999 9999999999999999999999988744 6       


Q ss_pred             -CCeEeEEEecc
Q 012923          197 -GNRMTACQLAS  207 (453)
Q Consensus       197 -~gr~~~v~~~~  207 (453)
                       .++.|.|.++.
T Consensus        99 ~~~~~l~v~~a~  110 (114)
T 1x5o_A           99 APTEPLLCKFSG  110 (114)
T ss_dssp             CCSSCBEEEECC
T ss_pred             CCCCceeEEccC
Confidence             57889998875

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.69  E-value=2.6e-17  Score=127.65  Aligned_cols=82  Identities=23%  Similarity=0.421  Sum_probs=75.1

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEec
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLA  206 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~  206 (453)
                      ....++|||+|||+++|+++|+++|++||.|..|+|++++ +++++|||||+|.+.++|.+|+. ....|.|+.|.|.++
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~-~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE-SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT-CCCEETTEECEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            3446899999999999999999999999999999999999 99999999999999999999999 556799999999998


Q ss_pred             ccCC
Q 012923          207 SIGP  210 (453)
Q Consensus       207 ~~~~  210 (453)
                      ....
T Consensus        84 ~~~~   87 (102)
T 2xs2_A           84 IRKQ   87 (102)
T ss_dssp             EECC
T ss_pred             CcCc
Confidence            7543

>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=99.69  E-value=8.9e-17  Score=123.83  Aligned_cols=78  Identities=24%  Similarity=0.341  Sum_probs=71.6

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ....++|||+|||+.+|+++|+++|++||.|..|+|+++      +|||||+|.+.++|.+||..|+ ..|.|++|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   85 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF   85 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEE
Confidence            345579999999999999999999999999999999865      8999999999999999999999 889999999999


Q ss_pred             ccCCC
Q 012923          323 AIDGP  327 (453)
Q Consensus       323 a~~~~  327 (453)
                      +..+.
T Consensus        86 a~~~~   90 (99)
T 2cpj_A           86 ACHSA   90 (99)
T ss_dssp             SSCCS
T ss_pred             cCCCC
Confidence            97654

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.1e-16  Score=123.82  Aligned_cols=82  Identities=28%  Similarity=0.383  Sum_probs=72.4

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~  204 (453)
                      .....++|||+|||+++|+++|+++|.+||.|   +|+.+ .+++++|||||+|.+.++|.+||..++. .|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            44567999999999999999999999999977   56776 4899999999999999999999998884 5999999999


Q ss_pred             ecccCCC
Q 012923          205 LASIGPA  211 (453)
Q Consensus       205 ~~~~~~~  211 (453)
                      ++.....
T Consensus        87 ~a~~~~~   93 (101)
T 2fc9_A           87 LQGPRGS   93 (101)
T ss_dssp             ECSSCCC
T ss_pred             EcCCCCC
Confidence            9976543

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

Probab=99.69  E-value=9.7e-17  Score=128.49  Aligned_cols=81  Identities=15%  Similarity=0.179  Sum_probs=71.5

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHH----HHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLI----DAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRM  200 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~----~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~  200 (453)
                      ....+++|||+|||+.+++++|+    ++|++||.|.+|.+.+   +++++|||||+|.+.++|.+|+..++ ..|.|+.
T Consensus        25 ~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~  101 (127)
T 2a3j_A           25 HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNP  101 (127)
T ss_dssp             CCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCE
Confidence            34557899999999999999876    6999999999998754   67899999999999999999999888 4599999


Q ss_pred             eEEEecccC
Q 012923          201 TACQLASIG  209 (453)
Q Consensus       201 ~~v~~~~~~  209 (453)
                      |.|.++...
T Consensus       102 l~V~~a~~~  110 (127)
T 2a3j_A          102 LVITFSETP  110 (127)
T ss_dssp             CEEEECCCC
T ss_pred             EEEEEccCc
Confidence            999998644

>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=99.69  E-value=2.1e-17  Score=128.37  Aligned_cols=79  Identities=18%  Similarity=0.203  Sum_probs=69.8

Q ss_pred             CCCCcCeEEEcCCCCC-CCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC---CccCCeEe
Q 012923          126 EDPVHRKIFVHGLGWD-TKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ---KKIGNRMT  201 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~-~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~---~~~~gr~~  201 (453)
                      ....+++|||+|||++ +|+++|+++|++||.|.+|+|++      ++|||||+|.+.++|.+|++.++   ..|.||.|
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l   94 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   94 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            3556789999999998 99999999999999999999874      47899999999999999999775   35899999


Q ss_pred             EEEecccCC
Q 012923          202 ACQLASIGP  210 (453)
Q Consensus       202 ~v~~~~~~~  210 (453)
                      .|.++....
T Consensus        95 ~V~~a~~~~  103 (112)
T 1x4f_A           95 KVDLSEKYK  103 (112)
T ss_dssp             EEEEECSCS
T ss_pred             EEEECcccc
Confidence            999986443

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.69  E-value=5.5e-17  Score=126.01  Aligned_cols=77  Identities=21%  Similarity=0.247  Sum_probs=70.0

Q ss_pred             cEEEEecC----CCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECC----HHH----HHHHHH--cCC-Cc
Q 012923          248 RKIFVSNV----GSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKT----VDA----AKKALE--EPH-KN  312 (453)
Q Consensus       248 ~~l~V~nL----p~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~----~~~----A~~Al~--~~~-~~  312 (453)
                      +.|||+||    |+.+++..|+.+|+.||.|.+|.++.|+.||+++|||||+|.+    .++    |.+|+.  .++ ..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            58999999    9999999999999999999999999999999999999999995    333    899988  778 89


Q ss_pred             cCCeEEEEEEcc
Q 012923          313 FEGHILNCQRAI  324 (453)
Q Consensus       313 l~g~~l~v~~a~  324 (453)
                      |+|++|+|.+..
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999999864

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.68  E-value=1.2e-17  Score=129.24  Aligned_cols=82  Identities=18%  Similarity=0.208  Sum_probs=73.7

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ....++|||+|||+++|+++|+++|++||.|.. .++++..+++++|||||+|.+.++|.+||+ ++ ..|.|+.|.|.+
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEE
Confidence            345689999999999999999999999999988 778887789999999999999999999999 66 669999999999


Q ss_pred             cccCC
Q 012923          206 ASIGP  210 (453)
Q Consensus       206 ~~~~~  210 (453)
                      +....
T Consensus        92 a~~~~   96 (101)
T 1fj7_A           92 PKGRD   96 (101)
T ss_dssp             CSCCC
T ss_pred             cCCCC
Confidence            86543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.68  E-value=3.9e-17  Score=126.62  Aligned_cols=81  Identities=25%  Similarity=0.484  Sum_probs=74.4

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEccC
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAID  325 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a~~  325 (453)
                      ..++|||+|||+.+|+++|+++|+.||.|..|+|++++ +++++|||||+|.+.++|.+||. ....|+|+.|.|.++..
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            44799999999999999999999999999999999998 99999999999999999999999 33889999999999976


Q ss_pred             CCC
Q 012923          326 GPK  328 (453)
Q Consensus       326 ~~~  328 (453)
                      +..
T Consensus        86 ~~~   88 (102)
T 2xs2_A           86 KQN   88 (102)
T ss_dssp             CC-
T ss_pred             Ccc
Confidence            543

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

Probab=99.68  E-value=5.8e-17  Score=124.02  Aligned_cols=77  Identities=18%  Similarity=0.349  Sum_probs=69.5

Q ss_pred             ccccEEEEecCCC-CccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          245 YTQRKIFVSNVGS-ELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       245 ~~~~~l~V~nLp~-~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      ...++|||+|||+ .+|+++|+++|++||.|..|+|.        +|||||+|.+.++|.+||..|| ..|.|++|.|.+
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            3457999999998 99999999999999999999983        7899999999999999999988 889999999999


Q ss_pred             ccCCCCC
Q 012923          323 AIDGPKP  329 (453)
Q Consensus       323 a~~~~~~  329 (453)
                      +.....+
T Consensus        80 a~~~~~~   86 (96)
T 2kvi_A           80 SSSNARP   86 (96)
T ss_dssp             EECCCC-
T ss_pred             cCcCCCC
Confidence            9776543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=1.3e-16  Score=122.30  Aligned_cols=78  Identities=15%  Similarity=0.167  Sum_probs=70.0

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|+.||.|. +.++.    ++++|||||+|.+.++|.+||..|| ..|+|+.|.|.++
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            3457999999999999999999999999997 67764    3679999999999999999999999 8999999999999


Q ss_pred             cCCC
Q 012923          324 IDGP  327 (453)
Q Consensus       324 ~~~~  327 (453)
                      ..+.
T Consensus        92 ~~~~   95 (97)
T 2e5j_A           92 RQQR   95 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7643

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

Probab=99.68  E-value=2.1e-16  Score=119.36  Aligned_cols=78  Identities=19%  Similarity=0.436  Sum_probs=70.2

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~  205 (453)
                      ....++|||+|||+++|+++|+++|++||.|..|+|+        +|||||+|.+.++|.+|+..+++ .|.|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   76 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEA   76 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEE
Confidence            4567899999999999999999999999999999987        57999999999999999998874 69999999999


Q ss_pred             cccCCCC
Q 012923          206 ASIGPAT  212 (453)
Q Consensus       206 ~~~~~~~  212 (453)
                      +......
T Consensus        77 a~~~~~~   83 (90)
T 2dnq_A           77 SKNKSKA   83 (90)
T ss_dssp             SSCCCCC
T ss_pred             CCCCCCC
Confidence            8765443

>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=99.68  E-value=3.3e-16  Score=122.61  Aligned_cols=77  Identities=16%  Similarity=0.240  Sum_probs=70.0

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCC-----eEe
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGN-----RMT  201 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~g-----r~~  201 (453)
                      ...++|||+|||+++|+++|+++|.+||.|..|+|+.+       |||||+|.+.++|.+||+.|+. .|.|     +.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i   85 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   85 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEE
Confidence            45689999999999999999999999999999999886       7999999999999999998885 5888     999


Q ss_pred             EEEecccCCC
Q 012923          202 ACQLASIGPA  211 (453)
Q Consensus       202 ~v~~~~~~~~  211 (453)
                      .|.++.....
T Consensus        86 ~V~~a~~~~~   95 (108)
T 1x4c_A           86 RVKVDGPRSP   95 (108)
T ss_dssp             EEEESSCCSC
T ss_pred             EEEeCCCCCC
Confidence            9999976543

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

Probab=99.68  E-value=2.7e-16  Score=121.06  Aligned_cols=76  Identities=13%  Similarity=0.186  Sum_probs=69.0

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhcc--CCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKY--GEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNC  320 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v  320 (453)
                      ....++|||+|||+.+|+++|+++|++|  |.|..|+++        +|||||+|.+.++|.+||..|| ..|+|++|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   83 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            3456799999999999999999999999  999998874        6799999999999999999998 8899999999


Q ss_pred             EEccCCC
Q 012923          321 QRAIDGP  327 (453)
Q Consensus       321 ~~a~~~~  327 (453)
                      .++..+.
T Consensus        84 ~~a~~~~   90 (99)
T 2cpd_A           84 TLAKPVD   90 (99)
T ss_dssp             ECCCCCC
T ss_pred             EECCCCC
Confidence            9997654

>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=99.68  E-value=2.1e-16  Score=124.04  Aligned_cols=81  Identities=20%  Similarity=0.445  Sum_probs=72.5

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      .....++|||+|||.++|+++|+++|++||.|..|+|+++      +|||||+|.+.++|.+||..++ ..|.|+.|.|.
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   94 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY   94 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            3455789999999999999999999999999999999876      6899999999999999998877 56999999999


Q ss_pred             ecccCCCC
Q 012923          205 LASIGPAT  212 (453)
Q Consensus       205 ~~~~~~~~  212 (453)
                      ++...+..
T Consensus        95 ~a~~~~~~  102 (109)
T 1x4g_A           95 WGKESPDM  102 (109)
T ss_dssp             CCCCCCSS
T ss_pred             ecCCCCCC
Confidence            99765543

>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=99.67  E-value=2e-16  Score=121.33  Aligned_cols=79  Identities=23%  Similarity=0.441  Sum_probs=70.4

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccC--CeEeE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIG--NRMTA  202 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~--gr~~~  202 (453)
                      .....++|||+|||+++|+++|+++|++||.|..|+|+.+      +|||||+|.+.++|.+|++.++ ..|.  |+.|.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~   86 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR   86 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEE
Confidence            3455689999999999999999999999999999998864      6899999999999999999877 5588  99999


Q ss_pred             EEecccCC
Q 012923          203 CQLASIGP  210 (453)
Q Consensus       203 v~~~~~~~  210 (453)
                      |.++...+
T Consensus        87 V~~a~~~~   94 (97)
T 1why_A           87 VDFAKSGP   94 (97)
T ss_dssp             EEECCCCC
T ss_pred             EEECCCCC
Confidence            99987543

>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=99.67  E-value=2.9e-16  Score=117.27  Aligned_cols=76  Identities=28%  Similarity=0.394  Sum_probs=68.9

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcC-C-CccCCeEeE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP-Q-KKIGNRMTA  202 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~-~-~~~~gr~~~  202 (453)
                      ..+...++|||+|||.++|+++|+++|++||.|..|+|+++      +|||||+|.+.++|.+|+..+ + ..+.|+.|.
T Consensus         7 ~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~   80 (85)
T 2ytc_A            7 GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLN   80 (85)
T ss_dssp             CSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECC
T ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEE
Confidence            34566789999999999999999999999999999999863      689999999999999999987 6 569999999


Q ss_pred             EEec
Q 012923          203 CQLA  206 (453)
Q Consensus       203 v~~~  206 (453)
                      |.++
T Consensus        81 v~~a   84 (85)
T 2ytc_A           81 VKWG   84 (85)
T ss_dssp             EEEC
T ss_pred             EEec
Confidence            9986

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

Probab=99.67  E-value=2.3e-16  Score=119.12  Aligned_cols=75  Identities=24%  Similarity=0.362  Sum_probs=68.7

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|++||.|..|+|++        +||||+|.+.++|.+||..|| ..|+|+.|.|.++
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 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELS   78 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            3457999999999999999999999999999999973        499999999999999999998 8899999999999


Q ss_pred             cCCC
Q 012923          324 IDGP  327 (453)
Q Consensus       324 ~~~~  327 (453)
                      ....
T Consensus        79 ~~~~   82 (90)
T 2dnp_A           79 TKGQ   82 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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=99.67  E-value=4.8e-17  Score=129.14  Aligned_cols=85  Identities=15%  Similarity=0.259  Sum_probs=72.4

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ....++|||+|||+++|+++|+++|.+||.|..|.+..+..+++++|||||+|.+.++|.+||..++ ..|.|+.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3457899999999999999999999999999544333333388999999999999999999999887 559999999999


Q ss_pred             cccCCC
Q 012923          206 ASIGPA  211 (453)
Q Consensus       206 ~~~~~~  211 (453)
                      +.....
T Consensus       102 a~~~~~  107 (115)
T 2cpx_A          102 GKNKKQ  107 (115)
T ss_dssp             CCCCSC
T ss_pred             ccCCCC
Confidence            976544

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

Probab=99.67  E-value=1.2e-16  Score=124.81  Aligned_cols=78  Identities=24%  Similarity=0.436  Sum_probs=70.4

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      .....++|||+|||+.+|+++|+++|++||.|..|.|+        +|||||+|.+.++|.+|+..|| ..|+|+.|.|.
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   98 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV   98 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            34456899999999999999999999999999999997        7899999999999999999988 88999999999


Q ss_pred             EccCCCC
Q 012923          322 RAIDGPK  328 (453)
Q Consensus       322 ~a~~~~~  328 (453)
                      ++...+.
T Consensus        99 ~a~~~~~  105 (108)
T 2jvo_A           99 YSKLPAK  105 (108)
T ss_dssp             SCSCCC-
T ss_pred             EecCCCC
Confidence            9976543

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.67  E-value=1.1e-16  Score=124.45  Aligned_cols=77  Identities=22%  Similarity=0.166  Sum_probs=68.7

Q ss_pred             CeEEEcCC----CCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEcc----HHH----HHHHHH--cCC-Cc
Q 012923          131 RKIFVHGL----GWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKT----RSG----ARKALK--EPQ-KK  195 (453)
Q Consensus       131 ~~lfV~nL----p~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~----~~~----a~~A~~--~~~-~~  195 (453)
                      ++|||+||    |+.+++.+|+++|+.||+|.+|.++.|+.||+++|||||+|.+    +++    |.+|+.  .++ ..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            58999999    9999999999999999999999999999999999999999996    322    888888  666 55


Q ss_pred             cCCeEeEEEecc
Q 012923          196 IGNRMTACQLAS  207 (453)
Q Consensus       196 ~~gr~~~v~~~~  207 (453)
                      |.||.|+|.+-.
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999999864

>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=99.67  E-value=1.3e-16  Score=125.38  Aligned_cols=75  Identities=17%  Similarity=0.138  Sum_probs=69.5

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .++|||+|||+.+|+++|+++|++||.|..|.|++      ++|||||+|.+.++|.+||..|| ..|.|++|.|.|+..
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            46999999999999999999999999999999875      48999999999999999999999 889999999999975


Q ss_pred             CC
Q 012923          326 GP  327 (453)
Q Consensus       326 ~~  327 (453)
                      ..
T Consensus        84 ~~   85 (111)
T 1whx_A           84 GV   85 (111)
T ss_dssp             TT
T ss_pred             Cc
Confidence            43

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.67  E-value=1.2e-16  Score=122.31  Aligned_cols=78  Identities=22%  Similarity=0.306  Sum_probs=70.3

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|+.||.|..+     ..+++++|||||+|.+.++|.+||..++ ..|+|+.|.|.++
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   88 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            345799999999999999999999999988766     3478899999999999999999999999 8899999999999


Q ss_pred             cCCC
Q 012923          324 IDGP  327 (453)
Q Consensus       324 ~~~~  327 (453)
                      ..+.
T Consensus        89 ~~~~   92 (96)
T 1fjc_A           89 GEKG   92 (96)
T ss_dssp             SSSC
T ss_pred             CCCC
Confidence            6654

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

Probab=99.67  E-value=2e-16  Score=122.61  Aligned_cols=84  Identities=27%  Similarity=0.428  Sum_probs=74.0

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ......++|||+|||+++|+++|+++|+.|   ..|++++++.+++++|||||+|.+.++|.+||+.++ ..|.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   86 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTL   86 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            344567899999999999999999999977   377888888899999999999999999999999877 5699999999


Q ss_pred             EecccCCC
Q 012923          204 QLASIGPA  211 (453)
Q Consensus       204 ~~~~~~~~  211 (453)
                      .++.....
T Consensus        87 ~~a~~~~~   94 (102)
T 2fc8_A           87 DWAKPKGE   94 (102)
T ss_dssp             EECCCCCS
T ss_pred             EEecCCCC
Confidence            99975543

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

Probab=99.67  E-value=9.6e-17  Score=124.15  Aligned_cols=75  Identities=19%  Similarity=0.266  Sum_probs=69.4

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|+.||.|..|+|++      ++|||||+|.+.++|.+||..|| ..|+|+.|+|.|+
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 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG   98 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEec
Confidence            3457999999999999999999999999999999974      48999999999999999999998 8899999999998


Q ss_pred             cC
Q 012923          324 ID  325 (453)
Q Consensus       324 ~~  325 (453)
                      .+
T Consensus        99 ~~  100 (101)
T 2la4_A           99 KE  100 (101)
T ss_dssp             CC
T ss_pred             cC
Confidence            64

>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=99.67  E-value=1.6e-16  Score=124.94  Aligned_cols=73  Identities=21%  Similarity=0.440  Sum_probs=67.8

Q ss_pred             cccEEEEecCCCC-ccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          246 TQRKIFVSNVGSE-LEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       246 ~~~~l~V~nLp~~-~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ..++|||+|||+. +|+++|+++|++||.|..|.|        ++|||||+|.+.++|.+||..|+ ..|+|+.|.|.++
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   97 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA   97 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEES
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            3479999999999 999999999999999999998        38999999999999999999998 8899999999999


Q ss_pred             cCC
Q 012923          324 IDG  326 (453)
Q Consensus       324 ~~~  326 (453)
                      ...
T Consensus        98 ~~~  100 (110)
T 1wf1_A           98 GEP  100 (110)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.48  E-value=5e-18  Score=134.99  Aligned_cols=85  Identities=27%  Similarity=0.376  Sum_probs=77.6

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeE--------EEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccC
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIED--------CKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIG  197 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~--------v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~  197 (453)
                      ....++|||+|||+++|+++|+++|++||.|..        |+|++++.+++++|||||+|.+.++|.+||..++ ..|.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            445689999999999999999999999999999        9999998899999999999999999999999888 5599


Q ss_pred             CeEeEEEecccCCC
Q 012923          198 NRMTACQLASIGPA  211 (453)
Q Consensus       198 gr~~~v~~~~~~~~  211 (453)
                      |+.|.|.++.....
T Consensus        84 g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           84 GNPIKVSFATRRAD   97 (116)
Confidence            99999999875544

>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=99.66  E-value=2.8e-16  Score=120.22  Aligned_cols=77  Identities=17%  Similarity=0.323  Sum_probs=69.3

Q ss_pred             ccccccEEEEecCCC-CccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEE
Q 012923          243 SEYTQRKIFVSNVGS-ELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNC  320 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~-~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v  320 (453)
                      .....++|||+|||+ .+++++|+++|+.||.|..|+|.        +|||||+|.+.++|.+||..+| ..|+|++|.|
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   89 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL   89 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            344567999999998 99999999999999999999982        7999999999999999999998 8899999999


Q ss_pred             EEccCCC
Q 012923          321 QRAIDGP  327 (453)
Q Consensus       321 ~~a~~~~  327 (453)
                      .++..+.
T Consensus        90 ~~a~~~~   96 (97)
T 2xnq_A           90 EVSSSNA   96 (97)
T ss_dssp             EECCCCC
T ss_pred             EecCCCC
Confidence            9986543

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

Probab=99.66  E-value=1.4e-16  Score=123.16  Aligned_cols=78  Identities=19%  Similarity=0.222  Sum_probs=69.6

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ......++|||+|||.++|+++|+++|++||.|..|+|+      +++|||||+|.+.++|.+|+..++ ..|.|+.|.|
T Consensus        22 ~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   95 (101)
T 2la4_A           22 SAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRT   95 (101)
T ss_dssp             TSCSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCC
T ss_pred             cCCCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            344557899999999999999999999999999999987      367999999999999999999877 5599999999


Q ss_pred             Eeccc
Q 012923          204 QLASI  208 (453)
Q Consensus       204 ~~~~~  208 (453)
                      .++..
T Consensus        96 ~~a~~  100 (101)
T 2la4_A           96 GWGKE  100 (101)
T ss_dssp             CBCCC
T ss_pred             EeccC
Confidence            98753

>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=99.66  E-value=9.4e-17  Score=123.24  Aligned_cols=79  Identities=23%  Similarity=0.379  Sum_probs=72.6

Q ss_pred             cccEEEEecCCCCccHHHHH----HHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEE
Q 012923          246 TQRKIFVSNVGSELEPQKLL----AFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNC  320 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~----~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v  320 (453)
                      ..++|||+|||+.+|+++|+    ++|++||.|..|.|++   ++.++|||||+|.+.++|.+|+..|| ..|+|+.|.|
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (97)
T 1nu4_A            7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   83 (97)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEE
Confidence            45799999999999999999    9999999999999874   57789999999999999999999988 8899999999


Q ss_pred             EEccCCC
Q 012923          321 QRAIDGP  327 (453)
Q Consensus       321 ~~a~~~~  327 (453)
                      .++....
T Consensus        84 ~~a~~~~   90 (97)
T 1nu4_A           84 QYAKTDS   90 (97)
T ss_dssp             EECSSCC
T ss_pred             EEccCCC
Confidence            9997654

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

Probab=99.66  E-value=2.2e-16  Score=134.67  Aligned_cols=83  Identities=18%  Similarity=0.336  Sum_probs=77.4

Q ss_pred             ccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          243 SEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      .....++|||+|||+.+|+++|+++|+.||.|..|.|+.+. ++.++|||||+|.+.++|.+||..|| ..|+|++|.|.
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~  162 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  162 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            33456899999999999999999999999999999999998 99999999999999999999999999 89999999999


Q ss_pred             EccCC
Q 012923          322 RAIDG  326 (453)
Q Consensus       322 ~a~~~  326 (453)
                      |+...
T Consensus       163 ~a~~~  167 (177)
T 2f3j_A          163 LVASQ  167 (177)
T ss_dssp             EESSG
T ss_pred             EecCC
Confidence            99654

>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=99.66  E-value=1.5e-16  Score=122.16  Aligned_cols=80  Identities=26%  Similarity=0.346  Sum_probs=72.0

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHH----HHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLI----DAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMT  201 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~----~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~  201 (453)
                      .+.+++|||+|||+++|+++|+    ++|++||.|..|+|+.   ++.++|||||+|.+.++|.+|+..++ ..|.|+.|
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            4567899999999999999999    9999999999999874   57889999999999999999999877 55999999


Q ss_pred             EEEecccC
Q 012923          202 ACQLASIG  209 (453)
Q Consensus       202 ~v~~~~~~  209 (453)
                      .|.++...
T Consensus        82 ~v~~a~~~   89 (97)
T 1nu4_A           82 RIQYAKTD   89 (97)
T ss_dssp             EEEECSSC
T ss_pred             EEEEccCC
Confidence            99998754

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

Probab=99.66  E-value=2e-16  Score=125.09  Aligned_cols=77  Identities=23%  Similarity=0.415  Sum_probs=69.2

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCC---CCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEE
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVS---GKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQ  204 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~---g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~  204 (453)
                      ...++|||+|||+++|+++|+++|++||.|. +.++.+..+   |+++|||||+|.+.++|.+||+.++ .+.|+.+.+.
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~-~~~G~~~~~~   83 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL-EEDGKLYLCV   83 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE-EETTEEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh-hcCCcEEEec
Confidence            4568999999999999999999999999999 888888876   7999999999999999999999884 4788888876


Q ss_pred             ec
Q 012923          205 LA  206 (453)
Q Consensus       205 ~~  206 (453)
                      .+
T Consensus        84 ~~   85 (114)
T 2dnl_A           84 SS   85 (114)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>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=99.66  E-value=2.7e-16  Score=121.12  Aligned_cols=79  Identities=25%  Similarity=0.339  Sum_probs=70.8

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      .....++|||+|||+++|+++|+++|++||.|..|+|+++      +|||||+|.+.++|.+|++.++ ..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   84 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVR   84 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEE
Confidence            3456789999999999999999999999999999998854      6899999999999999998887 55999999999


Q ss_pred             ecccCC
Q 012923          205 LASIGP  210 (453)
Q Consensus       205 ~~~~~~  210 (453)
                      ++....
T Consensus        85 ~a~~~~   90 (99)
T 2cpj_A           85 FACHSA   90 (99)
T ss_dssp             ESSCCS
T ss_pred             EcCCCC
Confidence            987543

>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=99.66  E-value=5.5e-16  Score=118.63  Aligned_cols=77  Identities=19%  Similarity=0.371  Sum_probs=68.0

Q ss_pred             CCCCCcCeEEEcCCCC-CCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeE
Q 012923          125 DEDPVHRKIFVHGLGW-DTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTA  202 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~-~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~  202 (453)
                      ...+.+++|||+|||+ ++|+++|+++|++||.|..|+|.        +|||||+|.+.++|.+|+..+++ .+.|+.|.
T Consensus        17 ~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   88 (97)
T 2xnq_A           17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLI   88 (97)
T ss_dssp             --CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            3456679999999998 99999999999999999999983        78999999999999999998874 58999999


Q ss_pred             EEecccC
Q 012923          203 CQLASIG  209 (453)
Q Consensus       203 v~~~~~~  209 (453)
                      |.++...
T Consensus        89 V~~a~~~   95 (97)
T 2xnq_A           89 LEVSSSN   95 (97)
T ss_dssp             EEECCCC
T ss_pred             EEecCCC
Confidence            9998643

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=2.2e-16  Score=121.03  Aligned_cols=79  Identities=18%  Similarity=0.331  Sum_probs=69.6

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      .....++|||+|||+++|+++|+++|.+||.|. ++++.+    +++|||||+|.+.++|.+|++.++ ..|.|+.|.|.
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   89 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVA   89 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            345578999999999999999999999999997 666654    688999999999999999999877 55999999999


Q ss_pred             ecccC
Q 012923          205 LASIG  209 (453)
Q Consensus       205 ~~~~~  209 (453)
                      ++...
T Consensus        90 ~a~~~   94 (97)
T 2e5j_A           90 LARQQ   94 (97)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            98654

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

Probab=99.66  E-value=2.8e-16  Score=139.13  Aligned_cols=81  Identities=16%  Similarity=0.241  Sum_probs=76.2

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      +.++|||+|||+.+|+++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|.+||..+| ..+.|+.|+|.++.
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            45799999999999999999999999999999999999999999999999999999999999999 88999999999986


Q ss_pred             CC
Q 012923          325 DG  326 (453)
Q Consensus       325 ~~  326 (453)
                      ..
T Consensus        94 ~~   95 (213)
T 4f02_A           94 RD   95 (213)
T ss_dssp             CC
T ss_pred             cc
Confidence            44

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=5.7e-16  Score=118.01  Aligned_cols=75  Identities=23%  Similarity=0.395  Sum_probs=67.0

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .++|||+|||+.+|+++|+++|+.||.|..|  +.++.+++   ||||+|.+.++|.+||. +| ..|+|+.|.|.++..
T Consensus         8 ~~~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            8 LRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQ   81 (94)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCc
Confidence            4699999999999999999999999999987  55665665   99999999999999999 88 899999999998864


Q ss_pred             CC
Q 012923          326 GP  327 (453)
Q Consensus       326 ~~  327 (453)
                      +.
T Consensus        82 ~~   83 (94)
T 2e5g_A           82 KE   83 (94)
T ss_dssp             SC
T ss_pred             CC
Confidence            43

>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=99.65  E-value=9.2e-17  Score=132.72  Aligned_cols=84  Identities=23%  Similarity=0.301  Sum_probs=72.6

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceee--eecc---CCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGP--LGID---KATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHI  317 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~--i~~d---~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~  317 (453)
                      ....++|||+|||+.+|+++|+++|+.||.|..+.  ++.+   ..+++++|||||+|.+.++|.+||..|| ..|.|+.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            34557999999999999999999999999998752  2222   3579999999999999999999999999 8999999


Q ss_pred             EEEEEccCCC
Q 012923          318 LNCQRAIDGP  327 (453)
Q Consensus       318 l~v~~a~~~~  327 (453)
                      |.|.++....
T Consensus       122 l~V~~a~~~~  131 (143)
T 3egn_A          122 MVVQFARSAR  131 (143)
T ss_dssp             CEEEECCCSC
T ss_pred             EEEEECCCCC
Confidence            9999997543

>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=99.65  E-value=2.2e-16  Score=124.04  Aligned_cols=77  Identities=19%  Similarity=0.178  Sum_probs=69.3

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLAS  207 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~  207 (453)
                      ..++|||+|||+++|+++|+++|++||.|..|+|+.      ++|||||+|.+.++|.+||..|+ ..|.|+.|.|.++.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   82 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            457999999999999999999999999999998874      57899999999999999999888 55999999999987


Q ss_pred             cCCC
Q 012923          208 IGPA  211 (453)
Q Consensus       208 ~~~~  211 (453)
                      ....
T Consensus        83 ~~~~   86 (111)
T 1whx_A           83 IGVF   86 (111)
T ss_dssp             TTTT
T ss_pred             CCcc
Confidence            5443

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

Probab=99.65  E-value=8.5e-16  Score=116.53  Aligned_cols=78  Identities=19%  Similarity=0.352  Sum_probs=69.9

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      .....++|||+|||+++|+++|+++|++||.|..|+|+++        ||||+|.+.++|.+|+..++ ..|.|+.|.|.
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   77 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQ   77 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS--------EEEEEESCHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Confidence            4456789999999999999999999999999999998843        99999999999999999877 55999999999


Q ss_pred             ecccCCC
Q 012923          205 LASIGPA  211 (453)
Q Consensus       205 ~~~~~~~  211 (453)
                      ++.....
T Consensus        78 ~a~~~~~   84 (92)
T 2dgt_A           78 LSTSRLR   84 (92)
T ss_dssp             ESSCCCS
T ss_pred             EccCCCC
Confidence            9976544

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

Probab=99.65  E-value=6.9e-16  Score=116.53  Aligned_cols=78  Identities=22%  Similarity=0.421  Sum_probs=69.8

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      .....++|||+|||+++|+++|+++|++||.|..|+|+++        ||||+|.+.++|.+|+..++ ..|.|+.|.|.
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   76 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQLNGKEVKGKRINVE   76 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS--------CEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            4456789999999999999999999999999999998843        99999999999999999877 55999999999


Q ss_pred             ecccCCC
Q 012923          205 LASIGPA  211 (453)
Q Consensus       205 ~~~~~~~  211 (453)
                      ++.....
T Consensus        77 ~a~~~~~   83 (90)
T 2dnp_A           77 LSTKGQK   83 (90)
T ss_dssp             ESCCCCC
T ss_pred             ECCCCCC
Confidence            9975543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.65  E-value=2.4e-16  Score=120.72  Aligned_cols=80  Identities=26%  Similarity=0.376  Sum_probs=70.4

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      .....++|||+|||+++|+++|+++|++||.|..+     ..+++++|||||+|.+.++|.+|+..++ ..|.|+.|.|.
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   86 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34557899999999999999999999999988766     2378999999999999999999999888 55999999999


Q ss_pred             ecccCC
Q 012923          205 LASIGP  210 (453)
Q Consensus       205 ~~~~~~  210 (453)
                      ++....
T Consensus        87 ~a~~~~   92 (96)
T 1fjc_A           87 YTGEKG   92 (96)
T ss_dssp             ECSSSC
T ss_pred             EcCCCC
Confidence            986543

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

Probab=99.65  E-value=3.4e-16  Score=122.26  Aligned_cols=79  Identities=20%  Similarity=0.440  Sum_probs=69.7

Q ss_pred             cCCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeE
Q 012923          124 ADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTA  202 (453)
Q Consensus       124 ~~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~  202 (453)
                      .......++|||+|||+++|+++|+++|++||.|..|+|+        +|||||+|.+.++|.+|+..++ ..|.|+.|.
T Consensus        25 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   96 (108)
T 2jvo_A           25 QEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLE   96 (108)
T ss_dssp             ---CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             cCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            3455677999999999999999999999999999999987        6899999999999999999877 559999999


Q ss_pred             EEecccCC
Q 012923          203 CQLASIGP  210 (453)
Q Consensus       203 v~~~~~~~  210 (453)
                      |.++....
T Consensus        97 V~~a~~~~  104 (108)
T 2jvo_A           97 VVYSKLPA  104 (108)
T ss_dssp             EESCSCCC
T ss_pred             EEEecCCC
Confidence            99987543

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

Probab=99.65  E-value=3.3e-16  Score=133.61  Aligned_cols=80  Identities=24%  Similarity=0.395  Sum_probs=74.9

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ...++|||+|||+++|+++|+++|++||.|..|+|+.++ ++.++|||||+|.+.++|.+||+.++ ..|.|+.|.|.++
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a  164 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            446899999999999999999999999999999999999 99999999999999999999999888 5699999999998


Q ss_pred             cc
Q 012923          207 SI  208 (453)
Q Consensus       207 ~~  208 (453)
                      ..
T Consensus       165 ~~  166 (177)
T 2f3j_A          165 AS  166 (177)
T ss_dssp             SS
T ss_pred             cC
Confidence            64

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=1.1e-15  Score=117.08  Aligned_cols=76  Identities=21%  Similarity=0.387  Sum_probs=68.6

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+||  .+|+++|+++|++||.|..|.|.      +++|||||+|.+.++|.+||..|| ..|.|++|.|.|+
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a   84 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   84 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECC
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC
Confidence            34579999996  89999999999999999999985      458999999999999999999999 8899999999999


Q ss_pred             cCCCC
Q 012923          324 IDGPK  328 (453)
Q Consensus       324 ~~~~~  328 (453)
                      ..++.
T Consensus        85 ~~~~~   89 (97)
T 1x5p_A           85 RKQPM   89 (97)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            76554

>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=99.65  E-value=3.9e-16  Score=117.27  Aligned_cols=77  Identities=17%  Similarity=0.276  Sum_probs=63.3

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEcc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAI  324 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a~  324 (453)
                      ...++|||+|||+.+|+++|+++|++||.|.+|+|+++     +||||||+|.+.++|.++. .....+.|+.|.|.++.
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~~~-~~~~~~~g~~v~v~~a~   82 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLC-GEDLIIKGISVHISNAE   82 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHHHT-TCEEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHHHc-CCCcccCCEEEEEEEcC
Confidence            34579999999999999999999999999999999875     6999999999999998432 22355779999999997


Q ss_pred             CCC
Q 012923          325 DGP  327 (453)
Q Consensus       325 ~~~  327 (453)
                      ++.
T Consensus        83 ~k~   85 (89)
T 3d2w_A           83 PKH   85 (89)
T ss_dssp             ---
T ss_pred             CCC
Confidence            543

>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=99.65  E-value=3.5e-16  Score=117.55  Aligned_cols=77  Identities=23%  Similarity=0.189  Sum_probs=62.9

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEec
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLA  206 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~  206 (453)
                      ....++|||+|||+++|+++|+++|++||.|.+|+|+++     ++|||||+|.+.++|.++.. ....+.++.|.|.++
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~~~~-~~~~~~g~~v~v~~a   81 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCG-EDLIIKGISVHISNA   81 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHHHTT-CEEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHHHcC-CCcccCCEEEEEEEc
Confidence            345689999999999999999999999999999999874     78999999999999985322 223367999999998


Q ss_pred             ccC
Q 012923          207 SIG  209 (453)
Q Consensus       207 ~~~  209 (453)
                      ..+
T Consensus        82 ~~k   84 (89)
T 3d2w_A           82 EPK   84 (89)
T ss_dssp             C--
T ss_pred             CCC
Confidence            644

>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=99.65  E-value=7.3e-16  Score=150.19  Aligned_cols=83  Identities=29%  Similarity=0.479  Sum_probs=77.2

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ...++|||+|||+.+|+++|+++|.+||.|..|+|+.++.+++++|||||+|.+.++|.+||..|+ ..|.|+.|.|.++
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            446899999999999999999999999999999999999899999999999999999999999888 5699999999999


Q ss_pred             ccCC
Q 012923          207 SIGP  210 (453)
Q Consensus       207 ~~~~  210 (453)
                      ....
T Consensus       180 ~~~~  183 (437)
T 3pgw_S          180 RGRT  183 (437)
T ss_pred             CCCC
Confidence            7543

>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=99.65  E-value=9e-16  Score=119.04  Aligned_cols=78  Identities=31%  Similarity=0.440  Sum_probs=69.3

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ....++|||+|||+++|+++|+++|.+||.|..|+|+        ++||||+|.+.++|.+||+.|+ ..|.|+.|.|.+
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   79 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVF   79 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEE
Confidence            3456899999999999999999999999999999987        3599999999999999999877 559999999999


Q ss_pred             cccCCCC
Q 012923          206 ASIGPAT  212 (453)
Q Consensus       206 ~~~~~~~  212 (453)
                      +......
T Consensus        80 a~~~~~~   86 (103)
T 2dgu_A           80 AKPPDQK   86 (103)
T ss_dssp             CCCCCCC
T ss_pred             cCCCccc
Confidence            9765443

>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=99.64  E-value=4.5e-16  Score=123.45  Aligned_cols=78  Identities=21%  Similarity=0.350  Sum_probs=71.8

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+|+++|+++|+.||.|..|.|+++   +.++|||||+|.+.++|.+||..|| ..|+|+.|.|.++.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            4579999999999999999999999999999999875   4559999999999999999999988 89999999999996


Q ss_pred             CC
Q 012923          325 DG  326 (453)
Q Consensus       325 ~~  326 (453)
                      ..
T Consensus        84 ~~   85 (115)
T 3lqv_A           84 AN   85 (115)
T ss_dssp             HH
T ss_pred             CC
Confidence            53

>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=99.64  E-value=4.6e-16  Score=118.31  Aligned_cols=75  Identities=16%  Similarity=0.345  Sum_probs=65.8

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCC-cceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC--CccCCeEEEEEE
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGE-IEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH--KNFEGHILNCQR  322 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~-i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~--~~l~g~~l~v~~  322 (453)
                      ..++|||+|||+.+|+++|+++|++||. |..+.+ .      ++|||||+|.+.++|.+||..||  ..|+|+.|+|.+
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~-~------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~   79 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-L------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDY   79 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE-E------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE-c------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEE
Confidence            4569999999999999999999999999 555555 2      38999999999999999999887  579999999999


Q ss_pred             ccCCC
Q 012923          323 AIDGP  327 (453)
Q Consensus       323 a~~~~  327 (453)
                      +..+.
T Consensus        80 a~~~~   84 (93)
T 2cqh_A           80 SVSKK   84 (93)
T ss_dssp             CCCCC
T ss_pred             ccCcc
Confidence            97654

>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=99.64  E-value=3.2e-16  Score=121.64  Aligned_cols=77  Identities=18%  Similarity=0.293  Sum_probs=68.5

Q ss_pred             ccccEEEE--ecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-Ccc-----CCe
Q 012923          245 YTQRKIFV--SNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNF-----EGH  316 (453)
Q Consensus       245 ~~~~~l~V--~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l-----~g~  316 (453)
                      .++++|||  +||++.+|+++|+++|++||.|..|.|+.+      ||||||+|.+.++|.+|+..|| ..|     .|+
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 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            34678999  669999999999999999999999988653      7999999999999999999999 766     689


Q ss_pred             EEEEEEccCCC
Q 012923          317 ILNCQRAIDGP  327 (453)
Q Consensus       317 ~l~v~~a~~~~  327 (453)
                      +|.|.++...+
T Consensus        97 ~l~v~~a~~~p  107 (114)
T 2cq2_A           97 TLYLNFVEKVQ  107 (114)
T ss_dssp             ECEEEEESCCC
T ss_pred             EEEEEecccCc
Confidence            99999997544

>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=99.64  E-value=7.7e-16  Score=133.36  Aligned_cols=78  Identities=15%  Similarity=0.264  Sum_probs=73.8

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~~  208 (453)
                      .++|||+|||+++|+++|+++|++||.|..|+|+++. +++++|||||+|.+.++|.+||..++..|.|+.|.|.++..
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhHH
Confidence            4899999999999999999999999999999999987 69999999999999999999999998899999999998753

>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=99.64  E-value=1.8e-15  Score=131.09  Aligned_cols=80  Identities=15%  Similarity=0.243  Sum_probs=74.5

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEccC
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAID  325 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a~~  325 (453)
                      ..++|||+|||+.+|+++|+++|++||.|..|+|+++. +++++|||||+|.+.++|.+||..++..|+|+.|.|.++..
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDD  186 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETTT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhHH
Confidence            34699999999999999999999999999999999986 58999999999999999999999988889999999999865


Q ss_pred             C
Q 012923          326 G  326 (453)
Q Consensus       326 ~  326 (453)
                      .
T Consensus       187 y  187 (193)
T 2voo_A          187 Y  187 (193)
T ss_dssp             C
T ss_pred             H
Confidence            3

>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=99.63  E-value=8.6e-16  Score=119.25  Aligned_cols=81  Identities=15%  Similarity=0.201  Sum_probs=69.1

Q ss_pred             CCCCcCeEEE--cCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-c-----C
Q 012923          126 EDPVHRKIFV--HGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-I-----G  197 (453)
Q Consensus       126 ~~~~~~~lfV--~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~-----~  197 (453)
                      ....+++|||  +||++++|+++|+++|++||.|..|.|+.      .+|||||+|.+.++|.+|++.|++. |     .
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~   94 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQ   94 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSC
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccCC
Confidence            3445789999  77999999999999999999999998764      3789999999999999999999854 5     5


Q ss_pred             CeEeEEEecccCCCC
Q 012923          198 NRMTACQLASIGPAT  212 (453)
Q Consensus       198 gr~~~v~~~~~~~~~  212 (453)
                      ++.|.|.++...+..
T Consensus        95 g~~l~v~~a~~~p~~  109 (114)
T 2cq2_A           95 KITLYLNFVEKVQWS  109 (114)
T ss_dssp             EEECEEEEESCCCCS
T ss_pred             CcEEEEEecccCccc
Confidence            899999998754443

>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=99.63  E-value=4e-16  Score=123.46  Aligned_cols=73  Identities=14%  Similarity=0.163  Sum_probs=64.5

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeE-----EE
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHI-----LN  319 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~-----l~  319 (453)
                      ..++|||+|||+.+|+++|+++|++||.|..|.|+.+       |||||+|.+.++|.+||..|| ..|+|+.     |+
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            3479999999999999999999999999999999765       899999999999999999999 8899988     66


Q ss_pred             EEEccC
Q 012923          320 CQRAID  325 (453)
Q Consensus       320 v~~a~~  325 (453)
                      |..+..
T Consensus        88 v~~~~~   93 (115)
T 3beg_B           88 VKVDGP   93 (115)
T ss_dssp             EEECC-
T ss_pred             eccCCC
Confidence            666543

>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=99.63  E-value=4.7e-16  Score=116.91  Aligned_cols=75  Identities=17%  Similarity=0.293  Sum_probs=65.3

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEccCC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAIDG  326 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a~~~  326 (453)
                      .++|||+|||+.+|+++|+++|++||.|..|+|+++     ++|||||+|.+.++|.+|+.. ...+.|++|.|.++.++
T Consensus         5 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~-~~~~~g~~l~v~~a~~~   78 (88)
T 1wf0_A            5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE-DLIIKGISVHISNAEPK   78 (88)
T ss_dssp             CCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC-EEEETTEEEEEECCCCC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC-CceeCCEEEEEEecCCC
Confidence            469999999999999999999999999999999865     599999999999999865433 35679999999998655


Q ss_pred             C
Q 012923          327 P  327 (453)
Q Consensus       327 ~  327 (453)
                      .
T Consensus        79 ~   79 (88)
T 1wf0_A           79 H   79 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.63  E-value=2.1e-15  Score=116.00  Aligned_cols=77  Identities=23%  Similarity=0.356  Sum_probs=68.2

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhcc--CCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQY--GEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~--G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ....++|||+|||+++|+++|+++|++|  |.|..|+++        +|||||+|.+.++|.+||..++ ..|.|+.|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   83 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            3456899999999999999999999999  999999865        5699999999999999999877 4599999999


Q ss_pred             EecccCCC
Q 012923          204 QLASIGPA  211 (453)
Q Consensus       204 ~~~~~~~~  211 (453)
                      .++.....
T Consensus        84 ~~a~~~~~   91 (99)
T 2cpd_A           84 TLAKPVDK   91 (99)
T ss_dssp             ECCCCCCC
T ss_pred             EECCCCCC
Confidence            99875543

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=1.6e-15  Score=115.55  Aligned_cols=77  Identities=17%  Similarity=0.295  Sum_probs=66.9

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ...++|||+|||+++|+++|+++|.+||.|..|  +.++.+++   ||||+|.+.++|.+||. ++ ..|.|+.|.|.++
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a   79 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEEC
Confidence            345799999999999999999999999999987  55555655   99999999999999999 66 5699999999987


Q ss_pred             ccCC
Q 012923          207 SIGP  210 (453)
Q Consensus       207 ~~~~  210 (453)
                      ....
T Consensus        80 ~~~~   83 (94)
T 2e5g_A           80 EQKE   83 (94)
T ss_dssp             CCSC
T ss_pred             CcCC
Confidence            6443

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

Probab=99.63  E-value=4.6e-16  Score=118.98  Aligned_cols=78  Identities=21%  Similarity=0.362  Sum_probs=68.1

Q ss_pred             CCCCcCeEEEcCCCC-CCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          126 EDPVHRKIFVHGLGW-DTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~-~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ..+..++|||+|||+ ++|+++|+++|++||.|..|+|.        +|||||+|.+.++|.+|+..++ ..+.|+.|.|
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   77 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLIL   77 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCE
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            345678999999998 99999999999999999999984        6899999999999999999877 5589999999


Q ss_pred             EecccCCC
Q 012923          204 QLASIGPA  211 (453)
Q Consensus       204 ~~~~~~~~  211 (453)
                      .++.....
T Consensus        78 ~~a~~~~~   85 (96)
T 2kvi_A           78 EVSSSNAR   85 (96)
T ss_dssp             EEEECCCC
T ss_pred             EEcCcCCC
Confidence            99975544

>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=99.63  E-value=7.1e-16  Score=117.25  Aligned_cols=78  Identities=13%  Similarity=0.214  Sum_probs=67.8

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCC-eeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC--ccCCeEeEE
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGE-IEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK--KIGNRMTAC  203 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~-i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~--~~~gr~~~v  203 (453)
                      ....++|||+|||+++|+++|+++|++||. |..+.+.       ++|||||+|.+.++|.+|++.+++  .|.|+.|.|
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v   77 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEV   77 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEE
Confidence            455689999999999999999999999999 6666552       578999999999999999998875  599999999


Q ss_pred             EecccCCC
Q 012923          204 QLASIGPA  211 (453)
Q Consensus       204 ~~~~~~~~  211 (453)
                      .++.....
T Consensus        78 ~~a~~~~~   85 (93)
T 2cqh_A           78 DYSVSKKL   85 (93)
T ss_dssp             EECCCCCC
T ss_pred             EEccCccc
Confidence            99975543

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

Probab=99.63  E-value=8.2e-16  Score=121.56  Aligned_cols=77  Identities=16%  Similarity=0.400  Sum_probs=68.8

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCC---CCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEE
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKAT---GKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQR  322 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~---g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~  322 (453)
                      ..++|||+|||+.+|+++|+++|++||.|. +.++.+..+   |+++|||||+|.+.++|.+||..++ .|+|+.|.+..
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~-~~~G~~~~~~~   84 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL-EEDGKLYLCVS   84 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE-EETTEEEEEEC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh-hcCCcEEEecc
Confidence            347999999999999999999999999999 888888877   7999999999999999999999984 47888887765


Q ss_pred             cc
Q 012923          323 AI  324 (453)
Q Consensus       323 a~  324 (453)
                      +.
T Consensus        85 ~~   86 (114)
T 2dnl_A           85 SP   86 (114)
T ss_dssp             CS
T ss_pred             CC
Confidence            43

>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=99.63  E-value=1.3e-15  Score=133.05  Aligned_cols=84  Identities=21%  Similarity=0.433  Sum_probs=76.8

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEc
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRA  323 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a  323 (453)
                      ....++|||+|||+.+|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+||...+..|.|+.|.|.++
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~~   89 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA   89 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeecc
Confidence            34557999999999999999999999999999999999999999999999999999999999999558899999999998


Q ss_pred             cCCC
Q 012923          324 IDGP  327 (453)
Q Consensus       324 ~~~~  327 (453)
                      ....
T Consensus        90 ~~~~   93 (196)
T 1l3k_A           90 VSRE   93 (196)
T ss_dssp             CC--
T ss_pred             cCcc
Confidence            6543

>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=99.62  E-value=1.4e-15  Score=119.56  Aligned_cols=76  Identities=20%  Similarity=0.455  Sum_probs=68.3

Q ss_pred             CCCCcCeEEEcCCCCC-CCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          126 EDPVHRKIFVHGLGWD-TKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~-~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      .....++|||+|||++ +|+++|+++|++||.|..|+|        ++|||||+|.+.++|.+||+.++ ..|.|+.|.|
T Consensus        23 ~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   94 (110)
T 1wf1_A           23 PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDI   94 (110)
T ss_dssp             CTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCE
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            3345689999999999 999999999999999999998        57899999999999999998877 5699999999


Q ss_pred             EecccC
Q 012923          204 QLASIG  209 (453)
Q Consensus       204 ~~~~~~  209 (453)
                      .++...
T Consensus        95 ~~a~~~  100 (110)
T 1wf1_A           95 NMAGEP  100 (110)
T ss_dssp             EESCCC
T ss_pred             EECCCC
Confidence            998643

>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=99.62  E-value=6.1e-16  Score=116.26  Aligned_cols=78  Identities=19%  Similarity=0.181  Sum_probs=66.5

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecc
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLAS  207 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~  207 (453)
                      ..+++|||+|||+++|+++|+++|++||.|..|+|+++     ++|||||+|.+.++|++|+.. ...+.++.|.|.++.
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            34689999999999999999999999999999999865     789999999999999875443 234689999999886


Q ss_pred             cCCC
Q 012923          208 IGPA  211 (453)
Q Consensus       208 ~~~~  211 (453)
                      ....
T Consensus        77 ~~~~   80 (88)
T 1wf0_A           77 PKHN   80 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            5543

>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=99.62  E-value=1.4e-15  Score=125.55  Aligned_cols=77  Identities=18%  Similarity=0.084  Sum_probs=69.1

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCC--eEEEEEEc
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEG--HILNCQRA  323 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g--~~l~v~~a  323 (453)
                      ..+|||+||++.+|+++|+++|++||.|.+|+|+.+    +++|||||+|.+.++|.+|+..|| ..|.|  ++|+|.|+
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~A  121 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  121 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEEC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEe
Confidence            358999999999999999999999999999999754    258999999999999999999999 88855  99999999


Q ss_pred             cCCC
Q 012923          324 IDGP  327 (453)
Q Consensus       324 ~~~~  327 (453)
                      +.+.
T Consensus       122 k~~~  125 (164)
T 1sjr_A          122 KLTS  125 (164)
T ss_dssp             SSSS
T ss_pred             cCCc
Confidence            7653

>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=99.62  E-value=8.9e-16  Score=127.88  Aligned_cols=80  Identities=23%  Similarity=0.389  Sum_probs=72.1

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ......++|||+|||+++|+++|+++|++||.|..|+|+++     ++|||||+|.+.++|.+||..++ ..|.|+.|.|
T Consensus        68 ~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  142 (150)
T 2i2y_A           68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRV  142 (150)
T ss_dssp             SSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            34456789999999999999999999999999999999886     58999999999999999999877 5699999999


Q ss_pred             EecccC
Q 012923          204 QLASIG  209 (453)
Q Consensus       204 ~~~~~~  209 (453)
                      .++...
T Consensus       143 ~~a~~~  148 (150)
T 2i2y_A          143 ELSNGE  148 (150)
T ss_dssp             EECCCC
T ss_pred             EEcCCC
Confidence            998643

>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=99.62  E-value=1e-15  Score=114.95  Aligned_cols=74  Identities=19%  Similarity=0.301  Sum_probs=67.5

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEecc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQLAS  207 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~~~  207 (453)
                      ..++|||+|||+++|+++|+++|++| .|..|+|.      +++|||||+|.+.++|.+|++.+++ .+.|+.|.|.++.
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            46899999999999999999999999 99999884      6789999999999999999998885 5999999999986


Q ss_pred             cC
Q 012923          208 IG  209 (453)
Q Consensus       208 ~~  209 (453)
                      ..
T Consensus        77 ~~   78 (88)
T 1wg1_A           77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.62  E-value=1.5e-15  Score=128.94  Aligned_cols=80  Identities=21%  Similarity=0.346  Sum_probs=75.9

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .++|||+|||+.+|+++|+++|+.||.|..|++++++.+|+++|||||+|.+.++|.+|+..++ ..|.|++|.|.++..
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            3699999999999999999999999999999999999899999999999999999999999888 889999999999864


Q ss_pred             C
Q 012923          326 G  326 (453)
Q Consensus       326 ~  326 (453)
                      .
T Consensus        82 ~   82 (167)
T 1fxl_A           82 S   82 (167)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.62  E-value=7.9e-16  Score=115.60  Aligned_cols=73  Identities=18%  Similarity=0.231  Sum_probs=67.6

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .++|||+|||+.+|+++|+++|++| .|..|+|.      +++|||||+|.+.++|.+|+..+| ..|.|++|+|.++..
T Consensus         5 ~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   77 (88)
T 1wg1_A            5 SSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCC
Confidence            4689999999999999999999999 99999985      459999999999999999999999 889999999999855


Q ss_pred             C
Q 012923          326 G  326 (453)
Q Consensus       326 ~  326 (453)
                      .
T Consensus        78 ~   78 (88)
T 1wg1_A           78 D   78 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.61  E-value=8.8e-16  Score=117.50  Aligned_cols=77  Identities=23%  Similarity=0.343  Sum_probs=69.5

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceee-eeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGP-LGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~-i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ..++|||+|||+.+|+++|+++|+.||.|..|+ |++++.+    +.|||+|.+.++|.+||..|| ..|.|++|.|.++
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 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET----AVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYI   89 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSS----EEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCC----CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            357999999999999999999999999999994 8877654    349999999999999999999 8999999999999


Q ss_pred             cCC
Q 012923          324 IDG  326 (453)
Q Consensus       324 ~~~  326 (453)
                      .++
T Consensus        90 ~~~   92 (96)
T 2e44_A           90 PDE   92 (96)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            765

>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=99.61  E-value=1.4e-15  Score=129.36  Aligned_cols=80  Identities=18%  Similarity=0.295  Sum_probs=75.9

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .++|||+|||+.+|+++|+++|+.||.|..|+|++++.+++++|||||+|.+.++|.+|+..++ ..|.|++|.|.++..
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            4699999999999999999999999999999999999899999999999999999999999888 889999999999865


Q ss_pred             C
Q 012923          326 G  326 (453)
Q Consensus       326 ~  326 (453)
                      .
T Consensus        83 ~   83 (168)
T 1b7f_A           83 G   83 (168)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.61  E-value=2.6e-16  Score=130.00  Aligned_cols=83  Identities=24%  Similarity=0.315  Sum_probs=70.8

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEE--EEccc---CCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeE
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDC--KAVCD---KVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRM  200 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v--~i~~d---~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~  200 (453)
                      ...+++|||+|||+++|+++|+++|++||.|..|  +++.+   ..+++++|||||+|.+.++|.+||..++ ..|.|+.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            4556899999999999999999999999998875  12222   2378999999999999999999999887 5599999


Q ss_pred             eEEEecccC
Q 012923          201 TACQLASIG  209 (453)
Q Consensus       201 ~~v~~~~~~  209 (453)
                      |.|.++...
T Consensus       122 l~V~~a~~~  130 (143)
T 3egn_A          122 MVVQFARSA  130 (143)
T ss_dssp             CEEEECCCS
T ss_pred             EEEEECCCC
Confidence            999998654

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

Probab=99.61  E-value=2.8e-15  Score=110.01  Aligned_cols=71  Identities=14%  Similarity=0.189  Sum_probs=63.7

Q ss_pred             EEEEecCCCCccHHH----HHHHHhcc-CCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          249 KIFVSNVGSELEPQK----LLAFFSKY-GEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       249 ~l~V~nLp~~~t~~~----l~~~F~~~-G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      +|||+|||+.+++++    |+++|++| |.|.+|       ++   |||||.|.+.++|.+|++.|+ ..|.||+|+|.+
T Consensus        11 ~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~   80 (96)
T 2diu_A           11 LLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIVSF   80 (96)
T ss_dssp             EEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEES
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEe
Confidence            499999999999988    55899999 599988       33   999999999999999999999 999999999999


Q ss_pred             ccCCCCC
Q 012923          323 AIDGPKP  329 (453)
Q Consensus       323 a~~~~~~  329 (453)
                      |..+..-
T Consensus        81 A~~~sd~   87 (96)
T 2diu_A           81 TPKNREL   87 (96)
T ss_dssp             SCCSCCC
T ss_pred             cCCCcce
Confidence            9876544

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

Probab=99.61  E-value=2.5e-15  Score=116.12  Aligned_cols=80  Identities=14%  Similarity=0.126  Sum_probs=71.1

Q ss_pred             cccEEEEecCCC-----CccHHHHHHHHhccCCcceeeeeccCCC-CCCceEEEEEECCHHHHHHHHHcCC-CccCCeEE
Q 012923          246 TQRKIFVSNVGS-----ELEPQKLLAFFSKYGEIEEGPLGIDKAT-GKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHIL  318 (453)
Q Consensus       246 ~~~~l~V~nLp~-----~~t~~~l~~~F~~~G~i~~v~i~~d~~~-g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l  318 (453)
                      .+++|+|+||..     ..++++|+++|++||.|.+|.|++++.+ ++++|||||+|.+.++|.+|+..|| ..|+||.|
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i   86 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV   86 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEE
Confidence            457999999963     2378999999999999999999998754 6899999999999999999999999 89999999


Q ss_pred             EEEEccC
Q 012923          319 NCQRAID  325 (453)
Q Consensus       319 ~v~~a~~  325 (453)
                      .|.++..
T Consensus        87 ~v~~a~~   93 (105)
T 2pe8_A           87 KACFYNL   93 (105)
T ss_dssp             EEEECCH
T ss_pred             EEEEcCH
Confidence            9999853

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.61  E-value=2.2e-15  Score=119.79  Aligned_cols=75  Identities=20%  Similarity=0.155  Sum_probs=68.3

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceE-EEEEECCHHHHHHHHHcCC-CccCC--eEEEEEEc
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGF-CLFVYKTVDAAKKALEEPH-KNFEG--HILNCQRA  323 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~-afV~F~~~~~A~~Al~~~~-~~l~g--~~l~v~~a  323 (453)
                      .+|||+||++.+|+++|+++|++||.|.+|+|+.+.     +|| |||+|.+.++|.+|+..|| ..|.|  +.|+|.|+
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 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  103 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEEC
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEec
Confidence            588999999999999999999999999999987642     788 9999999999999999999 88888  89999999


Q ss_pred             cCCC
Q 012923          324 IDGP  327 (453)
Q Consensus       324 ~~~~  327 (453)
                      +...
T Consensus       104 k~~~  107 (130)
T 3zzy_A          104 KLTS  107 (130)
T ss_dssp             SCSS
T ss_pred             CCCc
Confidence            7653

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=6.8e-15  Score=112.67  Aligned_cols=77  Identities=19%  Similarity=0.309  Sum_probs=68.2

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~  205 (453)
                      ....++|||+||  ++|+++|+++|++||.|..|+|.      +++|||||+|.+.++|.+||..++. .|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~   83 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   83 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            345689999996  99999999999999999999984      5789999999999999999998884 59999999999


Q ss_pred             cccCCC
Q 012923          206 ASIGPA  211 (453)
Q Consensus       206 ~~~~~~  211 (453)
                      +.....
T Consensus        84 a~~~~~   89 (97)
T 1x5p_A           84 ARKQPM   89 (97)
T ss_dssp             CSSCCC
T ss_pred             CCCCCC
Confidence            876544

>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=99.60  E-value=2e-14  Score=133.15  Aligned_cols=80  Identities=23%  Similarity=0.362  Sum_probs=73.3

Q ss_pred             ccccEEEEecCCCCccHHHHH----HHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEE
Q 012923          245 YTQRKIFVSNVGSELEPQKLL----AFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILN  319 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~----~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~  319 (453)
                      ...++|||+|||+.+|+++|+    ++|+.||.|..|+|++   +++++|||||+|.+.++|.+||..|| ..|.|+.|+
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            346799999999999999977    8999999999999875   78899999999999999999999999 889999999


Q ss_pred             EEEccCCC
Q 012923          320 CQRAIDGP  327 (453)
Q Consensus       320 v~~a~~~~  327 (453)
                      |.|+....
T Consensus        84 v~~a~~~~   91 (282)
T 3pgw_A           84 IQYAKTDS   91 (282)
T ss_pred             EEEeccCc
Confidence            99996654

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

Probab=99.59  E-value=2.4e-15  Score=115.01  Aligned_cols=78  Identities=19%  Similarity=0.231  Sum_probs=69.1

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEE-EEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDC-KAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v-~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ...++|||+|||+++|+++|+++|.+||.|..| .|+.++.++    .|||+|.+.++|.+|+..++ ..|.|+.|.|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            446899999999999999999999999999999 488876443    49999999999999999877 569999999999


Q ss_pred             cccC
Q 012923          206 ASIG  209 (453)
Q Consensus       206 ~~~~  209 (453)
                      +...
T Consensus        89 a~~~   92 (96)
T 2e44_A           89 IPDE   92 (96)
T ss_dssp             CCCC
T ss_pred             cCcc
Confidence            8754

>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=99.59  E-value=1.8e-15  Score=128.54  Aligned_cols=80  Identities=26%  Similarity=0.486  Sum_probs=74.0

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecccC
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASIG  209 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~~~  209 (453)
                      .++|||+|||+++|+++|+++|++||.|..|+|++++.++.++|||||+|.+.++|.+|++..+..+.|+.|.|.++..+
T Consensus        87 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A           87 TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             CEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHHCSEECSSSSCEEEEECCCC
T ss_pred             CCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHhCCCEEeCCeEEEEeecCCC
Confidence            56899999999999999999999999999999999988999999999999999999999994336699999999998643

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

Probab=99.59  E-value=4.2e-15  Score=126.07  Aligned_cols=82  Identities=27%  Similarity=0.439  Sum_probs=76.4

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      .....++|||+|||.++|+++|+++|++||.|..|++++++.++.++|||||+|.+.++|.+|+..++ ..|.|+.|.|.
T Consensus        83 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  162 (166)
T 3md3_A           83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN  162 (166)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Confidence            44567899999999999999999999999999999999998899999999999999999999999877 56999999999


Q ss_pred             ecc
Q 012923          205 LAS  207 (453)
Q Consensus       205 ~~~  207 (453)
                      ++.
T Consensus       163 ~a~  165 (166)
T 3md3_A          163 WAA  165 (166)
T ss_dssp             ESC
T ss_pred             ecC
Confidence            974

>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=99.59  E-value=2.9e-15  Score=112.34  Aligned_cols=70  Identities=23%  Similarity=0.510  Sum_probs=64.7

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhcc----C-------CcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-Ccc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKY----G-------EIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNF  313 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~----G-------~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l  313 (453)
                      ..++|||+|||+.+|+++|+++|++|    |       .|.++++.++      +|||||+|.+.++|.+|| .+| ..|
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~~   77 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGIIF   77 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCEE
Confidence            34799999999999999999999999    8       8999998765      899999999999999999 888 889


Q ss_pred             CCeEEEEEE
Q 012923          314 EGHILNCQR  322 (453)
Q Consensus       314 ~g~~l~v~~  322 (453)
                      +|+.|+|++
T Consensus        78 ~g~~l~V~r   86 (87)
T 2hzc_A           78 QGQSLKIRR   86 (87)
T ss_dssp             TTEECEEEC
T ss_pred             CCeEEEEeC
Confidence            999999974

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

Probab=99.59  E-value=4.3e-15  Score=131.87  Aligned_cols=85  Identities=22%  Similarity=0.442  Sum_probs=78.1

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ...++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+|+..++ ..|.|+.|.|.++
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            345899999999999999999999999999999999999899999999999999999999999877 5699999999999


Q ss_pred             ccCCCC
Q 012923          207 SIGPAT  212 (453)
Q Consensus       207 ~~~~~~  212 (453)
                      ...+..
T Consensus       203 ~~~~~~  208 (216)
T 2qfj_A          203 VTPPMP  208 (216)
T ss_dssp             SSCSST
T ss_pred             cCCCCC
Confidence            765443

>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=99.59  E-value=3.5e-15  Score=111.86  Aligned_cols=71  Identities=15%  Similarity=0.309  Sum_probs=64.1

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhcc----C-------CeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-Cc
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQY----G-------EIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KK  195 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~----G-------~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~  195 (453)
                      ...++|||+|||+++|+++|+++|++|    |       .|..|++.++      +|||||+|.+.++|.+|+ .++ ..
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~   76 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGII   76 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCE
Confidence            346899999999999999999999999    8       8999998764      789999999999999999 777 56


Q ss_pred             cCCeEeEEEe
Q 012923          196 IGNRMTACQL  205 (453)
Q Consensus       196 ~~gr~~~v~~  205 (453)
                      |.|+.|.|..
T Consensus        77 ~~g~~l~V~r   86 (87)
T 2hzc_A           77 FQGQSLKIRR   86 (87)
T ss_dssp             ETTEECEEEC
T ss_pred             ECCeEEEEeC
Confidence            9999999874

>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=99.59  E-value=3.1e-15  Score=127.78  Aligned_cols=80  Identities=24%  Similarity=0.392  Sum_probs=75.0

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ...++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+|++.++ ..|.|+.|.|.++
T Consensus        92 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            446899999999999999999999999999999999998899999999999999999999999877 5699999999987


Q ss_pred             c
Q 012923          207 S  207 (453)
Q Consensus       207 ~  207 (453)
                      .
T Consensus       172 s  172 (172)
T 2g4b_A          172 S  172 (172)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.58  E-value=8.8e-15  Score=115.88  Aligned_cols=75  Identities=13%  Similarity=0.097  Sum_probs=66.7

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceE-EEEEECCHHHHHHHHHcCC-CccCC--eEEEEEE
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGF-CLFVYKTVDAAKKALEEPH-KNFEG--HILNCQR  322 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~-afV~F~~~~~A~~Al~~~~-~~l~g--~~l~v~~  322 (453)
                      ...|||+||++.+|+++|+++|++||.|.+|+|+..      .|| |||+|.+.++|.+|+..|| ..|.|  +.|+|.+
T Consensus        25 vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~   98 (124)
T 2e5i_A           25 VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEY   98 (124)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEEC
T ss_pred             EEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEE
Confidence            346789999999999999999999999999999752      386 9999999999999999999 88887  6999999


Q ss_pred             ccCCC
Q 012923          323 AIDGP  327 (453)
Q Consensus       323 a~~~~  327 (453)
                      +..+.
T Consensus        99 Ak~~~  103 (124)
T 2e5i_A           99 ARPTR  103 (124)
T ss_dssp             CSCSC
T ss_pred             ecCCc
Confidence            97654

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

Probab=99.58  E-value=6.8e-15  Score=107.97  Aligned_cols=73  Identities=12%  Similarity=0.178  Sum_probs=63.2

Q ss_pred             cCe-EEEcCCCCCCCHHH----HHHHHhcc-CCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeE
Q 012923          130 HRK-IFVHGLGWDTKAET----LIDAFKQY-GEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTA  202 (453)
Q Consensus       130 ~~~-lfV~nLp~~~te~~----l~~~f~~~-G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~  202 (453)
                      +.| |||+|||+++++++    |+++|++| |.|.+|       ++   |+|||.|.+.++|.+|++.|++ .|.||.|+
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 99999999999988    55899999 599998       33   9999999999999999998885 59999999


Q ss_pred             EEecccCCCC
Q 012923          203 CQLASIGPAT  212 (453)
Q Consensus       203 v~~~~~~~~~  212 (453)
                      |.++......
T Consensus        78 v~~A~~~sd~   87 (96)
T 2diu_A           78 VSFTPKNREL   87 (96)
T ss_dssp             EESSCCSCCC
T ss_pred             EEecCCCcce
Confidence            9999765543

>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=99.58  E-value=2.1e-15  Score=119.30  Aligned_cols=72  Identities=17%  Similarity=0.268  Sum_probs=63.3

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeE-----eE
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRM-----TA  202 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~-----~~  202 (453)
                      ..++|||+|||+++|+++|+++|.+||.|..|+|+.+       |||||+|.+.++|.+||+.|+ ..|.|+.     |.
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            3579999999999999999999999999999999876       899999999999999999887 5588988     66


Q ss_pred             EEecc
Q 012923          203 CQLAS  207 (453)
Q Consensus       203 v~~~~  207 (453)
                      |....
T Consensus        88 v~~~~   92 (115)
T 3beg_B           88 VKVDG   92 (115)
T ss_dssp             EEECC
T ss_pred             eccCC
Confidence            65554

>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=99.58  E-value=7e-15  Score=121.37  Aligned_cols=77  Identities=13%  Similarity=0.180  Sum_probs=68.0

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCC--eEeEEEec
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGN--RMTACQLA  206 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~g--r~~~v~~~  206 (453)
                      -.+|||+||++.+|+++|+++|++||.|..|+|+.+    .++|||||+|.+.++|.+|++.|++. |.+  +.|+|.++
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~A  121 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  121 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEEC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEe
Confidence            457999999999999999999999999999998653    36799999999999999999999854 755  99999998


Q ss_pred             ccCC
Q 012923          207 SIGP  210 (453)
Q Consensus       207 ~~~~  210 (453)
                      ....
T Consensus       122 k~~~  125 (164)
T 1sjr_A          122 KLTS  125 (164)
T ss_dssp             SSSS
T ss_pred             cCCc
Confidence            7653

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

Probab=99.57  E-value=1.3e-14  Score=112.14  Aligned_cols=80  Identities=13%  Similarity=0.159  Sum_probs=70.2

Q ss_pred             CCcCeEEEcCCCC-----CCCHHHHHHHHhccCCeeEEEEcccCCC-CCcceEEEEEEccHHHHHHHHHcCCC-ccCCeE
Q 012923          128 PVHRKIFVHGLGW-----DTKAETLIDAFKQYGEIEDCKAVCDKVS-GKSKGYGFILFKTRSGARKALKEPQK-KIGNRM  200 (453)
Q Consensus       128 ~~~~~lfV~nLp~-----~~te~~l~~~f~~~G~i~~v~i~~d~~~-g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~  200 (453)
                      ..+++|+|+||..     +-++++|+++|++||.|.+|+|++++.+ ++++|||||+|.+.++|.+|+..|++ .+.||.
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            3468999999963     3378999999999999999999998754 68999999999999999999999884 599999


Q ss_pred             eEEEecc
Q 012923          201 TACQLAS  207 (453)
Q Consensus       201 ~~v~~~~  207 (453)
                      |.|.++.
T Consensus        86 i~v~~a~   92 (105)
T 2pe8_A           86 VKACFYN   92 (105)
T ss_dssp             CEEEECC
T ss_pred             EEEEEcC
Confidence            9999985

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

Probab=99.56  E-value=9.8e-15  Score=127.68  Aligned_cols=83  Identities=23%  Similarity=0.394  Sum_probs=77.1

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ...++|||+|||+++|+++|+++|++||.|..|+|++++.++.++|||||+|.+.++|.+|++.++ ..|.|+.|.|.++
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            456899999999999999999999999999999999998899999999999999999999999877 5699999999998


Q ss_pred             ccCC
Q 012923          207 SIGP  210 (453)
Q Consensus       207 ~~~~  210 (453)
                      ....
T Consensus       192 ~~~~  195 (198)
T 2yh0_A          192 SVGA  195 (198)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.56  E-value=1.4e-14  Score=115.09  Aligned_cols=76  Identities=13%  Similarity=0.228  Sum_probs=67.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceE-EEEEEccHHHHHHHHHcCCCc-cCC--eEeEEEec
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGY-GFILFKTRSGARKALKEPQKK-IGN--RMTACQLA  206 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~-afV~f~~~~~a~~A~~~~~~~-~~g--r~~~v~~~  206 (453)
                      -+|||+||++.+|+++|+++|++||.|.+|+|+.+     ++|| |||+|.+.++|.+|++.|++. |.+  +.|+|.++
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            47889999999999999999999999999988764     3688 999999999999999999954 777  89999998


Q ss_pred             ccCCC
Q 012923          207 SIGPA  211 (453)
Q Consensus       207 ~~~~~  211 (453)
                      .....
T Consensus       104 k~~~l  108 (130)
T 3zzy_A          104 KLTSL  108 (130)
T ss_dssp             SCSSC
T ss_pred             CCCce
Confidence            75543

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.56  E-value=4.5e-15  Score=131.11  Aligned_cols=81  Identities=21%  Similarity=0.299  Sum_probs=69.1

Q ss_pred             ccccEEEEecCCCCc---------cHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-Ccc-
Q 012923          245 YTQRKIFVSNVGSEL---------EPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNF-  313 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~---------t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l-  313 (453)
                      ...++|||+||+..+         ++++|+++|++||.|.+|+|+.+      +|||||+|.+.++|..|+..|+ ..| 
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~l~  205 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQTLL  205 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCCCC
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCEEe
Confidence            356799999999998         89999999999999999999864      8999999999999999999999 778 


Q ss_pred             -----------CCeEEEEEEccCCCCCCC
Q 012923          314 -----------EGHILNCQRAIDGPKPGK  331 (453)
Q Consensus       314 -----------~g~~l~v~~a~~~~~~~~  331 (453)
                                 .|+.|.|.||...+.+..
T Consensus       206 ~~~~~e~~~~~~gr~L~V~wA~~~pnp~~  234 (240)
T 3u1l_A          206 LPSDKEWDDRREGTGLLVKWANEDPDPAA  234 (240)
T ss_dssp             CTTSTTGGGGGGSCCCEEEECC-------
T ss_pred             ccccccccccCCCCEEEEEEccCCCCHHH
Confidence                       899999999988765543

>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=99.55  E-value=8.1e-15  Score=128.38  Aligned_cols=75  Identities=16%  Similarity=0.231  Sum_probs=69.9

Q ss_pred             ccEEEEecCC-CCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          247 QRKIFVSNVG-SELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       247 ~~~l~V~nLp-~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      .++|||+||| +.+|+++|+++|++||.|.+|+|++++     +|||||+|.+.++|.+||..|| ..|.|++|+|.++.
T Consensus         4 ~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~   78 (205)
T 3tyt_A            4 SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSK   78 (205)
T ss_dssp             CSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcc
Confidence            4699999999 899999999999999999999998763     8999999999999999999999 89999999999986


Q ss_pred             CC
Q 012923          325 DG  326 (453)
Q Consensus       325 ~~  326 (453)
                      ..
T Consensus        79 ~~   80 (205)
T 3tyt_A           79 QP   80 (205)
T ss_dssp             CS
T ss_pred             CC
Confidence            44

>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=99.54  E-value=2e-14  Score=122.94  Aligned_cols=80  Identities=24%  Similarity=0.439  Sum_probs=72.4

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccC---CeEe
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIG---NRMT  201 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~---gr~~  201 (453)
                      .....++|||+|||+++|+++|+++|++||.|..|+|+++. +++++|||||+|.+.++|.+|++.+++ .+.   ++.|
T Consensus        91 ~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l  169 (175)
T 3nmr_A           91 NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPM  169 (175)
T ss_dssp             SCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCC
T ss_pred             ccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCe
Confidence            34467899999999999999999999999999999999997 699999999999999999999999885 354   4999


Q ss_pred             EEEec
Q 012923          202 ACQLA  206 (453)
Q Consensus       202 ~v~~~  206 (453)
                      .|.++
T Consensus       170 ~V~~a  174 (175)
T 3nmr_A          170 VVKFA  174 (175)
T ss_dssp             EEEEC
T ss_pred             EEEec
Confidence            99987

>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=99.52  E-value=9.9e-14  Score=109.07  Aligned_cols=80  Identities=19%  Similarity=0.314  Sum_probs=68.0

Q ss_pred             cccccEEEEecCCCCcc-----------HHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-C
Q 012923          244 EYTQRKIFVSNVGSELE-----------PQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-K  311 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t-----------~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~  311 (453)
                      ...+++|+|+||....+           +++|+++|++||.|..|.| .++   .++|||||+|.+.++|.+||..|| .
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~   87 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGR   87 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCC
Confidence            34567999999954432           6899999999999999966 543   379999999999999999999999 8


Q ss_pred             ccCCeEEEEEEccCCC
Q 012923          312 NFEGHILNCQRAIDGP  327 (453)
Q Consensus       312 ~l~g~~l~v~~a~~~~  327 (453)
                      .|+|++|.|.++..+.
T Consensus        88 ~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           88 WFGGRQITAQAWDGTT  103 (112)
T ss_dssp             EETTEECEEEECCSCC
T ss_pred             EECCcEEEEEEeCCCC
Confidence            8999999999996654

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.51  E-value=5.7e-14  Score=111.22  Aligned_cols=73  Identities=12%  Similarity=0.109  Sum_probs=63.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceE-EEEEEccHHHHHHHHHcCCC-ccCC--eEeEEEecc
Q 012923          132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGY-GFILFKTRSGARKALKEPQK-KIGN--RMTACQLAS  207 (453)
Q Consensus       132 ~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~-afV~f~~~~~a~~A~~~~~~-~~~g--r~~~v~~~~  207 (453)
                      .|||+||++.+|+++|+++|++||.|..|+|+. +     .|| |||+|.+.++|..|++.|++ .|.|  +.|+|.++.
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 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR  100 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCS
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEec
Confidence            468999999999999999999999999999865 2     286 99999999999999999885 4776  689999987


Q ss_pred             cCC
Q 012923          208 IGP  210 (453)
Q Consensus       208 ~~~  210 (453)
                      ...
T Consensus       101 ~~~  103 (124)
T 2e5i_A          101 PTR  103 (124)
T ss_dssp             CSC
T ss_pred             CCc
Confidence            554

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.51  E-value=2.1e-14  Score=126.82  Aligned_cols=80  Identities=20%  Similarity=0.273  Sum_probs=68.7

Q ss_pred             CCCCcCeEEEcCCCCCC---------CHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-c
Q 012923          126 EDPVHRKIFVHGLGWDT---------KAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-K  195 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~---------te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~  195 (453)
                      .....++|||+||+..+         |+++|+++|++||.|.+|+|+.      ++|||||+|.+.++|+.|++.|++ .
T Consensus       130 ~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG~AFV~F~~~~~Ae~A~~am~g~~  203 (240)
T 3u1l_A          130 FRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMSNQT  203 (240)
T ss_dssp             -CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             cccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCCEEEEEeCCHHHHHHHHHHhCCCE
Confidence            35567999999999998         7999999999999999999985      479999999999999999998884 4


Q ss_pred             c------------CCeEeEEEecccCCC
Q 012923          196 I------------GNRMTACQLASIGPA  211 (453)
Q Consensus       196 ~------------~gr~~~v~~~~~~~~  211 (453)
                      |            .|+.|.|.|+...+.
T Consensus       204 l~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          204 LLLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CCCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             EeccccccccccCCCCEEEEEEccCCCC
Confidence            6            799999999986544

>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=99.50  E-value=3.7e-14  Score=109.60  Aligned_cols=79  Identities=15%  Similarity=0.142  Sum_probs=69.1

Q ss_pred             cccEEEEecCC--CCc--------cHHHHHHHHhccCCcceeeeeccCCC--CCCceEEEEEECCHHHHHHHHHcCC-Cc
Q 012923          246 TQRKIFVSNVG--SEL--------EPQKLLAFFSKYGEIEEGPLGIDKAT--GKPKGFCLFVYKTVDAAKKALEEPH-KN  312 (453)
Q Consensus       246 ~~~~l~V~nLp--~~~--------t~~~l~~~F~~~G~i~~v~i~~d~~~--g~~kg~afV~F~~~~~A~~Al~~~~-~~  312 (453)
                      ++++|+|.|+-  ..+        .+++|++.|++||.|.+|.|++++.+  ++++||+||+|.+.++|.+|+..|| ..
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            45799999983  223        34799999999999999999998755  4689999999999999999999999 89


Q ss_pred             cCCeEEEEEEcc
Q 012923          313 FEGHILNCQRAI  324 (453)
Q Consensus       313 l~g~~l~v~~a~  324 (453)
                      |+||+|.|.++.
T Consensus        84 f~GR~i~v~~~~   95 (105)
T 3v4m_A           84 FANRVVVTKYCD   95 (105)
T ss_dssp             ETTEECEEEEEC
T ss_pred             eCCCEEEEEEeC
Confidence            999999999974

>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=99.48  E-value=7.9e-14  Score=119.33  Aligned_cols=78  Identities=27%  Similarity=0.387  Sum_probs=69.6

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ....++|||+|||+++|+++|+++|++||.|..+     ..++.++|||||+|.+.++|.+|+..++ ..|.|+.|.|.+
T Consensus        96 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  170 (175)
T 1fje_B           96 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY  170 (175)
T ss_dssp             TGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEE
T ss_pred             cccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEe
Confidence            3457899999999999999999999999988766     4488999999999999999999999888 569999999999


Q ss_pred             cccC
Q 012923          206 ASIG  209 (453)
Q Consensus       206 ~~~~  209 (453)
                      +..+
T Consensus       171 a~~k  174 (175)
T 1fje_B          171 TGEK  174 (175)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            8654

>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=99.47  E-value=8.4e-14  Score=109.64  Aligned_cols=79  Identities=10%  Similarity=0.085  Sum_probs=69.7

Q ss_pred             cccEEEEecCCCC-----ccHHHHHHHHhccCCcceeeeeccCC----CCCCceEEEEEECCHHHHHHHHHcCC-CccCC
Q 012923          246 TQRKIFVSNVGSE-----LEPQKLLAFFSKYGEIEEGPLGIDKA----TGKPKGFCLFVYKTVDAAKKALEEPH-KNFEG  315 (453)
Q Consensus       246 ~~~~l~V~nLp~~-----~t~~~l~~~F~~~G~i~~v~i~~d~~----~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g  315 (453)
                      ++++|+|.||-..     -.+++|++.|++||.|.+|.|++++.    +++++||+||+|.+.++|.+|+..|| ..|+|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            5679999999422     24689999999999999999999864    46788999999999999999999999 99999


Q ss_pred             eEEEEEEcc
Q 012923          316 HILNCQRAI  324 (453)
Q Consensus       316 ~~l~v~~a~  324 (453)
                      |.|.|.++.
T Consensus        99 R~i~v~~~~  107 (118)
T 3ue2_A           99 RKVVAEVYD  107 (118)
T ss_dssp             EECEEEEEC
T ss_pred             cEEEEEEcC
Confidence            999999974

>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=99.45  E-value=1.1e-13  Score=123.72  Aligned_cols=78  Identities=19%  Similarity=0.316  Sum_probs=71.9

Q ss_pred             cccccEEEEecCCC-CccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          244 EYTQRKIFVSNVGS-ELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       244 ~~~~~~l~V~nLp~-~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      ....++|||+|||+ .+|+++|+++|+.||.|..|+|++++     +|||||+|.+.++|.+||..++ ..|.|+.|.|.
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            34567999999999 99999999999999999999999875     8999999999999999999888 88999999999


Q ss_pred             EccCC
Q 012923          322 RAIDG  326 (453)
Q Consensus       322 ~a~~~  326 (453)
                      ++...
T Consensus       106 ~a~~~  110 (229)
T 2adc_A          106 LSKHQ  110 (229)
T ss_dssp             CCSCC
T ss_pred             EecCc
Confidence            99755

>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=99.45  E-value=4.1e-13  Score=105.54  Aligned_cols=82  Identities=15%  Similarity=0.192  Sum_probs=68.3

Q ss_pred             CCCCCcCeEEEcCCCCCCC-----------HHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC
Q 012923          125 DEDPVHRKIFVHGLGWDTK-----------AETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ  193 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~t-----------e~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~  193 (453)
                      .....+++|+|+||....+           +++|+++|++||.|..|.| .++   .++|||||+|.+.++|.+|+..++
T Consensus        10 ~~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~ln   85 (112)
T 2dit_A           10 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLD   85 (112)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHST
T ss_pred             CCCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcC
Confidence            3455689999999944332           6899999999999999965 554   389999999999999999999888


Q ss_pred             -CccCCeEeEEEecccCC
Q 012923          194 -KKIGNRMTACQLASIGP  210 (453)
Q Consensus       194 -~~~~gr~~~v~~~~~~~  210 (453)
                       ..|.||.|.|.++....
T Consensus        86 g~~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           86 GRWFGGRQITAQAWDGTT  103 (112)
T ss_dssp             TCEETTEECEEEECCSCC
T ss_pred             CCEECCcEEEEEEeCCCC
Confidence             45999999999986543

>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=99.44  E-value=4.1e-14  Score=109.23  Aligned_cols=71  Identities=18%  Similarity=0.318  Sum_probs=62.6

Q ss_pred             EecCCCCccHHHHHHHH------------hccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEE
Q 012923          252 VSNVGSELEPQKLLAFF------------SKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHIL  318 (453)
Q Consensus       252 V~nLp~~~t~~~l~~~F------------~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l  318 (453)
                      +.||++.+++++|++.|            ++||.|.+|.|+++. +++++|||||+|.+.++|.+|+..|| ..|+||+|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            55677777887777666            999999999999876 47899999999999999999999999 89999999


Q ss_pred             EEEEc
Q 012923          319 NCQRA  323 (453)
Q Consensus       319 ~v~~a  323 (453)
                      .|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

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

Probab=99.44  E-value=1.3e-12  Score=99.47  Aligned_cols=75  Identities=23%  Similarity=0.252  Sum_probs=63.8

Q ss_pred             ccEEEEecCC-------CCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEE
Q 012923          247 QRKIFVSNVG-------SELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILN  319 (453)
Q Consensus       247 ~~~l~V~nLp-------~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~  319 (453)
                      .++|.|.-..       ..+|+++|+++|++||.|..|+|+     ++++|||||+|.+.++|.+||..++. +.+++|+
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~-~~g~~l~   83 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG-LVDNPLK   83 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB-CSSSBCE
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC-CCCCeEE
Confidence            3477776544       458999999999999999999997     36799999999999999999999654 6799999


Q ss_pred             EEEccCCC
Q 012923          320 CQRAIDGP  327 (453)
Q Consensus       320 v~~a~~~~  327 (453)
                      |.|+..++
T Consensus        84 V~~a~~~~   91 (100)
T 2d9o_A           84 ISWLEGQP   91 (100)
T ss_dssp             EECSSCCC
T ss_pred             EEEccCCC
Confidence            99987655

>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=99.43  E-value=3.6e-13  Score=103.99  Aligned_cols=79  Identities=15%  Similarity=0.173  Sum_probs=68.6

Q ss_pred             CcCeEEEcCC--CCCCC--------HHHHHHHHhccCCeeEEEEcccCCC--CCcceEEEEEEccHHHHHHHHHcCCC-c
Q 012923          129 VHRKIFVHGL--GWDTK--------AETLIDAFKQYGEIEDCKAVCDKVS--GKSKGYGFILFKTRSGARKALKEPQK-K  195 (453)
Q Consensus       129 ~~~~lfV~nL--p~~~t--------e~~l~~~f~~~G~i~~v~i~~d~~~--g~~~G~afV~f~~~~~a~~A~~~~~~-~  195 (453)
                      .++.|.|.|+  |.++.        +++|++.|++||.|.+|+|++++.+  ++++|||||+|.+.++|.+|+..||+ .
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            4689999998  44443        4699999999999999999998754  46899999999999999999999995 5


Q ss_pred             cCCeEeEEEecc
Q 012923          196 IGNRMTACQLAS  207 (453)
Q Consensus       196 ~~gr~~~v~~~~  207 (453)
                      +.||.|.|.++.
T Consensus        84 f~GR~i~v~~~~   95 (105)
T 3v4m_A           84 FANRVVVTKYCD   95 (105)
T ss_dssp             ETTEECEEEEEC
T ss_pred             eCCCEEEEEEeC
Confidence            999999999875

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

Probab=99.42  E-value=1.5e-13  Score=120.08  Aligned_cols=76  Identities=20%  Similarity=0.339  Sum_probs=70.6

Q ss_pred             ccEEEEecCCC-CccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          247 QRKIFVSNVGS-ELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       247 ~~~l~V~nLp~-~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      .++|||+|||+ .+|+++|+++|+.||.|..|+|++++     +|||||+|.+.++|.+||..++ ..|.|+.|.|.++.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            46999999999 99999999999999999999999875     8899999999999999999888 88999999999987


Q ss_pred             CCC
Q 012923          325 DGP  327 (453)
Q Consensus       325 ~~~  327 (453)
                      ...
T Consensus        78 ~~~   80 (198)
T 1qm9_A           78 HQN   80 (198)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            553

>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=99.41  E-value=4.3e-13  Score=122.48  Aligned_cols=75  Identities=21%  Similarity=0.339  Sum_probs=69.4

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|+.||.|..|.|.++      +|||||+|.+.++|.+||..++ ..|.|+.|.|.++
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a   93 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA   93 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeec
Confidence            44579999999999999999999999999999999764      8999999999999999999888 8899999999998


Q ss_pred             cC
Q 012923          324 ID  325 (453)
Q Consensus       324 ~~  325 (453)
                      ..
T Consensus        94 ~~   95 (261)
T 3sde_A           94 TH   95 (261)
T ss_dssp             CC
T ss_pred             cc
Confidence            64

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

Probab=99.40  E-value=3.1e-12  Score=97.35  Aligned_cols=77  Identities=16%  Similarity=0.142  Sum_probs=65.6

Q ss_pred             CcCeEEEcCCC-------CCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEe
Q 012923          129 VHRKIFVHGLG-------WDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMT  201 (453)
Q Consensus       129 ~~~~lfV~nLp-------~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~  201 (453)
                      ...+|.|....       .++|+++|+++|++||.|..|+|+     ++++|||||+|.+.++|..||+.++. +.++.|
T Consensus         9 ~~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~-~~g~~l   82 (100)
T 2d9o_A            9 GTPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG-LVDNPL   82 (100)
T ss_dssp             SSCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB-CSSSBC
T ss_pred             ccceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC-CCCCeE
Confidence            35678888765       458999999999999999999987     36899999999999999999998544 679999


Q ss_pred             EEEecccCCC
Q 012923          202 ACQLASIGPA  211 (453)
Q Consensus       202 ~v~~~~~~~~  211 (453)
                      .|.++...+.
T Consensus        83 ~V~~a~~~~~   92 (100)
T 2d9o_A           83 KISWLEGQPQ   92 (100)
T ss_dssp             EEECSSCCCC
T ss_pred             EEEEccCCCC
Confidence            9999875543

>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=99.40  E-value=1.3e-13  Score=106.41  Aligned_cols=71  Identities=17%  Similarity=0.321  Sum_probs=61.1

Q ss_pred             EcCCCCCCCHHHHHHHH------------hccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEe
Q 012923          135 VHGLGWDTKAETLIDAF------------KQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMT  201 (453)
Q Consensus       135 V~nLp~~~te~~l~~~f------------~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~  201 (453)
                      +.|||+.+++++|+++|            ++||.|.+|+|+++. +++++|||||+|.+.++|.+|+..+++ .+.||.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            45666677777776666            999999999999987 589999999999999999999998884 5999999


Q ss_pred             EEEec
Q 012923          202 ACQLA  206 (453)
Q Consensus       202 ~v~~~  206 (453)
                      .|.++
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=99.39  E-value=6.1e-13  Score=104.67  Aligned_cols=79  Identities=11%  Similarity=0.133  Sum_probs=68.7

Q ss_pred             CcCeEEEcCCC--CCC---CHHHHHHHHhccCCeeEEEEcccCC----CCCcceEEEEEEccHHHHHHHHHcCCC-ccCC
Q 012923          129 VHRKIFVHGLG--WDT---KAETLIDAFKQYGEIEDCKAVCDKV----SGKSKGYGFILFKTRSGARKALKEPQK-KIGN  198 (453)
Q Consensus       129 ~~~~lfV~nLp--~~~---te~~l~~~f~~~G~i~~v~i~~d~~----~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~g  198 (453)
                      .+++|+|+|+-  .++   .++||++.|++||.|.+|+|++++.    +++++||+||+|.+.++|.+|+..||+ .+.|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            46899999994  222   3789999999999999999999864    357889999999999999999999994 5999


Q ss_pred             eEeEEEecc
Q 012923          199 RMTACQLAS  207 (453)
Q Consensus       199 r~~~v~~~~  207 (453)
                      |.|.|.++.
T Consensus        99 R~i~v~~~~  107 (118)
T 3ue2_A           99 RKVVAEVYD  107 (118)
T ss_dssp             EECEEEEEC
T ss_pred             cEEEEEEcC
Confidence            999999875

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.33  E-value=3.5e-12  Score=99.55  Aligned_cols=76  Identities=14%  Similarity=0.155  Sum_probs=65.5

Q ss_pred             ccccEEEEecCCCCc----------cHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-Ccc
Q 012923          245 YTQRKIFVSNVGSEL----------EPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNF  313 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~----------t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l  313 (453)
                      ..+++|.|.||-...          .+++|++.|++||.|.+|.|.++.    ++||+||+|.+.++|.+|+..|| ..|
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f   80 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWF   80 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            356799999984322          246889999999999999997763    49999999999999999999999 899


Q ss_pred             CCeEEEEEEcc
Q 012923          314 EGHILNCQRAI  324 (453)
Q Consensus       314 ~g~~l~v~~a~  324 (453)
                      +||.|.|.++.
T Consensus        81 ~GR~i~v~~~~   91 (114)
T 3s6e_A           81 AGKMITAAYVP   91 (114)
T ss_dssp             TTEECEEEEEC
T ss_pred             CCEEEEEEEEc
Confidence            99999999984

>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=99.26  E-value=1.3e-11  Score=115.06  Aligned_cols=77  Identities=14%  Similarity=0.220  Sum_probs=64.0

Q ss_pred             cCCCCCcCeEEEcC--CCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-c---C
Q 012923          124 ADEDPVHRKIFVHG--LGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-I---G  197 (453)
Q Consensus       124 ~~~~~~~~~lfV~n--Lp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~---~  197 (453)
                      .-.+..+++|||+|  |++.+|+++|+++|++||.|..|++..      +||||||+|.+.++|++|++.||+. +   .
T Consensus        12 ~~~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~   85 (345)
T 3tht_A           12 ETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDL   85 (345)
T ss_dssp             CCCSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTT
T ss_pred             eecCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCcccccc
Confidence            34456678999999  579999999999999999999987653      5799999999999999999999954 3   3


Q ss_pred             Ce--EeEEEec
Q 012923          198 NR--MTACQLA  206 (453)
Q Consensus       198 gr--~~~v~~~  206 (453)
                      |+  .|.|.++
T Consensus        86 g~~~~ly~~~~   96 (345)
T 3tht_A           86 GQKITLYLNFV   96 (345)
T ss_dssp             SCEEECEEEEC
T ss_pred             CCceEEEEEEe
Confidence            55  4666665

>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=99.25  E-value=9.8e-12  Score=115.88  Aligned_cols=75  Identities=21%  Similarity=0.349  Sum_probs=63.9

Q ss_pred             cccccEEEEec--CCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-Ccc---CCe-
Q 012923          244 EYTQRKIFVSN--VGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNF---EGH-  316 (453)
Q Consensus       244 ~~~~~~l~V~n--Lp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l---~g~-  316 (453)
                      ..++++|||+|  |++.+|+++|+++|++||.|.+|.+++      +||||||+|.+.++|.+||+.|| ..+   .|+ 
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~   88 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCc
Confidence            44567999999  588999999999999999999988864      38999999999999999999999 555   355 


Q ss_pred             -EEEEEEcc
Q 012923          317 -ILNCQRAI  324 (453)
Q Consensus       317 -~l~v~~a~  324 (453)
                       .|.|.++.
T Consensus        89 ~~ly~~~~~   97 (345)
T 3tht_A           89 ITLYLNFVE   97 (345)
T ss_dssp             EECEEEECS
T ss_pred             eEEEEEEee
Confidence             67777774

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.17  E-value=9.9e-11  Score=91.32  Aligned_cols=75  Identities=8%  Similarity=0.086  Sum_probs=63.7

Q ss_pred             CcCeEEEcCCCCCC----------CHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccC
Q 012923          129 VHRKIFVHGLGWDT----------KAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIG  197 (453)
Q Consensus       129 ~~~~lfV~nLp~~~----------te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~  197 (453)
                      .++.|.|.|+=...          .+++|++.|++||.|.+|.|.++.    .+|||||+|.+.++|.+|+..||+ .+.
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            46789999984222          245889999999999999987763    589999999999999999999885 599


Q ss_pred             CeEeEEEecc
Q 012923          198 NRMTACQLAS  207 (453)
Q Consensus       198 gr~~~v~~~~  207 (453)
                      ||.|.|.++.
T Consensus        82 GR~i~v~~~~   91 (114)
T 3s6e_A           82 GKMITAAYVP   91 (114)
T ss_dssp             TEECEEEEEC
T ss_pred             CEEEEEEEEc
Confidence            9999999985

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.15  E-value=1.4e-10  Score=90.44  Aligned_cols=76  Identities=13%  Similarity=0.052  Sum_probs=66.7

Q ss_pred             ccccccEEEEecCCCC-ccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECC-HHHHHHHHHcCC---CccCCeE
Q 012923          243 SEYTQRKIFVSNVGSE-LEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKT-VDAAKKALEEPH---KNFEGHI  317 (453)
Q Consensus       243 ~~~~~~~l~V~nLp~~-~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~-~~~A~~Al~~~~---~~l~g~~  317 (453)
                      .....+.|||+||++. ++.++|+++|+.||.|.+|.++++..      .|||+|.+ ..+|..|+..+|   ..|+|..
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~   87 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKE   87 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSS
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcE
Confidence            3445679999999999 99999999999999999999998853      59999999 899999999985   6889988


Q ss_pred             EEEEEcc
Q 012923          318 LNCQRAI  324 (453)
Q Consensus       318 l~v~~a~  324 (453)
                      +.+....
T Consensus        88 ~~~evL~   94 (121)
T 1owx_A           88 VTWEVLE   94 (121)
T ss_dssp             EEEEECC
T ss_pred             EEEEECC
Confidence            8887653

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.13  E-value=2e-10  Score=83.48  Aligned_cols=72  Identities=17%  Similarity=0.175  Sum_probs=60.7

Q ss_pred             cccEEEEecCC----CCccH----HHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCe
Q 012923          246 TQRKIFVSNVG----SELEP----QKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGH  316 (453)
Q Consensus       246 ~~~~l~V~nLp----~~~t~----~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~  316 (453)
                      +..||+|..++    ..+..    .+|.+.|++||.|..++|+.++        +||+|.+.++|.+||. || ..|+||
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~Gr   76 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLNR   76 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETTE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCCe
Confidence            34588888776    23433    6788999999999999999873        8999999999999999 88 899999


Q ss_pred             EEEEEEccCC
Q 012923          317 ILNCQRAIDG  326 (453)
Q Consensus       317 ~l~v~~a~~~  326 (453)
                      .|+|+++.+.
T Consensus        77 ~LkV~lkt~d   86 (91)
T 2dnr_A           77 TITIALKSPS   86 (91)
T ss_dssp             EEEEEECCCS
T ss_pred             EEEEEeCCCC
Confidence            9999999654

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.11  E-value=2e-10  Score=89.54  Aligned_cols=75  Identities=24%  Similarity=0.189  Sum_probs=65.7

Q ss_pred             CCCcCeEEEcCCCCC-CCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEcc-HHHHHHHHHcCC---CccCCeEe
Q 012923          127 DPVHRKIFVHGLGWD-TKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKT-RSGARKALKEPQ---KKIGNRMT  201 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~-~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~-~~~a~~A~~~~~---~~~~gr~~  201 (453)
                      -+..+.|||+||+.+ ++.++|+++|++||.|..|.++++..      .|||.|.+ ..+|..|+..++   ..|.+..+
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~   88 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEV   88 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEE
Confidence            356789999999999 99999999999999999999998874      59999999 899999999885   45888888


Q ss_pred             EEEecc
Q 012923          202 ACQLAS  207 (453)
Q Consensus       202 ~v~~~~  207 (453)
                      .+.+..
T Consensus        89 ~~evL~   94 (121)
T 1owx_A           89 TWEVLE   94 (121)
T ss_dssp             EEEECC
T ss_pred             EEEECC
Confidence            877654

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.00  E-value=1.4e-09  Score=79.00  Aligned_cols=74  Identities=23%  Similarity=0.227  Sum_probs=61.7

Q ss_pred             CCcCeEEEcCCC----CCCCH----HHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCe
Q 012923          128 PVHRKIFVHGLG----WDTKA----ETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNR  199 (453)
Q Consensus       128 ~~~~~lfV~nLp----~~~te----~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr  199 (453)
                      +..-||+|.-++    .++-.    .+|.+.|.+||.|..++|+.++        +||+|.+.++|.+|+++....+.||
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            455689998877    33434    5789999999999999999986        8999999999999999444669999


Q ss_pred             EeEEEecccC
Q 012923          200 MTACQLASIG  209 (453)
Q Consensus       200 ~~~v~~~~~~  209 (453)
                      .|+|.++...
T Consensus        77 ~LkV~lkt~d   86 (91)
T 2dnr_A           77 TITIALKSPS   86 (91)
T ss_dssp             EEEEEECCCS
T ss_pred             EEEEEeCCCC
Confidence            9999998643

>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=98.97  E-value=7.2e-10  Score=80.91  Aligned_cols=72  Identities=14%  Similarity=0.190  Sum_probs=61.0

Q ss_pred             cccccEEEEecCCCC-----ccH----HHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-Ccc
Q 012923          244 EYTQRKIFVSNVGSE-----LEP----QKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNF  313 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~-----~t~----~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l  313 (453)
                      .++..||+|..++..     +..    .+|.+.|.+||.|..++|+.|+        +||+|.+.++|.+||. |+ ..|
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v   82 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKV   82 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEE
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeee
Confidence            344569999988743     322    5688999999999999999883        9999999999999999 88 999


Q ss_pred             CCeEEEEEEcc
Q 012923          314 EGHILNCQRAI  324 (453)
Q Consensus       314 ~g~~l~v~~a~  324 (453)
                      +||.|+|++..
T Consensus        83 ~Gr~L~V~~k~   93 (95)
T 1ufw_A           83 KGRAVKISGPS   93 (95)
T ss_dssp             TTEEEEEECCC
T ss_pred             CCeEEEEeccC
Confidence            99999998864

>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=98.83  E-value=1.1e-08  Score=90.76  Aligned_cols=77  Identities=10%  Similarity=0.101  Sum_probs=65.6

Q ss_pred             cEEEEecCC-----CCccHHHHHHHHhccCCcceeeeeccC----CCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeE
Q 012923          248 RKIFVSNVG-----SELEPQKLLAFFSKYGEIEEGPLGIDK----ATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHI  317 (453)
Q Consensus       248 ~~l~V~nLp-----~~~t~~~l~~~F~~~G~i~~v~i~~d~----~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~  317 (453)
                      ..+.+.|+-     ..-.+++|++.|++||.|.+|.|+++.    .+++++|++||+|.+.++|.+|+..|| ..|+||+
T Consensus       125 ~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~  204 (222)
T 3dxb_A          125 TVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRK  204 (222)
T ss_dssp             SEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSB
T ss_pred             ccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeE
Confidence            456666653     334678999999999999999998554    455899999999999999999999999 9999999


Q ss_pred             EEEEEcc
Q 012923          318 LNCQRAI  324 (453)
Q Consensus       318 l~v~~a~  324 (453)
                      |.|.+..
T Consensus       205 i~~~~~~  211 (222)
T 3dxb_A          205 VVAEVYD  211 (222)
T ss_dssp             CEEEECC
T ss_pred             EEEEEcC
Confidence            9999974

>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=98.82  E-value=4.7e-09  Score=76.62  Aligned_cols=75  Identities=16%  Similarity=0.154  Sum_probs=62.4

Q ss_pred             CCCCCcCeEEEcCCCCC-----CCH----HHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc
Q 012923          125 DEDPVHRKIFVHGLGWD-----TKA----ETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK  195 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~-----~te----~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~  195 (453)
                      .--+..-||+|.-++.+     +-.    .+|.+.|.+||+|..++|+.|+        +||+|.+.++|.+||++....
T Consensus        10 ~~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~ldG~~   81 (95)
T 1ufw_A           10 FQGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLDVDGMK   81 (95)
T ss_dssp             CCCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHHGGGSE
T ss_pred             ecCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHhcCCee
Confidence            34566779999988743     333    4688999999999999999986        999999999999999944467


Q ss_pred             cCCeEeEEEecc
Q 012923          196 IGNRMTACQLAS  207 (453)
Q Consensus       196 ~~gr~~~v~~~~  207 (453)
                      +.||.|+|.+..
T Consensus        82 v~Gr~L~V~~k~   93 (95)
T 1ufw_A           82 VKGRAVKISGPS   93 (95)
T ss_dssp             ETTEEEEEECCC
T ss_pred             eCCeEEEEeccC
Confidence            999999998864

>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=98.60  E-value=5.8e-08  Score=85.95  Aligned_cols=78  Identities=12%  Similarity=0.138  Sum_probs=63.9

Q ss_pred             cCeEEEcCCC-----CCCCHHHHHHHHhccCCeeEEEEcccCC----CCCcceEEEEEEccHHHHHHHHHcCCC-ccCCe
Q 012923          130 HRKIFVHGLG-----WDTKAETLIDAFKQYGEIEDCKAVCDKV----SGKSKGYGFILFKTRSGARKALKEPQK-KIGNR  199 (453)
Q Consensus       130 ~~~lfV~nLp-----~~~te~~l~~~f~~~G~i~~v~i~~d~~----~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr  199 (453)
                      .+.|.+.|+-     .+-.+++|++.|++||.|.+|.|+++..    +++++|++||+|.+.++|.+|+..|++ .+.||
T Consensus       124 s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr  203 (222)
T 3dxb_A          124 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR  203 (222)
T ss_dssp             CSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             cccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCe
Confidence            3455555552     3345779999999999999999986543    458999999999999999999999995 59999


Q ss_pred             EeEEEecc
Q 012923          200 MTACQLAS  207 (453)
Q Consensus       200 ~~~v~~~~  207 (453)
                      .|.+.+..
T Consensus       204 ~i~~~~~~  211 (222)
T 3dxb_A          204 KVVAEVYD  211 (222)
T ss_dssp             BCEEEECC
T ss_pred             EEEEEEcC
Confidence            99999875

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.50  E-value=4.3e-07  Score=67.51  Aligned_cols=71  Identities=15%  Similarity=0.251  Sum_probs=65.1

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhcc-----CCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEE
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKY-----GEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNC  320 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~-----G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v  320 (453)
                      .++|-|-|||..+++..|+.+++++     |.|+.|.+..|.      +=|+|+|.+...|.+|...|+ ..|.||+|+|
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            4689999999999999999999999     999999999884      459999999999999999999 8999999998


Q ss_pred             EEc
Q 012923          321 QRA  323 (453)
Q Consensus       321 ~~a  323 (453)
                      .-.
T Consensus        95 gTv   97 (117)
T 2l9w_A           95 GTI   97 (117)
T ss_dssp             ECH
T ss_pred             cCH
Confidence            643

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.46  E-value=1.3e-06  Score=64.60  Aligned_cols=71  Identities=17%  Similarity=0.173  Sum_probs=61.2

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhc-----cCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEE
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQ-----YGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTAC  203 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~-----~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v  203 (453)
                      ..++|.|.|||..+.++.|.-+|+.     =|+|..|....        +-|+|+|.+...|++.|+.-.+.|.+..|.|
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k~~H~L~~~~LsV   78 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQADHELHGAQLSL   78 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTCSCCBSSSSBCEE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcCCcceecCeEEEE
Confidence            4579999999999999999999987     25888887654        2599999999999999999888999999999


Q ss_pred             Eecc
Q 012923          204 QLAS  207 (453)
Q Consensus       204 ~~~~  207 (453)
                      ....
T Consensus        79 ~P~~   82 (104)
T 2dhx_A           79 RPAP   82 (104)
T ss_dssp             EECC
T ss_pred             EcCC
Confidence            7754

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.09  E-value=1.7e-05  Score=59.02  Aligned_cols=72  Identities=14%  Similarity=0.122  Sum_probs=63.8

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhcc-----CCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeE
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQY-----GEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTA  202 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~-----G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~  202 (453)
                      ..++|-|-|||-.++..-|+.|++++     |.|+.|.+..|-      +=|+|+|.+...|-+|.-.++ ..|.||+|+
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~Lr   93 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVIR   93 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEEE
Confidence            46899999999999999999999999     999999888875      249999999999999987777 459999999


Q ss_pred             EEec
Q 012923          203 CQLA  206 (453)
Q Consensus       203 v~~~  206 (453)
                      |...
T Consensus        94 ~gTv   97 (117)
T 2l9w_A           94 SGTI   97 (117)
T ss_dssp             EECH
T ss_pred             ecCH
Confidence            9754

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.01  E-value=6.5e-05  Score=55.52  Aligned_cols=74  Identities=12%  Similarity=0.120  Sum_probs=63.0

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhcc-----CCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEE
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKY-----GEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNC  320 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~-----G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v  320 (453)
                      ..++|.|.|||..+.++.|.-+|+.-     |.|..|....        +-|+|+|.+...|.+.|+.-.+.|.+..|.|
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k~~H~L~~~~LsV   78 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQADHELHGAQLSL   78 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTCSCCBSSSSBCEE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcCCcceecCeEEEE
Confidence            45699999999999999999999872     6788887754        3589999999999999999888899999999


Q ss_pred             EEccCCC
Q 012923          321 QRAIDGP  327 (453)
Q Consensus       321 ~~a~~~~  327 (453)
                      .....+.
T Consensus        79 ~P~~~~~   85 (104)
T 2dhx_A           79 RPAPPRA   85 (104)
T ss_dssp             EECCCCC
T ss_pred             EcCCCCC
Confidence            8765443

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.68  E-value=0.00011  Score=54.61  Aligned_cols=72  Identities=14%  Similarity=0.078  Sum_probs=61.0

Q ss_pred             ccEEEEecCCCCc-c----HHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEE
Q 012923          247 QRKIFVSNVGSEL-E----PQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNC  320 (453)
Q Consensus       247 ~~~l~V~nLp~~~-t----~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v  320 (453)
                      .++|+|.||+..+ +    .+.++.+|..|+.+.....++.-     + -..|.|.+.++|.+|...|+ ..|.|+.|+|
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF-----R-Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF-----K-RVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT-----T-EEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc-----e-EEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            3589999998765 2    36778999999999988877642     2 47899999999999999999 8899999999


Q ss_pred             EEcc
Q 012923          321 QRAI  324 (453)
Q Consensus       321 ~~a~  324 (453)
                      -++.
T Consensus        79 YFgq   82 (104)
T 1wey_A           79 YFAQ   82 (104)
T ss_dssp             ECCC
T ss_pred             EecC
Confidence            9986

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.54  E-value=0.00017  Score=52.62  Aligned_cols=53  Identities=15%  Similarity=0.253  Sum_probs=44.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcC
Q 012923          132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP  192 (453)
Q Consensus       132 ~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~  192 (453)
                      .||+-++|.++...||..+|+.||-| .|+-+.|.       .|||.|.+++.|..||..+
T Consensus        17 HVf~l~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           17 HVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             SEEEEECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHH
T ss_pred             eEEEEeCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhc
Confidence            34444999999999999999999965 55556664       6999999999999999976

>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=97.32  E-value=0.0015  Score=50.06  Aligned_cols=73  Identities=18%  Similarity=0.246  Sum_probs=58.9

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCC-eEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEG-HILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g-~~l~v~~a  323 (453)
                      ...+.|.|-++|... ...|...|++||.|++.....      ...+-.|.|.+..+|.+||......|++ -.|-|.+.
T Consensus        22 ~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~------~~NWihI~Y~s~~~A~rAL~kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           22 LDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEEC
T ss_pred             CCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC------CCCeEEEEeCCHHHHHHHHHhCCeEecCCEEEEEEEC
Confidence            345689999999886 556777899999999887621      2568999999999999999997777774 77888776


Q ss_pred             c
Q 012923          324 I  324 (453)
Q Consensus       324 ~  324 (453)
                      .
T Consensus        95 ~   95 (119)
T 1wwh_A           95 I   95 (119)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.24  E-value=0.00082  Score=48.98  Aligned_cols=53  Identities=17%  Similarity=0.241  Sum_probs=45.7

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcC
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP  309 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~  309 (453)
                      +.++| ++|..+...+|.++|+.||.| .|+.+-|.       -|||.|.+++.|..|+..+
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhc
Confidence            46666 999999999999999999955 67777663       5999999999999999976

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.23  E-value=0.00095  Score=48.77  Aligned_cols=63  Identities=8%  Similarity=-0.000  Sum_probs=52.4

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCC--CceEEEEEECCHHHHHHHHHcCC
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGK--PKGFCLFVYKTVDAAKKALEEPH  310 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~--~kg~afV~F~~~~~A~~Al~~~~  310 (453)
                      ++|.|++||+.+|++++.+.+..+..+.....+..+.+.+  .-..|||.|.+.+++..-...++
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~   66 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFD   66 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHT
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhC
Confidence            4899999999999999999999998887777766554333  24569999999999998888877

>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=97.17  E-value=0.00044  Score=50.60  Aligned_cols=53  Identities=17%  Similarity=0.287  Sum_probs=44.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC
Q 012923          132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ  193 (453)
Q Consensus       132 ~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~  193 (453)
                      .++| ++|.++...||..+|+.||-| .|+-+.|.       .|||.|.+++.|..||..+.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            4555 999999999999999999954 56666664       69999999999999999753

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.11  E-value=0.0016  Score=47.53  Aligned_cols=65  Identities=14%  Similarity=0.059  Sum_probs=52.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCC--cceEEEEEEccHHHHHHHHHcCCCc
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGK--SKGYGFILFKTRSGARKALKEPQKK  195 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~--~~G~afV~f~~~~~a~~A~~~~~~~  195 (453)
                      ++|.|++||+.+|++++.+.+..+..+.....+..+.+.+  .-.-|||.|.+.+++....+.+++.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~   68 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGY   68 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCc
Confidence            5799999999999999999999998877666655443322  2246999999999999999988754

>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=96.97  E-value=0.0055  Score=46.86  Aligned_cols=72  Identities=22%  Similarity=0.298  Sum_probs=57.8

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCC-eEeEEEecc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGN-RMTACQLAS  207 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~g-r~~~v~~~~  207 (453)
                      ..+-|.|-+.|... ...|...|++||.|.+....    +  ...+-.|.|.+..+|++||..+...|.+ -.|-|.+..
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----N--TGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCI   95 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC----S--SSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC----C--CCCeEEEEeCCHHHHHHHHHhCCeEecCCEEEEEEECC
Confidence            35789999999996 66788899999999988752    1  2348999999999999999998777764 566676653

>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=96.83  E-value=0.00092  Score=48.89  Aligned_cols=52  Identities=19%  Similarity=0.253  Sum_probs=44.7

Q ss_pred             EEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcC
Q 012923          249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP  309 (453)
Q Consensus       249 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~  309 (453)
                      .++| ++|..+...+|.++|+.||.| .|+.+-|.       -|||.|.+++.|..|+..+
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i   59 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVKIAVNTS   59 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEETT-------EEEEEEEEECHHHHHHHHH
T ss_pred             EEEE-eCChhhhhHHHHHHHhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhc
Confidence            5666 999999999999999999944 67777663       5999999999999999965

>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=96.75  E-value=0.0098  Score=44.15  Aligned_cols=72  Identities=13%  Similarity=0.004  Sum_probs=59.8

Q ss_pred             cCeEEEcCCCCCC-C----HHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCCeEeEE
Q 012923          130 HRKIFVHGLGWDT-K----AETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGNRMTAC  203 (453)
Q Consensus       130 ~~~lfV~nLp~~~-t----e~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~~~v  203 (453)
                      ..+|+|.||+.++ +    ...|+.+|..|+++.....++.-      .=..|.|.+.++|.+|-..+++. +.|+.++|
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            3689999999766 3    25778999999998887766543      13799999999999999999965 99999999


Q ss_pred             Eecc
Q 012923          204 QLAS  207 (453)
Q Consensus       204 ~~~~  207 (453)
                      .++.
T Consensus        79 YFgq   82 (104)
T 1wey_A           79 YFAQ   82 (104)
T ss_dssp             ECCC
T ss_pred             EecC
Confidence            9986

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.60  E-value=0.0084  Score=46.51  Aligned_cols=76  Identities=21%  Similarity=0.257  Sum_probs=56.3

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcce-eeeeccCC--------CC-----CCceEEEEEECCHHHHHHHHHcCCCcc
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEE-GPLGIDKA--------TG-----KPKGFCLFVYKTVDAAKKALEEPHKNF  313 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~-v~i~~d~~--------~g-----~~kg~afV~F~~~~~A~~Al~~~~~~l  313 (453)
                      ..|.|-+.|...+.. |.+.|++||.|.. +.+.+...        ..     ....+..|+|.+..+|.+||......|
T Consensus         8 ~~VtVFGFp~~~~~~-VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG~ii   86 (132)
T 3p3d_A            8 LAILVFGYPETMANQ-VIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGAVF   86 (132)
T ss_dssp             CEEEEECCCGGGHHH-HHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTTCEE
T ss_pred             eEEEEEecCHHHHHH-HHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCCeEe
Confidence            478888997766655 5668999999987 32221100        00     125678999999999999999988889


Q ss_pred             CCeEEEEEEcc
Q 012923          314 EGHILNCQRAI  324 (453)
Q Consensus       314 ~g~~l~v~~a~  324 (453)
                      +|..|-|.+..
T Consensus        87 ~G~mIGV~Py~   97 (132)
T 3p3d_A           87 NGVLLGVIPYT   97 (132)
T ss_dssp             TTEECEEEECC
T ss_pred             CcEEEEEEECC
Confidence            99988888874

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.54  E-value=0.005  Score=45.17  Aligned_cols=64  Identities=6%  Similarity=-0.021  Sum_probs=47.9

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCC--ceEEEEEECCHHHHHHHHHcCC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKP--KGFCLFVYKTVDAAKKALEEPH  310 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~--kg~afV~F~~~~~A~~Al~~~~  310 (453)
                      ..+|.||.||+.+|++++.+.++.+-.+.....+....+-+.  -..|||.|.+.++...-....+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~   74 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFD   74 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHST
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcC
Confidence            358999999999999999888887655554444433322221  3459999999999999998877

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.21  E-value=0.0088  Score=46.40  Aligned_cols=76  Identities=18%  Similarity=0.190  Sum_probs=56.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCC---------CC-----CcceEEEEEEccHHHHHHHHHcCCCcc
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKV---------SG-----KSKGYGFILFKTRSGARKALKEPQKKI  196 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~---------~g-----~~~G~afV~f~~~~~a~~A~~~~~~~~  196 (453)
                      .-|.|-+.|.+.+. .|...|++||.|.+-.-..+..         ..     ....+..|+|.+..+|.+||......|
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            46888899777655 6678999999987732111100         00     124578999999999999999999999


Q ss_pred             CCeEeEEEecc
Q 012923          197 GNRMTACQLAS  207 (453)
Q Consensus       197 ~gr~~~v~~~~  207 (453)
                      .|..|-|.+..
T Consensus        87 ~G~mIGV~Py~   97 (132)
T 3p3d_A           87 NGVLLGVIPYT   97 (132)
T ss_dssp             TTEECEEEECC
T ss_pred             CcEEEEEEECC
Confidence            99988888774

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.13  E-value=0.0067  Score=44.50  Aligned_cols=66  Identities=9%  Similarity=0.009  Sum_probs=47.0

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCC--cceEEEEEEccHHHHHHHHHcCCCc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGK--SKGYGFILFKTRSGARKALKEPQKK  195 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~--~~G~afV~f~~~~~a~~A~~~~~~~  195 (453)
                      +-+|.|+.||+.+|++++.+.+..+-.+.....+..+.+-+  .-.-|||.|.+.+++....+..++.
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~   76 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGY   76 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCc
Confidence            45799999999999999888887765543332222222111  1134999999999999999988854

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.92  E-value=0.0035  Score=60.46  Aligned_cols=56  Identities=13%  Similarity=0.188  Sum_probs=43.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcC
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP  192 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~  192 (453)
                      |+|||. .|..+++.+|.++|++||.|..+....+.     .-||.|+|.+.+++..++...
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~~~  109 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQNGT  109 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHSSC
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHhcc
Confidence            799998 89999999999999999999999776543     259999999999999888664

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.68  E-value=0.0067  Score=58.49  Aligned_cols=57  Identities=12%  Similarity=0.250  Sum_probs=44.1

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP  309 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~  309 (453)
                      .++|||. .|..+++.+|.++|++||.|.++.+..+.     .-||.|+|.+.+++..++...
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~~~  109 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQNGT  109 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHSSC
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHhcc
Confidence            3689997 79999999999999999999999887653     469999999999999887664

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=86.84  E-value=1.2  Score=43.78  Aligned_cols=55  Identities=16%  Similarity=0.241  Sum_probs=45.4

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH  310 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~  310 (453)
                      ...++|+ +|..|...+|.++|+.||.| +|+++-+       ..|||.|.+.+.|..++..++
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd-------t~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD-------TSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS-------SEEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC-------CeEEEEECCHHHHHHHHHHHH
Confidence            4567776 99999999999999999954 6666544       369999999999999999875

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=86.83  E-value=1.2  Score=43.87  Aligned_cols=54  Identities=17%  Similarity=0.283  Sum_probs=44.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ  193 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~  193 (453)
                      ..++|+ +|..+...+|.++|+.||.| +|+.+.+.       .|||.|.+.+.|..++..++
T Consensus       441 ~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widdt-------~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          441 HVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSSS-------EEEEECSCHHHHHHHHHHHT
T ss_pred             cEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcCC-------eEEEEECCHHHHHHHHHHHH
Confidence            355555 99999999999999999965 66656553       69999999999999998775

---

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	453
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-25
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-09
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-08
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	7e-16
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-12
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-14
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-12
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	8e-14
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-11
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-13
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-12
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	6e-13
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-12
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-12
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-10
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	3e-12
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-10
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	5e-12
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	4e-10
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	8e-12
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-11
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-11
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-10
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-11
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	8e-10
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-11
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-08
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	3e-11
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	9e-10
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-11
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-08
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-11
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-10
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	8e-11
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-09
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-10
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-09
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-10
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-09
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-10
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-07
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-10
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-08
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	5e-10
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-09
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	7e-10
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	8e-10
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	9e-10
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-08
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-09
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	4e-05
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-09
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-08
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-09
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-07
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	6e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-08
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	8e-09
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-08
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	3e-05
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-08
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	4e-07
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	9e-06
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-08
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	9e-07
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	5e-08
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	4e-08
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-07
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	2e-05
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	4e-08
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	5e-07
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-08
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-06
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	5e-08
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-06
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	7e-08
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-06
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-07
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	9e-06
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	2e-07
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	2e-06
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-07
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	6e-07
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-07
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	4e-07
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	2e-07
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-07
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-06
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	3e-07
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-06
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-07
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	7e-07
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	8e-07
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	8e-07
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	9e-07
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-06
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-06
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-06
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-06
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-06
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-06
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-06
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-06
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-05
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	4e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	3e-05
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-06
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	6e-06
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	2e-05
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	8e-06
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-05
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:) 1e-05
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:) 1e-04
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	6e-05
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	6e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	1e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-04
d2ayua1	301	d.305.1.1 (A:70-370) Nucleosome assembly protein,	1e-04
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	2e-04
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	0.002
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-04
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	0.004
d1qkla_	127	a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId:	2e-04
d1sdma_	364	c.37.1.9 (A:) Kinesin heavy chain-like protein {Po	0.001
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	0.002
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	0.003
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	0.004
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	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 =  101 bits (251), Expect = 1e-25
 Identities = 45/205 (21%), Positives = 85/205 (41%), Gaps = 29/205 (14%)

Query: 126 EDPVH-RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSG 184
           ++P   RK+F+ GL ++T  E+L   F+Q+G + DC  + D  + +S+G+GF+ + T   
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 185 ARKALKEPQKKIGNRMTACQLASIGPATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSE 244
              A+     K                             +     +   +       + 
Sbjct: 61  VDAAMNARPHK--------------------------VDGRVVEPKRAVSREDSQRPGAH 94

Query: 245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKK 304
            T +KIFV  +  + E   L  +F +YG+IE   +  D+ +GK +GF    +   D+  K
Sbjct: 95  LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 154

Query: 305 ALEEPHKNFEGHILNCQRAIDGPKP 329
            + + +    GH    ++A+   K 
Sbjct: 155 IVIQKYHTVNGHNCEVRKAL--SKQ 177

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.9 bits (128), Expect = 4e-09
 Identities = 28/96 (29%), Positives = 44/96 (45%)

Query: 111 ENHRDVASRVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGK 170
           E  R V+    Q        +KIFV G+  DT+   L D F+QYG+IE  + + D+ SGK
Sbjct: 78  EPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK 137

Query: 171 SKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLA 206
            +G+ F+ F       K + +    +       + A
Sbjct: 138 KRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA 173

>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 = 50.8 bits (120), Expect = 4e-08
 Identities = 19/92 (20%), Positives = 39/92 (42%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           RK+F+  +  E   + L + F ++G + +  +  D  T + +GF    Y TV+    A+ 
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66

Query: 308 EPHKNFEGHILNCQRAIDGPKPGKSRHHNAQN 339
                 +G ++  +RA+      +   H    
Sbjct: 67  ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVK 98

>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 = 70.0 bits (171), Expect = 7e-16
 Identities = 23/75 (30%), Positives = 47/75 (62%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K+F+ GL W T  E L + F Q+GE+++C  + D ++ +S+G+GF+ F  ++G  K L +
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 192 PQKKIGNRMTACQLA 206
            + ++ ++    ++A
Sbjct: 62  SRHELDSKTIDPKVA 76

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.4 bits (146), Expect = 2e-12
 Identities = 14/75 (18%), Positives = 33/75 (44%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           K+F+  +  +   + L  +F ++GE++E  +  D  T + +GF    +       K L +
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 309 PHKNFEGHILNCQRA 323
                +   ++ + A
Sbjct: 62  SRHELDSKTIDPKVA 76

>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 = 66.5 bits (162), Expect = 1e-14
 Identities = 23/75 (30%), Positives = 38/75 (50%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           KIFV GL  DT  E + + F  +GE+E  +   D  + K +G+ FI FK     +K +++
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 192 PQKKIGNRMTACQLA 206
               +G      ++A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.0 bits (145), Expect = 3e-12
 Identities = 22/75 (29%), Positives = 37/75 (49%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           KIFV  +  +   +K+  +F  +GE+E   L +D  T K +GFC   +K  +  KK +E+
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 309 PHKNFEGHILNCQRA 323
            + N        + A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>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 = 64.3 bits (156), Expect = 8e-14
 Identities = 24/82 (29%), Positives = 45/82 (54%), Gaps = 1/82 (1%)

Query: 126 EDPVH-RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSG 184
           ++P   RK+F+ GL ++T  E+L   F+Q+G + DC  + D  + +S+G+GF+ + T   
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 185 ARKALKEPQKKIGNRMTACQLA 206
              A+     K+  R+   + A
Sbjct: 61  VDAAMNARPHKVDGRVVEPKRA 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 = 57.4 bits (138), Expect = 2e-11
 Identities = 18/77 (23%), Positives = 37/77 (48%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           RK+F+  +  E   + L + F ++G + +  +  D  T + +GF    Y TV+    A+ 
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66

Query: 308 EPHKNFEGHILNCQRAI 324
                 +G ++  +RA+
Sbjct: 67  ARPHKVDGRVVEPKRAV 83

>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 = 63.1 bits (153), Expect = 2e-13
 Identities = 26/75 (34%), Positives = 45/75 (60%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K+F+ GL WDT  + L D F ++GE+ DC    D ++G+S+G+GF+LFK      K + +
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 192 PQKKIGNRMTACQLA 206
            + 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 = 59.2 bits (143), Expect = 5e-12
 Identities = 19/75 (25%), Positives = 42/75 (56%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           K+F+  +  +   + L  +FSK+GE+ +  L +D  TG+ +GF   ++K  ++  K +++
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 309 PHKNFEGHILNCQRA 323
                 G +++ +RA
Sbjct: 61  KEHKLNGKVIDPKRA 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 = 62.8 bits (152), Expect = 6e-13
 Identities = 28/95 (29%), Positives = 44/95 (46%)

Query: 239 HHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKT 298
           H  Q + T  KIFV  +        L  +F  +G+IEE  +  D+ TGK +G+       
Sbjct: 2   HGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMAD 61

Query: 299 VDAAKKALEEPHKNFEGHILNCQRAIDGPKPGKSR 333
             AA++A ++P+   +G   N   A  G KP   +
Sbjct: 62  RAAAERACKDPNPIIDGRKANVNLAYLGAKPRSLQ 96

>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 = 61.7 bits (149), Expect = 1e-12
 Identities = 31/89 (34%), Positives = 48/89 (53%)

Query: 122 QVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKT 181
             + +D    KIFV GL + T   +L   F+ +G+IE+   + D+ +GKS+GYGF+    
Sbjct: 2   HGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMAD 61

Query: 182 RSGARKALKEPQKKIGNRMTACQLASIGP 210
           R+ A +A K+P   I  R     LA +G 
Sbjct: 62  RAAAERACKDPNPIIDGRKANVNLAYLGA 90

>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 = 61.5 bits (149), Expect = 1e-12
 Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
             + V GL W T  + L + F  +GE+   +   D  +G SKG+GF+ F       K + 
Sbjct: 9   SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 68

Query: 191 EPQKKIGNRMTACQLA 206
           +    I  R   C+L 
Sbjct: 69  QRH-MIDGRWCDCKLP 83

>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 = 54.6 bits (131), Expect = 3e-10
 Identities = 18/86 (20%), Positives = 34/86 (39%), Gaps = 5/86 (5%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
             + V  +  +   Q L  +FS +GE+    +  D  TG  KGF    +   +   K + 
Sbjct: 9   SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 68

Query: 308 EPHKNFEGHILNCQRAIDGPKPGKSR 333
           + H   +G   +C+         +S+
Sbjct: 69  QRHM-IDGRWCDCKLP----NSKQSQ 89

>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 = 60.4 bits (146), Expect = 3e-12
 Identities = 19/91 (20%), Positives = 37/91 (40%)

Query: 116 VASRVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYG 175
           V   V  ++ E+   R +F   L    +   L D F   G++ D + + D+ S +SKG  
Sbjct: 4   VREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIA 63

Query: 176 FILFKTRSGARKALKEPQKKIGNRMTACQLA 206
           ++ F        A+    +++       Q +
Sbjct: 64  YVEFCEIQSVPLAIGLTGQRLLGVPIIVQAS 94

>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 = 55.0 bits (132), Expect = 2e-10
 Identities = 17/93 (18%), Positives = 38/93 (40%), Gaps = 4/93 (4%)

Query: 241 QQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVD 300
              E   R +F   + + + P+ L  FFS  G++ +  +  D+ + + KG     +  + 
Sbjct: 12  SPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQ 71

Query: 301 AAKKALEEPHKNFEGHILNCQRAIDGPKPGKSR 333
           +   A+    +   G  +  Q +    +  K+R
Sbjct: 72  SVPLAIGLTGQRLLGVPIIVQAS----QAEKNR 100

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.1 bits (145), Expect = 5e-12
 Identities = 24/81 (29%), Positives = 45/81 (55%)

Query: 126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGA 185
           E    RK+F+ GL ++T  E+L + ++Q+G++ DC  + D  S +S+G+GF+ F + +  
Sbjct: 16  EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEV 75

Query: 186 RKALKEPQKKIGNRMTACQLA 206
             A+      I  R+   + A
Sbjct: 76  DAAMAARPHSIDGRVVEPKRA 96

>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 = 54.7 bits (131), Expect = 4e-10
 Identities = 15/83 (18%), Positives = 41/83 (49%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           RK+F+  +  E   + L  ++ ++G++ +  +  D A+ + +GF    + ++     A+ 
Sbjct: 21  RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 80

Query: 308 EPHKNFEGHILNCQRAIDGPKPG 330
               + +G ++  +RA+   + G
Sbjct: 81  ARPHSIDGRVVEPKRAVAREESG 103

>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 = 58.6 bits (141), Expect = 8e-12
 Identities = 22/79 (27%), Positives = 40/79 (50%)

Query: 246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKA 305
           T +KIFV  +  + E   L  +F +YG+IE   +  D+ +GK +GF    +   D+  K 
Sbjct: 1   TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 60

Query: 306 LEEPHKNFEGHILNCQRAI 324
           + + +    GH    ++A+
Sbjct: 61  VIQKYHTVNGHNCEVRKAL 79

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.0 bits (137), Expect = 3e-11
 Identities = 24/76 (31%), Positives = 39/76 (51%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           +KIFV G+  DT+   L D F+QYG+IE  + + D+ SGK +G+ F+ F       K + 
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 62

Query: 191 EPQKKIGNRMTACQLA 206
           +    +       + A
Sbjct: 63  QKYHTVNGHNCEVRKA 78

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.8 bits (142), Expect = 1e-11
 Identities = 19/89 (21%), Positives = 36/89 (40%), Gaps = 4/89 (4%)

Query: 122 QVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCD-KVSGKSKGYGFILFK 180
           QV  +     KI V  + +      + + F  +GE++  +       +G  +G+GF+ F 
Sbjct: 1   QVPKKQT-TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFI 59

Query: 181 TRSGARKALKEPQ--KKIGNRMTACQLAS 207
           T+  A+KA         +  R    + A 
Sbjct: 60  TKQDAKKAFNALCHSTHLYGRRLVLEWAD 88

>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 = 4e-10
 Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 3/81 (3%)

Query: 246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGID-KATGKPKGFCLFVYKTVDAAKK 304
           T  KI V N+  +   +++   FS +GE++   L      TG  +GF    + T   AKK
Sbjct: 7   TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKK 66

Query: 305 ALEEPH--KNFEGHILNCQRA 323
           A        +  G  L  + A
Sbjct: 67  AFNALCHSTHLYGRRLVLEWA 87

>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 = 58.0 bits (140), Expect = 1e-11
 Identities = 16/76 (21%), Positives = 30/76 (39%), Gaps = 1/76 (1%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
            ++V  L  D     L + F   G I   +   D ++ +S GY ++ F+  + A +AL  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 192 PQ-KKIGNRMTACQLA 206
                I  +      +
Sbjct: 62  MNFDVIKGKPVRIMWS 77

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.0 bits (127), Expect = 8e-10
 Identities = 13/76 (17%), Positives = 30/76 (39%), Gaps = 1/76 (1%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
            ++V ++  ++    L   FS  G I    +  D  T +  G+    ++    A++AL+ 
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 309 -PHKNFEGHILNCQRA 323
                 +G  +    +
Sbjct: 62  MNFDVIKGKPVRIMWS 77

>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 = 57.4 bits (138), Expect = 2e-11
 Identities = 23/70 (32%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
             ++V GL      + L   F QYG I   + + D+V+G S+G GFI F  R  A +A+K
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 191 EPQ-KKIGNR 199
               +K    
Sbjct: 67  GLNGQKPSGA 76

>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 = 48.9 bits (116), Expect = 3e-08
 Identities = 15/70 (21%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
             ++VS +   +  ++L   FS+YG I    + +D+ TG  +G     +     A++A++
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 308 EPH-KNFEGH 316
             + +   G 
Sbjct: 67  GLNGQKPSGA 76

>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 = 56.7 bits (136), Expect = 3e-11
 Identities = 24/75 (32%), Positives = 43/75 (57%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           KIFV GL  +T  E +   F+Q+G+++D   + DK + + +G+GF+ F++     K  + 
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 192 PQKKIGNRMTACQLA 206
              +I N+M  C+ A
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 = 52.8 bits (126), Expect = 9e-10
 Identities = 17/75 (22%), Positives = 37/75 (49%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           KIFV  +      + +  +F ++G++++  L  DK T + +GF    +++ D  +K  E 
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 309 PHKNFEGHILNCQRA 323
                   ++ C++A
Sbjct: 61  HFHEINNKMVECKKA 75

>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 = 56.9 bits (137), Expect = 4e-11
 Identities = 16/66 (24%), Positives = 30/66 (45%)

Query: 126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGA 185
           E      ++V  L      + L   F +YG I     + DK++G+ +G  F+ +  R  A
Sbjct: 2   ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 61

Query: 186 RKALKE 191
           ++A+  
Sbjct: 62  QEAISA 67

>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 = 49.2 bits (117), Expect = 2e-08
 Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 3/79 (3%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
             ++V+N+   +   +L   F KYG I +  +  DK TG+P+G     Y   + A++A+ 
Sbjct: 7   TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 66

Query: 308 EPH-KNFEG--HILNCQRA 323
             +    EG    L+ + A
Sbjct: 67  ALNNVIPEGGSQPLSVRLA 85

>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 = 57.1 bits (137), Expect = 4e-11
 Identities = 18/89 (20%), Positives = 37/89 (41%), Gaps = 6/89 (6%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEG-----PLGIDKATGKPKGFCLFVYKTVDAA 302
           R+++V N+   +  + ++ FF+    +           +     + K F    +++VD  
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 303 KKALEEPHKNFEGHILNCQRAID-GPKPG 330
            +A+      F+G  L  +R  D  P PG
Sbjct: 62  TQAMAFDGIIFQGQSLKIRRPHDYQPLPG 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 = 54.8 bits (131), Expect = 2e-10
 Identities = 10/74 (13%), Positives = 26/74 (35%), Gaps = 5/74 (6%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCK-----AVCDKVSGKSKGYGFILFKTRSGA 185
           R+++V  + +    E ++D F     +          V      + K + F+ F++    
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 186 RKALKEPQKKIGNR 199
            +A+         +
Sbjct: 62  TQAMAFDGIIFQGQ 75

>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 = 55.8 bits (134), Expect = 8e-11
 Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 1/81 (1%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
            K+F+ GL      + + +    +G ++    V D  +G SKGY F  +   +   +A+ 
Sbjct: 2   HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61

Query: 191 EPQ-KKIGNRMTACQLASIGP 210
                ++G++    Q AS+G 
Sbjct: 62  GLNGMQLGDKKLLVQRASVGA 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 = 51.9 bits (124), Expect = 2e-09
 Identities = 19/82 (23%), Positives = 35/82 (42%), Gaps = 1/82 (1%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
            K+F+  + + L   ++    + +G ++   L  D ATG  KG+    Y  ++   +A+ 
Sbjct: 2   HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61

Query: 308 EPH-KNFEGHILNCQRAIDGPK 328
             +        L  QRA  G K
Sbjct: 62  GLNGMQLGDKKLLVQRASVGAK 83

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.4 bits (133), Expect = 1e-10
 Identities = 20/89 (22%), Positives = 42/89 (47%), Gaps = 5/89 (5%)

Query: 246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKA 305
           T+R ++V  +  E++ + L A F  +G+I +  + +D  T K +GF    ++  + A  A
Sbjct: 4   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63

Query: 306 LEEPH-KNFEGHILNCQRAIDGPKPGKSR 333
           ++  +     G  +    A    KP + +
Sbjct: 64  IDNMNESELFGRTIRVNLA----KPMRIK 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 = 52.7 bits (126), Expect = 1e-09
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 1/77 (1%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           R ++V GL  +   + L  AF  +G+I D +   D  + K +G+ F+ F+    A  A+ 
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65

Query: 191 EPQ-KKIGNRMTACQLA 206
                ++  R     LA
Sbjct: 66  NMNESELFGRTIRVNLA 82

>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 = 55.3 bits (133), Expect = 2e-10
 Identities = 15/78 (19%), Positives = 37/78 (47%), Gaps = 1/78 (1%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
             ++V  L + T  E + + F + G+I+      DK+   + G+ F+ + +R+ A  A++
Sbjct: 8   CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

Query: 191 EPQ-KKIGNRMTACQLAS 207
                ++ +R+      +
Sbjct: 68  YINGTRLDDRIIRTDWDA 85

>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 = 52.3 bits (125), Expect = 2e-09
 Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 2/85 (2%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
             ++V N+      +++   FSK G+I++  +G+DK      GFC   Y +   A+ A+ 
Sbjct: 8   CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

Query: 308 EPH-KNFEGHILNCQRAIDGPKPGK 331
             +    +  I+       G K G+
Sbjct: 68  YINGTRLDDRIIRTDWD-AGFKEGR 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 = 54.9 bits (132), Expect = 3e-10
 Identities = 18/92 (19%), Positives = 34/92 (36%), Gaps = 10/92 (10%)

Query: 117 ASRVRQVADEDPVHRKIFVHGLGWD-TKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYG 175
           +S      D   ++ ++F+  L     K   +   F +YG+I  C            G+ 
Sbjct: 2   SSGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFA 53

Query: 176 FILFKTRSGARKALKEPQ-KKIGNRMTACQLA 206
           F+ +     AR A+     + I  ++    LA
Sbjct: 54  FVQYVNERNARAAVAGEDGRMIAGQVLDINLA 85

>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 = 47.2 bits (112), Expect = 2e-07
 Identities = 21/87 (24%), Positives = 37/87 (42%), Gaps = 11/87 (12%)

Query: 248 RKIFVSNVGSEL-EPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKAL 306
            ++F+ N+ + + +   + A FSKYG+I              KGF    Y     A+ A+
Sbjct: 16  SRVFIGNLNTLVVKKSDVEAIFSKYGKIVG--------CSVHKGFAFVQYVNERNARAAV 67

Query: 307 EEPH-KNFEGHILNCQRAIDGPKPGKS 332
                +   G +L+   A + PK  +S
Sbjct: 68  AGEDGRMIAGQVLDINLAAE-PKVNRS 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 = 54.6 bits (131), Expect = 3e-10
 Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 1/85 (1%)

Query: 124 ADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRS 183
             E      ++V GL        L + F Q G + +     D+V+G+ +GYGF+ F +  
Sbjct: 3   ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE 62

Query: 184 GARKALKEPQ-KKIGNRMTACQLAS 207
            A  A+K     K+  +      AS
Sbjct: 63  DADYAIKIMDMIKLYGKPIRVNKAS 87

>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 = 49.6 bits (118), Expect = 2e-08
 Identities = 12/77 (15%), Positives = 31/77 (40%), Gaps = 1/77 (1%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
             ++V  +  ++    L   F + G +    +  D+ TG+ +G+    + + + A  A++
Sbjct: 10  ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 69

Query: 308 EPH-KNFEGHILNCQRA 323
                   G  +   +A
Sbjct: 70  IMDMIKLYGKPIRVNKA 86

>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 = 53.9 bits (129), Expect = 5e-10
 Identities = 22/84 (26%), Positives = 35/84 (41%), Gaps = 4/84 (4%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDK---ATGKPKGFCLFVYKTVDAAKKAL 306
           +F+ N+      + L   FSK G I+   +   K         GF    YK  + A+KAL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 307 EEPH-KNFEGHILNCQRAIDGPKP 329
           ++      +GH L  + +    KP
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 = 51.6 bits (123), Expect = 3e-09
 Identities = 26/87 (29%), Positives = 40/87 (45%), Gaps = 6/87 (6%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDK---VSGKSKGYGFILFKTRSGARKAL 189
           +F+  L + T  ETL   F + G I+ C     K       S G+GF+ +K    A+KAL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 190 KEPQ-KKIGNRMTACQLASIGPATTPA 215
           K+ Q   +       +++    AT PA
Sbjct: 61  KQLQGHTVDGHKLEVRISE--RATKPA 85

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 53.1 bits (127), Expect = 7e-10
 Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 1/79 (1%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
            + V+ L  D     L   F+  G I  C+ + D  +G S GY F+ F +   +++A+K 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 192 PQ-KKIGNRMTACQLASIG 209
                + N+      A  G
Sbjct: 64  LNGITVRNKRLKVSYARPG 82

>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 = 53.1 bits (127), Expect = 8e-10
 Identities = 15/83 (18%), Positives = 33/83 (39%), Gaps = 5/83 (6%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
            + V+ +  ++  ++L A F   G I    +  D  TG   G+    + +   +++A++ 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 309 PH-KNFEGHILNCQRAIDGPKPG 330
            +        L    A    +PG
Sbjct: 64  LNGITVRNKRLKVSYA----RPG 82

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.0 bits (127), Expect = 9e-10
 Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 2/77 (2%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K+ V  L +      + + F ++G ++    V    SG+S G   + F+ ++ A KA+K+
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAA-VHYDRSGRSLGTADVHFERKADALKAMKQ 60

Query: 192 PQ-KKIGNRMTACQLAS 207
                +  R    QL +
Sbjct: 61  YNGVPLDGRPMNIQLVT 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 = 48.8 bits (116), Expect = 2e-08
 Identities = 14/76 (18%), Positives = 35/76 (46%), Gaps = 2/76 (2%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           K+ VSN+   +    +   F+++G +++  +     +G+  G     ++    A KA+++
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAV-HYDRSGRSLGTADVHFERKADALKAMKQ 60

Query: 309 PH-KNFEGHILNCQRA 323
            +    +G  +N Q  
Sbjct: 61  YNGVPLDGRPMNIQLV 76

>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 = 52.8 bits (126), Expect = 1e-09
 Identities = 17/84 (20%), Positives = 31/84 (36%), Gaps = 1/84 (1%)

Query: 124 ADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRS 183
           +   P    I V  + +    + ++D F  Y  I     +     G   G   + F++R 
Sbjct: 3   SSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRD 62

Query: 184 GARKALKEPQ-KKIGNRMTACQLA 206
            A  A+ +   + IG+R     L 
Sbjct: 63  EATAAVIDLNDRPIGSRKVKLVLG 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 = 40.0 bits (93), Expect = 4e-05
 Identities = 14/77 (18%), Positives = 27/77 (35%), Gaps = 1/77 (1%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
             I V N+   +   ++L FF  Y  I           G P G  +  +++ D A  A+ 
Sbjct: 10  TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 69

Query: 308 EPH-KNFEGHILNCQRA 323
           + + +      +     
Sbjct: 70  DLNDRPIGSRKVKLVLG 86

>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 = 52.0 bits (124), Expect = 2e-09
 Identities = 19/91 (20%), Positives = 39/91 (42%), Gaps = 5/91 (5%)

Query: 240 HQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTV 299
           + +S+ T +++ VSN+        L   F ++G+I +  +  ++     KGF    ++  
Sbjct: 4   NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENS 61

Query: 300 DAAKKALEEPH-KNFEGHILNCQRAIDGPKP 329
             A +A E+ H    EG  +    A    + 
Sbjct: 62  ADADRAREKLHGTVVEGRKIEVNNAT--ARV 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 = 48.9 bits (116), Expect = 3e-08
 Identities = 17/84 (20%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 124 ADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRS 183
           ++     +++ V  + +  +   L   F Q+G+I D + + ++    SKG+GF+ F+  +
Sbjct: 5   SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSA 62

Query: 184 GARKALKEPQ-KKIGNRMTACQLA 206
            A +A ++     +  R      A
Sbjct: 63  DADRAREKLHGTVVEGRKIEVNNA 86

>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 = 51.6 bits (123), Expect = 3e-09
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 1/77 (1%)

Query: 125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSG 184
                +  + V GL   T    L + F +YG I D   V D+ S +S+G+ F+ F+    
Sbjct: 4   ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 63

Query: 185 ARKALKEPQ-KKIGNRM 200
           A++A +     ++  R 
Sbjct: 64  AKEAKERANGMELDGRR 80

>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 = 47.0 bits (111), Expect = 1e-07
 Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
             + V  +      + L   FSKYG I +  +  D+ + + +GF    ++ VD AK+A E
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 308 EPH-KNFEGHILN 319
             +    +G  + 
Sbjct: 70  RANGMELDGRRIR 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 = 50.9 bits (121), Expect = 6e-09
 Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVC-DKVSGKSKGYGFILFKTRSGARKALKE 191
           IF+  L  +   + L D F  +G I     +  D  +G SKGY FI F +   +  A++ 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 192 PQ-KKIGNRMTACQLA 206
              + + NR      A
Sbjct: 61  MNGQYLCNRPITVSYA 76

>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 = 49.0 bits (116), Expect = 2e-08
 Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 4/84 (4%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGP-LGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           IF+ N+  E++ + L   FS +G I + P +  D  TG  KG+    + + DA+  A+E 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 309 PH-KNFEGHILNCQRAIDGPKPGK 331
            + +      +    A    K  K
Sbjct: 61  MNGQYLCNRPITVSYAF--KKDSK 82

>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 = 51.0 bits (121), Expect = 8e-09
 Identities = 13/84 (15%), Positives = 30/84 (35%)

Query: 124 ADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRS 183
            D +       +  + +      ++   +     E+   V    +G+  G   + FK   
Sbjct: 2   GDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNED 61

Query: 184 GARKALKEPQKKIGNRMTACQLAS 207
            ARK+ +  +KK+  R     + +
Sbjct: 62  DARKSERLHRKKLNGREAFVHVVT 85

>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 = 43.7 bits (102), Expect = 2e-06
 Identities = 17/102 (16%), Positives = 30/102 (29%), Gaps = 5/102 (4%)

Query: 246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKA 305
            +    ++N+   +    +L F       E     +    G+  G  L  +K  D A+K+
Sbjct: 7   AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKS 66

Query: 306 LEEPHKNFEGHILNCQRAIDGPKPGKSRHHNAQNPHFQRNEG 347
                K   G               +      +NP  Q   G
Sbjct: 67  ERLHRKKLNGREAFVHVVTL-----EDMREIEKNPPAQGKSG 103

>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 = 51.1 bits (121), Expect = 2e-08
 Identities = 28/132 (21%), Positives = 52/132 (39%), Gaps = 2/132 (1%)

Query: 210 PATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFS 269
           P  +       T Q Q   Q Q QH             R + V+ + + ++  +L   F 
Sbjct: 5   PLVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFE 64

Query: 270 KYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDG-P 327
           +YG IE   +  D+ T + +G+    +++  +A++A+   +  N     L    A  G  
Sbjct: 65  RYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQ 124

Query: 328 KPGKSRHHNAQN 339
           +PG +      N
Sbjct: 125 RPGIAGAVGDGN 136

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 41.4 bits (96), Expect = 3e-05
 Identities = 33/120 (27%), Positives = 60/120 (50%), Gaps = 5/120 (4%)

Query: 89  PILSLLEPFSKDQLVNLLREAAENHRDVASRVRQVADEDPVHRKIFVHGLGWDTKAETLI 148
           P++S  +P+ +   +  L++  + H        Q+  E  V R + V+ +        L 
Sbjct: 5   PLVSQYDPYGQTAQLQQLQQQQQQHIPPT----QMNPEPDVLRNLMVNYIPTTVDEVQLR 60

Query: 149 DAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLAS 207
             F++YG IE  K VCD+ + +S+GYGF+ F++ S A++A+       I N+     LA+
Sbjct: 61  QLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA 120

>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 = 49.4 bits (117), Expect = 2e-08
 Identities = 17/84 (20%), Positives = 32/84 (38%), Gaps = 4/84 (4%)

Query: 248 RKIFVSNVGSELEPQKLL--AFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKA 305
           R+I + N+ +EL  + LL  +F       +       K           V++  D+A++A
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 306 LEEPHKNFEGHILNCQRAIDGPKP 329
           L+          ++   A    KP
Sbjct: 65  LQMNRSLLGNREISVSLAD--KKP 86

>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 = 45.5 bits (107), Expect = 4e-07
 Identities = 16/79 (20%), Positives = 31/79 (39%), Gaps = 2/79 (2%)

Query: 130 HRKIFVHGLGWDTKAETLIDAF--KQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARK 187
            R+I +  L  +   E L+           +       K    +    F++F+ +  A +
Sbjct: 4   GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 188 ALKEPQKKIGNRMTACQLA 206
           AL+  +  +GNR  +  LA
Sbjct: 64  ALQMNRSLLGNREISVSLA 82

>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 = 49.7 bits (118), Expect = 2e-08
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 1/82 (1%)

Query: 126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGA 185
           E P    +F++ L  +   + L+  F  +G +   K   DK +  SK +GF+ +     A
Sbjct: 14  EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSA 73

Query: 186 RKALKEPQ-KKIGNRMTACQLA 206
           + A++     +IG +    QL 
Sbjct: 74  QAAIQSMNGFQIGMKRLKVQLK 95

>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 = 42.4 bits (99), Expect = 9e-06
 Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 1/77 (1%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
             +F+ ++  E   Q LL  F  +G +    + IDK T   K F    Y    +A+ A++
Sbjct: 19  ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 78

Query: 308 EPH-KNFEGHILNCQRA 323
             +        L  Q  
Sbjct: 79  SMNGFQIGMKRLKVQLK 95

>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 = 3e-08
 Identities = 15/80 (18%), Positives = 33/80 (41%), Gaps = 4/80 (5%)

Query: 128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARK 187
            V+R +++  L +   AE + D F +YG I          + +++G  +++++    A+ 
Sbjct: 5   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIFDAKN 61

Query: 188 ALKEPQ-KKIGNRMTACQLA 206
           A        + NR       
Sbjct: 62  ACDHLSGFNVCNRYLVVLYY 81

>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 = 45.4 bits (107), Expect = 9e-07
 Identities = 17/92 (18%), Positives = 33/92 (35%), Gaps = 4/92 (4%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           R +++ N+  ++  +++   F KYG I +        T + +G    VY+ +  AK A +
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQIR---VGNTPETRGTAYVVYEDIFDAKNACD 64

Query: 308 EPH-KNFEGHILNCQRAIDGPKPGKSRHHNAQ 338
                N     L            K      +
Sbjct: 65  HLSGFNVCNRYLVVLYYNANRAFQKMDTKKKE 96

>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 = 48.2 bits (114), Expect = 4e-08
 Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 1/77 (1%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
             + V+ L  +   E     F   GEIE CK V DK++G+S GYGF+ +     A KA+ 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 191 EPQ-KKIGNRMTACQLA 206
                ++  +      A
Sbjct: 63  TLNGLRLQTKTIKVSYA 79

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 5e-08
 Identities = 17/79 (21%), Positives = 33/79 (41%), Gaps = 1/79 (1%)

Query: 246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKA 305
           ++  + V+ +   +  ++  + F   GEIE   L  DK TG+  G+    Y     A+KA
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 306 LEEPH-KNFEGHILNCQRA 323
           +   +    +   +    A
Sbjct: 61  INTLNGLRLQTKTIKVSYA 79

>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 = 48.5 bits (115), Expect = 4e-08
 Identities = 21/77 (27%), Positives = 33/77 (42%), Gaps = 1/77 (1%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
             I V+N+  +     L   F  +G I    L  DK TG+ KGF    +   + A +A+ 
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

Query: 308 EPH-KNFEGHILNCQRA 323
                 ++  ILN + A
Sbjct: 69  GVSGFGYDHLILNVEWA 85

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

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

 Score = 46.2 bits (109), Expect = 3e-07
 Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 1/77 (1%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
             I V  L  DT+   L + F+ +G I       DK +G+SKG+ FI F  R  A +A+ 
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

Query: 191 EPQ-KKIGNRMTACQLA 206
                   + +   + A
Sbjct: 69  GVSGFGYDHLILNVEWA 85

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.4 bits (115), Expect = 4e-08
 Identities = 20/85 (23%), Positives = 34/85 (40%), Gaps = 7/85 (8%)

Query: 130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
             ++FV  L  D   E +   F++YG+  +     DK       +GFI  +TR+ A  A 
Sbjct: 8   RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAK 61

Query: 190 KE-PQKKIGNRMTACQLASIGPATT 213
            E     +  +    + A    + T
Sbjct: 62  VELDNMPLRGKQLRVRFACHSASLT 86

>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 = 41.1 bits (96), Expect = 2e-05
 Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 8/84 (9%)

Query: 242 QSEYTQR-KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVD 300
           +  +TQR ++FV N+  ++  +++   F KYG+        +    K KGF     +T  
Sbjct: 2   EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKA------GEVFIHKDKGFGFIRLETRT 55

Query: 301 AAKKALEEPH-KNFEGHILNCQRA 323
            A+ A  E       G  L  + A
Sbjct: 56  LAEIAKVELDNMPLRGKQLRVRFA 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 = 48.6 bits (115), Expect = 4e-08
 Identities = 25/91 (27%), Positives = 37/91 (40%), Gaps = 9/91 (9%)

Query: 125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVC--------DKVSGKSKGYGF 176
           DED  +  I+V GL      + L D FKQ G ++  K           DK +GK KG   
Sbjct: 3   DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 62

Query: 177 ILFKTRSGARKALKEPQ-KKIGNRMTACQLA 206
           + ++    A+ A++    K          LA
Sbjct: 63  VSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA 93

>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 = 45.9 bits (108), Expect = 5e-07
 Identities = 26/94 (27%), Positives = 38/94 (40%), Gaps = 11/94 (11%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPL--------GIDKATGKPKGFCLFVYKTV 299
             I+V  +   +    L  FF + G ++             +DK TGKPKG     Y+  
Sbjct: 9   SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 68

Query: 300 DAAKKALEEPH-KNFEGHILNCQRAIDGPKPGKS 332
             AK A+E    K+F+G  L    A    KP  +
Sbjct: 69  PTAKAAVEWFDGKDFQGSKLKVSLAR--KKPPMN 100

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.1 bits (114), Expect = 5e-08
 Identities = 19/86 (22%), Positives = 34/86 (39%), Gaps = 3/86 (3%)

Query: 123 VADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTR 182
           + ++D   R ++V  L  D     ++  F Q G  + CK + +     +  Y F+ F   
Sbjct: 1   MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEH 58

Query: 183 SGARKALKEPQ-KKIGNRMTACQLAS 207
             A  AL     +KI  +      A+
Sbjct: 59  RDAAAALAAMNGRKILGKEVKVNWAT 84

>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 = 44.3 bits (104), Expect = 1e-06
 Identities = 15/87 (17%), Positives = 31/87 (35%), Gaps = 7/87 (8%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           R ++V N+  ++    +L  FS+ G  +   +  +  +  P  F    +     A  AL 
Sbjct: 9   RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFV--EFYEHRDAAAALA 66

Query: 308 EPH-KNFEGHILNCQRAIDGPKPGKSR 333
             + +   G  +    A        S+
Sbjct: 67  AMNGRKILGKEVKVNWA----TTPSSQ 89

>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 = 48.4 bits (115), Expect = 5e-08
 Identities = 15/83 (18%), Positives = 28/83 (33%), Gaps = 7/83 (8%)

Query: 125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSG 184
              P +  ++  G+      + +   F  +G+I + +          KGY F+ F T   
Sbjct: 13  QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------PEKGYSFVRFSTHES 66

Query: 185 ARKALKEPQ-KKIGNRMTACQLA 206
           A  A+       I   +  C   
Sbjct: 67  AAHAIVSVNGTTIEGHVVKCYWG 89

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.8 bits (103), Expect = 2e-06
 Identities = 21/96 (21%), Positives = 39/96 (40%), Gaps = 7/96 (7%)

Query: 233 QHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFC 292
           Q + +    QS      ++   + S L  Q +   FS +G+I E  +         KG+ 
Sbjct: 4   QLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRV------FPEKGYS 57

Query: 293 LFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGP 327
              + T ++A  A+   +    EGH++ C    + P
Sbjct: 58  FVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP 93

>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 = 47.8 bits (113), Expect = 7e-08
 Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 1/78 (1%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
            K+FV GL +DT  ++L   F +YG+I +   V D+ + +S+G+GF+ F+    A+ A+ 
Sbjct: 6   GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 65

Query: 191 EPQ-KKIGNRMTACQLAS 207
               K +  R      A 
Sbjct: 66  AMNGKSVDGRQIRVDQAG 83

>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 = 44.4 bits (104), Expect = 1e-06
 Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 1/78 (1%)

Query: 247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKAL 306
           + K+FV  +  +   Q L   FSKYG+I E  +  D+ T + +GF    ++ +D AK A+
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 64

Query: 307 EEPH-KNFEGHILNCQRA 323
              + K+ +G  +   +A
Sbjct: 65  MAMNGKSVDGRQIRVDQA 82

>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 = 47.0 bits (111), Expect = 1e-07
 Identities = 14/86 (16%), Positives = 28/86 (32%), Gaps = 10/86 (11%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
           K+++ N+   +    L   F            +        G+    Y   + A +A+E 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLP------LAGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 309 PHKNFE--GHILNCQRAIDGPKPGKS 332
                E  G I+    ++   K  +S
Sbjct: 57  LSGKVELHGKIMEVDYSV--SKKLRS 80

>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 = 41.6 bits (97), Expect = 9e-06
 Identities = 11/65 (16%), Positives = 24/65 (36%), Gaps = 6/65 (9%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
           K+++  L     A+ L   F         +           GY F+ +  ++ A +A++ 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQ------VLLKSGYAFVDYPDQNWAIRAIET 56

Query: 192 PQKKI 196
              K+
Sbjct: 57  LSGKV 61

>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 = 46.9 bits (110), Expect = 2e-07
 Identities = 14/83 (16%), Positives = 30/83 (36%), Gaps = 1/83 (1%)

Query: 124 ADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRS 183
             E      +F+  L  +     L  A  +     D   V  + +G ++ +G++ F++  
Sbjct: 7   GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAE 65

Query: 184 GARKALKEPQKKIGNRMTACQLA 206
              KAL+    K+       +  
Sbjct: 66  DLEKALELTGLKVFGNEIKLEKP 88

>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 = 43.8 bits (102), Expect = 2e-06
 Identities = 13/78 (16%), Positives = 31/78 (39%), Gaps = 1/78 (1%)

Query: 246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKA 305
           T   +F+ N+       +L    S+     +  +   + TG  + F    +++ +  +KA
Sbjct: 12  TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEKA 70

Query: 306 LEEPHKNFEGHILNCQRA 323
           LE       G+ +  ++ 
Sbjct: 71  LELTGLKVFGNEIKLEKP 88

>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 = 47.0 bits (111), Expect = 2e-07
 Identities = 12/86 (13%), Positives = 26/86 (30%), Gaps = 2/86 (2%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
              F+ N+  ++  + +  FF                  + KGF    ++ +D+   AL 
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 308 EPHKNFEGHILNCQRAIDGPKPGKSR 333
              ++     +    A       K  
Sbjct: 76  LNEESLGNKRIRVDVAD--QAQDKDS 99

>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 = 45.5 bits (107), Expect = 6e-07
 Identities = 16/91 (17%), Positives = 33/91 (36%), Gaps = 2/91 (2%)

Query: 117 ASRVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGF 176
            S   ++    P     F+  L +D   E++ + F+                 + KG+G+
Sbjct: 4   GSSGSRLPKSPP--YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGY 61

Query: 177 ILFKTRSGARKALKEPQKKIGNRMTACQLAS 207
             F+       AL   ++ +GN+     +A 
Sbjct: 62  AEFEDLDSLLSALSLNEESLGNKRIRVDVAD 92

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.7 bits (110), Expect = 2e-07
 Identities = 13/81 (16%), Positives = 34/81 (41%), Gaps = 1/81 (1%)

Query: 126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGA 185
            D  +R +++ G   D   + + +  +  G++ + + +   +    KG  F++F +   A
Sbjct: 2   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ-MRRTLHKAFKGSIFVVFDSIESA 60

Query: 186 RKALKEPQKKIGNRMTACQLA 206
           +K ++ P +K           
Sbjct: 61  KKFVETPGQKYKETDLLILFK 81

>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 = 45.5 bits (107), Expect = 4e-07
 Identities = 12/84 (14%), Positives = 33/84 (39%), Gaps = 1/84 (1%)

Query: 242 QSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDA 301
           +++   R +++    ++     +  +    G++              KG    V+ ++++
Sbjct: 1   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ-MRRTLHKAFKGSIFVVFDSIES 59

Query: 302 AKKALEEPHKNFEGHILNCQRAID 325
           AKK +E P + ++   L      D
Sbjct: 60  AKKFVETPGQKYKETDLLILFKDD 83

>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 = 46.1 bits (109), Expect = 2e-07
 Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 7/68 (10%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
            + V G    + A  ++  F QYG I             +  +  I ++++  ARKAL +
Sbjct: 6   WVTVFGFPQAS-ASYILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALSK 58

Query: 192 PQKKIGNR 199
             +  G  
Sbjct: 59  DGRIFGES 66

>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 = 46.2 bits (109), Expect = 3e-07
 Identities = 15/86 (17%), Positives = 30/86 (34%), Gaps = 8/86 (9%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
             +FV     ++   +L  FFS+YG++ +            + F    +     A+    
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMD-----VFIPKPFRAFAFVTFADDQIAQSLCG 60

Query: 308 EPHKNFEGHILNCQRAIDGPKPGKSR 333
           E     +G  ++   A   PK   + 
Sbjct: 61  EDLI-IKGISVHISNAE--PKHNSNS 83

>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 = 44.3 bits (104), Expect = 1e-06
 Identities = 15/76 (19%), Positives = 24/76 (31%), Gaps = 6/76 (7%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
             +FV     D   + L + F QYG++ D            + + F+ F     A+    
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQSLCG 60

Query: 191 EPQKKIGNRMTACQLA 206
           E    I         A
Sbjct: 61  EDL-IIKGISVHISNA 75

>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 = 45.8 bits (108), Expect = 3e-07
 Identities = 19/85 (22%), Positives = 30/85 (35%), Gaps = 9/85 (10%)

Query: 125 DEDPV--HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTR 182
           DED +   + ++V  L   T  E +   F         +        K + Y F+ F  R
Sbjct: 1   DEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNR 54

Query: 183 SGARKALKEPQ-KKIGNRMTACQLA 206
             A +A+K    K +        LA
Sbjct: 55  EDAVEAMKALNGKVLDGSPIEVTLA 79

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.9 bits (103), Expect = 2e-06
 Identities = 11/86 (12%), Positives = 29/86 (33%), Gaps = 9/86 (10%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           + ++V N+      + +   F+             +   K + +    +   + A +A++
Sbjct: 9   KILYVRNLMLSTSEEMIEKEFNNIKPGA------VERVKKIRDYAFVHFSNREDAVEAMK 62

Query: 308 EPH-KNFEGHILNCQRAIDGPKPGKS 332
             + K  +G  +    A   P    S
Sbjct: 63  ALNGKVLDGSPIEVTLAK--PVDKDS 86

>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 = 45.6 bits (107), Expect = 6e-07
 Identities = 18/77 (23%), Positives = 36/77 (46%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
             + + GL +    E ++  F     + +   +     G+S G  F+ F ++  A KALK
Sbjct: 16  GFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK 75

Query: 191 EPQKKIGNRMTACQLAS 207
           + +++IG+R      +S
Sbjct: 76  KHKERIGHRYIEIFKSS 92

>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 = 45.1 bits (106), Expect = 7e-07
 Identities = 20/77 (25%), Positives = 32/77 (41%), Gaps = 1/77 (1%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
            ++FV  L + +  E L   F  YG + +     D ++ K KG+ F+ F     A KA  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 191 EPQ-KKIGNRMTACQLA 206
           E   +    RM     +
Sbjct: 69  EVDGQVFQGRMLHVLPS 85

>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 = 45.1 bits (106), Expect = 8e-07
 Identities = 25/86 (29%), Positives = 39/86 (45%), Gaps = 1/86 (1%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
            ++FV N+      + L   FS YG + E    ID  T KPKGF    +   + A KA  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 308 EPH-KNFEGHILNCQRAIDGPKPGKS 332
           E   + F+G +L+   +    +  +S
Sbjct: 69  EVDGQVFQGRMLHVLPSTIKKEASQS 94

>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 = 45.4 bits (107), Expect = 8e-07
 Identities = 11/69 (15%), Positives = 24/69 (34%), Gaps = 5/69 (7%)

Query: 123 VADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTR 182
           +A + PV  +I V  L +    + L   F ++G +             ++    + +   
Sbjct: 1   MAGQSPV-LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADP 55

Query: 183 SGARKALKE 191
             A+ A   
Sbjct: 56  VSAQHAKLS 64

>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 = 44.4 bits (104), Expect = 9e-07
 Identities = 7/77 (9%), Positives = 25/77 (32%), Gaps = 1/77 (1%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
             +++           + D  +    +     +       S+ + +I   ++  AR  ++
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 191 EPQ-KKIGNRMTACQLA 206
           +    KI       +++
Sbjct: 62  KLNGLKIEGYTLVTKVS 78

>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 = 43.6 bits (102), Expect = 2e-06
 Identities = 7/77 (9%), Positives = 24/77 (31%), Gaps = 1/77 (1%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
             ++++N       + +         +              + F      + + A+  +E
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 308 EPH-KNFEGHILNCQRA 323
           + +    EG+ L  + +
Sbjct: 62  KLNGLKIEGYTLVTKVS 78

>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 = 44.7 bits (105), Expect = 1e-06
 Identities = 16/84 (19%), Positives = 33/84 (39%), Gaps = 4/84 (4%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
            +I+V N+  ++  + +   F KYG I +      K       F    ++    A+ A+ 
Sbjct: 15  CRIYVGNLPPDIRTKDIEDVFYKYGAIRDID---LKNRRGGPPFAFVEFEDPRDAEDAVY 71

Query: 308 EPH-KNFEGHILNCQRAIDGPKPG 330
                +++G+ L  +    G   G
Sbjct: 72  GRDGYDYDGYRLRVEFPRSGRGTG 95

>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 = 43.9 bits (103), Expect = 2e-06
 Identities = 16/90 (17%), Positives = 30/90 (33%), Gaps = 6/90 (6%)

Query: 118 SRVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFI 177
             +R  A  +    +I+V  L  D + + + D F +YG I D      +       + F+
Sbjct: 4   GVIRGPAGNND--CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFV 58

Query: 178 LFKTRSGARKALKEPQ-KKIGNRMTACQLA 206
            F+    A  A+               +  
Sbjct: 59  EFEDPRDAEDAVYGRDGYDYDGYRLRVEFP 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 = 44.3 bits (104), Expect = 1e-06
 Identities = 14/86 (16%), Positives = 28/86 (32%), Gaps = 5/86 (5%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEG--PLGIDKATGKPKGFCLFVYKTVDAAKKAL 306
           ++F+  +    + +++L   +K  E               K +GF    Y++  AA  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 307 EEPHKN---FEGHILNCQRAIDGPKP 329
            +         GH +    A      
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 = 44.3 bits (104), Expect = 2e-06
 Identities = 10/62 (16%), Positives = 27/62 (43%), Gaps = 2/62 (3%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDC--KAVCDKVSGKSKGYGFILFKTRSGARKAL 189
           ++F+ G+    K E +++   +  E               K++G+ F+ +++   A  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 190 KE 191
           ++
Sbjct: 63  RK 64

>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 = 44.3 bits (104), Expect = 1e-06
 Identities = 20/86 (23%), Positives = 31/86 (36%), Gaps = 8/86 (9%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           R +   N+   +   +L   F    EI      +    GK KG     +K+   A+K LE
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADAEKNLE 71

Query: 308 EPH-KNFEGHILNCQRAIDGPKPGKS 332
           E      +G  ++      G K G  
Sbjct: 72  EKQGAEIDGRSVSLYYT--GEKGGTR 95

>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 = 43.9 bits (103), Expect = 2e-06
 Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 6/77 (7%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           R +    L ++   + L + F+        +       GKSKG  +I FK+ + A K L+
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKSEADAEKNLE 71

Query: 191 EPQ-KKIGNRMTACQLA 206
           E Q  +I  R  +    
Sbjct: 72  EKQGAEIDGRSVSLYYT 88

>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 = 43.6 bits (102), Expect = 2e-06
 Identities = 17/77 (22%), Positives = 34/77 (44%), Gaps = 1/77 (1%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
             +FV  +  + + + + + F  YGEI++     D+ +G SKGY  + ++T   A  A +
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 191 EPQ-KKIGNRMTACQLA 206
                +I  +       
Sbjct: 68  ALNGAEIMGQTIQVDWC 84

>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 = 43.2 bits (101), Expect = 3e-06
 Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 1/78 (1%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
             +FV+++  E +  ++   F  YGEI+   L +D+ TG  KG+ L  Y+T   A  A E
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 308 EPH-KNFEGHILNCQRAI 324
             +     G  +      
Sbjct: 68  ALNGAEIMGQTIQVDWCF 85

>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 = 44.0 bits (103), Expect = 2e-06
 Identities = 25/96 (26%), Positives = 41/96 (42%), Gaps = 1/96 (1%)

Query: 246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKA 305
           + R +FV N+  E   ++L   FS+ G +    L  D+ TGKPKG+    Y+  + A  A
Sbjct: 7   SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSA 66

Query: 306 LEEPH-KNFEGHILNCQRAIDGPKPGKSRHHNAQNP 340
           +   + + F G  L    A       + +      P
Sbjct: 67  MRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAP 102

>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 = 42.1 bits (98), Expect = 1e-05
 Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 1/84 (1%)

Query: 125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSG 184
             D   R +FV  + ++   E L D F + G +   + V D+ +GK KGYGF  ++ +  
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 185 ARKALKEPQ-KKIGNRMTACQLAS 207
           A  A++    ++   R      A+
Sbjct: 63  ALSAMRNLNGREFSGRALRVDNAA 86

>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 = 43.3 bits (101), Expect = 4e-06
 Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 7/83 (8%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           + +F+  L +D++ E L +  +Q+G+++  + V    +  SKG  F  F T+  A+K L 
Sbjct: 9   KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 68

Query: 191 EPQ-------KKIGNRMTACQLA 206
                      K+  R     LA
Sbjct: 69  AASLEAEGGGLKLDGRQLKVDLA 91

>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 = 40.6 bits (94), Expect = 3e-05
 Identities = 16/85 (18%), Positives = 34/85 (40%), Gaps = 7/85 (8%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           + +F+ N+  + E + L     ++G+++   + +   T   KG     + T +AA+K L 
Sbjct: 9   KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 68

Query: 308 EPH-------KNFEGHILNCQRAID 325
                        +G  L    A+ 
Sbjct: 69  AASLEAEGGGLKLDGRQLKVDLAVT 93

>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 = 42.8 bits (100), Expect = 6e-06
 Identities = 13/95 (13%), Positives = 30/95 (31%), Gaps = 2/95 (2%)

Query: 124 ADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRS 183
           + +      + + GL +      + + F           +     G+  G   + F T  
Sbjct: 9   SFQSTTGHCVHMRGLPYRATENDIYNFFSPLNP--MRVHIEIGPDGRVTGEADVEFATHE 66

Query: 184 GARKALKEPQKKIGNRMTACQLASIGPATTPAVAS 218
            A  A+ + +  + +R     L S    +    +S
Sbjct: 67  DAVAAMAKDKANMQHRYVELFLNSTAGTSGSGPSS 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 = 42.3 bits (99), Expect = 6e-06
 Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 8/81 (9%)

Query: 131 RKIFVHGLGWDTKAETL----IDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGAR 186
             I+++ L    K + L       F ++G+I D        S K +G  F++FK  S A 
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDIL---VSRSLKMRGQAFVIFKEVSSAT 60

Query: 187 KALKEPQ-KKIGNRMTACQLA 206
            AL+  Q     ++    Q A
Sbjct: 61  NALRSMQGFPFYDKPMRIQYA 81

>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 = 40.8 bits (95), Expect = 2e-05
 Identities = 18/81 (22%), Positives = 37/81 (45%), Gaps = 8/81 (9%)

Query: 248 RKIFVSNVGSELEPQKL----LAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAK 303
             I+++N+  +++  +L     A FS++G+I +    +   + K +G    ++K V +A 
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI---LVSRSLKMRGQAFVIFKEVSSAT 60

Query: 304 KALEEPH-KNFEGHILNCQRA 323
            AL       F    +  Q A
Sbjct: 61  NALRSMQGFPFYDKPMRIQYA 81

>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 = 41.9 bits (98), Expect = 8e-06
 Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 3/78 (3%)

Query: 130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKAL 189
              IF+  L      + L D F  +G I  CK VCD+    SKGYGF+ F+T+  A +A+
Sbjct: 8   VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAI 65

Query: 190 KEPQ-KKIGNRMTACQLA 206
           ++     + +R       
Sbjct: 66  EKMNGMLLNDRKVFVGRF 83

>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 = 41.2 bits (96), Expect = 1e-05
 Identities = 19/86 (22%), Positives = 36/86 (41%), Gaps = 7/86 (8%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
            IF+ N+   ++ + L   FS +G I      +       KG+    ++T +AA++A+E+
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGNILS--CKVVCDENGSKGYGFVHFETQEAAERAIEK 67

Query: 309 PH-KNFEGHILNCQRAIDGPKPGKSR 333
            +        +   R     K  K R
Sbjct: 68  MNGMLLNDRKVFVGRF----KSRKER 89

>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 = 41.6 bits (97), Expect = 1e-05
 Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 2/76 (2%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
             + +     +   E   +  ++YGE+E+   VCD +     G  ++ F+    A KA+ 
Sbjct: 28  SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMN-VCDNLGDHLVGNVYVKFRREEDAEKAVI 86

Query: 191 EPQ-KKIGNRMTACQL 205
           +   +    +    +L
Sbjct: 87  DLNNRWFNGQPIHAEL 102

>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 = 39.2 bits (91), Expect = 1e-04
 Identities = 15/96 (15%), Positives = 35/96 (36%), Gaps = 2/96 (2%)

Query: 227 QHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATG 286
            + +++     Q           + +     E   +       KYGE+EE  +  D    
Sbjct: 7   LNIYRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNV-CDNLGD 65

Query: 287 KPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ 321
              G     ++  + A+KA+ + + + F G  ++ +
Sbjct: 66  HLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101

>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 = 40.3 bits (93), Expect = 6e-05
 Identities = 21/84 (25%), Positives = 43/84 (51%), Gaps = 1/84 (1%)

Query: 117 ASRVRQVADEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGF 176
             R R  +  +     +++ GL ++ + + +ID FK+   +ED   +    +GK+ G GF
Sbjct: 6   QKRSRSRSPHEA-GFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGF 64

Query: 177 ILFKTRSGARKALKEPQKKIGNRM 200
           + F+  +  + AL   ++ +GNR 
Sbjct: 65  VEFRNEADYKAALCRHKQYMGNRF 88

>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 = 37.2 bits (85), Expect = 6e-04
 Identities = 13/89 (14%), Positives = 28/89 (31%)

Query: 235 QHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLF 294
           Q +   +        +++  +  E E + ++ FF K   +E+         GK  G    
Sbjct: 6   QKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFV 65

Query: 295 VYKTVDAAKKALEEPHKNFEGHILNCQRA 323
            ++     K AL    +      +     
Sbjct: 66  EFRNEADYKAALCRHKQYMGNRFIQVHPI 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 = 39.4 bits (91), Expect = 1e-04
 Identities = 13/77 (16%), Positives = 31/77 (40%), Gaps = 1/77 (1%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
           + +++  L        L+  F ++ E +        ++G+ +G  FI F  +  A +AL 
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 191 EPQ-KKIGNRMTACQLA 206
                K+  ++   +  
Sbjct: 79  LVNGYKLYGKILVIEFG 95

>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 = 38.2 bits (88), Expect = 2e-04
 Identities = 14/77 (18%), Positives = 35/77 (45%), Gaps = 1/77 (1%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
           + +++ N+   +  + L++ F+++ E +  P+     TG+ +G     +   + A +AL 
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 308 EPH-KNFEGHILNCQRA 323
             +     G IL  +  
Sbjct: 79  LVNGYKLYGKILVIEFG 95

>d2ayua1 d.305.1.1 (A:70-370) Nucleosome assembly protein, NAP {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 301

class: Alpha and beta proteins (a+b)
fold: NAP-like
superfamily: NAP-like
family: NAP-like
domain: Nucleosome assembly protein, NAP
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 41.5 bits (97), Expect = 1e-04
 Identities = 19/86 (22%), Positives = 37/86 (43%), Gaps = 15/86 (17%)

Query: 20  KQLQQEPPKQEEPIEEEEYEEEVEEE---------------GEEEGEEEEEEEEEEEEEE 64
           K LQ E  + E+  + E +E E +                 G+E+ + E+  + +E  E 
Sbjct: 31  KTLQSELFEVEKEFQVEMFELENKFLQKYKPIWEQRSRIISGQEQPKPEQIAKGQEIVES 90

Query: 65  EKADQKEDEEEEEKADQNDEEDDEPI 90
               +   +EEE+  + ++EE  + I
Sbjct: 91  LNETELLVDEEEKAQNDSEEEQVKGI 116

>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 = 37.5 bits (86), Expect = 2e-04
 Identities = 14/68 (20%), Positives = 21/68 (30%), Gaps = 2/68 (2%)

Query: 132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE 191
            + V  L        +   FK  G I            K+  +  I F    GA  A+ +
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA--DSLKKNFRFARIEFARYDGALAAITK 59

Query: 192 PQKKIGNR 199
             K +G  
Sbjct: 60  THKVVGQN 67

>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 = 35.2 bits (80), Expect = 0.002
 Identities = 13/75 (17%), Positives = 25/75 (33%), Gaps = 2/75 (2%)

Query: 249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE 308
            + V N+       K+  +F   G I    + +  +  K   F    +   D A  A+ +
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPII--HVDVADSLKKNFRFARIEFARYDGALAAITK 59

Query: 309 PHKNFEGHILNCQRA 323
            HK    + +     
Sbjct: 60  THKVVGQNEIIVSHL 74

>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 = 37.4 bits (86), Expect = 2e-04
 Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 1/69 (1%)

Query: 133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEP 192
           +++ GL   T  + L+   + YG+I   KA+ DK + K KGYGF+ F + S A+KA+   
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 193 Q-KKIGNRM 200
           +   +  +M
Sbjct: 61  KASGVQAQM 69

>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 = 34.0 bits (77), Expect = 0.004
 Identities = 15/70 (21%), Positives = 29/70 (41%), Gaps = 1/70 (1%)

Query: 250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP 309
           +++  +      Q L+     YG+I      +DK T K KG+    + +  AA+KA+   
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 310 H-KNFEGHIL 318
                +  + 
Sbjct: 61  KASGVQAQMA 70

>d1qkla_ a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId: 9606]} Length = 127

class: All alpha proteins
fold: RPB6/omega subunit-like
superfamily: RPB6/omega subunit-like
family: RPB6
domain: RPB6
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.6 bits (90), Expect = 2e-04
 Identities = 13/59 (22%), Positives = 27/59 (45%)

Query: 37 EYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEEEEKADQNDEEDDEPILSLLE 95
          + E+  + +  ++ EE+E  ++ E  EEE  +  E     E+   N +    P ++  E
Sbjct: 3  DNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKYE 61

>d1sdma_ c.37.1.9 (A:) Kinesin heavy chain-like protein {Potato (Solanum tuberosum) [TaxId: 4113]} Length = 364

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin heavy chain-like protein
species: Potato (Solanum tuberosum) [TaxId: 4113]

 Score = 38.8 bits (89), Expect = 0.001
 Identities = 11/45 (24%), Positives = 22/45 (48%)

Query: 20  KQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEE 64
           + +  +P K     E    ++ V    E+ G + ++EE EE ++E
Sbjct: 320 RSIVNDPSKNVSSKEVARLKKLVSYWKEQAGRKGDDEELEEIQDE 364

>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 = 35.1 bits (80), Expect = 0.002
 Identities = 13/82 (15%), Positives = 23/82 (28%), Gaps = 8/82 (9%)

Query: 248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALE 307
             I V N+  +   Q++      Y               + K          + A+ A++
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDL-------KYCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 308 EPH-KNFEGHILNCQRAIDGPK 328
             H  +F G  L  Q       
Sbjct: 59  MFHQYSFRGKDLIVQLQPTDAL 80

>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 = 34.7 bits (79), Expect = 0.003
 Identities = 15/89 (16%), Positives = 26/89 (29%), Gaps = 8/89 (8%)

Query: 131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALK 190
             I V  L  D+  + + D  K Y               ++K   F+       A+ A++
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLKYCYV-------DRNKRTAFVTLLNGEQAQNAIQ 58

Query: 191 E-PQKKIGNRMTACQLASIGPATTPAVAS 218
              Q     +    QL           +S
Sbjct: 59  MFHQYSFRGKDLIVQLQPTDALLCSGPSS 87

>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 = 34.5 bits (79), Expect = 0.004
 Identities = 10/68 (14%), Positives = 19/68 (27%), Gaps = 5/68 (7%)

Query: 140 WDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGN 198
            +   E L     ++G+I               G   + F+    A   ++    +  G 
Sbjct: 29  LNEIREDLRVECSKFGQIRKLLLFDRHP----DGVASVSFRDPEEADYCIQTLDGRWFGG 84

Query: 199 RMTACQLA 206
           R    Q  
Sbjct: 85  RQITAQAW 92

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.6 bits (84), Expect = 0.004
 Identities = 10/65 (15%), Positives = 32/65 (49%)

Query: 16  EPPQKQLQQEPPKQEEPIEEEEYEEEVEEEGEEEGEEEEEEEEEEEEEEEKADQKEDEEE 75
           E  ++  Q+   +  E +E +  +   E+E     + +E+E+  +E  ++++   ++E +
Sbjct: 235 EQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQKESRIMKNEIQ 294

Query: 76  EEKAD 80
           + +  
Sbjct: 295 DLQTK 299

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	453
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	100.0
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.86
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.85
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.85
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.85
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.84
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.84
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.84
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.84
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.84
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.84
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.84
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.83
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.83
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.83
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.83
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.83
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.83
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.83
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.83
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.83
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.83
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.83
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.83
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.83
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.83
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.83
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.82
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.82
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.82
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.82
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.82
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.82
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.82
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.82
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.82
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.82
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.82
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.81
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.81
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.81
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.81
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.81
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.81
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.81
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.81
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.81
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.8
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.8
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.8
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.8
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.8
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.8
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.79
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.79
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.79
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.79
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.79
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.79
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.79
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.79
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.79
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.79
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.78
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.78
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.78
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.78
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.78
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.78
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.78
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.77
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.77
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.76
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.76
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.76
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.76
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.76
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.76
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.75
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.75
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.75
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.74
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.74
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.74
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.74
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.74
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.74
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.74
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.74
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.74
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.73
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.73
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.73
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.73
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.73
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.73
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.73
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.72
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.72
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.72
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.72
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.72
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.72
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.72
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.72
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.72
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.71
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.71
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.71
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.71
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.71
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.71
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.71
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.71
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.7
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.7
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.7
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.7
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.7
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.7
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.7
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.69
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.69
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.69
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.69
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.68
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.68
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.68
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.68
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.68
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.68
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.67
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.67
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.67
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.67
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.66
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.66
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.66
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.66
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.65
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.65
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.65
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.65
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.64
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.64
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.63
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.63
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.63
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.63
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.61
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.6
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.59
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.58
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.57
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.53
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	99.52
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	99.5
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.49
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.44
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.43
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.43
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.42
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.42
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.39
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.36
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.34
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.25
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.64
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.47
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.36
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.3
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.23
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.54
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.26
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	95.8

>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=100.00  E-value=2.1e-34  Score=248.20  Aligned_cols=171  Identities=26%  Similarity=0.520  Sum_probs=152.7

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecccC
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASIG  209 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~~~  209 (453)
                      .|||||+|||+++|+++|+++|++||.|.+++|+++..++.++|||||+|.+.++|.+|+..++..+..+.+.+......
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~~   85 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSR   85 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCCT
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhhc
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999988876533


Q ss_pred             CCCCCCcCcccccccccccccccccccccccccccccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCc
Q 012923          210 PATTPAVASTATHQHQHQHQHQHQHQHQQHHQQSEYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPK  289 (453)
Q Consensus       210 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~k  289 (453)
                      ....                          ........++|||+|||+.+|+++|+++|+.||.|..+.|+.+..++.++
T Consensus        86 ~~~~--------------------------~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~  139 (183)
T d1u1qa_          86 EDSQ--------------------------RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKR  139 (183)
T ss_dssp             TGGG--------------------------STTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEE
T ss_pred             cccc--------------------------ccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccc
Confidence            2211                          11223345699999999999999999999999999999999999999999


Q ss_pred             eEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEccCC
Q 012923          290 GFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAIDG  326 (453)
Q Consensus       290 g~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a~~~  326 (453)
                      |||||+|.+.++|.+||+.++..|+|++|+|.+|.++
T Consensus       140 g~~fV~f~~~e~A~~Al~~~~~~~~G~~i~V~~A~~k  176 (183)
T d1u1qa_         140 GFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSK  176 (183)
T ss_dssp             EEEEEEESCHHHHHHHHTSSCEEETTEEEEEEECCCH
T ss_pred             eeEEEEECCHHHHHHHHHhCCCeECCEEEEEEecCCc
Confidence            9999999999999999986558899999999998653

>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=99.86  E-value=1.4e-21  Score=149.38  Aligned_cols=84  Identities=31%  Similarity=0.493  Sum_probs=78.8

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEccC
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAID  325 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a~~  325 (453)
                      ..++|||+|||+.+|+++|+++|+.||.|.+|+|++++.+|+++|||||+|.+.++|.+||+.+|..|+|++|.|.++..
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~Gr~l~V~~a~~   88 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAYL   88 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEESTT
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEcCC
Confidence            44689999999999999999999999999999999999999999999999999999999999999889999999999986


Q ss_pred             CCCC
Q 012923          326 GPKP  329 (453)
Q Consensus       326 ~~~~  329 (453)
                      ..++
T Consensus        89 ~~~p   92 (103)
T d2cqda1          89 GAKP   92 (103)
T ss_dssp             TCCC
T ss_pred             CCCC
Confidence            6544

>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=99.85  E-value=2.4e-21  Score=147.97  Aligned_cols=87  Identities=36%  Similarity=0.664  Sum_probs=80.1

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQ  204 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~  204 (453)
                      ..+...++|||+|||+++|+++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|.+||+.+++.|.||.|.|.
T Consensus         5 ~~d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~Gr~l~V~   84 (103)
T d2cqda1           5 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVN   84 (103)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEE
T ss_pred             CCCCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCEEEEEE
Confidence            34455678999999999999999999999999999999999999999999999999999999999999989999999999


Q ss_pred             ecccCCC
Q 012923          205 LASIGPA  211 (453)
Q Consensus       205 ~~~~~~~  211 (453)
                      ++.....
T Consensus        85 ~a~~~~~   91 (103)
T d2cqda1          85 LAYLGAK   91 (103)
T ss_dssp             ESTTTCC
T ss_pred             EcCCCCC
Confidence            9875433

>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=99.85  E-value=1.9e-21  Score=142.52  Aligned_cols=78  Identities=29%  Similarity=0.594  Sum_probs=74.7

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLAS  207 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~  207 (453)
                      .++|||+|||+++|+++|+++|++||.|..|+|++|+.+++++|||||+|.+.++|.+||+.+++.|.||.|.|..|.
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            479999999999999999999999999999999999999999999999999999999999987788999999998874

>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=99.85  E-value=2.9e-21  Score=143.18  Aligned_cols=81  Identities=27%  Similarity=0.509  Sum_probs=75.1

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecc
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLAS  207 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~  207 (453)
                      ...++|||+|||+++|+++|+++|++||.|.+|+|++|+.+|+++|||||+|.+.++|.+||+.++ .|.|+.|.|.++.
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~~-~l~Gr~i~v~~a~   84 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH-MIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCE-EETTEEEEEECCC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcCC-ccCCEEeEEEeCC
Confidence            346789999999999999999999999999999999999999999999999999999999999654 7999999999986


Q ss_pred             cC
Q 012923          208 IG  209 (453)
Q Consensus       208 ~~  209 (453)
                      .+
T Consensus        85 ~k   86 (90)
T d2cqga1          85 SK   86 (90)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.84  E-value=2.5e-21  Score=143.47  Aligned_cols=81  Identities=26%  Similarity=0.411  Sum_probs=76.7

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+|+++|+++|+.||.|.+|+|++++.+|+++|||||+|.+.++|.+||..|| ..|.|++|+|.||.
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~   85 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF   85 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEec
Confidence            44699999999999999999999999999999999999999999999999999999999999988 88999999999997


Q ss_pred             CC
Q 012923          325 DG  326 (453)
Q Consensus       325 ~~  326 (453)
                      ++
T Consensus        86 ~k   87 (88)
T d1rk8a_          86 VK   87 (88)
T ss_dssp             EC
T ss_pred             CC
Confidence            64

>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=99.84  E-value=5.7e-21  Score=139.91  Aligned_cols=79  Identities=23%  Similarity=0.480  Sum_probs=74.8

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a~~  325 (453)
                      .++|||+|||+.+|+++|+++|+.||.|..|+|++|+.+|+++|||||+|.+.++|.+||..+++.|+|+.|+|..|.+
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~V~~A~s   84 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVS   84 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEeeeC
Confidence            3699999999999999999999999999999999999999999999999999999999999766899999999999863

>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=99.84  E-value=5.1e-21  Score=141.83  Aligned_cols=81  Identities=21%  Similarity=0.376  Sum_probs=75.0

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEccC
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAID  325 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a~~  325 (453)
                      ..++|||+|||+.+|+++|+++|+.||.|..|+|++|+.+|+++|||||+|.+.++|.+||+.++ .|+|+.|.|.++.+
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~~-~l~Gr~i~v~~a~~   85 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH-MIDGRWCDCKLPNS   85 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCE-EETTEEEEEECCCT
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcCC-ccCCEEeEEEeCCC
Confidence            34689999999999999999999999999999999999999999999999999999999999654 79999999999976


Q ss_pred             CC
Q 012923          326 GP  327 (453)
Q Consensus       326 ~~  327 (453)
                      +.
T Consensus        86 k~   87 (90)
T d2cqga1          86 KQ   87 (90)
T ss_dssp             TC
T ss_pred             CC
Confidence            43

>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=99.84  E-value=9e-21  Score=143.95  Aligned_cols=81  Identities=30%  Similarity=0.447  Sum_probs=76.9

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .++|||+|||+.+|+++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|.+||..|| ..|.|++|+|.++..
T Consensus         8 ~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~~   87 (99)
T d1whwa_           8 SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTI   87 (99)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCC
T ss_pred             CCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4689999999999999999999999999999999999999999999999999999999999999 889999999999976


Q ss_pred             CC
Q 012923          326 GP  327 (453)
Q Consensus       326 ~~  327 (453)
                      +.
T Consensus        88 ~~   89 (99)
T d1whwa_          88 KK   89 (99)
T ss_dssp             CS
T ss_pred             CC
Confidence            54

>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=99.84  E-value=1.3e-21  Score=140.64  Aligned_cols=76  Identities=30%  Similarity=0.705  Sum_probs=72.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEec
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLA  206 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~  206 (453)
                      |+|||+|||+++|+++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|.+||+...+.|.||.|.|.+|
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            6899999999999999999999999999999999999999999999999999999999997668899999999886

>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=99.84  E-value=8.5e-21  Score=142.01  Aligned_cols=81  Identities=21%  Similarity=0.384  Sum_probs=76.7

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      .+++|||+|||+.+|+++|+++|++||.|.+|+|++++.++.++|||||+|.+.++|..||..|| ..|+|++|+|.|+.
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~   85 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA   85 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            34699999999999999999999999999999999999999999999999999999999999999 88999999999985


Q ss_pred             CC
Q 012923          325 DG  326 (453)
Q Consensus       325 ~~  326 (453)
                      ..
T Consensus        86 ~~   87 (93)
T d1h2vz_          86 GF   87 (93)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.84  E-value=2e-20  Score=151.72  Aligned_cols=82  Identities=21%  Similarity=0.383  Sum_probs=77.4

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+|+++|+++|+.||.|.+|+|++++.+++++|||||+|.+.++|.+||..|| ..|+|+.|+|.++.
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~  120 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA  120 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45689999999999999999999999999999999999999999999999999999999999998 89999999999996


Q ss_pred             CCC
Q 012923          325 DGP  327 (453)
Q Consensus       325 ~~~  327 (453)
                      .+.
T Consensus       121 ~~~  123 (139)
T d1u6fa1         121 SGH  123 (139)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.84  E-value=6.3e-21  Score=142.74  Aligned_cols=81  Identities=15%  Similarity=0.302  Sum_probs=77.2

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .++|||+|||+.+|+++|+++|++||.|.+|+|++++.+|.++|||||+|.+.++|.+||..|| ..|+|+.|+|.||.+
T Consensus         9 ~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~   88 (93)
T d1x5ua1           9 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASA   88 (93)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTT
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            4699999999999999999999999999999999999999999999999999999999999999 889999999999976


Q ss_pred             CC
Q 012923          326 GP  327 (453)
Q Consensus       326 ~~  327 (453)
                      +.
T Consensus        89 ~~   90 (93)
T d1x5ua1          89 HN   90 (93)
T ss_dssp             TS
T ss_pred             CC
Confidence            54

>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=99.83  E-value=8.7e-21  Score=141.96  Aligned_cols=83  Identities=25%  Similarity=0.351  Sum_probs=77.0

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ...++|||+|||+++|+++|+++|++||.|..|+|++++.++.++|||||+|.+.++|.+||+.++ ..|.|+.|+|.++
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            345799999999999999999999999999999999999999999999999999999999999888 5599999999998


Q ss_pred             ccCC
Q 012923          207 SIGP  210 (453)
Q Consensus       207 ~~~~  210 (453)
                      ....
T Consensus        87 ~~~~   90 (93)
T d1x5ua1          87 SAHN   90 (93)
T ss_dssp             TTTS
T ss_pred             CCCC
Confidence            7543

>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=99.83  E-value=7.7e-21  Score=138.11  Aligned_cols=76  Identities=17%  Similarity=0.264  Sum_probs=74.0

Q ss_pred             EEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       249 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      +|||+|||+.+|+++|+++|++||.|.+|+|++++.+|+++|||||+|.+.++|.+||..|+ ..|.|++|+|.|+.
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            69999999999999999999999999999999999999999999999999999999999999 89999999999984

>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=99.83  E-value=3.6e-21  Score=140.93  Aligned_cols=78  Identities=17%  Similarity=0.272  Sum_probs=75.0

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      ++|||+|||+.+|+++|+++|++||.|.+|+|++++.+|+++|||||+|.+.++|.+||..|| ..|.|++|+|.|+.+
T Consensus         3 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           3 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            589999999999999999999999999999999999999999999999999999999999999 899999999999853

>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=99.83  E-value=5e-21  Score=137.06  Aligned_cols=75  Identities=35%  Similarity=0.771  Sum_probs=71.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEec
Q 012923          132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLA  206 (453)
Q Consensus       132 ~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~  206 (453)
                      +|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|++||+..+..|.|+.|.|..|
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            599999999999999999999999999999999999999999999999999999999998778899999998653

>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=99.83  E-value=3.2e-21  Score=137.50  Aligned_cols=75  Identities=31%  Similarity=0.515  Sum_probs=71.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEec
Q 012923          132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLA  206 (453)
Q Consensus       132 ~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~  206 (453)
                      +|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||+..++.|.|+.|.|..|
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            599999999999999999999999999999999999999999999999999999999998888999999998764

>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=99.83  E-value=1.7e-20  Score=140.32  Aligned_cols=81  Identities=19%  Similarity=0.350  Sum_probs=75.9

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ..++||||+|||+++|+++|+++|++||.|.+|+|++++.++.++|||||+|.+.++|..||+.++ ..|.|+.|.|.|+
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            346899999999999999999999999999999999999999999999999999999999999887 5599999999998


Q ss_pred             cc
Q 012923          207 SI  208 (453)
Q Consensus       207 ~~  208 (453)
                      ..
T Consensus        85 ~~   86 (93)
T d1h2vz_          85 AG   86 (93)
T ss_dssp             SC
T ss_pred             CC
Confidence            53

>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=99.83  E-value=7.3e-21  Score=139.28  Aligned_cols=79  Identities=24%  Similarity=0.395  Sum_probs=74.4

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~  208 (453)
                      +++|||+|||+++|+++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++||+.++ ..|.|+.|+|.++.+
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            4789999999999999999999999999999999999899999999999999999999999877 569999999999853

>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=99.83  E-value=1.1e-20  Score=139.99  Aligned_cols=82  Identities=21%  Similarity=0.333  Sum_probs=75.8

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ....++|||+|||.++|+++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|++|+..++ ..|.|+.|.|.|
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~   83 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3456899999999999999999999999999999999999899999999999999999999999877 559999999999


Q ss_pred             ccc
Q 012923          206 ASI  208 (453)
Q Consensus       206 ~~~  208 (453)
                      +..
T Consensus        84 a~~   86 (88)
T d1rk8a_          84 CFV   86 (88)
T ss_dssp             SEE
T ss_pred             ecC
Confidence            864

>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=99.83  E-value=4.5e-21  Score=142.44  Aligned_cols=79  Identities=22%  Similarity=0.425  Sum_probs=75.6

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .++|||+|||+.+|+++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|.+||..+| ..|+|++|.|.|+.+
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            4699999999999999999999999999999999999999999999999999999999999988 889999999999954

>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=99.83  E-value=5.8e-21  Score=140.31  Aligned_cols=80  Identities=23%  Similarity=0.394  Sum_probs=76.3

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCC
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDG  326 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~  326 (453)
                      .+|||+|||+.+|+++|+++|++||.|..|+|++|+.||+++|||||+|.+.++|.+|+..+| ..|.|++|.|.|+...
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            379999999999999999999999999999999999999999999999999999999999999 8999999999999754


Q ss_pred             C
Q 012923          327 P  327 (453)
Q Consensus       327 ~  327 (453)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.83  E-value=1.6e-20  Score=136.41  Aligned_cols=76  Identities=21%  Similarity=0.331  Sum_probs=72.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEecc
Q 012923          132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQLAS  207 (453)
Q Consensus       132 ~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~~~  207 (453)
                      +|||+|||+++|+++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|..|++.+++ .|.||.|+|.++.
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            699999999999999999999999999999999999999999999999999999999998884 5999999999984

>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=99.83  E-value=3.7e-21  Score=137.22  Aligned_cols=75  Identities=29%  Similarity=0.527  Sum_probs=71.9

Q ss_pred             EEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEc
Q 012923          249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRA  323 (453)
Q Consensus       249 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a  323 (453)
                      +|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||+..++.|+|+.|.|+.|
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            599999999999999999999999999999999999999999999999999999999988778999999999875

>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=99.83  E-value=8.3e-21  Score=141.01  Aligned_cols=80  Identities=25%  Similarity=0.412  Sum_probs=75.3

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLAS  207 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~  207 (453)
                      ..++|||+|||+++|+++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|.+|+..++ ..|.|+.|.|.++.
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            45899999999999999999999999999999999999999999999999999999999999887 55999999999986


Q ss_pred             c
Q 012923          208 I  208 (453)
Q Consensus       208 ~  208 (453)
                      .
T Consensus        84 p   84 (89)
T d2cqba1          84 P   84 (89)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.83  E-value=1.3e-20  Score=143.52  Aligned_cols=82  Identities=22%  Similarity=0.294  Sum_probs=77.5

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+|+++|+++|+.||.|..++++.++.+|+++|||||+|.+.++|..||..|| ..|.|++|+|.|+.
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~   96 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR   96 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            45689999999999999999999999999999999999999999999999999999999999999 88999999999997


Q ss_pred             CCC
Q 012923          325 DGP  327 (453)
Q Consensus       325 ~~~  327 (453)
                      ++.
T Consensus        97 ~k~   99 (102)
T d2cpza1          97 SKN   99 (102)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            654

>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=99.83  E-value=1.3e-20  Score=138.03  Aligned_cols=78  Identities=22%  Similarity=0.347  Sum_probs=74.8

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      ++|||+|||+.+|+++|+++|++||.|..|+|+++..+++++|||||+|.+.++|.+|+..|| ..|.|++|+|.||++
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            589999999999999999999999999999999999999999999999999999999999988 899999999999853

>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=99.83  E-value=2.5e-20  Score=141.46  Aligned_cols=83  Identities=25%  Similarity=0.403  Sum_probs=77.0

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ..+++|||+|||+++|+++|+++|.+||.|.+|+|++|+.+++++|||||+|.+.++|.+||+.|+ ..|.||.|.|.++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            446789999999999999999999999999999999999999999999999999999999999888 5599999999998


Q ss_pred             ccCC
Q 012923          207 SIGP  210 (453)
Q Consensus       207 ~~~~  210 (453)
                      ..+.
T Consensus        86 ~~~~   89 (99)
T d1whwa_          86 TIKK   89 (99)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            7554

>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=99.82  E-value=1.2e-20  Score=140.41  Aligned_cols=81  Identities=26%  Similarity=0.417  Sum_probs=76.7

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||..+|+++|+++|++||.|.+|+|++++.++.++|||||+|.+.++|.+||..|| ..|+|+.|+|.||.
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            34689999999999999999999999999999999999999999999999999999999999999 89999999999996


Q ss_pred             CC
Q 012923          325 DG  326 (453)
Q Consensus       325 ~~  326 (453)
                      ++
T Consensus        87 p~   88 (90)
T d2cq0a1          87 PS   88 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.82  E-value=1.4e-20  Score=143.11  Aligned_cols=80  Identities=29%  Similarity=0.588  Sum_probs=75.3

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecccC
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLASIG  209 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~~~  209 (453)
                      .++|||+|||+++|+++|+++|++||.|..++|++|+.++.++|||||+|.+.++|.+||+.++..|.|+.|.|.++..+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a~~k   99 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAR   99 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSSC
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEECccc
Confidence            37899999999999999999999999999999999999999999999999999999999988778899999999988654

>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=99.82  E-value=1.7e-20  Score=142.59  Aligned_cols=81  Identities=17%  Similarity=0.443  Sum_probs=75.8

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEccCC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAIDG  326 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a~~~  326 (453)
                      .++|||+|||+++|+++|+++|++||.|..+.|++|+.++.++|||||+|.+.++|.+||...++.|+|+.|.|.+|.++
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a~~k   99 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAR   99 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSSC
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEECccc
Confidence            36899999999999999999999999999999999999999999999999999999999986558899999999998765


Q ss_pred             C
Q 012923          327 P  327 (453)
Q Consensus       327 ~  327 (453)
                      .
T Consensus       100 e  100 (103)
T d1x4ba1         100 E  100 (103)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.82  E-value=4.9e-21  Score=137.55  Aligned_cols=77  Identities=18%  Similarity=0.403  Sum_probs=72.6

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEcc
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAI  324 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a~  324 (453)
                      ++|||+|||+.+|+++|+++|++||.|.+++|++|+.+|++||||||+|.+.++|.+||...++.|+||.|.|++|.
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~~~~~~i~Gr~i~V~~Af   77 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAF   77 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEECC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEEECC
Confidence            47999999999999999999999999999999999999999999999999999999999863399999999999873

>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=99.82  E-value=1.1e-20  Score=135.34  Aligned_cols=75  Identities=25%  Similarity=0.627  Sum_probs=70.9

Q ss_pred             EEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEc
Q 012923          249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRA  323 (453)
Q Consensus       249 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a  323 (453)
                      +|||+|||+++|+++|+++|++||.|..|.|++++.+++++|||||+|.+.++|.+||...+..|+|+.|.|+.|
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            499999999999999999999999999999999999999999999999999999999986558899999999754

>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=99.82  E-value=2.2e-20  Score=137.51  Aligned_cols=80  Identities=21%  Similarity=0.382  Sum_probs=73.2

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCC--eEeEE
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGN--RMTAC  203 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~g--r~~~v  203 (453)
                      +...++|||+|||+++|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||+.+++ .+.|  ++|.|
T Consensus         3 ~~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V   82 (85)
T d1b7fa2           3 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV   82 (85)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999998885 4655  88999


Q ss_pred             Eec
Q 012923          204 QLA  206 (453)
Q Consensus       204 ~~~  206 (453)
                      .+|
T Consensus        83 ~~A   85 (85)
T d1b7fa2          83 RLA   85 (85)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            886

>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=99.82  E-value=2.1e-20  Score=137.26  Aligned_cols=79  Identities=24%  Similarity=0.423  Sum_probs=74.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecccC
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASIG  209 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~~  209 (453)
                      .+|||+|||+++|+++|+++|++||+|..|+|++|+.+|+++|||||+|.+.++|..|++.++ ..|.|+.|.|.++...
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            479999999999999999999999999999999999999999999999999999999999888 5699999999999754

>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=99.82  E-value=1.9e-20  Score=137.83  Aligned_cols=78  Identities=27%  Similarity=0.467  Sum_probs=73.2

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCC--eEEEEEE
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEG--HILNCQR  322 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g--~~l~v~~  322 (453)
                      ..++|||+|||+.+|+++|+++|++||.|..|+|++++.+++++|||||+|.+.++|.+||+.+| ..+.|  ++|.|+|
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            34689999999999999999999999999999999999999999999999999999999999998 77766  8999998


Q ss_pred             c
Q 012923          323 A  323 (453)
Q Consensus       323 a  323 (453)
                      |
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=99.82  E-value=2.9e-20  Score=138.36  Aligned_cols=81  Identities=27%  Similarity=0.390  Sum_probs=75.8

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~~  206 (453)
                      ...++|||+|||.++|+++|+++|++||.|..|+|++|+.++.++|||||+|.+.++|.+||+.+++ .|.|+.|.|.++
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            3457999999999999999999999999999999999998999999999999999999999999884 699999999998


Q ss_pred             cc
Q 012923          207 SI  208 (453)
Q Consensus       207 ~~  208 (453)
                      ..
T Consensus        86 kp   87 (90)
T d2cq0a1          86 KP   87 (90)
T ss_dssp             SC
T ss_pred             eC
Confidence            64

>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=99.82  E-value=8.3e-21  Score=143.97  Aligned_cols=78  Identities=21%  Similarity=0.309  Sum_probs=73.3

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLAS  207 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~  207 (453)
                      .++|||+|||+++|+++|+++|+.||.|.+|+|++++.+|+++|||||+|.+.++|.+||+..+..|.|+.|.|.++.
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~   95 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEECC
Confidence            479999999999999999999999999999999999999999999999999999999999854567999999999874

>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=99.82  E-value=2.9e-20  Score=136.25  Aligned_cols=76  Identities=26%  Similarity=0.440  Sum_probs=71.2

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      ..+++|||+|||+++|+++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|.+||..++ ..|.||.|+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            346899999999999999999999999999999999999899999999999999999999999877 4599999987

>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=99.81  E-value=2.8e-20  Score=136.72  Aligned_cols=77  Identities=21%  Similarity=0.390  Sum_probs=72.5

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCC--eEEEEEEc
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEG--HILNCQRA  323 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g--~~l~v~~a  323 (453)
                      .++|||+|||+.+|+++|+++|++||.|.+|+|++++.+|+++|||||+|.+.++|.+|+..|| ..|.|  ++|.|.||
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            4689999999999999999999999999999999999999999999999999999999999998 88887  56999886

>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=99.81  E-value=3.6e-20  Score=135.79  Aligned_cols=78  Identities=24%  Similarity=0.431  Sum_probs=73.2

Q ss_pred             EEEecCCCCccHHHHHHHHhccCCccee-eeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCCC
Q 012923          250 IFVSNVGSELEPQKLLAFFSKYGEIEEG-PLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDGP  327 (453)
Q Consensus       250 l~V~nLp~~~t~~~l~~~F~~~G~i~~v-~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~~  327 (453)
                      |||+|||+++|+++|+++|++||.|..+ +|++++.+|+++|||||+|.+.++|.+||+.++ ..|+|++|+|.|+.++.
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            8999999999999999999999999765 789999999999999999999999999999999 89999999999997554

>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=99.81  E-value=4.7e-20  Score=134.94  Aligned_cols=77  Identities=30%  Similarity=0.498  Sum_probs=73.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecc
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLAS  207 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~  207 (453)
                      ++|||+|||+++|+++|+++|++||.|..|+|+++..+++++|||||+|.+.++|++|++.++ ..|.|+.|.|.++.
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~Ak   80 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            579999999999999999999999999999999999899999999999999999999999877 56999999999974

>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=99.81  E-value=4.1e-20  Score=140.77  Aligned_cols=85  Identities=24%  Similarity=0.387  Sum_probs=77.9

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      ..+..++|||+|||+++|+++|+++|+.||.|..|+++.++.++.++|||||+|.+.++|..||+.++ ..|.|+.|+|.
T Consensus        14 ~~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~   93 (102)
T d2cpza1          14 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ   93 (102)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            33556889999999999999999999999999999999999999999999999999999999998877 55999999999


Q ss_pred             ecccCC
Q 012923          205 LASIGP  210 (453)
Q Consensus       205 ~~~~~~  210 (453)
                      ++..+.
T Consensus        94 ~a~~k~   99 (102)
T d2cpza1          94 LKRSKN   99 (102)
T ss_dssp             CCCCSC
T ss_pred             EeCCCC
Confidence            986543

>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=99.81  E-value=7e-20  Score=132.90  Aligned_cols=76  Identities=32%  Similarity=0.534  Sum_probs=72.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEec
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLA  206 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~  206 (453)
                      ++|||+|||+++|+++|+++|++||.|..++++.++.++.++|||||+|.+.++|.+|++..+..|.||.|.|..|
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            7999999999999999999999999999999999999999999999999999999999987668899999999876

>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=99.81  E-value=3.4e-20  Score=136.25  Aligned_cols=78  Identities=31%  Similarity=0.491  Sum_probs=71.2

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCC--eEeEEEe
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGN--RMTACQL  205 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~g--r~~~v~~  205 (453)
                      ..++|||+|||+++|+++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|.+|++.++ ..+.|  ++|.|.|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            35789999999999999999999999999999999999899999999999999999999999887 45776  5588887


Q ss_pred             c
Q 012923          206 A  206 (453)
Q Consensus       206 ~  206 (453)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.81  E-value=3.8e-20  Score=138.69  Aligned_cols=82  Identities=28%  Similarity=0.381  Sum_probs=75.4

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccC-CCCCCceEEEEEECCHHHHHHHHHcC-C-CccCCeEEEEEE
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDK-ATGKPKGFCLFVYKTVDAAKKALEEP-H-KNFEGHILNCQR  322 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~-~~g~~kg~afV~F~~~~~A~~Al~~~-~-~~l~g~~l~v~~  322 (453)
                      ..++|||+|||+.+++++|+++|+.||.|..|+|+++. .+|+++|||||+|.+.++|.+||..| | ..|+|++|.|.|
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            34689999999999999999999999999999999885 47999999999999999999999987 6 789999999999


Q ss_pred             ccCCC
Q 012923          323 AIDGP  327 (453)
Q Consensus       323 a~~~~  327 (453)
                      |....
T Consensus        87 A~~~~   91 (94)
T d2cpha1          87 ADSEV   91 (94)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            97654

>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=99.81  E-value=3.3e-20  Score=135.95  Aligned_cols=75  Identities=24%  Similarity=0.399  Sum_probs=71.7

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEE
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNC  320 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v  320 (453)
                      +.++|||+|||+.+|+++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|.+||..|| ..|+|++|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            34689999999999999999999999999999999999999999999999999999999999988 8899999987

>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=99.81  E-value=4.1e-20  Score=133.39  Aligned_cols=76  Identities=20%  Similarity=0.391  Sum_probs=72.5

Q ss_pred             EEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       249 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      +|||+|||+.+|+++|+++|++||.|.+|+|++++ +++++|||||+|.+.++|.+||..+| ..|+|++|+|+++.+
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            69999999999999999999999999999999986 89999999999999999999999988 899999999999853

>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=99.81  E-value=5.4e-20  Score=137.10  Aligned_cols=83  Identities=29%  Similarity=0.547  Sum_probs=76.4

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      .+.++|||+|||+++|+++|+++|++||.|..|.++++..++.++|||||+|.+.++|..||..++ ..|.|+.|.|.++
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a   82 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   82 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            346789999999999999999999999999999999999899999999999999999999998877 5699999999998


Q ss_pred             ccCC
Q 012923          207 SIGP  210 (453)
Q Consensus       207 ~~~~  210 (453)
                      ....
T Consensus        83 ~~~~   86 (90)
T d1x5sa1          83 GKSS   86 (90)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            6543

>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=99.80  E-value=4.5e-20  Score=135.92  Aligned_cols=78  Identities=26%  Similarity=0.421  Sum_probs=72.3

Q ss_pred             EEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCC---CCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATG---KPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       250 l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g---~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      |||+|||+++|+++|+++|++||.|.+|.|++++.++   +++|||||+|.+.++|.+||..+| ..|+|+.|.|.|+..
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            8999999999999999999999999999999987665   469999999999999999999999 899999999999864


Q ss_pred             CC
Q 012923          326 GP  327 (453)
Q Consensus       326 ~~  327 (453)
                      ..
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            44

>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=99.80  E-value=8.2e-20  Score=136.85  Aligned_cols=83  Identities=20%  Similarity=0.409  Sum_probs=75.2

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCC-CCCcceEEEEEEccHHHHHHHHHcC-C-CccCCeEeEEE
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKV-SGKSKGYGFILFKTRSGARKALKEP-Q-KKIGNRMTACQ  204 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~-~g~~~G~afV~f~~~~~a~~A~~~~-~-~~~~gr~~~v~  204 (453)
                      ..+++|||+|||+++|+++|+++|++||.|..|+|+++.. +|+++|||||+|.+.++|.+||..| + ..|.|+.|.|.
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            3457899999999999999999999999999999998864 7999999999999999999999987 5 45999999999


Q ss_pred             ecccCC
Q 012923          205 LASIGP  210 (453)
Q Consensus       205 ~~~~~~  210 (453)
                      ++....
T Consensus        86 ~A~~~~   91 (94)
T d2cpha1          86 WADSEV   91 (94)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            997543

>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=99.80  E-value=4.7e-20  Score=137.41  Aligned_cols=81  Identities=28%  Similarity=0.488  Sum_probs=76.6

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .++|||+|||+.+|+++|+++|++||.|..|.++++..++.++|||||+|.++++|.+||..|+ ..|+|++|+|.++..
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~   84 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGK   84 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEEC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            3589999999999999999999999999999999999999999999999999999999999988 899999999999975


Q ss_pred             CC
Q 012923          326 GP  327 (453)
Q Consensus       326 ~~  327 (453)
                      +.
T Consensus        85 ~~   86 (90)
T d1x5sa1          85 SS   86 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.80  E-value=2.6e-20  Score=142.82  Aligned_cols=80  Identities=30%  Similarity=0.498  Sum_probs=76.1

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .++|||+|||+.+|+++|+++|++||.|.+|+|++++.+|+++|||||+|.+.++|.+||..|| ..|.|++|+|.++..
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4689999999999999999999999999999999999999999999999999999999999998 899999999999865


Q ss_pred             C
Q 012923          326 G  326 (453)
Q Consensus       326 ~  326 (453)
                      .
T Consensus        88 ~   88 (104)
T d1p1ta_          88 E   88 (104)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.80  E-value=7.5e-20  Score=132.00  Aligned_cols=75  Identities=24%  Similarity=0.433  Sum_probs=71.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecc
Q 012923          132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLAS  207 (453)
Q Consensus       132 ~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~  207 (453)
                      +|||+|||+++|+++|+++|++||.|..|+|+.++ +++++|||||+|.+.++|.+|++.++ ..+.|+.|+|.++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            69999999999999999999999999999999997 89999999999999999999999877 56999999999875

>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=99.80  E-value=5.8e-20  Score=140.84  Aligned_cols=79  Identities=27%  Similarity=0.504  Sum_probs=74.5

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~  208 (453)
                      .|||||+|||+++|+++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|.+||+.++ ..|.|+.|.|.++..
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4789999999999999999999999999999999999999999999999999999999999887 569999999999754

>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=99.80  E-value=1.5e-19  Score=146.44  Aligned_cols=84  Identities=32%  Similarity=0.515  Sum_probs=77.2

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ...++|||+|||+++|+++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|.+||+.++ ..|.||.|+|.++
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            345789999999999999999999999999999999999999999999999999999999999887 5699999999998


Q ss_pred             ccCCC
Q 012923          207 SIGPA  211 (453)
Q Consensus       207 ~~~~~  211 (453)
                      .....
T Consensus       120 ~~~~~  124 (139)
T d1u6fa1         120 ASGHQ  124 (139)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            75443

>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=99.80  E-value=6e-20  Score=133.92  Aligned_cols=78  Identities=9%  Similarity=0.103  Sum_probs=67.8

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      ++|||+|||+++|+++|+++|+.||.|..+.++.+..+|+++|||||+|.+.++|.+||+.|| ..|+|++|.|.++.+
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            589999999999999999999999999999988888899999999999999999999999998 899999999999853

>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=99.79  E-value=2.5e-19  Score=134.03  Aligned_cols=82  Identities=22%  Similarity=0.368  Sum_probs=74.8

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|++||.|..|+|+++.  +.++|||||+|.+.++|.+||..|| ..|+|++|+|.||
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            345689999999999999999999999999999999885  4479999999999999999999998 8999999999999


Q ss_pred             cCCCC
Q 012923          324 IDGPK  328 (453)
Q Consensus       324 ~~~~~  328 (453)
                      .+++.
T Consensus        87 ~~r~~   91 (93)
T d2cq3a1          87 TARVM   91 (93)
T ss_dssp             CSSCC
T ss_pred             CcCCC
Confidence            77653

>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=99.79  E-value=8.5e-20  Score=134.41  Aligned_cols=80  Identities=23%  Similarity=0.324  Sum_probs=69.2

Q ss_pred             ccEEEEecCCCCcc-HHHHHHHHhccCCcceeeeecc-CCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          247 QRKIFVSNVGSELE-PQKLLAFFSKYGEIEEGPLGID-KATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       247 ~~~l~V~nLp~~~t-~~~l~~~F~~~G~i~~v~i~~d-~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      .++|||+|||+.+| ++.|+++|++||.|.+|+|+++ ..+++++|||||+|.+.++|.+||+ +| ..|+|+.|+|.++
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~a   82 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEEC
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEEc
Confidence            46999999999976 5669999999999999998764 5789999999999999999999996 67 8899999999999


Q ss_pred             cCCC
Q 012923          324 IDGP  327 (453)
Q Consensus       324 ~~~~  327 (453)
                      ..+|
T Consensus        83 ~~kP   86 (86)
T d2ghpa3          83 DKKP   86 (86)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.79  E-value=2.2e-19  Score=133.47  Aligned_cols=81  Identities=25%  Similarity=0.394  Sum_probs=73.3

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~  204 (453)
                      ++...+||||+|||.++|+++|+++|+.||.|..|+|++++.+  .+|||||+|.+.++|.+|+..+++ .|.|+.|+|.
T Consensus         4 d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~   81 (90)
T d2cqia1           4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   81 (90)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc--cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            4556789999999999999999999999999999999998754  478999999999999999998885 5999999999


Q ss_pred             eccc
Q 012923          205 LASI  208 (453)
Q Consensus       205 ~~~~  208 (453)
                      ++..
T Consensus        82 ~a~~   85 (90)
T d2cqia1          82 WATT   85 (90)
T ss_dssp             ECCC
T ss_pred             EcCC
Confidence            9864

>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=99.79  E-value=7.8e-20  Score=133.30  Aligned_cols=77  Identities=9%  Similarity=0.130  Sum_probs=66.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecc
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLAS  207 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~  207 (453)
                      +||||+|||+++|+++|+++|++||.|..+.++.+..+++++|||||+|.+.++|.+|++.++ ..+.|+.|.|.++.
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~   79 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN   79 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcc
Confidence            799999999999999999999999999999998888899999999999999999999999887 56999999999985

>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=99.79  E-value=2.3e-19  Score=131.59  Aligned_cols=77  Identities=16%  Similarity=0.284  Sum_probs=72.1

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLAS  207 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~  207 (453)
                      .++|||+|||+++|+++|+++|+.||.|..|+|.++. +++++|||||+|.+.++|.+||+..+..+.|+.|.|.+..
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEcC
Confidence            4799999999999999999999999999999998876 8999999999999999999999876678999999999864

>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=99.79  E-value=2.3e-19  Score=130.10  Aligned_cols=76  Identities=28%  Similarity=0.552  Sum_probs=72.1

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEc
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRA  323 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a  323 (453)
                      ++|||+|||+++|+++|+++|+.||.|..+.++.++.++.++|||||+|.+.++|.+|+...+..|+||+|.|++|
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            6999999999999999999999999999999999999999999999999999999999975448999999999987

>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=99.79  E-value=2.1e-19  Score=133.65  Aligned_cols=79  Identities=16%  Similarity=0.336  Sum_probs=72.5

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||..+|+++|+++|+.||.|.+|+|++++.++  +|||||+|.+.++|.+|+..++ ..|.|+.|+|.|+.
T Consensus         7 ~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           7 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            34699999999999999999999999999999999986554  7899999999999999999998 88999999999996


Q ss_pred             CC
Q 012923          325 DG  326 (453)
Q Consensus       325 ~~  326 (453)
                      +.
T Consensus        85 ~~   86 (90)
T d2cqia1          85 TP   86 (90)
T ss_dssp             CT
T ss_pred             CC
Confidence            43

>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=99.79  E-value=6.6e-20  Score=138.91  Aligned_cols=78  Identities=18%  Similarity=0.357  Sum_probs=73.8

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .++|||+|||+.+|+++|+++|+.||.|.+|+|+++..+|+++|||||+|.+.++|.+||. || ..|.|+.|.|.++..
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
Confidence            4689999999999999999999999999999999999999999999999999999999996 66 889999999999753

>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=99.79  E-value=1.9e-19  Score=131.88  Aligned_cols=77  Identities=29%  Similarity=0.404  Sum_probs=71.3

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeeE-EEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecccC
Q 012923          133 IFVHGLGWDTKAETLIDAFKQYGEIED-CKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASIG  209 (453)
Q Consensus       133 lfV~nLp~~~te~~l~~~f~~~G~i~~-v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~~  209 (453)
                      |||+|||+++|+++|+++|++||.|.. ++|++++.+++++|||||+|.+.++|.+||+.++ ..|.|+.|+|.++..+
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK   79 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCC
Confidence            899999999999999999999999866 4789999899999999999999999999999888 5599999999998644

>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=99.79  E-value=1.3e-19  Score=133.43  Aligned_cols=81  Identities=23%  Similarity=0.389  Sum_probs=68.9

Q ss_pred             CcCeEEEcCCCCCCC-HHHHHHHHhccCCeeEEEEccc-CCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEec
Q 012923          129 VHRKIFVHGLGWDTK-AETLIDAFKQYGEIEDCKAVCD-KVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLA  206 (453)
Q Consensus       129 ~~~~lfV~nLp~~~t-e~~l~~~f~~~G~i~~v~i~~d-~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~  206 (453)
                      ..++|||+|||+++| +++|+++|++||.|..|+|+++ ..+++++|||||+|.+.++|.+||+..+..|.|+.|.|.++
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~V~~a   82 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEEC
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEEEc
Confidence            468999999999986 5669999999999999998775 45889999999999999999999974446699999999998


Q ss_pred             ccC
Q 012923          207 SIG  209 (453)
Q Consensus       207 ~~~  209 (453)
                      ..+
T Consensus        83 ~~k   85 (86)
T d2ghpa3          83 DKK   85 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>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=99.78  E-value=2.5e-19  Score=131.87  Aligned_cols=76  Identities=29%  Similarity=0.515  Sum_probs=70.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCC---CcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEeccc
Q 012923          133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSG---KSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASI  208 (453)
Q Consensus       133 lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g---~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~  208 (453)
                      |||+|||+++|+++|+++|++||.|.+|+|++++.++   +++|||||+|.+.++|.+|++.++ ..|.|+.|.|.++..
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            8999999999999999999999999999999987655   579999999999999999999888 569999999999853

>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=99.78  E-value=2e-19  Score=129.20  Aligned_cols=75  Identities=32%  Similarity=0.621  Sum_probs=70.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEec
Q 012923          132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLA  206 (453)
Q Consensus       132 ~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~  206 (453)
                      +|||+|||+++|+++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|++..+..|.||.|.|.+|
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            599999999999999999999999999999999998999999999999999999999985557899999999875

>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=99.78  E-value=1.9e-19  Score=129.27  Aligned_cols=74  Identities=24%  Similarity=0.587  Sum_probs=70.9

Q ss_pred             EEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       249 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      +|||+|||+++|+++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+||+ +| +.|+|++|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            59999999999999999999999999999999999999999999999999999999997 66 9999999999986

>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=99.78  E-value=3.5e-19  Score=135.14  Aligned_cols=84  Identities=25%  Similarity=0.437  Sum_probs=75.9

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-------CccCC
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-------KKIGN  198 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-------~~~~g  198 (453)
                      +....++|||+|||+++|+++|+++|++||.|..++++.++.++.++|||||+|.+.++|.+||+.++       ..|.|
T Consensus         4 ~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~g   83 (98)
T d1x4ha1           4 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   83 (98)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             CCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECC
Confidence            34456899999999999999999999999999999999999899999999999999999999999775       23789


Q ss_pred             eEeEEEecccC
Q 012923          199 RMTACQLASIG  209 (453)
Q Consensus       199 r~~~v~~~~~~  209 (453)
                      |.|+|.++..+
T Consensus        84 r~l~v~~a~~k   94 (98)
T d1x4ha1          84 RQLKVDLAVTR   94 (98)
T ss_dssp             CEEEEECCCCC
T ss_pred             EEEEEEECCCC
Confidence            99999998654

>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=99.78  E-value=6.9e-19  Score=131.52  Aligned_cols=83  Identities=20%  Similarity=0.400  Sum_probs=74.1

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      .....++|||+|||+++|+++|+++|++||.|..|+|+.++  +.++|||||+|.+.++|.+||..++ ..|.|+.|.|.
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~   84 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   84 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34456789999999999999999999999999999999986  3479999999999999999999877 56999999999


Q ss_pred             ecccCC
Q 012923          205 LASIGP  210 (453)
Q Consensus       205 ~~~~~~  210 (453)
                      ++..+.
T Consensus        85 ~A~~r~   90 (93)
T d2cq3a1          85 NATARV   90 (93)
T ss_dssp             ECCSSC
T ss_pred             ecCcCC
Confidence            997654

>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=99.78  E-value=3.5e-19  Score=132.09  Aligned_cols=78  Identities=22%  Similarity=0.364  Sum_probs=72.3

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCC
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDG  326 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~  326 (453)
                      .+|||+|||+.+|+++|+++|+.||.|..++|+.+.  +.++|||||+|.+.++|.+||..|| ..|+|++|.|.++.++
T Consensus         9 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2           9 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             TEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            489999999999999999999999999999999885  4478999999999999999999999 8999999999999754


Q ss_pred             C
Q 012923          327 P  327 (453)
Q Consensus       327 ~  327 (453)
                      .
T Consensus        87 ~   87 (89)
T d1cvja2          87 K   87 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.78  E-value=4.4e-19  Score=134.57  Aligned_cols=82  Identities=20%  Similarity=0.353  Sum_probs=75.4

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-------CccCCeEE
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-------KNFEGHIL  318 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-------~~l~g~~l  318 (453)
                      ..++|||+|||+.+|+++|+++|++||.|..+.++.+..+++++|||||+|.+.++|.+||..+|       ..|.|+.|
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            34689999999999999999999999999999999999999999999999999999999999875       35789999


Q ss_pred             EEEEccCCC
Q 012923          319 NCQRAIDGP  327 (453)
Q Consensus       319 ~v~~a~~~~  327 (453)
                      +|.++.++.
T Consensus        87 ~v~~a~~k~   95 (98)
T d1x4ha1          87 KVDLAVTRD   95 (98)
T ss_dssp             EEECCCCCC
T ss_pred             EEEECCCCC
Confidence            999997654

>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=99.77  E-value=4.7e-19  Score=135.17  Aligned_cols=84  Identities=30%  Similarity=0.426  Sum_probs=75.7

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcc--------eeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCC
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIE--------EGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEG  315 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~--------~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g  315 (453)
                      ...++|||+|||+.+|+++|+++|+.||.|.        .+.+.+++.+++++|||||+|.+.++|.+||..|| ..|+|
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   85 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   85 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC
Confidence            3457999999999999999999999999874        56777888889999999999999999999999998 89999


Q ss_pred             eEEEEEEccCCCC
Q 012923          316 HILNCQRAIDGPK  328 (453)
Q Consensus       316 ~~l~v~~a~~~~~  328 (453)
                      ++|+|.++..++.
T Consensus        86 r~i~V~~a~~~~p   98 (101)
T d2cpea1          86 SKLKVSLARKKPP   98 (101)
T ss_dssp             EECEEECSSCCCC
T ss_pred             EEEEEEEcCCCCC
Confidence            9999999976543

>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=99.77  E-value=1e-18  Score=127.98  Aligned_cols=78  Identities=15%  Similarity=0.266  Sum_probs=71.9

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a~~  325 (453)
                      .++|||+|||+.+|+++|+++|+.||.|..|+|+++. +++++|||||+|.+.++|.+||+..+..|.|+.|.|.|+..
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~d   83 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDD   83 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEGGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEcCC
Confidence            4699999999999999999999999999999998875 89999999999999999999997644899999999999753

>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=99.76  E-value=1.2e-18  Score=129.21  Aligned_cols=78  Identities=31%  Similarity=0.572  Sum_probs=71.2

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~  208 (453)
                      ..+|||+|||+++|+++|+++|++||.|..|+|+.+.  +.++|||||+|.+.++|.+||+.++ ..|.|+.|.|.++..
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            3579999999999999999999999999999999986  3478999999999999999999988 559999999999864


Q ss_pred             C
Q 012923          209 G  209 (453)
Q Consensus       209 ~  209 (453)
                      +
T Consensus        86 ~   86 (89)
T d1cvja2          86 R   86 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.76  E-value=1.3e-18  Score=132.67  Aligned_cols=85  Identities=28%  Similarity=0.348  Sum_probs=76.0

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCee--------EEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-Cc
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIE--------DCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KK  195 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~--------~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~  195 (453)
                      +++...++|||+|||+++|+++|+++|+.||.|.        .+++.+++.+++++|||||+|.+.++|.+||+.++ ..
T Consensus         3 ~~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~   82 (101)
T d2cpea1           3 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD   82 (101)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE
T ss_pred             CCCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCE
Confidence            3456678999999999999999999999999874        56778888889999999999999999999999887 55


Q ss_pred             cCCeEeEEEecccC
Q 012923          196 IGNRMTACQLASIG  209 (453)
Q Consensus       196 ~~gr~~~v~~~~~~  209 (453)
                      |.||.|+|.++..+
T Consensus        83 ~~gr~i~V~~a~~~   96 (101)
T d2cpea1          83 FQGSKLKVSLARKK   96 (101)
T ss_dssp             ETTEECEEECSSCC
T ss_pred             ECCEEEEEEEcCCC
Confidence            99999999998754

>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=99.76  E-value=8.5e-19  Score=131.59  Aligned_cols=76  Identities=24%  Similarity=0.459  Sum_probs=70.8

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||..+++++|+++|++||.|.+|+|+++      +|||||+|.+.++|.+||..|| ..|.|+.|+|.|++
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak   90 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            3468999999999999999999999999999999976      8999999999999999999988 88999999999997


Q ss_pred             CCC
Q 012923          325 DGP  327 (453)
Q Consensus       325 ~~~  327 (453)
                      .+|
T Consensus        91 ~~p   93 (96)
T d1x4ga1          91 ESP   93 (96)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.76  E-value=2.4e-19  Score=133.16  Aligned_cols=79  Identities=16%  Similarity=0.176  Sum_probs=72.2

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|+.||.|..++|+.+ .+|+++|||||+|.+.++|.+||+ +| ..|+|++|+|.++
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            34569999999999999999999999999999988754 689999999999999999999997 67 8999999999998


Q ss_pred             cC
Q 012923          324 ID  325 (453)
Q Consensus       324 ~~  325 (453)
                      ..
T Consensus        89 k~   90 (91)
T d1fjeb1          89 KG   90 (91)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.76  E-value=1.5e-19  Score=134.34  Aligned_cols=82  Identities=17%  Similarity=0.197  Sum_probs=72.8

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEe
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQL  205 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~  205 (453)
                      .....++|||+|||+++|+++|+++|+.||.|..|+|+.+. +|+++|||||+|.+.++|.+||+..+..|.|+.|+|.+
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~-~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~   87 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEK   87 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEE-EETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecC-CCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEe
Confidence            34456799999999999999999999999999999887654 89999999999999999999998544679999999998


Q ss_pred             ccc
Q 012923          206 ASI  208 (453)
Q Consensus       206 ~~~  208 (453)
                      +..
T Consensus        88 ak~   90 (91)
T d1fjeb1          88 PKG   90 (91)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            853

>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=99.76  E-value=1.6e-18  Score=130.46  Aligned_cols=82  Identities=17%  Similarity=0.192  Sum_probs=73.3

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCC-cceeeeeccC-CCCCCceEEEEEECCHHHHHHHHHcCC---CccCCeEEEEEE
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGE-IEEGPLGIDK-ATGKPKGFCLFVYKTVDAAKKALEEPH---KNFEGHILNCQR  322 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~-i~~v~i~~d~-~~g~~kg~afV~F~~~~~A~~Al~~~~---~~l~g~~l~v~~  322 (453)
                      ++|||+|||..+|+++|+++|+.||. |..|+|+++. .+++++|||||+|.++++|..||..|+   ..+.|++|+|.|
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            58999999999999999999999996 8999999885 468999999999999999999999986   456899999999


Q ss_pred             ccCCCCC
Q 012923          323 AIDGPKP  329 (453)
Q Consensus       323 a~~~~~~  329 (453)
                      |.+...+
T Consensus        82 A~p~~~~   88 (96)
T d2disa1          82 AEPEIDV   88 (96)
T ss_dssp             SCSSCST
T ss_pred             cCCCCCC
Confidence            9765443

>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=99.75  E-value=2.2e-18  Score=134.47  Aligned_cols=77  Identities=19%  Similarity=0.393  Sum_probs=70.2

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ..+++|||+|||+++|+++|+++|++||.|.+|+|..   ++.++|||||+|.+.++|..||+.|+ ..|.|+.|.|.++
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~---~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   81 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYY   81 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC---STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc---cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            3468999999999999999999999999999999876   45679999999999999999999887 5599999999997


Q ss_pred             c
Q 012923          207 S  207 (453)
Q Consensus       207 ~  207 (453)
                      .
T Consensus        82 ~   82 (114)
T d2f9da1          82 N   82 (114)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.75  E-value=4.3e-18  Score=130.08  Aligned_cols=84  Identities=21%  Similarity=0.316  Sum_probs=74.5

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEec
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLA  206 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~  206 (453)
                      .....+|||+|||+++|+++|++||..||.|..+.++.+..+++++|||||+|.+.++|++|++..+..|.+|.|.|.++
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS   91 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEEC
Confidence            34456899999999999999999999999998877777777999999999999999999999986667899999999998


Q ss_pred             ccCC
Q 012923          207 SIGP  210 (453)
Q Consensus       207 ~~~~  210 (453)
                      ....
T Consensus        92 ~~~~   95 (104)
T d1wg5a_          92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            7554

>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=99.75  E-value=5.6e-19  Score=134.96  Aligned_cols=82  Identities=17%  Similarity=0.365  Sum_probs=77.0

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ++++|||+|||..+|+++|+++|+.||.|..+.++.+..+|+++|||||+|.+.++|.+||..|| ..|.|++|+|.|+.
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            45799999999999999999999999999999999988899999999999999999999999999 89999999999997


Q ss_pred             CCC
Q 012923          325 DGP  327 (453)
Q Consensus       325 ~~~  327 (453)
                      .+.
T Consensus        97 ~k~   99 (102)
T d2cpxa1          97 NKK   99 (102)
T ss_dssp             CCS
T ss_pred             Ccc
Confidence            543

>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=99.74  E-value=3.4e-18  Score=121.85  Aligned_cols=74  Identities=19%  Similarity=0.224  Sum_probs=67.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEec
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLA  206 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~  206 (453)
                      +||||+|||+++|+++|+++|+.||.|..|+|+.++.  ..++||||+|.+.++|.+||...+..|.|+.|.|..+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            4899999999999999999999999999999999874  3457999999999999999987668899999999865

>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=99.74  E-value=2.6e-18  Score=126.65  Aligned_cols=77  Identities=18%  Similarity=0.225  Sum_probs=70.4

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      .++|||+|||+.+++++|+++|+.||.|....++.+..+++++|||||+|.+.++|.+||..|| ..|+||+|+|.++
T Consensus         9 ~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           9 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4589999999999999999999999999876555556789999999999999999999999999 8999999999875

>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=99.74  E-value=4.4e-18  Score=128.03  Aligned_cols=81  Identities=16%  Similarity=0.274  Sum_probs=72.3

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCC-eeEEEEcccCC-CCCcceEEEEEEccHHHHHHHHHcCCC---ccCCeEeEEE
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGE-IEDCKAVCDKV-SGKSKGYGFILFKTRSGARKALKEPQK---KIGNRMTACQ  204 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~-i~~v~i~~d~~-~g~~~G~afV~f~~~~~a~~A~~~~~~---~~~gr~~~v~  204 (453)
                      +|+|||+|||.++|+++|+++|++||. |..|+|+++.. +++++|||||+|.+.++|..|++.++.   .+.|+.|.|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            378999999999999999999999996 99999998864 689999999999999999999998862   3579999999


Q ss_pred             ecccCC
Q 012923          205 LASIGP  210 (453)
Q Consensus       205 ~~~~~~  210 (453)
                      |+....
T Consensus        81 ~A~p~~   86 (96)
T d2disa1          81 WAEPEI   86 (96)
T ss_dssp             ESCSSC
T ss_pred             EcCCCC
Confidence            996543

>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=99.74  E-value=6.5e-18  Score=129.30  Aligned_cols=79  Identities=16%  Similarity=0.257  Sum_probs=69.8

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccC-CCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDK-ATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~-~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      +.++|||+|||+.+|+++|+++|+.|| |..++++++. .+++++|||||+|.+.++|.+|+. +| ..|+|+.|+|.++
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEEC
Confidence            347999999999999999999999998 7788877765 578899999999999999987776 56 8999999999998


Q ss_pred             cCC
Q 012923          324 IDG  326 (453)
Q Consensus       324 ~~~  326 (453)
                      ..+
T Consensus        92 ~~~   94 (104)
T d1wi8a_          92 DQA   94 (104)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.74  E-value=4.1e-18  Score=127.82  Aligned_cols=78  Identities=21%  Similarity=0.465  Sum_probs=70.2

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      .+..++|||+|||.++|+++|+++|++||.|.+|+|+++      +|||||+|.+.++|.+|+..++ ..|.|+.|+|.|
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            345689999999999999999999999999999999876      6899999999999999999877 559999999999


Q ss_pred             cccCC
Q 012923          206 ASIGP  210 (453)
Q Consensus       206 ~~~~~  210 (453)
                      +...+
T Consensus        89 ak~~p   93 (96)
T d1x4ga1          89 GKESP   93 (96)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            86543

>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=99.74  E-value=3.3e-18  Score=133.39  Aligned_cols=76  Identities=22%  Similarity=0.339  Sum_probs=70.6

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .++|||+|||+.+|+++|+++|++||.|.+|++..   ++.++|||||+|.+.++|..||..|| ..|+|+.|.|.++..
T Consensus         7 ~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~---~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   83 (114)
T d2f9da1           7 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC---STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc---cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            46999999999999999999999999999999975   45679999999999999999999999 899999999999854

>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=99.74  E-value=5.8e-18  Score=129.59  Aligned_cols=81  Identities=19%  Similarity=0.335  Sum_probs=71.2

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCC-CCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKV-SGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLAS  207 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~-~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~  207 (453)
                      ..++|||+|||+++|+++|+++|++|| |..++++++.. +++++|||||+|.+.++|++|++..+..|.||.|+|.++.
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            458999999999999999999999999 77888877664 7899999999999999999888765577999999999986


Q ss_pred             cCC
Q 012923          208 IGP  210 (453)
Q Consensus       208 ~~~  210 (453)
                      ...
T Consensus        93 ~~~   95 (104)
T d1wi8a_          93 QAQ   95 (104)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.74  E-value=3.2e-18  Score=130.24  Aligned_cols=83  Identities=14%  Similarity=0.213  Sum_probs=72.8

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEe
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQL  205 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~  205 (453)
                      ......+|||+|||+++|+++|+++|..|| |..|+++.+. ++.++|||||+|.+.++|++||++.+..|.||.|+|.+
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V~~   88 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFL   88 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345567999999999999999999999998 4578888877 78999999999999999999998656789999999999


Q ss_pred             cccCC
Q 012923          206 ASIGP  210 (453)
Q Consensus       206 ~~~~~  210 (453)
                      +....
T Consensus        89 s~~~~   93 (102)
T d1weza_          89 NSTAG   93 (102)
T ss_dssp             ECCCC
T ss_pred             cCCCC
Confidence            87554

>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=99.74  E-value=8.4e-18  Score=128.44  Aligned_cols=83  Identities=12%  Similarity=0.172  Sum_probs=73.6

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEcc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAI  324 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a~  324 (453)
                      ....+|||+|||+++|+++|+++|..||.|..+.++.+..+++++|||||+|.+.++|.+||...+..|+||.|.|.++.
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~~~   92 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSS   92 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEECC
Confidence            34458999999999999999999999999988777777789999999999999999999999744488999999999986


Q ss_pred             CCC
Q 012923          325 DGP  327 (453)
Q Consensus       325 ~~~  327 (453)
                      ...
T Consensus        93 ~~~   95 (104)
T d1wg5a_          93 RAE   95 (104)
T ss_dssp             TTT
T ss_pred             HHH
Confidence            543

>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=99.73  E-value=1.4e-18  Score=132.08  Aligned_cols=80  Identities=16%  Similarity=0.308  Sum_probs=71.9

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQ  204 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~  204 (453)
                      .+.+.++|||+|||+++|+++|+++|++||.|..++++.+. ++.++|||||+|.+.++|.+||+.+| ..|.||.+.|.
T Consensus        14 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~   92 (101)
T d1x5oa1          14 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   92 (101)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccC
Confidence            34556899999999999999999999999999999998886 88999999999999999999999877 55899988876


Q ss_pred             ec
Q 012923          205 LA  206 (453)
Q Consensus       205 ~~  206 (453)
                      ++
T Consensus        93 ~~   94 (101)
T d1x5oa1          93 PT   94 (101)
T ss_dssp             CS
T ss_pred             CC
Confidence            54

>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=99.73  E-value=6.9e-18  Score=126.63  Aligned_cols=78  Identities=18%  Similarity=0.305  Sum_probs=70.5

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|+.||.|..+.+.++   ..+++||||+|.+.++|.+||+.|| ..|.|++|+|.|+
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a   88 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   88 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            34468999999999999999999999999999988553   4569999999999999999999999 8999999999998


Q ss_pred             cC
Q 012923          324 ID  325 (453)
Q Consensus       324 ~~  325 (453)
                      ..
T Consensus        89 ~~   90 (95)
T d1x4aa1          89 RS   90 (95)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>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=99.73  E-value=8.3e-18  Score=119.84  Aligned_cols=74  Identities=18%  Similarity=0.236  Sum_probs=66.7

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEc
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRA  323 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a  323 (453)
                      ++|||+|||+.+++++|+++|+.||.|..|+|++++.  ..++||||+|.+.++|.+||...+..|+|++|.|..+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            4899999999999999999999999999999998864  3467999999999999999975448999999999875

>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=99.73  E-value=3.8e-18  Score=125.24  Aligned_cols=74  Identities=26%  Similarity=0.384  Sum_probs=69.3

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .++|||+|||..+++++|+++|++||.|.+|+++++      +|||||+|.+.++|.+|+..|| ..|.|++|+|+||..
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            358999999999999999999999999999999876      7899999999999999999999 899999999999965


Q ss_pred             C
Q 012923          326 G  326 (453)
Q Consensus       326 ~  326 (453)
                      .
T Consensus        82 ~   82 (86)
T d2cpja1          82 S   82 (86)
T ss_dssp             C
T ss_pred             c
Confidence            4

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.73  E-value=6.6e-18  Score=127.00  Aligned_cols=78  Identities=22%  Similarity=0.302  Sum_probs=70.0

Q ss_pred             ccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          245 YTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ...++|||+|||+.+|+++|+++|+.||.|..++.     +++++|||||+|.+.++|.+||..|| ..|+|++|+|.|+
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a   88 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            34579999999999999999999999998876643     67889999999999999999999999 8999999999999


Q ss_pred             cCCC
Q 012923          324 IDGP  327 (453)
Q Consensus       324 ~~~~  327 (453)
                      .++.
T Consensus        89 ~~k~   92 (96)
T d1fjca_          89 GEKG   92 (96)
T ss_dssp             SSSC
T ss_pred             CCCC
Confidence            7554

>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=99.73  E-value=1e-17  Score=125.70  Aligned_cols=79  Identities=18%  Similarity=0.256  Sum_probs=70.6

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ....++|||+|||+++|+++|+++|++||.|..+++..+   ..++|||||+|.+.++|.+||+.|+ ..|.|+.|.|.+
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            355679999999999999999999999999999987654   4578999999999999999999877 569999999999


Q ss_pred             ccc
Q 012923          206 ASI  208 (453)
Q Consensus       206 ~~~  208 (453)
                      +..
T Consensus        88 a~~   90 (95)
T d1x4aa1          88 PRS   90 (95)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            864

>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=99.73  E-value=3.8e-18  Score=125.68  Aligned_cols=79  Identities=22%  Similarity=0.333  Sum_probs=69.0

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      +..++|||+|||+++|+++|+++|..||.|..+.++.+..+++++|||||+|.+.++|.+||+.++ ..|.||.|+|.++
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            445679999999999999999999999999774344444589999999999999999999999877 5699999999874

>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=99.72  E-value=1.4e-18  Score=132.62  Aligned_cols=82  Identities=16%  Similarity=0.271  Sum_probs=75.9

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ..+++|||+|||.++|+++|+++|.+||.|..+.++.+..+++++|||||+|.+.++|..||+.++ ..|.|+.|.|.++
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            346899999999999999999999999999999999888899999999999999999999999888 5599999999998


Q ss_pred             ccC
Q 012923          207 SIG  209 (453)
Q Consensus       207 ~~~  209 (453)
                      ..+
T Consensus        96 k~k   98 (102)
T d2cpxa1          96 KNK   98 (102)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            643

>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=99.72  E-value=6.7e-18  Score=123.26  Aligned_cols=74  Identities=16%  Similarity=0.217  Sum_probs=67.6

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-Ccc-CCeEEEEEEc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNF-EGHILNCQRA  323 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l-~g~~l~v~~a  323 (453)
                      ++++|||+|||..+|+++|+++|+.||.|..|++++++     +|||||+|.+.++|..|+..|+ ..| +|++|+|.|+
T Consensus         7 P~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~a   81 (83)
T d2b0ga1           7 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFA   81 (83)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEe
Confidence            45799999999999999999999999999999998753     7899999999999999999998 667 5799999998


Q ss_pred             c
Q 012923          324 I  324 (453)
Q Consensus       324 ~  324 (453)
                      +
T Consensus        82 k   82 (83)
T d2b0ga1          82 K   82 (83)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.72  E-value=5.7e-18  Score=122.28  Aligned_cols=73  Identities=21%  Similarity=0.358  Sum_probs=67.3

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .++|||+||+  +|+++|+++|++||.|.+|++.++      +|||||+|.+.++|.+|+..|| ..|+|++|+|.|++.
T Consensus         5 ~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~   76 (79)
T d2bz2a1           5 GNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK   76 (79)
T ss_dssp             CCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCS
T ss_pred             CCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecC
Confidence            4699999996  899999999999999999999765      7899999999999999999999 899999999999976


Q ss_pred             CC
Q 012923          326 GP  327 (453)
Q Consensus       326 ~~  327 (453)
                      +|
T Consensus        77 ~P   78 (79)
T d2bz2a1          77 QP   78 (79)
T ss_dssp             SC
T ss_pred             CC
Confidence            54

>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=99.72  E-value=8.1e-18  Score=127.94  Aligned_cols=81  Identities=14%  Similarity=0.135  Sum_probs=71.4

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQR  322 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~  322 (453)
                      .....+|||+|||+.+|+++|+++|..|| |..|+++++. ++.++|||||+|.+.++|.+||. +| ..|+||.|+|.+
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~   88 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            34456999999999999999999999997 5688888875 68999999999999999999997 56 999999999999


Q ss_pred             ccCCC
Q 012923          323 AIDGP  327 (453)
Q Consensus       323 a~~~~  327 (453)
                      +...+
T Consensus        89 s~~~~   93 (102)
T d1weza_          89 NSTAG   93 (102)
T ss_dssp             ECCCC
T ss_pred             cCCCC
Confidence            87554

>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=99.72  E-value=2.5e-18  Score=130.59  Aligned_cols=78  Identities=12%  Similarity=0.211  Sum_probs=71.6

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+|+++|+++|+.||.|..++++.+. ++.++|||||+|.+.++|.+||+.|| ..|.|+++.|.++.
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~   95 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE   95 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCC
Confidence            34689999999999999999999999999999998874 88999999999999999999999999 89999998886653

>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=99.72  E-value=3.5e-18  Score=123.65  Aligned_cols=74  Identities=18%  Similarity=0.365  Sum_probs=67.4

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-C-ccCCeEEEEEEccC
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-K-NFEGHILNCQRAID  325 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~-~l~g~~l~v~~a~~  325 (453)
                      ++|||+|||+.+|+++|+++|++||.|..+++++.      +|||||+|.+.++|.+||+.|| . .|+|++|+|.|+.+
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 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            37999999999999999999999999998888764      8999999999999999999998 4 58999999999975


Q ss_pred             CC
Q 012923          326 GP  327 (453)
Q Consensus       326 ~~  327 (453)
                      +.
T Consensus        76 k~   77 (80)
T d2cqha1          76 KK   77 (80)
T ss_dssp             CC
T ss_pred             cC
Confidence            43

>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=99.72  E-value=6.1e-18  Score=131.35  Aligned_cols=76  Identities=17%  Similarity=0.142  Sum_probs=69.5

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ..++|||+|||+.+|+++|+++|+.||.|..|.|.+      ++|||||+|.+.++|.+||..|| ..|.|++|.|.|+.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~   82 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            346999999999999999999999999999998853      38999999999999999999999 89999999999997


Q ss_pred             CCC
Q 012923          325 DGP  327 (453)
Q Consensus       325 ~~~  327 (453)
                      ...
T Consensus        83 ~~~   85 (111)
T d1whxa_          83 IGV   85 (111)
T ss_dssp             TTT
T ss_pred             CCc
Confidence            654

>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=99.72  E-value=5.9e-18  Score=124.96  Aligned_cols=75  Identities=16%  Similarity=0.275  Sum_probs=66.2

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCCeEEEEEEccCC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEGHILNCQRAIDG  326 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g~~l~v~~a~~~  326 (453)
                      .++|||+|||+.+|+++|+++|++||.|..|++..     .++|||||+|.+.++|.+||. .++.|+|++|.|.++.++
T Consensus         5 s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~-~~~~i~g~~l~v~~a~~k   78 (88)
T d1wf0a_           5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG-EDLIIKGISVHISNAEPK   78 (88)
T ss_dssp             CCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT-CEEEETTEEEEEECCCCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh-CCCEECCEEeEEEeCCCC
Confidence            46999999999999999999999999999998754     358999999999999999986 237899999999998654


Q ss_pred             C
Q 012923          327 P  327 (453)
Q Consensus       327 ~  327 (453)
                      .
T Consensus        79 ~   79 (88)
T d1wf0a_          79 H   79 (88)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.72  E-value=3e-18  Score=126.68  Aligned_cols=75  Identities=16%  Similarity=0.317  Sum_probs=68.7

Q ss_pred             ccEEEEecCCCCccHHHH---HHHHhccCCcceeeeeccCCCCCC---ceEEEEEECCHHHHHHHHHcCC-CccCCeEEE
Q 012923          247 QRKIFVSNVGSELEPQKL---LAFFSKYGEIEEGPLGIDKATGKP---KGFCLFVYKTVDAAKKALEEPH-KNFEGHILN  319 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l---~~~F~~~G~i~~v~i~~d~~~g~~---kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~  319 (453)
                      .++|||+|||+.+++++|   +++|++||.|..|.|++++.++.+   +|||||+|.+.++|.+||..|| ..|+|++|+
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            458999999999999999   678999999999999999877655   4999999999999999999999 899999999


Q ss_pred             EE
Q 012923          320 CQ  321 (453)
Q Consensus       320 v~  321 (453)
                      |+
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            85

>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=99.71  E-value=1.9e-18  Score=122.64  Aligned_cols=70  Identities=33%  Similarity=0.590  Sum_probs=65.6

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeE
Q 012923          133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTA  202 (453)
Q Consensus       133 lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~  202 (453)
                      |||+|||+++|+++|+++|++||.|..+++++++.++.++|||||+|.+.++|.+|++.++ ..|.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            8999999999999999999999999999999999999999999999999999999999888 458887663

>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=99.71  E-value=1.6e-18  Score=123.07  Aligned_cols=70  Identities=21%  Similarity=0.380  Sum_probs=67.1

Q ss_pred             EEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEE
Q 012923          250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILN  319 (453)
Q Consensus       250 l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~  319 (453)
                      |||+|||+++|+++|+++|++||.|..+++++++.++.++|||||+|.+.++|.+||..|| ..|+|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            7999999999999999999999999999999999999999999999999999999999999 889998763

>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=99.71  E-value=1.8e-17  Score=124.70  Aligned_cols=72  Identities=25%  Similarity=0.474  Sum_probs=65.8

Q ss_pred             cccEEEEecCC-CCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          246 TQRKIFVSNVG-SELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       246 ~~~~l~V~nLp-~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      ..++|||+||+ ..+++++|+++|++||.|.+|+|.        +|||||+|.+.++|.+||..|| ..|+|++|+|.|+
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   85 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLA   85 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEET
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34689999996 578899999999999999999982        7999999999999999999999 8999999999998


Q ss_pred             cC
Q 012923          324 ID  325 (453)
Q Consensus       324 ~~  325 (453)
                      ..
T Consensus        86 ~~   87 (98)
T d1wf2a_          86 AE   87 (98)
T ss_dssp             TS
T ss_pred             CC
Confidence            64

>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=99.71  E-value=2e-17  Score=121.69  Aligned_cols=75  Identities=11%  Similarity=0.124  Sum_probs=67.9

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .++|||+|||+.+|+++|+++|++||.|..+.+.+      ++|||||+|.+.++|.+||..|| ..|.|+.|.|.|+.+
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP   81 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   81 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccC
Confidence            36899999999999999999999999998877743      48999999999999999999999 889999999999864


Q ss_pred             CC
Q 012923          326 GP  327 (453)
Q Consensus       326 ~~  327 (453)
                      ..
T Consensus        82 ~~   83 (86)
T d2cpda1          82 VD   83 (86)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.71  E-value=7.4e-18  Score=128.68  Aligned_cols=80  Identities=15%  Similarity=0.218  Sum_probs=69.8

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecc
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLAS  207 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~  207 (453)
                      ....+|||+|||+++|+++|+++|..||.|..+.++....+|+++|||||+|.+.++|++||+..+..|.||.|.|.++.
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEEC
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEECC
Confidence            34578999999999999999999999999987555555559999999999999999999999854467999999998874

>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=99.71  E-value=1.9e-17  Score=120.82  Aligned_cols=78  Identities=22%  Similarity=0.308  Sum_probs=69.1

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-cc-CCeEeE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KI-GNRMTA  202 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~-~gr~~~  202 (453)
                      .+.+.+++|||+|||.++|+++|+++|++||.|..|++++++     +|||||+|.+.++|..|+..|++ .| .++.|.
T Consensus         3 ~~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~   77 (83)
T d2b0ga1           3 TEQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMK   77 (83)
T ss_dssp             CCCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEE
Confidence            345668999999999999999999999999999999998653     68999999999999999999885 45 578999


Q ss_pred             EEecc
Q 012923          203 CQLAS  207 (453)
Q Consensus       203 v~~~~  207 (453)
                      |.|+.
T Consensus        78 v~~ak   82 (83)
T d2b0ga1          78 ITFAK   82 (83)
T ss_dssp             EEECC
T ss_pred             EEEec
Confidence            99874

>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=99.71  E-value=1.1e-17  Score=127.75  Aligned_cols=78  Identities=18%  Similarity=0.191  Sum_probs=70.9

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      ..+|||+|||+.+|+++|+++|..||.|..+.++.+..+|+++|||||+|.+.++|.+||. +| ..|+||.|.|.++..
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~~   86 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVTL   86 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEECH
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECCH
Confidence            4689999999999999999999999999886666667799999999999999999999997 66 889999999999753

>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=99.71  E-value=1.7e-17  Score=124.75  Aligned_cols=79  Identities=27%  Similarity=0.381  Sum_probs=69.7

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEe
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQL  205 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~  205 (453)
                      ....++|||+|||+++|+++|+++|.+||.|..++.     +++++|||||+|.+.++|.+|++.++ ..|.|+.|.|.+
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~   87 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345689999999999999999999999998876642     67899999999999999999999888 569999999999


Q ss_pred             cccCC
Q 012923          206 ASIGP  210 (453)
Q Consensus       206 ~~~~~  210 (453)
                      +..+.
T Consensus        88 a~~k~   92 (96)
T d1fjca_          88 TGEKG   92 (96)
T ss_dssp             CSSSC
T ss_pred             eCCCC
Confidence            87553

>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=99.70  E-value=1.9e-17  Score=128.01  Aligned_cols=75  Identities=20%  Similarity=0.347  Sum_probs=68.7

Q ss_pred             ccEEEEecCCC-CccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          247 QRKIFVSNVGS-ELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       247 ~~~l~V~nLp~-~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      .++|||+||++ .+|+++|+++|+.||.|..|+|++++     +|||||+|.+.++|.+||..|| ..|.|+.|+|.|+.
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            35999999965 59999999999999999999998874     8999999999999999999999 88999999999986


Q ss_pred             CC
Q 012923          325 DG  326 (453)
Q Consensus       325 ~~  326 (453)
                      ..
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.70  E-value=1.3e-17  Score=129.51  Aligned_cols=76  Identities=20%  Similarity=0.209  Sum_probs=68.0

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLAS  207 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~  207 (453)
                      .+++|||+|||+++|+++|+++|++||.|..|.|.      +++|||||+|.+.++|.+||+.|| ..|.|+.|.|.++.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~------~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~   82 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            45799999999999999999999999999999874      357899999999999999999888 55999999999986


Q ss_pred             cCC
Q 012923          208 IGP  210 (453)
Q Consensus       208 ~~~  210 (453)
                      ...
T Consensus        83 ~~~   85 (111)
T d1whxa_          83 IGV   85 (111)
T ss_dssp             TTT
T ss_pred             CCc
Confidence            544

>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=99.70  E-value=1.1e-17  Score=123.41  Aligned_cols=77  Identities=18%  Similarity=0.167  Sum_probs=67.3

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecc
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLAS  207 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~  207 (453)
                      ..+++|||+|||+++|+++|+++|++||.|.+|++..     .++|||||+|.+.++|++||. ....|.|+.|.|.++.
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~-~~~~i~g~~l~v~~a~   76 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG-EDLIIKGISVHISNAE   76 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT-CEEEETTEEEEEECCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh-CCCEECCEEeEEEeCC
Confidence            3468999999999999999999999999999998654     468899999999999999986 3467999999999986


Q ss_pred             cCC
Q 012923          208 IGP  210 (453)
Q Consensus       208 ~~~  210 (453)
                      .+.
T Consensus        77 ~k~   79 (88)
T d1wf0a_          77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.70  E-value=2.2e-17  Score=121.11  Aligned_cols=74  Identities=27%  Similarity=0.388  Sum_probs=67.9

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~~  208 (453)
                      .++|||+|||.++++++|+++|++||.|.+|+++++      +|||||+|.+.++|.+|+..++ ..|.|+.|.|.++..
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            468999999999999999999999999999998865      5799999999999999999888 569999999999875


Q ss_pred             C
Q 012923          209 G  209 (453)
Q Consensus       209 ~  209 (453)
                      .
T Consensus        82 ~   82 (86)
T d2cpja1          82 S   82 (86)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.70  E-value=8.3e-18  Score=124.26  Aligned_cols=75  Identities=15%  Similarity=0.240  Sum_probs=67.1

Q ss_pred             cCeEEEcCCCCCCCHHHH---HHHHhccCCeeEEEEcccCCCCCc---ceEEEEEEccHHHHHHHHHcCCC-ccCCeEeE
Q 012923          130 HRKIFVHGLGWDTKAETL---IDAFKQYGEIEDCKAVCDKVSGKS---KGYGFILFKTRSGARKALKEPQK-KIGNRMTA  202 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l---~~~f~~~G~i~~v~i~~d~~~g~~---~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~  202 (453)
                      .++|||+|||+++|+++|   +++|++||.|..|+|++++.++.+   +|||||+|.+.++|.+|++.+|+ .|.||.|+
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            367999999999999999   678999999999999999876654   49999999999999999998884 59999998


Q ss_pred             EE
Q 012923          203 CQ  204 (453)
Q Consensus       203 v~  204 (453)
                      |.
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            73

>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=99.70  E-value=3.4e-18  Score=126.00  Aligned_cols=71  Identities=13%  Similarity=0.083  Sum_probs=65.8

Q ss_pred             EEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCC
Q 012923          249 KIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDG  326 (453)
Q Consensus       249 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~  326 (453)
                      +|||+|||+.+|+++|+++|++||.|.+++|++       +|||||+|.+.++|.+||..|| ..|.|+.|.|.++...
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-------TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhcccccccccc-------cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            799999999999999999999999999999865       4899999999999999999999 8999999999887544

>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=99.70  E-value=3.8e-17  Score=122.83  Aligned_cols=76  Identities=22%  Similarity=0.465  Sum_probs=67.0

Q ss_pred             CCCCcCeEEEcCCC-CCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          126 EDPVHRKIFVHGLG-WDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       126 ~~~~~~~lfV~nLp-~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      .....++|||+||| ..+++++|+++|++||.|..|+|        ++|||||+|.+.++|.+||+.++ ..|.|+.|+|
T Consensus        11 ~~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V   82 (98)
T d1wf2a_          11 PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDI   82 (98)
T ss_dssp             CSSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEE
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34456789999996 67889999999999999999987        46899999999999999999988 5699999999


Q ss_pred             EecccC
Q 012923          204 QLASIG  209 (453)
Q Consensus       204 ~~~~~~  209 (453)
                      .++...
T Consensus        83 ~~a~~~   88 (98)
T d1wf2a_          83 NLAAEP   88 (98)
T ss_dssp             EETTSC
T ss_pred             EECCCC
Confidence            998643

>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=99.69  E-value=3.1e-17  Score=120.89  Aligned_cols=74  Identities=18%  Similarity=0.217  Sum_probs=64.4

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccC
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAID  325 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~  325 (453)
                      .++|||+|||+.+|+++|+++|++|| |..+.+      ++++|||||+|.+.++|.+||..|| ..|.|++|.|+++..
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            45899999999999999999999999 334444      3448999999999999999999999 889999999999955


Q ss_pred             CC
Q 012923          326 GP  327 (453)
Q Consensus       326 ~~  327 (453)
                      ..
T Consensus        78 ~~   79 (88)
T d1wg1a_          78 DA   79 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.69  E-value=3e-17  Score=123.54  Aligned_cols=76  Identities=22%  Similarity=0.357  Sum_probs=68.7

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCC--eEEEEEE
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEG--HILNCQR  322 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g--~~l~v~~  322 (453)
                      ++++|||+|||+.+|+++|+++|++||.|..|+++++      ++||||+|.+.++|.+|++.|| ..|.|  ++|+|.|
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~   89 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEe
Confidence            4579999999999999999999999999999999765      7899999999999999999999 77876  6899999


Q ss_pred             ccCCC
Q 012923          323 AIDGP  327 (453)
Q Consensus       323 a~~~~  327 (453)
                      ++..+
T Consensus        90 ak~~~   94 (97)
T d1whya_          90 AKSGP   94 (97)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            97544

>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=99.69  E-value=3.1e-17  Score=121.26  Aligned_cols=77  Identities=22%  Similarity=0.323  Sum_probs=68.1

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-Ccc-CCeEEEEEEc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNF-EGHILNCQRA  323 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l-~g~~l~v~~a  323 (453)
                      ++++|||+|||+.+|+++|+++|+.||.|..+.++..    +++|||||+|.+.++|.+|+..|+ ..| +|++|+|.|+
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            4579999999999999999999999999988877643    458899999999999999999998 666 6899999998


Q ss_pred             cCC
Q 012923          324 IDG  326 (453)
Q Consensus       324 ~~~  326 (453)
                      +++
T Consensus        85 k~~   87 (88)
T d2adca2          85 KST   87 (88)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            653

>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=99.69  E-value=6.3e-17  Score=125.02  Aligned_cols=75  Identities=17%  Similarity=0.276  Sum_probs=67.8

Q ss_pred             cCeEEEcCCCC-CCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecc
Q 012923          130 HRKIFVHGLGW-DTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLAS  207 (453)
Q Consensus       130 ~~~lfV~nLp~-~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~  207 (453)
                      +++|||+|||+ .+|+++|+++|+.||.|..|+|++++     +|||||+|.+.++|.+||+.++ ..|.|+.|.|.++.
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            57999999965 59999999999999999999999874     7899999999999999999888 55999999999986


Q ss_pred             cC
Q 012923          208 IG  209 (453)
Q Consensus       208 ~~  209 (453)
                      ..
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.68  E-value=1.3e-17  Score=129.05  Aligned_cols=80  Identities=24%  Similarity=0.444  Sum_probs=71.3

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEecc
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQLAS  207 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~~~  207 (453)
                      ...++|||+|||+++|+++|++||+.||.|..+.++.+..+|.++|||||+|.+.++|++||+..+..|.||.|.|.++.
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEEC
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEcC
Confidence            34568999999999999999999999999987666666669999999999999999999999865577999999998874

>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=99.68  E-value=6.2e-17  Score=119.01  Aligned_cols=73  Identities=21%  Similarity=0.263  Sum_probs=65.7

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEeccc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQLASI  208 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~~~~  208 (453)
                      .++|||+|||+++|+++|+++|++||.|..+++.      +++|||||+|.+.++|..||..+++ .|.|+.|.|.++.+
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP   81 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   81 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccC
Confidence            4789999999999999999999999999887753      4678999999999999999998884 59999999999863

>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=99.68  E-value=1.1e-16  Score=121.96  Aligned_cols=77  Identities=14%  Similarity=0.113  Sum_probs=69.4

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC---CccCCeEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH---KNFEGHILNC  320 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~---~~l~g~~l~v  320 (453)
                      ...+++|||+|||..+|+++|+++|++||.|..|++.++      |+||||+|.+.++|..||..++   ..+.|++|+|
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v   85 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEE
Confidence            345679999999999999999999999999999999865      7899999999999999999774   5789999999


Q ss_pred             EEccCC
Q 012923          321 QRAIDG  326 (453)
Q Consensus       321 ~~a~~~  326 (453)
                      .|+...
T Consensus        86 ~~s~~~   91 (104)
T d1wexa_          86 NYSTSK   91 (104)
T ss_dssp             EECSSS
T ss_pred             EEcCCC
Confidence            999654

>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=99.68  E-value=1.5e-17  Score=123.66  Aligned_cols=78  Identities=22%  Similarity=0.371  Sum_probs=69.8

Q ss_pred             ccEEEEecCCCCccHHHHHH----HHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          247 QRKIFVSNVGSELEPQKLLA----FFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~----~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      +++|||+|||+.+|+++|++    +|++||.|.+|++.+   +++++|||||+|.+.++|.+|+..+| ..|.|+.|.|.
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            46999999999999999864    689999999998854   56789999999999999999999998 88999999999


Q ss_pred             EccCCC
Q 012923          322 RAIDGP  327 (453)
Q Consensus       322 ~a~~~~  327 (453)
                      |+....
T Consensus        80 ~ak~~~   85 (91)
T d1nu4a_          80 YAKTDS   85 (91)
T ss_dssp             ECSSCC
T ss_pred             EeCCCc
Confidence            997643

>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=99.68  E-value=2.7e-17  Score=122.23  Aligned_cols=78  Identities=27%  Similarity=0.362  Sum_probs=68.9

Q ss_pred             CcCeEEEcCCCCCCCHHHHHH----HHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEE
Q 012923          129 VHRKIFVHGLGWDTKAETLID----AFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTAC  203 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~----~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v  203 (453)
                      .++||||+|||+++|+++|++    +|++||+|.+|++..   +++++|||||+|.+.++|.+|++.++ ..+.|+.|.|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            368999999999999999864    689999999998765   56789999999999999999999887 5599999999


Q ss_pred             EecccC
Q 012923          204 QLASIG  209 (453)
Q Consensus       204 ~~~~~~  209 (453)
                      .++...
T Consensus        79 ~~ak~~   84 (91)
T d1nu4a_          79 QYAKTD   84 (91)
T ss_dssp             EECSSC
T ss_pred             EEeCCC
Confidence            998643

>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=99.68  E-value=7e-17  Score=119.27  Aligned_cols=76  Identities=14%  Similarity=0.182  Sum_probs=67.3

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-cc-CCeEeEEEe
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KI-GNRMTACQL  205 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~-~gr~~~v~~  205 (453)
                      +.+++|||+|||+++|+++|+++|++||.|..+.++..    +++|||||+|.+.++|.+|+..|++ .| .|+.|+|.+
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~   83 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            56789999999999999999999999999988876643    4678999999999999999998885 46 589999999


Q ss_pred             cc
Q 012923          206 AS  207 (453)
Q Consensus       206 ~~  207 (453)
                      +.
T Consensus        84 sk   85 (88)
T d2adca2          84 SK   85 (88)
T ss_dssp             CS
T ss_pred             CC
Confidence            75

>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=99.67  E-value=4.9e-17  Score=119.76  Aligned_cols=74  Identities=19%  Similarity=0.303  Sum_probs=63.7

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEecc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQLAS  207 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~~~  207 (453)
                      .+++|||+|||+++|+++|+++|.+|| +..+.+      ++++|||||+|.+.++|++|++.|++ .|.|+.|.|.++.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            357899999999999999999999999 333432      35689999999999999999998885 4999999999986


Q ss_pred             cC
Q 012923          208 IG  209 (453)
Q Consensus       208 ~~  209 (453)
                      ..
T Consensus        77 ~~   78 (88)
T d1wg1a_          77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.67  E-value=3.7e-17  Score=122.92  Aligned_cols=75  Identities=16%  Similarity=0.167  Sum_probs=68.8

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ...+|||+|||+.+++++|+++|+.||.|..|.|.+       +|||||+|.+.++|.+||+.|| ..|.|+.|+|.++.
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            446899999999999999999999999999999864       6899999999999999999999 89999999999986


Q ss_pred             CCC
Q 012923          325 DGP  327 (453)
Q Consensus       325 ~~~  327 (453)
                      .++
T Consensus        87 ~~~   89 (98)
T d1wg4a_          87 VYP   89 (98)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            554

>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=99.67  E-value=6.7e-17  Score=119.32  Aligned_cols=77  Identities=12%  Similarity=0.111  Sum_probs=69.0

Q ss_pred             cccccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcC--C-CccCCeEEEE
Q 012923          244 EYTQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEP--H-KNFEGHILNC  320 (453)
Q Consensus       244 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~--~-~~l~g~~l~v  320 (453)
                      ..++++|||+|||+.+|+++|+++|++||.|..++++++      ++||||+|.+.++|.+|+..+  + ..|.|++|+|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v   78 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   78 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEE
Confidence            345679999999999999999999999999999999865      689999999999999999865  3 6799999999


Q ss_pred             EEccCC
Q 012923          321 QRAIDG  326 (453)
Q Consensus       321 ~~a~~~  326 (453)
                      .|+..+
T Consensus        79 ~~sk~~   84 (88)
T d2cq1a1          79 QYSNHK   84 (88)
T ss_dssp             EECSCS
T ss_pred             EECCCC
Confidence            998644

>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=99.67  E-value=5.2e-17  Score=125.61  Aligned_cols=79  Identities=16%  Similarity=0.248  Sum_probs=71.7

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ...+|||+|||+.+|+++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|.+||. +| ..|+||.|.|.++.
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEEC
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEcC
Confidence            45699999999999999999999999999887777777899999999999999999999997 56 88999999999875


Q ss_pred             C
Q 012923          325 D  325 (453)
Q Consensus       325 ~  325 (453)
                      .
T Consensus        96 ~   96 (112)
T d1wela1          96 K   96 (112)
T ss_dssp             H
T ss_pred             h
Confidence            3

>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=99.66  E-value=1.1e-16  Score=115.48  Aligned_cols=75  Identities=19%  Similarity=0.293  Sum_probs=66.5

Q ss_pred             CCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          128 PVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      ...+||||+||+  +|+++|+++|++||.|.+|++.++      +|||||+|.+.++|..|+..++ ..|.|+.|+|.++
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            346899999996  899999999999999999998754      5799999999999999999888 5699999999999


Q ss_pred             ccCC
Q 012923          207 SIGP  210 (453)
Q Consensus       207 ~~~~  210 (453)
                      ...|
T Consensus        75 ~~~P   78 (79)
T d2bz2a1          75 RKQP   78 (79)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            6543

>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=99.66  E-value=1.4e-16  Score=113.36  Aligned_cols=70  Identities=17%  Similarity=0.239  Sum_probs=62.8

Q ss_pred             EEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEccCC
Q 012923          250 IFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAIDG  326 (453)
Q Consensus       250 l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~~~  326 (453)
                      |||+|||+.+|+++|+++|++|| |..+.+      ++++|||||+|.+.++|.+|+..|| ..|.|++|.|+|+...
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 555554      3458999999999999999999999 8999999999999654

>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=99.66  E-value=1.8e-16  Score=119.14  Aligned_cols=78  Identities=23%  Similarity=0.443  Sum_probs=68.0

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCC--eEeEE
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGN--RMTAC  203 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~g--r~~~v  203 (453)
                      .+.+++|||+|||+++|+++|+++|++||.|..|+++++      ++||||+|.+.++|.+|++.|++ .|.|  +.|+|
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v   87 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEE
Confidence            355789999999999999999999999999999998764      57999999999999999999884 4655  58999


Q ss_pred             EecccCC
Q 012923          204 QLASIGP  210 (453)
Q Consensus       204 ~~~~~~~  210 (453)
                      .|+...+
T Consensus        88 ~~ak~~~   94 (97)
T d1whya_          88 DFAKSGP   94 (97)
T ss_dssp             EECCCCC
T ss_pred             EeCCCCC
Confidence            9986543

>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=99.66  E-value=5.6e-17  Score=117.21  Aligned_cols=73  Identities=14%  Similarity=0.217  Sum_probs=65.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-c-cCCeEeEEEeccc
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-K-IGNRMTACQLASI  208 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~-~~gr~~~v~~~~~  208 (453)
                      .+|||+|||.++|+++|+++|++||.|..+++++      ++|||||+|.+.++|.+|++.+++ . +.|+.|.|.++..
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            3799999999999999999999999998776654      468999999999999999998884 3 8999999999875


Q ss_pred             C
Q 012923          209 G  209 (453)
Q Consensus       209 ~  209 (453)
                      +
T Consensus        76 k   76 (80)
T d2cqha1          76 K   76 (80)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.65  E-value=1.2e-16  Score=122.75  Aligned_cols=77  Identities=18%  Similarity=0.084  Sum_probs=68.2

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-Ccc--CCeEEEEEE
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNF--EGHILNCQR  322 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l--~g~~l~v~~  322 (453)
                      ...+|||+|||+.+|+++|+++|++||.|..|.|++++    ++|||||+|.+.++|.+||..|| ..|  .+++|.|.+
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~   81 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF   81 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEE
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEe
Confidence            34689999999999999999999999999999998764    48999999999999999999998 666  578888888


Q ss_pred             ccCC
Q 012923          323 AIDG  326 (453)
Q Consensus       323 a~~~  326 (453)
                      +...
T Consensus        82 s~~~   85 (108)
T d2adba1          82 SKLT   85 (108)
T ss_dssp             CSSC
T ss_pred             cCCc
Confidence            7554

>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=99.65  E-value=1.7e-16  Score=112.89  Aligned_cols=70  Identities=23%  Similarity=0.392  Sum_probs=61.7

Q ss_pred             EEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEecccC
Q 012923          133 IFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQLASIG  209 (453)
Q Consensus       133 lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~~~~~  209 (453)
                      |||+|||+++|+++|+++|++|| +..+++      ++++|||||+|.+.++|.+|+..+|+ .+.|+.|.|.++...
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            89999999999999999999999 545543      45789999999999999999998885 599999999998644

>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=99.65  E-value=2.2e-16  Score=116.52  Aligned_cols=78  Identities=13%  Similarity=0.146  Sum_probs=69.1

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC---CccCCeEeE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ---KKIGNRMTA  202 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~---~~~~gr~~~  202 (453)
                      +.+.+++|||+|||+++|+++|+++|++||.|..|+++++      ++||||+|.+.++|.+|++.++   ..+.|+.|+
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~   77 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   77 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEE
Confidence            3567899999999999999999999999999999998865      4799999999999999998653   468999999


Q ss_pred             EEecccC
Q 012923          203 CQLASIG  209 (453)
Q Consensus       203 v~~~~~~  209 (453)
                      |.++..+
T Consensus        78 v~~sk~~   84 (88)
T d2cq1a1          78 IQYSNHK   84 (88)
T ss_dssp             EEECSCS
T ss_pred             EEECCCC
Confidence            9998644

>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=99.65  E-value=3.7e-17  Score=120.34  Aligned_cols=69  Identities=17%  Similarity=0.257  Sum_probs=63.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecc
Q 012923          132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLAS  207 (453)
Q Consensus       132 ~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~  207 (453)
                      +|||+|||+++|+++|+++|++||.|..|+|+++       |||||+|.+.++|.+||+.|+ ..|.|+.|.|.++.
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~   71 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   71 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEe
Confidence            6999999999999999999999999999998764       799999999999999998877 55999999887764

>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=99.64  E-value=1.6e-16  Score=119.68  Aligned_cols=76  Identities=18%  Similarity=0.180  Sum_probs=67.4

Q ss_pred             ccccEEEEecCCCC-ccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHc--CC-CccCCeEEEE
Q 012923          245 YTQRKIFVSNVGSE-LEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEE--PH-KNFEGHILNC  320 (453)
Q Consensus       245 ~~~~~l~V~nLp~~-~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~--~~-~~l~g~~l~v  320 (453)
                      ...++|||+|||.. +|+++|+++|++||.|.+|+++++      +|||||+|.+.++|.+||..  ++ ..|.|++|+|
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V   89 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   89 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEE
Confidence            34579999999985 899999999999999999999876      78999999999999999984  44 6899999999


Q ss_pred             EEccCC
Q 012923          321 QRAIDG  326 (453)
Q Consensus       321 ~~a~~~  326 (453)
                      .|+...
T Consensus        90 ~~s~~~   95 (99)
T d1x4fa1          90 DLSEKY   95 (99)
T ss_dssp             EEECSC
T ss_pred             EEcCCc
Confidence            998643

>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=99.64  E-value=2.4e-16  Score=118.38  Aligned_cols=75  Identities=16%  Similarity=0.255  Sum_probs=67.0

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-ccCCeEeEEEecc
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-KIGNRMTACQLAS  207 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-~~~gr~~~v~~~~  207 (453)
                      ..++|||+|||+++++++|+++|++||.|..|+|.+       +|||||+|.+.++|.+||+.||+ .|.|+.|.|.+..
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            456899999999999999999999999999999864       47999999999999999998885 5999999999876


Q ss_pred             cCC
Q 012923          208 IGP  210 (453)
Q Consensus       208 ~~~  210 (453)
                      ..+
T Consensus        87 ~~~   89 (98)
T d1wg4a_          87 VYP   89 (98)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            443

>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=99.63  E-value=3e-16  Score=115.60  Aligned_cols=76  Identities=13%  Similarity=0.081  Sum_probs=67.7

Q ss_pred             ccccEEEEecCCCC-ccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC---CccCCeEEEE
Q 012923          245 YTQRKIFVSNVGSE-LEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH---KNFEGHILNC  320 (453)
Q Consensus       245 ~~~~~l~V~nLp~~-~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~---~~l~g~~l~v  320 (453)
                      ..+++|||+|||.. +|+++|+++|++||.|.+|.++++      +++|||+|.+.++|..|+..++   ..++|++|+|
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            34579999999986 899999999999999999999876      6799999999999999999763   5799999999


Q ss_pred             EEccCC
Q 012923          321 QRAIDG  326 (453)
Q Consensus       321 ~~a~~~  326 (453)
                      .|+...
T Consensus        80 ~~s~~~   85 (89)
T d1x4da1          80 HLSQKY   85 (89)
T ss_dssp             EEECCC
T ss_pred             EECCCc
Confidence            998643

>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=99.63  E-value=7.6e-16  Score=117.31  Aligned_cols=81  Identities=16%  Similarity=0.182  Sum_probs=70.4

Q ss_pred             CCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC---CccCCeEeE
Q 012923          126 EDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ---KKIGNRMTA  202 (453)
Q Consensus       126 ~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~---~~~~gr~~~  202 (453)
                      ....+++|||+|||.++|+++|+++|++||.|..|+++++      +|||||+|.+.++|..||..++   ..+.|+.|+
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~   84 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEE
Confidence            3456789999999999999999999999999999998754      5799999999999999998764   358899999


Q ss_pred             EEecccCCCC
Q 012923          203 CQLASIGPAT  212 (453)
Q Consensus       203 v~~~~~~~~~  212 (453)
                      |.++......
T Consensus        85 v~~s~~~~~~   94 (104)
T d1wexa_          85 FNYSTSKRIT   94 (104)
T ss_dssp             EEECSSSSCC
T ss_pred             EEEcCCCccC
Confidence            9999755443

>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=99.63  E-value=4.4e-16  Score=118.00  Aligned_cols=75  Identities=12%  Similarity=0.031  Sum_probs=66.7

Q ss_pred             ccEEEEecCCCCc-c----HHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEE
Q 012923          247 QRKIFVSNVGSEL-E----PQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNC  320 (453)
Q Consensus       247 ~~~l~V~nLp~~~-t----~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v  320 (453)
                      .++|||+||+..+ +    +++|+.+|++||.|..+++++.      ++||||+|.+.++|.+||..|| ..|+|++|+|
T Consensus         5 ~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v   78 (104)
T d1weya_           5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCCEeEE
Confidence            4689999999886 3    3569999999999999999864      7899999999999999999999 8999999999


Q ss_pred             EEccCCC
Q 012923          321 QRAIDGP  327 (453)
Q Consensus       321 ~~a~~~~  327 (453)
                      .|+....
T Consensus        79 ~~a~~~~   85 (104)
T d1weya_          79 YFAQTLH   85 (104)
T ss_dssp             ECCCCSS
T ss_pred             eecccCC
Confidence            9996543

>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=99.63  E-value=2.5e-16  Score=120.97  Aligned_cols=77  Identities=12%  Similarity=0.166  Sum_probs=67.8

Q ss_pred             CcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-c--CCeEeEEEe
Q 012923          129 VHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-I--GNRMTACQL  205 (453)
Q Consensus       129 ~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~--~gr~~~v~~  205 (453)
                      ...+|||+|||+++|+++|+++|++||.|..|+|++++    ++|||||+|.+.++|..||..+++. |  .++.|.|.+
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~   81 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF   81 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEE
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEe
Confidence            34689999999999999999999999999999998764    5899999999999999999998854 5  578888888


Q ss_pred             cccC
Q 012923          206 ASIG  209 (453)
Q Consensus       206 ~~~~  209 (453)
                      +...
T Consensus        82 s~~~   85 (108)
T d2adba1          82 SKLT   85 (108)
T ss_dssp             CSSC
T ss_pred             cCCc
Confidence            7644

>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=99.61  E-value=1.3e-15  Score=129.38  Aligned_cols=83  Identities=29%  Similarity=0.466  Sum_probs=77.0

Q ss_pred             CCCCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEE
Q 012923          125 DEDPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQ  204 (453)
Q Consensus       125 ~~~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~  204 (453)
                      ......++|||+|||+.+|+++|+++|+.||.|..+.|+.+..+++++|||||+|.+.++|.+||+.+++.|.|+.|.|.
T Consensus        92 ~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~~~~~~~~G~~i~V~  171 (183)
T d1u1qa_          92 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR  171 (183)
T ss_dssp             TTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHTSSCEEETTEEEEEE
T ss_pred             ccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHHhCCCeECCEEEEEE
Confidence            44556789999999999999999999999999999999999989999999999999999999999977778999999999


Q ss_pred             ecc
Q 012923          205 LAS  207 (453)
Q Consensus       205 ~~~  207 (453)
                      ++.
T Consensus       172 ~A~  174 (183)
T d1u1qa_         172 KAL  174 (183)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            875

>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=99.60  E-value=2.2e-17  Score=122.60  Aligned_cols=76  Identities=18%  Similarity=0.390  Sum_probs=67.2

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeee-----ccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEE
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLG-----IDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQ  321 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~-----~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~  321 (453)
                      ++|||+|||+.+|+++|+++|+.||.|..+.+.     .+..+++++|||||+|.+.++|.+|+. || ..|.|+.|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            589999999999999999999999998877664     345678899999999999999999996 77 89999999997


Q ss_pred             Ecc
Q 012923          322 RAI  324 (453)
Q Consensus       322 ~a~  324 (453)
                      +++
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            544

>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=99.59  E-value=2.9e-17  Score=121.95  Aligned_cols=76  Identities=12%  Similarity=0.231  Sum_probs=65.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEc-----ccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeEeEEEe
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAV-----CDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRMTACQL  205 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~-----~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~~~v~~  205 (453)
                      |+|||+|||+++|+++|+++|+.||.|..+.+.     .+..+++++|||||+|.+.++|.+|++..+..+.|+.|+|..
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            789999999999999999999999988777654     345577899999999999999999997444679999999965


Q ss_pred             c
Q 012923          206 A  206 (453)
Q Consensus       206 ~  206 (453)
                      +
T Consensus        82 ~   82 (90)
T d1u2fa_          82 P   82 (90)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.58  E-value=1.4e-15  Score=114.45  Aligned_cols=77  Identities=18%  Similarity=0.223  Sum_probs=66.7

Q ss_pred             CCCcCeEEEcCCCCC-CCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHc--CC-CccCCeEeE
Q 012923          127 DPVHRKIFVHGLGWD-TKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKE--PQ-KKIGNRMTA  202 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~-~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~--~~-~~~~gr~~~  202 (453)
                      ...+++|||+|||.+ +|+++|+++|++||.|.+|+|+++      +|||||+|.+.++|..|++.  ++ ..+.|+.|+
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~   88 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   88 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEE
Confidence            345689999999985 899999999999999999998865      57999999999999999973  33 468999999


Q ss_pred             EEecccC
Q 012923          203 CQLASIG  209 (453)
Q Consensus       203 v~~~~~~  209 (453)
                      |.++...
T Consensus        89 V~~s~~~   95 (99)
T d1x4fa1          89 VDLSEKY   95 (99)
T ss_dssp             EEEECSC
T ss_pred             EEEcCCc
Confidence            9998543

>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=99.57  E-value=3e-15  Score=110.13  Aligned_cols=76  Identities=13%  Similarity=0.135  Sum_probs=66.9

Q ss_pred             CCCcCeEEEcCCCCC-CCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC---CccCCeEeE
Q 012923          127 DPVHRKIFVHGLGWD-TKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ---KKIGNRMTA  202 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~-~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~---~~~~gr~~~  202 (453)
                      ...+++|||+|||.. +|+++|.++|++||.|.+|+++.++      ++|||+|.+.++|..|++.++   ..+.|++|.
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k------~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            455789999999986 7899999999999999999998754      589999999999999998653   459999999


Q ss_pred             EEeccc
Q 012923          203 CQLASI  208 (453)
Q Consensus       203 v~~~~~  208 (453)
                      |.++..
T Consensus        79 V~~s~~   84 (89)
T d1x4da1          79 VHLSQK   84 (89)
T ss_dssp             EEEECC
T ss_pred             EEECCC
Confidence            999863

>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=99.53  E-value=7.5e-15  Score=111.10  Aligned_cols=78  Identities=13%  Similarity=-0.028  Sum_probs=66.8

Q ss_pred             CCcCeEEEcCCCCCC-CH----HHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc-cCCeEe
Q 012923          128 PVHRKIFVHGLGWDT-KA----ETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK-IGNRMT  201 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~-te----~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~-~~gr~~  201 (453)
                      ..+++|||+||+.++ ++    ++|+.+|++||.|.++++++      +++||||+|.+.++|.+|+..|++. |.|+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            346799999999886 33    56999999999999999874      4679999999999999999999954 999999


Q ss_pred             EEEecccCCC
Q 012923          202 ACQLASIGPA  211 (453)
Q Consensus       202 ~v~~~~~~~~  211 (453)
                      .|.|+.....
T Consensus        77 ~v~~a~~~~~   86 (104)
T d1weya_          77 KLYFAQTLHI   86 (104)
T ss_dssp             EEECCCCSSC
T ss_pred             EEeecccCCC
Confidence            9999864433

>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=99.52  E-value=7.2e-16  Score=116.83  Aligned_cols=75  Identities=17%  Similarity=0.239  Sum_probs=70.3

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEc
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRA  323 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a  323 (453)
                      +.++|++++..+++++|+++|++||.|.+|+|+++ .+++++|||||+|.+.++|.+|+..|| ..|+||+|.|.+.
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            46888999999999999999999999999999876 589999999999999999999999999 9999999999885

>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=99.50  E-value=1e-15  Score=115.97  Aligned_cols=74  Identities=15%  Similarity=0.221  Sum_probs=68.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEec
Q 012923          132 KIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLA  206 (453)
Q Consensus       132 ~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~  206 (453)
                      .|+|++++.++++++|+++|++||.|.+|+|+++. +++++|||||+|.+.++|.+|+..++ ..+.||.|.|.+.
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC-CCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            58888999999999999999999999999998875 89999999999999999999999988 5599999999875

>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=99.49  E-value=2.6e-14  Score=110.19  Aligned_cols=73  Identities=14%  Similarity=0.087  Sum_probs=64.2

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCH-HHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTV-DAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~-~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      ...+||+|||+.+|+++|+++|++||.|.+|.|+++      +|||||+|.+. ++|..|+..++ ..|.++.+.|.|+.
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            457799999999999999999999999999999865      89999999985 78999999999 77877777777765


Q ss_pred             C
Q 012923          325 D  325 (453)
Q Consensus       325 ~  325 (453)
                      .
T Consensus        85 ~   85 (113)
T d1owxa_          85 L   85 (113)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.44  E-value=8.8e-14  Score=104.57  Aligned_cols=63  Identities=22%  Similarity=0.428  Sum_probs=56.8

Q ss_pred             ccccEEEEec--CCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-Ccc
Q 012923          245 YTQRKIFVSN--VGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNF  313 (453)
Q Consensus       245 ~~~~~l~V~n--Lp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l  313 (453)
                      .++++|||.|  ||..+|+++|+++|++||.|..|+++++      ++||||+|.+.++|.+|+..|| ..|
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            3456899966  9999999999999999999999999875      7899999999999999999999 555

>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=99.43  E-value=1.2e-13  Score=106.48  Aligned_cols=71  Identities=25%  Similarity=0.186  Sum_probs=61.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccH-HHHHHHHHcCC-CccCCeEeEEEecc
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTR-SGARKALKEPQ-KKIGNRMTACQLAS  207 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~-~~a~~A~~~~~-~~~~gr~~~v~~~~  207 (453)
                      ..+||+|||+.+|+++|+++|++||+|..|+|+++      +|||||.|.+. ++|..|+..++ ..+.++.+.|.+..
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            45699999999999999999999999999999864      68999999996 67888888888 45777777777764

>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=99.43  E-value=3.1e-13  Score=101.19  Aligned_cols=78  Identities=18%  Similarity=0.253  Sum_probs=66.6

Q ss_pred             ccccEEEEecC--CCCc---------cHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-Cc
Q 012923          245 YTQRKIFVSNV--GSEL---------EPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KN  312 (453)
Q Consensus       245 ~~~~~l~V~nL--p~~~---------t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~  312 (453)
                      ...++|+|+||  |..+         .+++|++.|++||.|..|.+..+    ..+|||||+|.+.++|.+|+..|| ..
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            34579999999  5432         23689999999999999998765    458999999999999999999999 89


Q ss_pred             cCCeEEEEEEccCC
Q 012923          313 FEGHILNCQRAIDG  326 (453)
Q Consensus       313 l~g~~l~v~~a~~~  326 (453)
                      |+||+|.|.++..+
T Consensus        82 ~~gr~i~v~~~~g~   95 (99)
T d2dita1          82 FGGRQITAQAWDGT   95 (99)
T ss_dssp             ETTEECEEEECCSC
T ss_pred             ECCEEEEEEEeCCc
Confidence            99999999998654

>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=99.42  E-value=1.7e-13  Score=97.97  Aligned_cols=71  Identities=21%  Similarity=0.273  Sum_probs=60.4

Q ss_pred             ccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeE-EEEEEcc
Q 012923          247 QRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHI-LNCQRAI  324 (453)
Q Consensus       247 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~-l~v~~a~  324 (453)
                      .+.|+|.+||++++++.| ++|++||.|.++++.++      ++||||+|.+.++|.+||+ +| ..|+|+. |.|..+.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~------~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC------CCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            458999999999997655 57999999999988543      8999999999999999996 67 8899975 6788775


Q ss_pred             C
Q 012923          325 D  325 (453)
Q Consensus       325 ~  325 (453)
                      .
T Consensus        76 ~   76 (81)
T d1wwha1          76 D   76 (81)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.42  E-value=1.7e-13  Score=102.93  Aligned_cols=64  Identities=17%  Similarity=0.282  Sum_probs=56.6

Q ss_pred             CCCCcCeEEEcC--CCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCc
Q 012923          126 EDPVHRKIFVHG--LGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKK  195 (453)
Q Consensus       126 ~~~~~~~lfV~n--Lp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~  195 (453)
                      .....++|||.|  ||.++|+++|+++|++||.|..|+++.+      ++||||+|.+.++|.+|+..|++.
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~   79 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGK   79 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTC
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCC
Confidence            345567899965  9999999999999999999999998765      469999999999999999999954

>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=99.39  E-value=3.2e-13  Score=96.54  Aligned_cols=71  Identities=20%  Similarity=0.304  Sum_probs=58.7

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCCeE-eEEEecc
Q 012923          130 HRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGNRM-TACQLAS  207 (453)
Q Consensus       130 ~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~gr~-~~v~~~~  207 (453)
                      .+.|+|.+||++++++ |.++|++||+|.++++.      +++|||||+|.+.++|++||+.....|.|+. |.|.++.
T Consensus         4 ~~wV~V~G~p~~~~~~-il~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASY-ILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHH-HHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECC
T ss_pred             ccEEEEECCChHHHHH-HHHHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeCC
Confidence            4689999999999865 45689999999999864      3468999999999999999975446688874 5687765

>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=99.36  E-value=1.1e-12  Score=98.09  Aligned_cols=79  Identities=15%  Similarity=0.156  Sum_probs=66.6

Q ss_pred             CCCcCeEEEcCC--CCCC---------CHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCC-
Q 012923          127 DPVHRKIFVHGL--GWDT---------KAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQK-  194 (453)
Q Consensus       127 ~~~~~~lfV~nL--p~~~---------te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~-  194 (453)
                      ...+++|+|+||  |.++         .+++|++.|++||.|..|++..+    ..+|||||+|.+.++|.+|+..|++ 
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~   80 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGR   80 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCc
Confidence            456789999999  5543         23689999999999999988765    3679999999999999999999995 


Q ss_pred             ccCCeEeEEEecccC
Q 012923          195 KIGNRMTACQLASIG  209 (453)
Q Consensus       195 ~~~gr~~~v~~~~~~  209 (453)
                      .+.||.|.|.+....
T Consensus        81 ~~~gr~i~v~~~~g~   95 (99)
T d2dita1          81 WFGGRQITAQAWDGT   95 (99)
T ss_dssp             EETTEECEEEECCSC
T ss_pred             EECCEEEEEEEeCCc
Confidence            599999999998644

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=6.2e-13  Score=100.62  Aligned_cols=79  Identities=15%  Similarity=0.149  Sum_probs=67.2

Q ss_pred             cccEEEEecC--CCCc--------cHHHHHHHHhccCCcceeeeeccCCCC--CCceEEEEEECCHHHHHHHHHcCC-Cc
Q 012923          246 TQRKIFVSNV--GSEL--------EPQKLLAFFSKYGEIEEGPLGIDKATG--KPKGFCLFVYKTVDAAKKALEEPH-KN  312 (453)
Q Consensus       246 ~~~~l~V~nL--p~~~--------t~~~l~~~F~~~G~i~~v~i~~d~~~g--~~kg~afV~F~~~~~A~~Al~~~~-~~  312 (453)
                      ++++|.|.||  +..+        ..++|++.|++||.|++|.|+++..+.  ...|++||+|.+.++|.+|+..|| ..
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            4579999999  3332        346799999999999999998866443  347899999999999999999999 89


Q ss_pred             cCCeEEEEEEcc
Q 012923          313 FEGHILNCQRAI  324 (453)
Q Consensus       313 l~g~~l~v~~a~  324 (453)
                      |+||+|.|.+..
T Consensus        83 f~gR~v~v~f~~   94 (104)
T d1o0pa_          83 FANRVVVTKYCD   94 (104)
T ss_dssp             SSSSCCEEEEEC
T ss_pred             ECCeEEEEEEcC
Confidence            999999999974

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.25  E-value=3.7e-12  Score=96.25  Aligned_cols=80  Identities=15%  Similarity=0.167  Sum_probs=67.2

Q ss_pred             CCcCeEEEcCC--CCCC--------CHHHHHHHHhccCCeeEEEEcccCCCC--CcceEEEEEEccHHHHHHHHHcCCC-
Q 012923          128 PVHRKIFVHGL--GWDT--------KAETLIDAFKQYGEIEDCKAVCDKVSG--KSKGYGFILFKTRSGARKALKEPQK-  194 (453)
Q Consensus       128 ~~~~~lfV~nL--p~~~--------te~~l~~~f~~~G~i~~v~i~~d~~~g--~~~G~afV~f~~~~~a~~A~~~~~~-  194 (453)
                      +.++.|.|+||  |.++        ..+||++.|++||.|.+|.|.++..+.  ...|++||+|.+.++|.+|+..|++ 
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            35789999999  4443        345799999999999999998876443  4569999999999999999999985 


Q ss_pred             ccCCeEeEEEecc
Q 012923          195 KIGNRMTACQLAS  207 (453)
Q Consensus       195 ~~~gr~~~v~~~~  207 (453)
                      .+.||.|.|.+..
T Consensus        82 ~f~gR~v~v~f~~   94 (104)
T d1o0pa_          82 KFANRVVVTKYCD   94 (104)
T ss_dssp             CSSSSCCEEEEEC
T ss_pred             EECCeEEEEEEcC
Confidence            5899999999875

>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=97.64  E-value=8.5e-05  Score=51.24  Aligned_cols=71  Identities=15%  Similarity=0.203  Sum_probs=57.3

Q ss_pred             ccccEEEEecCCCCccH---------HHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCCCccCC
Q 012923          245 YTQRKIFVSNVGSELEP---------QKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPHKNFEG  315 (453)
Q Consensus       245 ~~~~~l~V~nLp~~~t~---------~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~~~l~g  315 (453)
                      ++.-+|.|.-+..+..+         .+|.+.|..||+|.-||++.+        -.+|+|.+-++|.+|+.....+++|
T Consensus        13 PpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~l~g~~v~G   84 (95)
T d1ufwa_          13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLDVDGMKVKG   84 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHHGGGSEETT
T ss_pred             CCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhccCCeEEcc
Confidence            34457888655444333         467888999999999999877        4899999999999999988899999


Q ss_pred             eEEEEEEc
Q 012923          316 HILNCQRA  323 (453)
Q Consensus       316 ~~l~v~~a  323 (453)
                      +.|.|...
T Consensus        85 ~~l~It~~   92 (95)
T d1ufwa_          85 RAVKISGP   92 (95)
T ss_dssp             EEEEEECC
T ss_pred             eEEEEecC
Confidence            99999764

>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=97.47  E-value=0.00012  Score=50.50  Aligned_cols=72  Identities=17%  Similarity=0.186  Sum_probs=58.1

Q ss_pred             CCcCeEEEcCCCCCCCH---------HHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCCCccCC
Q 012923          128 PVHRKIFVHGLGWDTKA---------ETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQKKIGN  198 (453)
Q Consensus       128 ~~~~~lfV~nLp~~~te---------~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~~~~~g  198 (453)
                      +..-||.|.=+..+..+         .+|.+.|..||+|.-||++.+.        .+|+|.+-++|.+|+.....+++|
T Consensus        13 PpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d~--------mwVTF~dG~SAL~al~l~g~~v~G   84 (95)
T d1ufwa_          13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLDVDGMKVKG   84 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHHGGGSEETT
T ss_pred             CCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCCe--------EEEEECCcHHHHHHhccCCeEEcc
Confidence            44567777644433322         3677889999999999999885        999999999999999999899999


Q ss_pred             eEeEEEecc
Q 012923          199 RMTACQLAS  207 (453)
Q Consensus       199 r~~~v~~~~  207 (453)
                      +.|.|....
T Consensus        85 ~~l~It~~~   93 (95)
T d1ufwa_          85 RAVKISGPS   93 (95)
T ss_dssp             EEEEEECCC
T ss_pred             eEEEEecCC
Confidence            999997653

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.36  E-value=0.0002  Score=50.33  Aligned_cols=63  Identities=10%  Similarity=0.053  Sum_probs=53.5

Q ss_pred             cEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCC--ceEEEEEECCHHHHHHHHHcCC
Q 012923          248 RKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKP--KGFCLFVYKTVDAAKKALEEPH  310 (453)
Q Consensus       248 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~--kg~afV~F~~~~~A~~Al~~~~  310 (453)
                      ++|.|+.||+.+|++++.+.+...+.+........+.+.+.  -..|||.|.+.+++..-....+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~   66 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFD   66 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHT
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcC
Confidence            48999999999999999999999999988887776654332  3469999999999988888877

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.30  E-value=0.00034  Score=45.63  Aligned_cols=60  Identities=15%  Similarity=0.127  Sum_probs=50.8

Q ss_pred             HHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC-CccCCeEEEEEEcc
Q 012923          262 QKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH-KNFEGHILNCQRAI  324 (453)
Q Consensus       262 ~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~-~~l~g~~l~v~~a~  324 (453)
                      +.|...|.+|+.|.++.|.... .+..  .|-|...+.++|.-|+..|+ ..|++++|.|.++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~-dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHT-DYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC-STTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEecc-CCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            4566789999999999987643 3333  48999999999999999999 89999999999975

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.23  E-value=0.00039  Score=48.83  Aligned_cols=65  Identities=14%  Similarity=0.068  Sum_probs=53.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCc--ceEEEEEEccHHHHHHHHHcCCCc
Q 012923          131 RKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKS--KGYGFILFKTRSGARKALKEPQKK  195 (453)
Q Consensus       131 ~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~--~G~afV~f~~~~~a~~A~~~~~~~  195 (453)
                      ++|.|+.||+++|++++.+.+...+.+.....+..+.+-+.  -.-|||.|.+.+++....+..++.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~   68 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGY   68 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCc
Confidence            57999999999999999999999999888776655443221  245999999999999999887744

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.54  E-value=0.0059  Score=39.69  Aligned_cols=59  Identities=19%  Similarity=0.235  Sum_probs=49.2

Q ss_pred             HHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC-CccCCeEeEEEecc
Q 012923          146 TLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ-KKIGNRMTACQLAS  207 (453)
Q Consensus       146 ~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~-~~~~gr~~~v~~~~  207 (453)
                      -|...|.+++.|..+.|.... .+..  .|-|...+..+|..|+..++ .+|..+.|.|.++.
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~~-dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPHT-DYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCC-STTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHhheeEEEEEEEecc-CCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            455788999999999886643 3433  69999999999999999998 56999999998874

>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=96.26  E-value=0.0062  Score=42.54  Aligned_cols=59  Identities=15%  Similarity=0.244  Sum_probs=47.9

Q ss_pred             CCCcCeEEEcCCCCCCCHHHHHHHHhccCCeeEEEEcccCCCCCcceEEEEEEccHHHHHHHHHcCC
Q 012923          127 DPVHRKIFVHGLGWDTKAETLIDAFKQYGEIEDCKAVCDKVSGKSKGYGFILFKTRSGARKALKEPQ  193 (453)
Q Consensus       127 ~~~~~~lfV~nLp~~~te~~l~~~f~~~G~i~~v~i~~d~~~g~~~G~afV~f~~~~~a~~A~~~~~  193 (453)
                      .+...-||.-.+|..+...||.++|++||.|.--.| .|.       -|||...+.++|..++..+.
T Consensus        12 ~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-ddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          12 QPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCcceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cCc-------eEEEEecCHHHHHHHHHHhc
Confidence            344456999999999999999999999999855544 332       59999999999999987543

>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=95.80  E-value=0.017  Score=40.22  Aligned_cols=57  Identities=14%  Similarity=0.222  Sum_probs=46.3

Q ss_pred             cccEEEEecCCCCccHHHHHHHHhccCCcceeeeeccCCCCCCceEEEEEECCHHHHHHHHHcCC
Q 012923          246 TQRKIFVSNVGSELEPQKLLAFFSKYGEIEEGPLGIDKATGKPKGFCLFVYKTVDAAKKALEEPH  310 (453)
Q Consensus       246 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~d~~~g~~kg~afV~F~~~~~A~~Al~~~~  310 (453)
                      ....||.-.+|..|...+|.++|++||.|. |..+-|.       -|||...+.++|..++..++
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc-------eEEEEecCHHHHHHHHHHhc
Confidence            345788889999999999999999999874 4444442       59999999999988887654