Citrus Sinensis ID: 023765

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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-------
Protein Sequence
MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDSRRSYSRSPSRSPYYSRSRSRSPYYSRSRSPSRSWSYSPRSRSYSPRGKYSRRSPSLSPARSASQRSPSGSPPRSFSRSGSFARTWGVGY
Secondary Structure (PSIPRED)
cccccccEEEEccccccccHHHHHHHHHHccccEEEEEccccccccEEEEEEccHHHHHHHHHHHcccccccccEEEEEcccccccccccccccccccccccccccccccEEEEEcccccccccccccccccccccEEEccEEcccccEEEEEcccHHHHHHHHHHHccccccccccEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccEEEEccccccccHHHHHHHHHHcccEEEEEEEcccccccEEEEEEccHHHHHHHHHccccccccccEEEEEEccccccccccccccccccccccccccccccEEEEEEcccccccHHHHHHHHHHcccEEEEEEEEcccccEEEEEEccHHHHHHHHHHcccccEcccccEEEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mssrssrtlyvgnlpgdtrMREVEDLfykygpivdidlkipprppgyaflefedyrdaedairgrdgynfdgYRLRVELAhggrrhsssmdryssyssggsrgvsrrsdyRVLVTglpssaswQDLKDHMRRagdvcfsqvfrdrggmtgivdytsyddMKYAIRKLDRSEFRNAFSRSYVRVReydsrrsysrspsrspyysrsrsrspyysrsrspsrswsysprsrsysprgkysrrspslsparsasqrspsgspprsfsrsgsfartwgvgy
Flexible Loop (DISEMBL)
mssrssrtlyvgnlpgdtrmREVEDLFYKYGPivdidlkippRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELahggrrhsssmdryssyssggsrgvsrrsDYRVLVTGLpssaswqdlKDHMRRAGDVCfsqvfrdrggmtgivdytsydDMKYAIRkldrsefrnafsrsyvrvreydsrrsysrspsrspyysrsrsrspyysrsrspsrswsysprsrsysprgkysrrspslsparsasqrspsgspprsfsrsgsfartwgvgy
Low Complexity Region (SEG)
MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGrrhsssmdryssyssggsrgvsrrsdyrVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFsrsyvrvreydsrrsysrspsrspyysrsrsrspyysrsrspsrswsysprsrsysprgkysrrspslsparsasqrspsgspprsfsrsgsfarTWGVGY
Disordered region (IsUnstruct)
*********YVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA*****************************YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV**********************************************************************************************
Disordered Region (DISOPRED)
*****SR**YVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSAS***********************************************************************************************************************************************************
Disordered Region (DISEMBL)
********LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH*************************RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV************************************************************************************SFARTWGVGY
Disordered Region (DISPRO)
*****SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH**********************VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDS*****************************************************************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDSRRSYSRSPSRSPYYSRSRSRSPYYSRSRSPSRSWSYSPRSRSYSPRGKYSRRSPSLSPARSASQRSPSGSPPRSFSRSGSFARTWGVGY
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	277	2.2.26 [Sep-21-2011]
O22315	303	Pre-mRNA-splicing factor	no	no	0.703	0.643	0.712	9e-78
Q5ZML3	257	Serine/arginine-rich spli	yes	no	0.682	0.735	0.524	1e-45
Q6NYA0	245	Serine/arginine-rich spli	yes	no	0.624	0.706	0.547	3e-43
Q5R7H2	248	Serine/arginine-rich spli	yes	no	0.624	0.697	0.530	5e-42
Q3YLA6	248	Serine/arginine-rich spli	yes	no	0.624	0.697	0.530	5e-42
Q6PDM2	248	Serine/arginine-rich spli	yes	no	0.624	0.697	0.530	5e-42
Q07955	248	Serine/arginine-rich spli	yes	no	0.624	0.697	0.530	5e-42
Q0VCY7	248	Serine/arginine-rich spli	yes	no	0.624	0.697	0.530	5e-42
Q9NEW6	258	Probable splicing factor,	yes	no	0.631	0.678	0.494	8e-42
Q7SXP4	257	Serine/arginine-rich spli	no	no	0.624	0.673	0.523	8e-42

>sp|O22315|SRSF1_ARATH Pre-mRNA-splicing factor SF2 OS=Arabidopsis thaliana GN=SF2 PE=1 SV=1

 Score =  290 bits (741), Expect = 9e-78,   Method: Compositional matrix adjust.
 Identities = 146/205 (71%), Positives = 164/205 (80%), Gaps = 10/205 (4%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
           MSSRSSRT+YVGNLPGD R REVEDLF KYGP+V IDLK+PPRPPGYAF+EF+D RDAED
Sbjct: 1   MSSRSSRTVYVGNLPGDIREREVEDLFSKYGPVVQIDLKVPPRPPGYAFVEFDDARDAED 60

Query: 61  AIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGV---------SRRSDYR 111
           AI GRDGY+FDG+RLRVELAHGGRR S       +    G             SRRS++R
Sbjct: 61  AIHGRDGYDFDGHRLRVELAHGGRRSSDDTRGSFNGGGRGGGRGRGDGGSRGPSRRSEFR 120

Query: 112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSE 171
           VLVTGLPSSASWQDLKDHMR+ GDVCFSQV+RD  G TG+VDYT Y+DMKYA++KLD +E
Sbjct: 121 VLVTGLPSSASWQDLKDHMRKGGDVCFSQVYRDARGTTGVVDYTCYEDMKYALKKLDDTE 180

Query: 172 FRNAFSRSYVRVREYDSRRSYSRSP 196
           FRNAFS  YVRVREYDSR+  SRSP
Sbjct: 181 FRNAFSNGYVRVREYDSRKD-SRSP 204

Can promote splice site selection in vitro presumably by antagonizing the effects of the A1 heterogeneous nuclear ribonucleoprotein. May have an essential function during early plant development.
Arabidopsis thaliana (taxid: 3702)

>sp|Q5ZML3|SRSF1_CHICK Serine/arginine-rich splicing factor 1 OS=Gallus gallus GN=SRSF1 PE=1 SV=3

 Score =  183 bits (464), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 107/204 (52%), Positives = 134/204 (65%), Gaps = 15/204 (7%)

Query: 9   LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
           +YVGNLP D R +++ED+FYKYG I DIDLK     P +AF+EFED RDAEDA+ GRDGY
Sbjct: 18  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 77

Query: 69  NFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGV--SRRSDYRVLVTGLPSSASWQDL 126
           ++DGYRLRVE    GR             +   R    SRRS+YRV+V+GLP S SWQDL
Sbjct: 78  DYDGYRLRVEFPRSGRGTGRGGGGGGGGGAPRGRYGPPSRRSEYRVIVSGLPPSGSWQDL 137

Query: 127 KDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFR-NAFSRSYVRVRE 185
           KDHMR AGDVC++ VFRD    TG+V++   +DM YA+RKLD ++FR +    +Y+RV+ 
Sbjct: 138 KDHMREAGDVCYADVFRD---GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK- 193

Query: 186 YDSRRSYSRSPSRSPYYSRSRSRS 209
                       RSP Y RSRSRS
Sbjct: 194 --------VDGPRSPSYGRSRSRS 209

May play a role in preventing exon skipping, ensuring the accuracy of splicing and regulating alternative splicing.

Gallus gallus (taxid: 9031)

>sp|Q6NYA0|SRS1B_DANRE Serine/arginine-rich splicing factor 1B OS=Danio rerio GN=srsf1b PE=2 SV=1

 Score =  175 bits (443), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 98/179 (54%), Positives = 124/179 (69%), Gaps = 6/179 (3%)

Query: 9   LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
           +YVGNLP D R ++VED+FYKYG I DIDLK     P +AF+EFED RDAEDA+ GRDGY
Sbjct: 17  IYVGNLPPDIRTKDVEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 76

Query: 69  NFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSR--GVSRRSDYRVLVTGLPSSASWQDL 126
           ++DGYRLRVE    GR             +   R    SRRS+YRV+V+GLP S SWQDL
Sbjct: 77  DYDGYRLRVEFPRSGRGGGRGGGGGGGVGAPRGRYGPPSRRSEYRVIVSGLPPSGSWQDL 136

Query: 127 KDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFR-NAFSRSYVRVR 184
           KDHMR AGDVC++ VFRD    TG+V++   +DM YA+RKLD ++FR +    +Y+RV+
Sbjct: 137 KDHMREAGDVCYADVFRD---GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK 192

May play a role in preventing exon skipping, ensuring the accuracy of splicing and regulating alternative splicing.

Danio rerio (taxid: 7955)

>sp|Q5R7H2|SRSF1_PONAB Serine/arginine-rich splicing factor 1 OS=Pongo abelii GN=SRSF1 PE=2 SV=3

 Score =  171 bits (433), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 95/179 (53%), Positives = 123/179 (68%), Gaps = 6/179 (3%)

Query: 9   LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
           +YVGNLP D R +++ED+FYKYG I DIDLK     P +AF+EFED RDAEDA+ GRDGY
Sbjct: 18  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 77

Query: 69  NFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGV--SRRSDYRVLVTGLPSSASWQDL 126
           ++DGYRLRVE    GR             +   R    SRRS+ RV+V+GLP S SWQDL
Sbjct: 78  DYDGYRLRVEFPRSGRGTGRGGGGGGGGGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDL 137

Query: 127 KDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFR-NAFSRSYVRVR 184
           KDHMR AGDVC++ V+RD    TG+V++   +DM YA+RKLD ++FR +    +Y+RV+
Sbjct: 138 KDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK 193

Plays a role in preventing exon skipping, ensuring the accuracy of splicing and regulating alternative splicing. Interacts with other spliceosomal components, via the RS domains, to form a bridge between the 5'- and 3'-splice site binding components, U1 snRNP and U2AF. Can stimulate binding of U1 snRNP to a 5'-splice site-containing pre-mRNA. Binds to purine-rich RNA sequences, either the octamer, 5'-RGAAGAAC-3' (r=A or G) or the decamers, AGGACAGAGC/AGGACGAAGC. Binds preferentially to the 5'-CGAGGCG-3' motif in vitro. Three copies of the octamer constitute a powerful splicing enhancer in vitro, the ASF/SF2 splicing enhancer (ASE) which can specifically activate ASE-dependent splicing.

Pongo abelii (taxid: 9601)

>sp|Q3YLA6|SRSF1_PIG Serine/arginine-rich splicing factor 1 OS=Sus scrofa GN=SRSF1 PE=2 SV=3

 Score =  171 bits (433), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 95/179 (53%), Positives = 123/179 (68%), Gaps = 6/179 (3%)

Query: 9   LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
           +YVGNLP D R +++ED+FYKYG I DIDLK     P +AF+EFED RDAEDA+ GRDGY
Sbjct: 18  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 77

Query: 69  NFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGV--SRRSDYRVLVTGLPSSASWQDL 126
           ++DGYRLRVE    GR             +   R    SRRS+ RV+V+GLP S SWQDL
Sbjct: 78  DYDGYRLRVEFPRSGRGTGRGGGGGGGGGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDL 137

Query: 127 KDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFR-NAFSRSYVRVR 184
           KDHMR AGDVC++ V+RD    TG+V++   +DM YA+RKLD ++FR +    +Y+RV+
Sbjct: 138 KDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK 193

Plays a role in preventing exon skipping, ensuring the accuracy of splicing and regulating alternative splicing. Interacts with other spliceosomal components, via the RS domains, to form a bridge between the 5'- and 3'-splice site binding components, U1 snRNP and U2AF. Can stimulate binding of U1 snRNP to a 5'-splice site-containing pre-mRNA. Binds to purine-rich RNA sequences, either the octamer, 5'-RGAAGAAC-3' (r=A or G) or the decamers, AGGACAGAGC/AGGACGAAGC. Binds preferentially to the 5'-CGAGGCG-3' motif in vitro. Three copies of the octamer constitute a powerful splicing enhancer in vitro, the ASF/SF2 splicing enhancer (ASE) which can specifically activate ASE-dependent splicing.

Sus scrofa (taxid: 9823)

>sp|Q6PDM2|SRSF1_MOUSE Serine/arginine-rich splicing factor 1 OS=Mus musculus GN=Srsf1 PE=1 SV=3

 Score =  171 bits (433), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 95/179 (53%), Positives = 123/179 (68%), Gaps = 6/179 (3%)

Query: 9   LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
           +YVGNLP D R +++ED+FYKYG I DIDLK     P +AF+EFED RDAEDA+ GRDGY
Sbjct: 18  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 77

Query: 69  NFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGV--SRRSDYRVLVTGLPSSASWQDL 126
           ++DGYRLRVE    GR             +   R    SRRS+ RV+V+GLP S SWQDL
Sbjct: 78  DYDGYRLRVEFPRSGRGTGRGGGGGGGGGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDL 137

Query: 127 KDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFR-NAFSRSYVRVR 184
           KDHMR AGDVC++ V+RD    TG+V++   +DM YA+RKLD ++FR +    +Y+RV+
Sbjct: 138 KDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK 193

Plays a role in preventing exon skipping, ensuring the accuracy of splicing and regulating alternative splicing. Interacts with other spliceosomal components, via the RS domains, to form a bridge between the 5'- and 3'-splice site binding components, U1 snRNP and U2AF. Can stimulate binding of U1 snRNP to a 5'-splice site-containing pre-mRNA. Binds to purine-rich RNA sequences, either the octamer, 5'-RGAAGAAC-3' (r=A or G) or the decamers, AGGACAGAGC/AGGACGAAGC. Binds preferentially to the 5'-CGAGGCG-3' motif in vitro. Three copies of the octamer constitute a powerful splicing enhancer in vitro, the ASF/SF2 splicing enhancer (ASE) which can specifically activate ASE-dependent splicing (By similarity). Specifically regulates alternative splicing of cardiac isoforms of CAMK2D, LDB3/CYPHER and TNNT2/CTNT during heart remodeling at the juvenile to adult transition. The inappropriate accumulation of a neonatal and neuronal isoform of CAMKD2 in the adult heart results in aberrant calcium handling and defective excitation-contraction coupling in cardiomyocytes.

Mus musculus (taxid: 10090)

>sp|Q07955|SRSF1_HUMAN Serine/arginine-rich splicing factor 1 OS=Homo sapiens GN=SRSF1 PE=1 SV=2

 Score =  171 bits (433), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 95/179 (53%), Positives = 123/179 (68%), Gaps = 6/179 (3%)

Query: 9   LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
           +YVGNLP D R +++ED+FYKYG I DIDLK     P +AF+EFED RDAEDA+ GRDGY
Sbjct: 18  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 77

Query: 69  NFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGV--SRRSDYRVLVTGLPSSASWQDL 126
           ++DGYRLRVE    GR             +   R    SRRS+ RV+V+GLP S SWQDL
Sbjct: 78  DYDGYRLRVEFPRSGRGTGRGGGGGGGGGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDL 137

Query: 127 KDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFR-NAFSRSYVRVR 184
           KDHMR AGDVC++ V+RD    TG+V++   +DM YA+RKLD ++FR +    +Y+RV+
Sbjct: 138 KDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK 193

Plays a role in preventing exon skipping, ensuring the accuracy of splicing and regulating alternative splicing. Interacts with other spliceosomal components, via the RS domains, to form a bridge between the 5'- and 3'-splice site binding components, U1 snRNP and U2AF. Can stimulate binding of U1 snRNP to a 5'-splice site-containing pre-mRNA. Binds to purine-rich RNA sequences, either the octamer, 5'-RGAAGAAC-3' (r=A or G) or the decamers, AGGACAGAGC/AGGACGAAGC. Binds preferentially to the 5'-CGAGGCG-3' motif in vitro. Three copies of the octamer constitute a powerful splicing enhancer in vitro, the ASF/SF2 splicing enhancer (ASE) which can specifically activate ASE-dependent splicing. Isoform ASF-2 and isoform ASF-3 act as splicing repressors.

Homo sapiens (taxid: 9606)

>sp|Q0VCY7|SRSF1_BOVIN Serine/arginine-rich splicing factor 1 OS=Bos taurus GN=SRSF1 PE=2 SV=1

 Score =  171 bits (433), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 95/179 (53%), Positives = 123/179 (68%), Gaps = 6/179 (3%)

Query: 9   LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
           +YVGNLP D R +++ED+FYKYG I DIDLK     P +AF+EFED RDAEDA+ GRDGY
Sbjct: 18  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 77

Query: 69  NFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGV--SRRSDYRVLVTGLPSSASWQDL 126
           ++DGYRLRVE    GR             +   R    SRRS+ RV+V+GLP S SWQDL
Sbjct: 78  DYDGYRLRVEFPRSGRGTGRGGGGGGGGGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDL 137

Query: 127 KDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFR-NAFSRSYVRVR 184
           KDHMR AGDVC++ V+RD    TG+V++   +DM YA+RKLD ++FR +    +Y+RV+
Sbjct: 138 KDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK 193

Plays a role in preventing exon skipping, ensuring the accuracy of splicing and regulating alternative splicing. Interacts with other spliceosomal components, via the RS domains, to form a bridge between the 5'- and 3'-splice site binding components, U1 snRNP and U2AF. Can stimulate binding of U1 snRNP to a 5'-splice site-containing pre-mRNA. Binds to purine-rich RNA sequences, either the octamer, 5'-RGAAGAAC-3' (r=A or G) or the decamers, AGGACAGAGC/AGGACGAAGC. Binds preferentially to the 5'-CGAGGCG-3' motif in vitro. Three copies of the octamer constitute a powerful splicing enhancer in vitro, the ASF/SF2 splicing enhancer (ASE) which can specifically activate ASE-dependent splicing.

Bos taurus (taxid: 9913)

>sp|Q9NEW6|RSP3_CAEEL Probable splicing factor, arginine/serine-rich 3 OS=Caenorhabditis elegans GN=rsp-3 PE=1 SV=2

 Score =  170 bits (431), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 97/196 (49%), Positives = 125/196 (63%), Gaps = 21/196 (10%)

Query: 5   SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRG 64
             + +YVGNLPGD R +EVED+F+KYG I  +D+K   R P +AF+EFED+RDAEDA+R 
Sbjct: 7   EDQKVYVGNLPGDVREKEVEDIFHKYGRIKYVDIK-SGRGPAFAFVEFEDHRDAEDAVRA 65

Query: 65  RDGYNFDGYRLRVE--------------LAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDY 110
           RDGY FDG R+RVE              L  GG                   G  RR+ Y
Sbjct: 66  RDGYEFDGRRIRVEFTRGVGPRGPGGRPLQDGGDHRGGDFRGGRGGGR--GGGPQRRTGY 123

Query: 111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRS 170
           RV+V GLP + SWQDLKDHMR AGDVC++ V RD    TG+V++T Y+D+KYA+RKLD +
Sbjct: 124 RVIVEGLPPTGSWQDLKDHMRDAGDVCYADVARD---GTGVVEFTRYEDVKYAVRKLDDT 180

Query: 171 EFR-NAFSRSYVRVRE 185
           +FR +    +Y+RVRE
Sbjct: 181 KFRSHEGETAYIRVRE 196

Plays an essential role in embryogenesis.

Caenorhabditis elegans (taxid: 6239)

>sp|Q7SXP4|SRS1A_DANRE Serine/arginine-rich splicing factor 1A OS=Danio rerio GN=srsf1a PE=2 SV=2

 Score =  170 bits (431), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 99/189 (52%), Positives = 124/189 (65%), Gaps = 16/189 (8%)

Query: 9   LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
           +YVGNLP D R ++VED+FYKYG I DIDLK     P +AF+EFED RDAEDA+  RDGY
Sbjct: 17  IYVGNLPPDIRTKDVEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYARDGY 76

Query: 69  NFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGV------------SRRSDYRVLVTG 116
           ++DGYRLRVE    GR              GG  G             SRRS+YRV+V+G
Sbjct: 77  DYDGYRLRVEFPRSGRGMGRGGFGGGGGGGGGGGGGGGGAPRGRYGPPSRRSEYRVIVSG 136

Query: 117 LPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFR-NA 175
           LP S SWQDLKDHMR AGDVC++ VFRD    TG+V++   +DM YA+RKLD ++FR + 
Sbjct: 137 LPPSGSWQDLKDHMREAGDVCYADVFRD---GTGVVEFVRKEDMTYAVRKLDNTKFRSHE 193

Query: 176 FSRSYVRVR 184
              +Y+RV+
Sbjct: 194 GETAYIRVK 202

May play a role in preventing exon skipping, ensuring the accuracy of splicing and regulating alternative splicing.

Danio rerio (taxid: 7955)

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	277
449485688	322	PREDICTED: pre-mRNA-splicing factor SF2-	0.877	0.754	0.782	7e-94
357441751	290	Pre-mRNA-splicing factor SF2 [Medicago t	0.877	0.837	0.792	2e-91
388515137	259	unknown [Medicago truncatula]	0.877	0.938	0.792	7e-91
255542756	300	arginine/serine-rich splicing factor, pu	0.935	0.863	0.783	8e-91
449435631	315	PREDICTED: pre-mRNA-splicing factor SF2-	0.855	0.752	0.761	2e-90
217073712	246	unknown [Medicago truncatula]	0.862	0.971	0.793	1e-89
148909953	331	unknown [Picea sitchensis]	0.671	0.561	0.867	2e-87
357441755	316	Pre-mRNA-splicing factor SF2 [Medicago t	0.830	0.727	0.789	5e-87
357441753	322	Pre-mRNA-splicing factor SF2 [Medicago t	0.830	0.714	0.789	6e-87
357441749	334	Pre-mRNA-splicing factor SF2 [Medicago t	0.830	0.688	0.789	8e-87

>gi|449485688|ref|XP_004157245.1| PREDICTED: pre-mRNA-splicing factor SF2-like [Cucumis sativus]

 Score =  349 bits (896), Expect = 7e-94,   Method: Compositional matrix adjust.
 Identities = 201/257 (78%), Positives = 213/257 (82%), Gaps = 14/257 (5%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
           MSSR+SRT+YVGNLPGD R+REVEDLFYKYGPIVDIDLKIPPRPPGYAF+EFED RDAED
Sbjct: 1   MSSRNSRTIYVGNLPGDIRLREVEDLFYKYGPIVDIDLKIPPRPPGYAFVEFEDVRDAED 60

Query: 61  AIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRG-VSRRSDYRVLVTGLPS 119
           AI GRDGY FDG RLRVE AHGGR HSSS+DRYS   SG SRG V RR+DYRVLVTGLPS
Sbjct: 61  AIYGRDGYKFDGCRLRVEFAHGGRGHSSSVDRYSR--SGSSRGGVPRRTDYRVLVTGLPS 118

Query: 120 SASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRS 179
           SASWQDLKDHMRRAGDVCFS+VFRDRGGM GIVDYT+YDDMKYAIRKLD SEFRNAFSR+
Sbjct: 119 SASWQDLKDHMRRAGDVCFSEVFRDRGGMAGIVDYTNYDDMKYAIRKLDDSEFRNAFSRA 178

Query: 180 YVRVREYDSRRSYSRSP---SRSPYYSRSRSRSPYYSRSRSPSRSWSYSPRSR------- 229
           YVRV+EYDSR SYSRSP   SR   YSRS SRSPY  R RS SRS S S           
Sbjct: 179 YVRVKEYDSRHSYSRSPSLDSRRSDYSRSPSRSPYRGRGRSQSRSRSRSRSRSRSYSGRS 238

Query: 230 -SYSPRGKYSRRSPSLS 245
            S SPR K+SRRS S+S
Sbjct: 239 TSLSPRHKHSRRSRSVS 255

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357441751|ref|XP_003591153.1| Pre-mRNA-splicing factor SF2 [Medicago truncatula] gi|355480201|gb|AES61404.1| Pre-mRNA-splicing factor SF2 [Medicago truncatula]

 Score =  341 bits (874), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 195/246 (79%), Positives = 210/246 (85%), Gaps = 3/246 (1%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
           MS RSSRTLYVGNLPGD R+REVEDLFYKYGPIVDIDLKIPP+PPGYAF+EFED RDA+D
Sbjct: 32  MSGRSSRTLYVGNLPGDIRLREVEDLFYKYGPIVDIDLKIPPKPPGYAFVEFEDARDAQD 91

Query: 61  AIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSS-GGSRGVSRRSDYRVLVTGLPS 119
           AI  RDGY+FDGYRL VELAHGGR  SSS+DRYS +S   GSRGVSRRSDYRVLVTGLP 
Sbjct: 92  AIYYRDGYDFDGYRLLVELAHGGRGSSSSVDRYSRHSGRSGSRGVSRRSDYRVLVTGLPP 151

Query: 120 SASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRS 179
           SASWQDLKDHMR+AG VCFSQVFR+RGG+TGIVDYT+YDD+KYAIRKLD SEFRNAFSRS
Sbjct: 152 SASWQDLKDHMRKAGHVCFSQVFRERGGLTGIVDYTNYDDVKYAIRKLDDSEFRNAFSRS 211

Query: 180 YVRVREYDSRRSYSRSPSRSPYYSRSRSRSPYYSRSRSPSRSWSYSPRSRSYSPRGKYSR 239
           Y+RVREYD   S S S       S SRSRSPY SRSRS S S SYS RSRS SP+ K+SR
Sbjct: 212 YIRVREYDRSHSRSPSRDSRR--SYSRSRSPYVSRSRSCSLSHSYSGRSRSLSPKAKHSR 269

Query: 240 RSPSLS 245
           RS SLS
Sbjct: 270 RSFSLS 275

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388515137|gb|AFK45630.1| unknown [Medicago truncatula]

 Score =  339 bits (870), Expect = 7e-91,   Method: Compositional matrix adjust.
 Identities = 195/246 (79%), Positives = 210/246 (85%), Gaps = 3/246 (1%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
           MS RSSRTLYVGNLPGD R+REVEDLFYKYGPIVDIDLKIPP+PPGYAF+EFED RDA+D
Sbjct: 1   MSGRSSRTLYVGNLPGDIRLREVEDLFYKYGPIVDIDLKIPPKPPGYAFVEFEDARDAQD 60

Query: 61  AIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSS-GGSRGVSRRSDYRVLVTGLPS 119
           AI  RDGY+FDGYRL VELAHGGR  SSS+DRYS +S   GSRGVSRRSDYRVLVTGLP 
Sbjct: 61  AIYYRDGYDFDGYRLLVELAHGGRGSSSSVDRYSRHSGRSGSRGVSRRSDYRVLVTGLPP 120

Query: 120 SASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRS 179
           SASWQDLKDHMR+AG VCFSQVFR+RGG+TGIVDYT+YDD+KYAIRKLD SEFRNAFSRS
Sbjct: 121 SASWQDLKDHMRKAGHVCFSQVFRERGGLTGIVDYTNYDDVKYAIRKLDDSEFRNAFSRS 180

Query: 180 YVRVREYDSRRSYSRSPSRSPYYSRSRSRSPYYSRSRSPSRSWSYSPRSRSYSPRGKYSR 239
           Y+RVREYD   S S S       S SRSRSPY SRSRS S S SYS RSRS SP+ K+SR
Sbjct: 181 YIRVREYDRSHSRSPSRDSRR--SYSRSRSPYVSRSRSCSLSHSYSGRSRSLSPKAKHSR 238

Query: 240 RSPSLS 245
           RS SLS
Sbjct: 239 RSFSLS 244

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255542756|ref|XP_002512441.1| arginine/serine-rich splicing factor, putative [Ricinus communis] gi|223548402|gb|EEF49893.1| arginine/serine-rich splicing factor, putative [Ricinus communis]

 Score =  339 bits (869), Expect = 8e-91,   Method: Compositional matrix adjust.
 Identities = 210/268 (78%), Positives = 221/268 (82%), Gaps = 9/268 (3%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
           MSSR+SRTLYVGNLPGD R REV+DLFYKYGPIV++DLKIPPRPPGYAF+EFED RDAED
Sbjct: 38  MSSRASRTLYVGNLPGDIRQREVKDLFYKYGPIVEVDLKIPPRPPGYAFVEFEDARDAED 97

Query: 61  AIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGV-SRRSDYRVLVTGLPS 119
           AIRGRDGYNFDG RLRVELAHGGRRHSS  DRYSSYS        SRRSDYRVLVTGLPS
Sbjct: 98  AIRGRDGYNFDGCRLRVELAHGGRRHSSPGDRYSSYSGRSGSRGPSRRSDYRVLVTGLPS 157

Query: 120 SASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRS 179
           SASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYT+YDDMK+AI+KLD SEFRNAFSRS
Sbjct: 158 SASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRS 217

Query: 180 YVRVREYDSRRSYSRSPSRSPYYSRSRSRSPYYSRSRSPSRSWSYSPRSRSYSPRGKYSR 239
           YVRVREYDSRRSYSRSPS  PY    RSRS   SR+RS    W     SRS SP  KY  
Sbjct: 218 YVRVREYDSRRSYSRSPSCGPY---DRSRSRSRSRTRSRHSDW-----SRSKSPGAKYHS 269

Query: 240 RSPSLSPARSASQRSPSGSPPRSFSRSG 267
           RS S+SP RS S RS +GS PRS S  G
Sbjct: 270 RSLSVSPGRSVSPRSHAGSSPRSSSNLG 297

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449435631|ref|XP_004135598.1| PREDICTED: pre-mRNA-splicing factor SF2-like [Cucumis sativus]

 Score =  338 bits (866), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 195/256 (76%), Positives = 207/256 (80%), Gaps = 19/256 (7%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
           MSSR+SRT+YVGNLPGD R+REVEDLFYKYGPIVDIDLKIPPRPPGYAF+EFED RDAED
Sbjct: 1   MSSRNSRTIYVGNLPGDIRLREVEDLFYKYGPIVDIDLKIPPRPPGYAFVEFEDVRDAED 60

Query: 61  AIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSS 120
           AI GRDGY FDG RLRVE AHGGR HSSS+DRYS   SG SR      D+ VLVTGLPSS
Sbjct: 61  AIYGRDGYKFDGCRLRVEFAHGGRGHSSSVDRYS--RSGSSR------DFAVLVTGLPSS 112

Query: 121 ASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSY 180
           ASWQDLKDHMRRAGDVCFS+VFRDRGGM GIVDYT+YDDMKYAIRKLD SEFRNAFSR+Y
Sbjct: 113 ASWQDLKDHMRRAGDVCFSEVFRDRGGMAGIVDYTNYDDMKYAIRKLDDSEFRNAFSRAY 172

Query: 181 VRVREYDSRRSYSRSP---SRSPYYSRSRSRSPYYSRSRSPSRSWSYSPRSR-------- 229
           VRV+EYDSR SYSRSP   SR   YSRS SRSPY  R RS SRS S S            
Sbjct: 173 VRVKEYDSRHSYSRSPSLDSRRSDYSRSPSRSPYRGRGRSQSRSRSRSRSRSRSYSGRST 232

Query: 230 SYSPRGKYSRRSPSLS 245
           S SPR K+SRRS S+S
Sbjct: 233 SLSPRHKHSRRSRSVS 248

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217073712|gb|ACJ85216.1| unknown [Medicago truncatula]

 Score =  335 bits (860), Expect = 1e-89,   Method: Compositional matrix adjust.
 Identities = 192/242 (79%), Positives = 207/242 (85%), Gaps = 3/242 (1%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
           MS RSSRTLYVGNLPGD R+REVEDLFYKYGPIVDIDLKIPP+PPGYAF+EFED RDA+D
Sbjct: 1   MSGRSSRTLYVGNLPGDIRLREVEDLFYKYGPIVDIDLKIPPKPPGYAFVEFEDARDAQD 60

Query: 61  AIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSS-GGSRGVSRRSDYRVLVTGLPS 119
           AI  RDGY+FDGYRL VELAHGGR  SSS+DRYS +S   GSRGVSRRSDYRVLVTGLP 
Sbjct: 61  AIYYRDGYDFDGYRLLVELAHGGRGSSSSVDRYSRHSGRSGSRGVSRRSDYRVLVTGLPP 120

Query: 120 SASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRS 179
           SASWQDLKDHMR+AG VCFSQVFR+RGG+TGIVDYT+YDD+KYAIRKLD SEFRNAFSRS
Sbjct: 121 SASWQDLKDHMRKAGHVCFSQVFRERGGLTGIVDYTNYDDVKYAIRKLDDSEFRNAFSRS 180

Query: 180 YVRVREYDSRRSYSRSPSRSPYYSRSRSRSPYYSRSRSPSRSWSYSPRSRSYSPRGKYSR 239
           Y+RVREYD   S S S       S SRSRSPY SRSRS S S SYS RSRS SP+ K+SR
Sbjct: 181 YIRVREYDRSHSRSPSRDSRR--SYSRSRSPYVSRSRSCSLSHSYSGRSRSLSPKAKHSR 238

Query: 240 RS 241
           RS
Sbjct: 239 RS 240

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|148909953|gb|ABR18062.1| unknown [Picea sitchensis]

 Score =  328 bits (840), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 163/188 (86%), Positives = 171/188 (90%), Gaps = 2/188 (1%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
           MSSR+SRTLYVGNLPGD R REVEDLFYKYGPIVDIDLKIPPRPPGY F+EFED RDAED
Sbjct: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIVDIDLKIPPRPPGYCFIEFEDARDAED 60

Query: 61  AIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSR--GVSRRSDYRVLVTGLP 118
           AIRGRDGYNFDG RLRVELAHGGR  SS+ DRYSSYSS G R  GVSRRS+YRVLV+GLP
Sbjct: 61  AIRGRDGYNFDGNRLRVELAHGGRGQSSTNDRYSSYSSAGGRSGGVSRRSEYRVLVSGLP 120

Query: 119 SSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR 178
           SSASWQDLKDHMRRAGDVCFSQVFRD  G TGIVDYT+YDDMKYAIRKLD SEFRNAFSR
Sbjct: 121 SSASWQDLKDHMRRAGDVCFSQVFRDSSGTTGIVDYTNYDDMKYAIRKLDDSEFRNAFSR 180

Query: 179 SYVRVREY 186
            Y+RV+EY
Sbjct: 181 GYIRVKEY 188

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357441755|ref|XP_003591155.1| Pre-mRNA-splicing factor SF2 [Medicago truncatula] gi|355480203|gb|AES61406.1| Pre-mRNA-splicing factor SF2 [Medicago truncatula]

 Score =  326 bits (836), Expect = 5e-87,   Method: Compositional matrix adjust.
 Identities = 184/233 (78%), Positives = 199/233 (85%), Gaps = 3/233 (1%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
           MS RSSRTLYVGNLPGD R+REVEDLFYKYGPIVDIDLKIPP+PPGYAF+EFED RDA+D
Sbjct: 32  MSGRSSRTLYVGNLPGDIRLREVEDLFYKYGPIVDIDLKIPPKPPGYAFVEFEDARDAQD 91

Query: 61  AIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSS-GGSRGVSRRSDYRVLVTGLPS 119
           AI  RDGY+FDGYRL VELAHGGR  SSS+DRYS +S   GSRGVSRRSDYRVLVTGLP 
Sbjct: 92  AIYYRDGYDFDGYRLLVELAHGGRGSSSSVDRYSRHSGRSGSRGVSRRSDYRVLVTGLPP 151

Query: 120 SASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRS 179
           SASWQDLKDHMR+AG VCFSQVFR+RGG+TGIVDYT+YDD+KYAIRKLD SEFRNAFSRS
Sbjct: 152 SASWQDLKDHMRKAGHVCFSQVFRERGGLTGIVDYTNYDDVKYAIRKLDDSEFRNAFSRS 211

Query: 180 YVRVREYDSRRSYSRSPSRSPYYSRSRSRSPYYSRSRSPSRSWSYSPRSRSYS 232
           Y+RVREYD   S S S       S SRSRSPY SRSRS S S SYS RSR ++
Sbjct: 212 YIRVREYDRSHSRSPSRDSRR--SYSRSRSPYVSRSRSCSLSHSYSGRSRRFT 262

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357441753|ref|XP_003591154.1| Pre-mRNA-splicing factor SF2 [Medicago truncatula] gi|355480202|gb|AES61405.1| Pre-mRNA-splicing factor SF2 [Medicago truncatula]

 Score =  326 bits (836), Expect = 6e-87,   Method: Compositional matrix adjust.
 Identities = 184/233 (78%), Positives = 199/233 (85%), Gaps = 3/233 (1%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
           MS RSSRTLYVGNLPGD R+REVEDLFYKYGPIVDIDLKIPP+PPGYAF+EFED RDA+D
Sbjct: 32  MSGRSSRTLYVGNLPGDIRLREVEDLFYKYGPIVDIDLKIPPKPPGYAFVEFEDARDAQD 91

Query: 61  AIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSS-GGSRGVSRRSDYRVLVTGLPS 119
           AI  RDGY+FDGYRL VELAHGGR  SSS+DRYS +S   GSRGVSRRSDYRVLVTGLP 
Sbjct: 92  AIYYRDGYDFDGYRLLVELAHGGRGSSSSVDRYSRHSGRSGSRGVSRRSDYRVLVTGLPP 151

Query: 120 SASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRS 179
           SASWQDLKDHMR+AG VCFSQVFR+RGG+TGIVDYT+YDD+KYAIRKLD SEFRNAFSRS
Sbjct: 152 SASWQDLKDHMRKAGHVCFSQVFRERGGLTGIVDYTNYDDVKYAIRKLDDSEFRNAFSRS 211

Query: 180 YVRVREYDSRRSYSRSPSRSPYYSRSRSRSPYYSRSRSPSRSWSYSPRSRSYS 232
           Y+RVREYD   S S S       S SRSRSPY SRSRS S S SYS RSR ++
Sbjct: 212 YIRVREYDRSHSRSPSRDSRR--SYSRSRSPYVSRSRSCSLSHSYSGRSRRFT 262

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357441749|ref|XP_003591152.1| Pre-mRNA-splicing factor SF2 [Medicago truncatula] gi|355480200|gb|AES61403.1| Pre-mRNA-splicing factor SF2 [Medicago truncatula]

 Score =  326 bits (835), Expect = 8e-87,   Method: Compositional matrix adjust.
 Identities = 184/233 (78%), Positives = 199/233 (85%), Gaps = 3/233 (1%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
           MS RSSRTLYVGNLPGD R+REVEDLFYKYGPIVDIDLKIPP+PPGYAF+EFED RDA+D
Sbjct: 32  MSGRSSRTLYVGNLPGDIRLREVEDLFYKYGPIVDIDLKIPPKPPGYAFVEFEDARDAQD 91

Query: 61  AIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSS-GGSRGVSRRSDYRVLVTGLPS 119
           AI  RDGY+FDGYRL VELAHGGR  SSS+DRYS +S   GSRGVSRRSDYRVLVTGLP 
Sbjct: 92  AIYYRDGYDFDGYRLLVELAHGGRGSSSSVDRYSRHSGRSGSRGVSRRSDYRVLVTGLPP 151

Query: 120 SASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRS 179
           SASWQDLKDHMR+AG VCFSQVFR+RGG+TGIVDYT+YDD+KYAIRKLD SEFRNAFSRS
Sbjct: 152 SASWQDLKDHMRKAGHVCFSQVFRERGGLTGIVDYTNYDDVKYAIRKLDDSEFRNAFSRS 211

Query: 180 YVRVREYDSRRSYSRSPSRSPYYSRSRSRSPYYSRSRSPSRSWSYSPRSRSYS 232
           Y+RVREYD   S S S       S SRSRSPY SRSRS S S SYS RSR ++
Sbjct: 212 YIRVREYDRSHSRSPSRDSR--RSYSRSRSPYVSRSRSCSLSHSYSGRSRRFT 262

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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	277
TAIR|locus:2195346	268	SR30 "Serine/Arginine-Rich Pro	0.631	0.652	0.704	5.4e-63
TAIR|locus:2024770	303	SR34 "Serine/Arginine-Rich Pro	0.635	0.580	0.659	7.1e-61
TAIR|locus:2133249	278	SR34b "Serine/Arginine-Rich Pr	0.624	0.622	0.650	1.4e-57
TAIR|locus:2114643	300	SR34a "Serine/Arginine-Rich Pr	0.628	0.58	0.602	3.4e-54
WB|WBGene00004700	258	rsp-3 [Caenorhabditis elegans	0.263	0.282	0.635	3.6e-42
UNIPROTKB|Q9NEW6	258	rsp-3 "Probable splicing facto	0.263	0.282	0.635	3.6e-42
UNIPROTKB|Q5ZML3	257	SRSF1 "Serine/arginine-rich sp	0.588	0.634	0.517	1.6e-40
ZFIN|ZDB-GENE-040426-1467	258	srsf1b "serine/arginine-rich s	0.588	0.631	0.523	1.6e-40
UNIPROTKB|Q0VCY7	248	SRSF1 "Serine/arginine-rich sp	0.588	0.657	0.511	4.2e-40
UNIPROTKB|E2RJL3	253	SRSF1 "Uncharacterized protein	0.588	0.644	0.511	4.2e-40

TAIR|locus:2195346 SR30 "Serine/Arginine-Rich Protein Splicing Factor 30" [Arabidopsis thaliana (taxid:3702)]

 Score = 643 (231.4 bits), Expect = 5.4e-63, P = 5.4e-63
 Identities = 124/176 (70%), Positives = 137/176 (77%)

Query:     1 MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
             MSSR +RT+YVGNLPGD R  EVEDLFYKYGPIVDIDLKIPPRPPGYAF+EFED RDA+D
Sbjct:     1 MSSRWNRTIYVGNLPGDIRKCEVEDLFYKYGPIVDIDLKIPPRPPGYAFVEFEDPRDADD 60

Query:    61 AIRGRDGYNFDGYRLRVELAHGGXXXXXXXXXXXXXXXXXXXXXXXXXXXXVLVTGLPSS 120
             AI GRDGY+FDG RLRVE+AHGG                            VLVTGLP S
Sbjct:    61 AIYGRDGYDFDGCRLRVEIAHGGRRFSPSVDRYSSSYSASRAPSRRSDYR-VLVTGLPPS 119

Query:   121 ASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAF 176
             ASWQDLKDHMR+AGDVCFS+VF DR GM+G+VDY++YDDMKYAIRKLD +EFRNAF
Sbjct:   120 ASWQDLKDHMRKAGDVCFSEVFPDRKGMSGVVDYSNYDDMKYAIRKLDATEFRNAF 175

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0005681 "spliceosomal complex" evidence=NAS

GO:0003729 "mRNA binding" evidence=ISS

GO:0006376 "mRNA splice site selection" evidence=IMP

GO:0048024 "regulation of mRNA splicing, via spliceosome" evidence=TAS

GO:0035061 "interchromatin granule" evidence=IDA

GO:0016607 "nuclear speck" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

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

TAIR|locus:2024770 SR34 "Serine/Arginine-Rich Protein Splicing Factor 34" [Arabidopsis thaliana (taxid:3702)]

 Score = 623 (224.4 bits), Expect = 7.1e-61, P = 7.1e-61
 Identities = 122/185 (65%), Positives = 136/185 (73%)

Query:     1 MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
             MSSRSSRT+YVGNLPGD R REVEDLF KYGP+V IDLK+PPRPPGYAF+EF+D RDAED
Sbjct:     1 MSSRSSRTVYVGNLPGDIREREVEDLFSKYGPVVQIDLKVPPRPPGYAFVEFDDARDAED 60

Query:    61 AIRGRDGYNFDGYRLRVELAHGGXXXXXXXXXXXXXXXXXXXXX---------XXXXXXX 111
             AI GRDGY+FDG+RLRVELAHGG                                     
Sbjct:    61 AIHGRDGYDFDGHRLRVELAHGGRRSSDDTRGSFNGGGRGGGRGRGDGGSRGPSRRSEFR 120

Query:   112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSE 171
             VLVTGLPSSASWQDLKDHMR+ GDVCFSQV+RD  G TG+VDYT Y+DMKYA++KLD +E
Sbjct:   121 VLVTGLPSSASWQDLKDHMRKGGDVCFSQVYRDARGTTGVVDYTCYEDMKYALKKLDDTE 180

Query:   172 FRNAF 176
             FRNAF
Sbjct:   181 FRNAF 185

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;ISS

GO:0035061 "interchromatin granule" evidence=IDA

GO:0016607 "nuclear speck" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

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

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

TAIR|locus:2133249 SR34b "Serine/Arginine-Rich Protein Splicing Factor 34b" [Arabidopsis thaliana (taxid:3702)]

 Score = 592 (213.5 bits), Expect = 1.4e-57, P = 1.4e-57
 Identities = 121/186 (65%), Positives = 133/186 (71%)

Query:     1 MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
             MSSRSSRT+YVGNLPGD R REVEDLF KYGP+V IDLKIPPRPPGYAF+EFED RDA+D
Sbjct:     1 MSSRSSRTIYVGNLPGDIREREVEDLFSKYGPVVQIDLKIPPRPPGYAFVEFEDARDADD 60

Query:    61 AIRGRDGYNFDGYRLRVELAHGGXXXXXXXXXXXXXXXXXXXXX----------XXXXXX 110
             AI GRDGY+FDG+ LRVELAHGG                                     
Sbjct:    61 AIYGRDGYDFDGHHLRVELAHGGRRSSHDARGSYSGRGRGGRGGGDGGGRERGPSRRSEY 120

Query:   111 XVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRS 170
              V+V+GLPSSASWQDLKDHMR+ G+VCFSQVFRD  G TGIVDYTSY+DMKYA   LD +
Sbjct:   121 RVVVSGLPSSASWQDLKDHMRKGGEVCFSQVFRDGRGTTGIVDYTSYEDMKYA---LDDT 177

Query:   171 EFRNAF 176
             EFRNAF
Sbjct:   178 EFRNAF 183

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

GO:0016926 "protein desumoylation" evidence=RCA

GO:0050665 "hydrogen peroxide biosynthetic process" evidence=RCA

TAIR|locus:2114643 SR34a "Serine/Arginine-Rich Protein Splicing Factor 34a" [Arabidopsis thaliana (taxid:3702)]

 Score = 560 (202.2 bits), Expect = 3.4e-54, P = 3.4e-54
 Identities = 112/186 (60%), Positives = 127/186 (68%)

Query:     1 MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
             MS R SR++YVGNLPGD R  E+ED+FYKYG IVDI+LK+PPRPP Y F+EFE  RDAED
Sbjct:     1 MSGRFSRSIYVGNLPGDIREHEIEDIFYKYGRIVDIELKVPPRPPCYCFVEFEHSRDAED 60

Query:    61 AIRGRDGYNFDGYRLRVELAHGGXXXXXXXXXXXXXXX------------XXXXXXXXXX 108
             AI+GRDGYN DG RLRVELAHGG                                     
Sbjct:    61 AIKGRDGYNLDGCRLRVELAHGGRGQSSSDRRGGYGGGGSGYGGGGGGGGSARFGVSRHS 120

Query:   109 XXXVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLD 168
                V+V GLPSSASWQDLKDHMR+AGDVCF++V RD  G  G+VDYT+YDDMKYAIRKLD
Sbjct:   121 EFRVIVRGLPSSASWQDLKDHMRKAGDVCFAEVTRDSDGTYGVVDYTNYDDMKYAIRKLD 180

Query:   169 RSEFRN 174
              +EFRN
Sbjct:   181 DTEFRN 186

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0005730 "nucleolus" evidence=IDA

GO:0008380 "RNA splicing" evidence=NAS

GO:0005829 "cytosol" evidence=IDA

WB|WBGene00004700 rsp-3 [Caenorhabditis elegans (taxid:6239)]

 Score = 254 (94.5 bits), Expect = 3.6e-42, Sum P(2) = 3.6e-42
 Identities = 47/74 (63%), Positives = 58/74 (78%)

Query:     9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
             +YVGNLPGD R +EVED+F+KYG I  +D+K   R P +AF+EFED+RDAEDA+R RDGY
Sbjct:    11 VYVGNLPGDVREKEVEDIFHKYGRIKYVDIK-SGRGPAFAFVEFEDHRDAEDAVRARDGY 69

Query:    69 NFDGYRLRVELAHG 82
              FDG R+RVE   G
Sbjct:    70 EFDGRRIRVEFTRG 83

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0009790 "embryo development" evidence=IMP

GO:0001703 "gastrulation with mouth forming first" evidence=IMP

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

GO:0040011 "locomotion" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0006376 "mRNA splice site selection" evidence=ISS

GO:0003723 "RNA binding" evidence=ISS

UNIPROTKB|Q9NEW6 rsp-3 "Probable splicing factor, arginine/serine-rich 3" [Caenorhabditis elegans (taxid:6239)]

 Score = 254 (94.5 bits), Expect = 3.6e-42, Sum P(2) = 3.6e-42
 Identities = 47/74 (63%), Positives = 58/74 (78%)

Query:     9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
             +YVGNLPGD R +EVED+F+KYG I  +D+K   R P +AF+EFED+RDAEDA+R RDGY
Sbjct:    11 VYVGNLPGDVREKEVEDIFHKYGRIKYVDIK-SGRGPAFAFVEFEDHRDAEDAVRARDGY 69

Query:    69 NFDGYRLRVELAHG 82
              FDG R+RVE   G
Sbjct:    70 EFDGRRIRVEFTRG 83

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

GO:0005515 "protein binding" evidence=IPI

GO:0008380 "RNA splicing" evidence=NAS

GO:0003723 "RNA binding" evidence=NAS

UNIPROTKB|Q5ZML3 SRSF1 "Serine/arginine-rich splicing factor 1" [Gallus gallus (taxid:9031)]

 Score = 431 (156.8 bits), Expect = 1.6e-40, P = 1.6e-40
 Identities = 87/168 (51%), Positives = 109/168 (64%)

Query:     9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
             +YVGNLP D R +++ED+FYKYG I DIDLK     P +AF+EFED RDAEDA+ GRDGY
Sbjct:    18 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 77

Query:    69 NFDGYRLRVELAHGGXXXXXXXXXXXXXXXXXXXXX--XXXXXXXVLVTGLPSSASWQDL 126
             ++DGYRLRVE    G                              V+V+GLP S SWQDL
Sbjct:    78 DYDGYRLRVEFPRSGRGTGRGGGGGGGGGAPRGRYGPPSRRSEYRVIVSGLPPSGSWQDL 137

Query:   127 KDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRN 174
             KDHMR AGDVC++ VFRD G  TG+V++   +DM YA+RKLD ++FR+
Sbjct:   138 KDHMREAGDVCYADVFRD-G--TGVVEFVRKEDMTYAVRKLDNTKFRS 182

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

ZFIN|ZDB-GENE-040426-1467 srsf1b "serine/arginine-rich splicing factor 1b" [Danio rerio (taxid:7955)]

 Score = 431 (156.8 bits), Expect = 1.6e-40, P = 1.6e-40
 Identities = 88/168 (52%), Positives = 109/168 (64%)

Query:     9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
             +YVGNLP D R ++VED+FYKYG I DIDLK     P +AF+EFED RDAEDA+ GRDGY
Sbjct:    17 IYVGNLPPDIRTKDVEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 76

Query:    69 NFDGYRLRVELAHGGXXXXXXXXXXXXXXXXXXXXX--XXXXXXXVLVTGLPSSASWQDL 126
             ++DGYRLRVE    G                              V+V+GLP S SWQDL
Sbjct:    77 DYDGYRLRVEFPRSGRGGGRGGGGGGGVGAPRGRYGPPSRRSEYRVIVSGLPPSGSWQDL 136

Query:   127 KDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRN 174
             KDHMR AGDVC++ VFRD G  TG+V++   +DM YA+RKLD ++FR+
Sbjct:   137 KDHMREAGDVCYADVFRD-G--TGVVEFVRKEDMTYAVRKLDNTKFRS 181

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|Q0VCY7 SRSF1 "Serine/arginine-rich splicing factor 1" [Bos taurus (taxid:9913)]

 Score = 427 (155.4 bits), Expect = 4.2e-40, P = 4.2e-40
 Identities = 86/168 (51%), Positives = 109/168 (64%)

Query:     9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
             +YVGNLP D R +++ED+FYKYG I DIDLK     P +AF+EFED RDAEDA+ GRDGY
Sbjct:    18 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 77

Query:    69 NFDGYRLRVELAHGGXXXXXXXXXXXXXXXXXXXXX--XXXXXXXVLVTGLPSSASWQDL 126
             ++DGYRLRVE    G                              V+V+GLP S SWQDL
Sbjct:    78 DYDGYRLRVEFPRSGRGTGRGGGGGGGGGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDL 137

Query:   127 KDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRN 174
             KDHMR AGDVC++ V+RD G  TG+V++   +DM YA+RKLD ++FR+
Sbjct:   138 KDHMREAGDVCYADVYRD-G--TGVVEFVRKEDMTYAVRKLDNTKFRS 182

GO:0001701 "in utero embryonic development" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005654 "nucleoplasm" evidence=ISS

GO:0003723 "RNA binding" evidence=ISS

GO:0000395 "mRNA 5'-splice site recognition" evidence=ISS

GO:0016607 "nuclear speck" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0060048 "cardiac muscle contraction" evidence=IEA

GO:0050733 "RS domain binding" evidence=IEA

UNIPROTKB|E2RJL3 SRSF1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 427 (155.4 bits), Expect = 4.2e-40, P = 4.2e-40
 Identities = 86/168 (51%), Positives = 109/168 (64%)

Query:     9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
             +YVGNLP D R +++ED+FYKYG I DIDLK     P +AF+EFED RDAEDA+ GRDGY
Sbjct:    18 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 77

Query:    69 NFDGYRLRVELAHGGXXXXXXXXXXXXXXXXXXXXX--XXXXXXXVLVTGLPSSASWQDL 126
             ++DGYRLRVE    G                              V+V+GLP S SWQDL
Sbjct:    78 DYDGYRLRVEFPRSGRGTGRGGGGGGGGGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDL 137

Query:   127 KDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRN 174
             KDHMR AGDVC++ V+RD G  TG+V++   +DM YA+RKLD ++FR+
Sbjct:   138 KDHMREAGDVCYADVYRD-G--TGVVEFVRKEDMTYAVRKLDNTKFRS 182

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q07955	SRSF1_HUMAN	No assigned EC number	0.5307	0.6245	0.6975	yes	no
Q3YLA6	SRSF1_PIG	No assigned EC number	0.5307	0.6245	0.6975	yes	no
Q6PDM2	SRSF1_MOUSE	No assigned EC number	0.5307	0.6245	0.6975	yes	no
Q5R7H2	SRSF1_PONAB	No assigned EC number	0.5307	0.6245	0.6975	yes	no
Q0VCY7	SRSF1_BOVIN	No assigned EC number	0.5307	0.6245	0.6975	yes	no
Q6NYA0	SRS1B_DANRE	No assigned EC number	0.5474	0.6245	0.7061	yes	no
Q5ZML3	SRSF1_CHICK	No assigned EC number	0.5245	0.6823	0.7354	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: fgenesh4_pg.C_LG_XIII000080 hypothetical protein (224 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	277
cd12602	76	cd12602, RRM2_SF2_plant_like, RNA recognition moti	8e-43
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	2e-41
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	3e-36
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	3e-30
cd12601	74	cd12601, RRM2_SRSF1_like, RNA recognition motif 2	1e-27
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	9e-26
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	3e-23
smart00360	73	smart00360, RRM, RNA recognition motif	1e-21
cd12768	76	cd12768, RRM2_SRSF9, RNA recognition motif 2 in ve	7e-21
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	5e-20
cd12767	76	cd12767, RRM2_SRSF1, RNA recognition motif 2 in se	9e-20
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	1e-19
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	8e-19
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	1e-18
cd12600	72	cd12600, RRM2_SRSF4_like, RNA recognition motif 2	3e-18
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	2e-15
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	2e-14
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	2e-14
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	4e-14
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-13
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	3e-13
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-12
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	2e-12
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	2e-12
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	5e-12
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	8e-12
cd12764	72	cd12764, RRM2_SRSF4, RNA recognition motif 2 in ve	1e-11
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	2e-11
cd12765	75	cd12765, RRM2_SRSF5, RNA recognition motif 2 in ve	2e-11
cd12766	73	cd12766, RRM2_SRSF6, RNA recognition motif 2 found	2e-11
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	5e-11
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	7e-11
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-10
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-10
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	1e-10
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	1e-10
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	3e-10
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	4e-10
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	7e-10
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-09
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	1e-09
smart00360	73	smart00360, RRM, RNA recognition motif	2e-09
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	2e-09
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-09
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-09
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-09
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	2e-09
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	3e-09
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	3e-09
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	3e-09
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	3e-09
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	4e-09
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	6e-09
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-08
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	1e-08
cd12467	78	cd12467, RRM_Srp1p_like, RNA recognition motif 1 i	1e-08
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	3e-08
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	4e-08
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	4e-08
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	5e-08
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	5e-08
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	6e-08
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	6e-08
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	8e-08
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	8e-08
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	1e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-07
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	2e-07
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	2e-07
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	2e-07
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	3e-07
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	4e-07
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	4e-07
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	4e-07
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	4e-07
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	5e-07
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	5e-07
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	7e-07
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	1e-06
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	1e-06
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	1e-06
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	1e-06
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	2e-06
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-06
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-06
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-06
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	3e-06
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	3e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	4e-06
cd12250	82	cd12250, RRM2_hnRNPR_like, RNA recognition motif 2	4e-06
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	4e-06
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	4e-06
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	5e-06
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	5e-06
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	6e-06
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	6e-06
cd12420	79	cd12420, RRM_RBPMS_like, RNA recognition motif in	7e-06
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	8e-06
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	1e-05
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-05
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	1e-05
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	1e-05
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	1e-05
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	1e-05
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	2e-05
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	2e-05
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	2e-05
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	2e-05
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	2e-05
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	2e-05
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	2e-05
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	2e-05
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	2e-05
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	2e-05
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	4e-05
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	4e-05
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	4e-05
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	4e-05
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	5e-05
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	6e-05
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	6e-05
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	6e-05
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	7e-05
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	7e-05
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	8e-05
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	9e-05
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	1e-04
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	1e-04
cd12657	76	cd12657, RRM1_hnRNPM, RNA recognition motif 1 in v	1e-04
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	1e-04
cd12658	76	cd12658, RRM1_MYEF2, RNA recognition motif 1 in ve	1e-04
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	2e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-04
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	2e-04
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	2e-04
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-04
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	2e-04
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	2e-04
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	2e-04
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	2e-04
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	3e-04
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	3e-04
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	3e-04
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	4e-04
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	4e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	4e-04
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	4e-04
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	4e-04
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	4e-04
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	5e-04
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	5e-04
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	5e-04
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	5e-04
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	5e-04
cd12281	92	cd12281, RRM1_TatSF1_like, RNA recognition motif 1	5e-04
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	5e-04
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	5e-04
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	5e-04
cd12533	84	cd12533, RRM_EWS, RNA recognition motif in vertebr	5e-04
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	6e-04
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	6e-04
cd12461	81	cd12461, RRM_SCAF4, RNA recognition motif found in	7e-04
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	7e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	7e-04
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	7e-04
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	8e-04
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	8e-04
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	8e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.001
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	0.001
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	0.001
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	0.001
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	0.001
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	0.001
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	0.001
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	0.001
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	0.001
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	0.002
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	0.002
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	0.002
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	0.002
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	0.002
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	0.002
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.002
cd12664	70	cd12664, RRM1_RAVER2, RNA recognition motif 1 in v	0.002
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	0.002
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	0.002
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	0.002
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	0.002
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	0.003
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	0.003
cd12724	92	cd12724, RRM1_CPEB2_like, RNA recognition motif 1	0.003
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	0.003
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	0.004
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	0.004

>gnl|CDD|241046 cd12602, RRM2_SF2_plant_like, RNA recognition motif 2 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score =  140 bits (355), Expect = 8e-43
 Identities = 65/76 (85%), Positives = 71/76 (93%)

Query: 110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDR 169
           +RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD  G TGIVD+T+YDDMKYAIRKLD 
Sbjct: 1   FRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGRGTTGIVDFTNYDDMKYAIRKLDD 60

Query: 170 SEFRNAFSRSYVRVRE 185
           +EFRN FSR+Y+RVRE
Sbjct: 61  TEFRNPFSRAYIRVRE 76

This subfamily corresponds to the RRM2 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 76

>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score =  137 bits (346), Expect = 2e-41
 Identities = 64/72 (88%), Positives = 68/72 (94%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDG 67
          T+YVGNLPGD R REVEDLFYKYGPIVDIDLK+PPRPPGYAF+EFED RDAEDAIRGRDG
Sbjct: 1  TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDG 60

Query: 68 YNFDGYRLRVEL 79
          Y+FDG RLRVEL
Sbjct: 61 YDFDGQRLRVEL 72

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score =  123 bits (311), Expect = 3e-36
 Identities = 53/72 (73%), Positives = 60/72 (83%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDG 67
           +YVGNLPGD R R++EDLFYKYGPI  IDLK   R P +AF+EFED RDAEDA+RGRDG
Sbjct: 1  RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDAVRGRDG 60

Query: 68 YNFDGYRLRVEL 79
          Y+FDGYRLRVE 
Sbjct: 61 YDFDGYRLRVEF 72

This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues. . Length = 72

>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score =  107 bits (270), Expect = 3e-30
 Identities = 41/76 (53%), Positives = 55/76 (72%), Gaps = 5/76 (6%)

Query: 110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDR 169
           +RV+V+GLP  ASWQDLKD  R+AGDV ++ V RD+ G  G+V++TS +DM+ A+RKLD 
Sbjct: 1   FRVVVSGLPEGASWQDLKDFGRQAGDVTYADVDRDQEG-EGVVEFTSQEDMERALRKLDG 59

Query: 170 SEFRNAFSRSYVRVRE 185
           +EFR       VRV E
Sbjct: 60  TEFRGR----RVRVEE 71

This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C) and plant pre-mRNA-splicing factor SF2 (SR1). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 71

>gnl|CDD|241045 cd12601, RRM2_SRSF1_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF9 and similar proteins

 Score =  101 bits (254), Expect = 1e-27
 Identities = 45/77 (58%), Positives = 61/77 (79%), Gaps = 4/77 (5%)

Query: 110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDR 169
           YRV+V+GLP + SWQDLKDHMR AGDVC++ V+RD    TG+V++  Y+DMKYA++KLD 
Sbjct: 1   YRVIVSGLPPTGSWQDLKDHMREAGDVCYADVYRDG---TGVVEFLRYEDMKYAVKKLDD 57

Query: 170 SEFRN-AFSRSYVRVRE 185
           S+FR+     SY+RV+E
Sbjct: 58  SKFRSHEGETSYIRVKE 74

This subfamily corresponds to the RRM2 of serine/arginine-rich splicing factor SRSF1, SRSF9 and similar proteins. SRSF1, also termed ASF-1, is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9, also termed SRp30C, has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 74

>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 96.4 bits (240), Expect = 9e-26
 Identities = 49/70 (70%), Positives = 58/70 (82%), Gaps = 1/70 (1%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          +YVGNLP D R +++EDLFYKYG I DIDLK    PP +AF+EFED RDAEDA+ GRDGY
Sbjct: 2  IYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRGPP-FAFVEFEDPRDAEDAVYGRDGY 60

Query: 69 NFDGYRLRVE 78
          ++DGYRLRVE
Sbjct: 61 DYDGYRLRVE 70

This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 73

>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 89.6 bits (223), Expect = 3e-23
 Identities = 39/74 (52%), Positives = 49/74 (66%), Gaps = 2/74 (2%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          +YVGNL      RE+ED F KYGP+    + +   PPG+AF+EFED RDAEDA+R  DG 
Sbjct: 2  VYVGNLGPRATKRELEDEFEKYGPL--RSVWVARNPPGFAFVEFEDPRDAEDAVRALDGR 59

Query: 69 NFDGYRLRVELAHG 82
             G R+RVEL+ G
Sbjct: 60 RICGNRVRVELSRG 73

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|214636 smart00360, RRM, RNA recognition motif

 Score = 85.7 bits (213), Expect = 1e-21
 Identities = 30/73 (41%), Positives = 42/73 (57%), Gaps = 3/73 (4%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRG 64
          TL+VGNLP DT   E+ +LF K+G +  + L       +  G+AF+EFE   DAE A+  
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 65 RDGYNFDGYRLRV 77
           +G   DG  L+V
Sbjct: 61 LNGKELDGRPLKV 73

Length = 73

>gnl|CDD|241212 cd12768, RRM2_SRSF9, RNA recognition motif 2 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 83.9 bits (207), Expect = 7e-21
 Identities = 42/77 (54%), Positives = 58/77 (75%), Gaps = 4/77 (5%)

Query: 110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDR 169
           +RV+V+GLP S SWQDLKDHMR AGDVC++ V +D  GM G+V++   +DM+YA+RKLD 
Sbjct: 1   FRVIVSGLPPSGSWQDLKDHMREAGDVCYADVQKD--GM-GVVEFLRKEDMEYALRKLDD 57

Query: 170 SEFRNAFSR-SYVRVRE 185
           ++FR+     SY+RV  
Sbjct: 58  TKFRSHEGETSYIRVMP 74

This subgroup corresponds to the RRM2 of SRSF9, also termed pre-mRNA-splicing factor SRp30C, an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. . Length = 76

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

 Score = 81.5 bits (202), Expect = 5e-20
 Identities = 32/70 (45%), Positives = 42/70 (60%), Gaps = 2/70 (2%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDAEDAIRGRD 66
          L+VGNLP DT   +++DLF K+GPI  I +      R  G+AF+EFED  DAE A+   +
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 67 GYNFDGYRLR 76
          G    G  LR
Sbjct: 61 GKELGGRELR 70

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

>gnl|CDD|241211 cd12767, RRM2_SRSF1, RNA recognition motif 2 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 80.9 bits (199), Expect = 9e-20
 Identities = 42/75 (56%), Positives = 57/75 (76%), Gaps = 4/75 (5%)

Query: 111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRS 170
           RV+V+GLP S SWQDLKDHMR AGDVC++ VFRD    TG+V++   +DM YA+RKLD +
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREAGDVCYADVFRDG---TGVVEFVRKEDMTYAVRKLDNT 58

Query: 171 EFRNAFSRS-YVRVR 184
           +FR+    + Y+RV+
Sbjct: 59  KFRSHEGETAYIRVK 73

This subgroup corresponds to the RRM2 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit, a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal SR domains rich in serine-arginine dipeptides. . Length = 76

>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 80.2 bits (198), Expect = 1e-19
 Identities = 42/70 (60%), Positives = 52/70 (74%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          +YVGNLP D R +++EDLFYKYG I DI+LK       +AF+ FED RDAEDA+ GR+GY
Sbjct: 2  IYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVPFAFVRFEDPRDAEDAVFGRNGY 61

Query: 69 NFDGYRLRVE 78
          +F   RLRVE
Sbjct: 62 DFGQCRLRVE 71

This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

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

 Score = 78.1 bits (193), Expect = 8e-19
 Identities = 28/72 (38%), Positives = 42/72 (58%), Gaps = 2/72 (2%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDAEDAIRGRD 66
          L+VGNLP DT   ++ +LF K+G I  + +      +  G+AF+EFE   DAE A+   +
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 67 GYNFDGYRLRVE 78
          G   DG +L+V 
Sbjct: 61 GKELDGRKLKVS 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|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 77.3 bits (191), Expect = 1e-18
 Identities = 31/71 (43%), Positives = 41/71 (57%), Gaps = 7/71 (9%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDID-LKIPPRPPGYAFLEFEDYRDAEDAIRGRDG 67
          L+VGNLP  T   E+  LF KYG + + D +K       Y F+  E+  DAEDAI+  +G
Sbjct: 2  LFVGNLPDATTSEELRALFEKYGTVTECDVVK------NYGFVHMEEEEDAEDAIKALNG 55

Query: 68 YNFDGYRLRVE 78
          Y F G R+ VE
Sbjct: 56 YEFMGKRINVE 66

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|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 76.6 bits (189), Expect = 3e-18
 Identities = 30/63 (47%), Positives = 42/63 (66%), Gaps = 1/63 (1%)

Query: 110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDR 169
           YR++V  L S  SWQDLKD MR+AG+V ++   + R    G+V++ +Y DMK AI KLD 
Sbjct: 1   YRLIVENLSSRVSWQDLKDFMRKAGEVTYADAHKQRPN-EGVVEFATYSDMKRAIEKLDG 59

Query: 170 SEF 172
           +E 
Sbjct: 60  TEL 62

This subfamily corresponds to the RRM2 of three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and is essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 69.3 bits (170), Expect = 2e-15
 Identities = 33/74 (44%), Positives = 44/74 (59%), Gaps = 5/74 (6%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          +Y+G LP   R R+VE  F  YG I +I+LK      G+ F+EFED RDA+DA+   +G 
Sbjct: 2  VYIGRLPYRARERDVERFFKGYGRIREINLK-----NGFGFVEFEDPRDADDAVYELNGK 56

Query: 69 NFDGYRLRVELAHG 82
             G R+ VE A G
Sbjct: 57 ELCGERVIVEHARG 70

This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 67.0 bits (163), Expect = 2e-14
 Identities = 36/77 (46%), Positives = 49/77 (63%), Gaps = 2/77 (2%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          +YVGNL  +    E+E  F  YGP+  +   +   PPG+AF+EFED RDA DA+R  DG 
Sbjct: 7  VYVGNLGNNGNKTELERAFGYYGPLRSV--WVARNPPGFAFVEFEDPRDAADAVRELDGR 64

Query: 69 NFDGYRLRVELAHGGRR 85
             G R+RVEL++G +R
Sbjct: 65 TLCGCRVRVELSNGEKR 81

This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that 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. SRSF3 can shuttle between the nucleus and cytoplasm. It contains 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 = 81

>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 66.3 bits (162), Expect = 2e-14
 Identities = 24/73 (32%), Positives = 42/73 (57%)

Query: 5  SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRG 64
          ++RTL++GNL   T   ++ + F ++G I+DID+K     P YAF+++ D      A+R 
Sbjct: 1  ATRTLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRK 60

Query: 65 RDGYNFDGYRLRV 77
           DG      R+++
Sbjct: 61 MDGEYLGNNRVKL 73

This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 74

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

 Score = 65.7 bits (161), Expect = 4e-14
 Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 3/76 (3%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRG 64
           L+V  L   T  +E+E LF K+G + ++ L   P      G+ F+ FE   DA+ AIR 
Sbjct: 3  KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 65 RDGYNFDGYRLRVELA 80
           +G   +G  ++VE A
Sbjct: 63 LNGKELEGRVIKVEKA 78

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

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

 Score = 64.6 bits (158), Expect = 1e-13
 Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 3/76 (3%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRG 64
           LYVGNLP +    +++DLF ++G +    +       R  G+ F+E E   +A  AI  
Sbjct: 1  NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 65 RDGYNFDGYRLRVELA 80
           +G +F G  L V  A
Sbjct: 61 LNGTDFGGRTLTVNEA 76

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

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

 Score = 63.5 bits (155), Expect = 3e-13
 Identities = 34/81 (41%), Positives = 50/81 (61%), Gaps = 3/81 (3%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRG 64
          +LYV N+   TR  ++  LF KYGPIVD+ + +     RP G+A+++FED RDAEDA+  
Sbjct: 2  SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61

Query: 65 RDGYNFDGYRLRVELAHGGRR 85
           D   F G  + ++ A G R+
Sbjct: 62 LDRTRFLGREIEIQFAQGDRK 82

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 61.0 bits (149), Expect = 2e-12
 Identities = 26/69 (37%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-RPPGYAFLEFEDYRDAEDAIRGRDG 67
          LYV NLP      ++ + F  YG +  + L     RP G+AF+EF    DAE A++  +G
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 68 YNFDGYRLR 76
             DG  LR
Sbjct: 61 LVLDGRTLR 69

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

>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins

 Score = 60.9 bits (148), Expect = 2e-12
 Identities = 29/74 (39%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 8  TLYVGNL-PGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRD 66
          TL+V    PG TR  ++E LF  +GP+V  D++       +AF+EFED  DA  A+    
Sbjct: 1  TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDIRKT-----FAFVEFEDSEDATKALEALH 55

Query: 67 GYNFDGYRLRVELA 80
          G   DG  L VE  
Sbjct: 56 GSRIDGSVLTVEFV 69

This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus. Length = 70

>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 61.2 bits (148), Expect = 2e-12
 Identities = 39/77 (50%), Positives = 48/77 (62%), Gaps = 2/77 (2%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          +YVGNL       E+E  F  YGP+  +   I   PPG+AF+EFED RDAEDA+RG DG 
Sbjct: 2  VYVGNLGTGAGKGELERAFSYYGPLRTV--WIARNPPGFAFVEFEDPRDAEDAVRGLDGK 59

Query: 69 NFDGYRLRVELAHGGRR 85
             G R+RVEL+ G  R
Sbjct: 60 VICGSRVRVELSTGMPR 76

This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that 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. 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. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, 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 = 77

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

 Score = 59.9 bits (146), Expect = 5e-12
 Identities = 30/74 (40%), Positives = 42/74 (56%), Gaps = 3/74 (4%)

Query: 10 YVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRGRD 66
          +VGN+P D    ++ ++F + GP+V   L       +P GY F EFED   A  AIR  +
Sbjct: 2  FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 67 GYNFDGYRLRVELA 80
          GY F+G  LRV+ A
Sbjct: 62 GYEFNGRALRVDFA 75

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

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

 Score = 59.1 bits (143), Expect = 8e-12
 Identities = 36/76 (47%), Positives = 45/76 (59%), Gaps = 7/76 (9%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRD 66
          R ++ GN   D R  E+E LF KYG +  +D+K      G+AF+  ED RDAEDAIRG D
Sbjct: 1  RPVFCGNFEYDARQSEIERLFGKYGRVDRVDMK-----SGFAFVYMEDERDAEDAIRGLD 55

Query: 67 GYNF--DGYRLRVELA 80
           + F     RLRVE A
Sbjct: 56 NFEFGRQRRRLRVEWA 71

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

>gnl|CDD|241208 cd12764, RRM2_SRSF4, RNA recognition motif 2 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 59.0 bits (142), Expect = 1e-11
 Identities = 29/62 (46%), Positives = 43/62 (69%), Gaps = 1/62 (1%)

Query: 110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDR 169
           YR++V  L S  SWQDLKD+MR+AG+V ++   + R    G++++ SY DMK A+ KLD 
Sbjct: 1   YRLIVENLSSRCSWQDLKDYMRQAGEVTYADAHKGRKN-EGVIEFRSYSDMKRALEKLDG 59

Query: 170 SE 171
           +E
Sbjct: 60  TE 61

This subgroup corresponds to the RRM2 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4), a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFRS4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, SRSF4 activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 59.2 bits (144), Expect = 2e-11
 Identities = 28/83 (33%), Positives = 42/83 (50%), Gaps = 3/83 (3%)

Query: 6  SRTLYVGNLPGDTR-MREVEDLFYKYGPIVDIDLKIPPR--PPGYAFLEFEDYRDAEDAI 62
          SR L+V  LP   R +  +  LF + G      L I P   P G+AF+E+    DAE+A 
Sbjct: 2  SRCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQ 61

Query: 63 RGRDGYNFDGYRLRVELAHGGRR 85
          +  +G++  G  +RV   + GR 
Sbjct: 62 QALNGHSLQGSPIRVSFGNPGRP 84

This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 92

>gnl|CDD|241209 cd12765, RRM2_SRSF5, RNA recognition motif 2 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)

 Score = 58.5 bits (141), Expect = 2e-11
 Identities = 30/65 (46%), Positives = 42/65 (64%), Gaps = 1/65 (1%)

Query: 107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRK 166
           R++ R++V  L S  SWQDLKD MR+AG+V F+   R +    G+V++ SY D+K AI K
Sbjct: 1   RTENRLIVENLSSRVSWQDLKDFMRQAGEVTFADAHRPKLN-EGVVEFASYSDLKNAIEK 59

Query: 167 LDRSE 171
           L   E
Sbjct: 60  LSGKE 64

This subgroup corresponds to the RRM2 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5), is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 75

>gnl|CDD|241210 cd12766, RRM2_SRSF6, RNA recognition motif 2 found in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 58.1 bits (140), Expect = 2e-11
 Identities = 29/62 (46%), Positives = 43/62 (69%), Gaps = 1/62 (1%)

Query: 110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDR 169
           YR++V  L S  SWQDLKD MR+AG+V ++   ++R    G++++ SY DMK A+ KLD 
Sbjct: 1   YRLIVENLSSRCSWQDLKDFMRQAGEVTYADAHKERAN-EGVIEFRSYSDMKRALEKLDG 59

Query: 170 SE 171
           +E
Sbjct: 60  TE 61

This subgroup corresponds to the RRM2 of SRSF6, also termed pre-mRNA-splicing factor SRp55, an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 73

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

 Score = 57.2 bits (139), Expect = 5e-11
 Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 3/66 (4%)

Query: 112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMT---GIVDYTSYDDMKYAIRKLD 168
           + V  LP   + +DLKD   + G +   ++ RD  G +     V++   +D + A+  L+
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 169 RSEFRN 174
             E   
Sbjct: 61  GKELGG 66

(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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 56.0 bits (136), Expect = 7e-11
 Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 2/56 (3%)

Query: 25 DLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA 80
           LF  +G +  I  K+  + PG+AF+EF     AE A++  +G  F G  LRV+ +
Sbjct: 3  KLFSPFGNVEKI--KLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

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

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

 Score = 56.7 bits (137), Expect = 1e-10
 Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGR 65
           L+V  LP      E+E LF K+G +  + L      +P G A++E+E+   A  A+   
Sbjct: 4  KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 66 DGYNFDGYRLRVELA 80
          DG       + V ++
Sbjct: 64 DGTEIKEKTISVAIS 78

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

 Score = 56.5 bits (137), Expect = 1e-10
 Identities = 31/82 (37%), Positives = 42/82 (51%), Gaps = 10/82 (12%)

Query: 8  TLYVGNLPGDTRMREVE--DLFYKYGPIVDID---LKIPP---RPPGYAFLEFEDYRDAE 59
           L++GNL  D+R+ E     LF KYG I   D    K  P   +P GY F+ FE   +AE
Sbjct: 1  RLWIGNL--DSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAE 58

Query: 60 DAIRGRDGYNFDGYRLRVELAH 81
           A++  +G    G +L V  AH
Sbjct: 59 KALKSLNGKTALGKKLVVRWAH 80

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

>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 56.1 bits (136), Expect = 1e-10
 Identities = 28/73 (38%), Positives = 36/73 (49%)

Query: 5  SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRG 64
           +R LYV NLP      E+ DLF KYG I  I +       G AF+ +ED  DA++A   
Sbjct: 1  VNRILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDH 60

Query: 65 RDGYNFDGYRLRV 77
            G+N     L V
Sbjct: 61 LSGFNVANRYLVV 73

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

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

 Score = 56.2 bits (136), Expect = 1e-10
 Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 3/76 (3%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAI 62
          S  L+VGNLP D    E+++ F ++G ++++ +       R P + F+ F+D    +  +
Sbjct: 3  SHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKIL 62

Query: 63 RGRDGYNFDGYRLRVE 78
            +  Y    +RL VE
Sbjct: 63 ANKPIYFRGDHRLNVE 78

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

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

 Score = 59.2 bits (142), Expect = 3e-10
 Identities = 44/143 (30%), Positives = 70/143 (48%), Gaps = 7/143 (4%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRD 57
            S   + TL+VGNLP D    ++ +LF K+GP+  + L   +   +  G+AF+EFE    
Sbjct: 110 KSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEES 169

Query: 58  AEDAIRGRDGYNFDGYRLRVELA--HGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRV--L 113
           AE AI   +G   +G  LRV+ A      R   S +  +S++   SRG +   +      
Sbjct: 170 AEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLY 229

Query: 114 VTGLPSSASWQDLKDHMRRAGDV 136
           V  LP   + ++L D  +  GD+
Sbjct: 230 VGNLPLKTAEEELADLFKSRGDI 252

Length = 306

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

 Score = 54.6 bits (132), Expect = 4e-10
 Identities = 30/75 (40%), Positives = 39/75 (52%), Gaps = 9/75 (12%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP------GYAFLEFEDYRDAEDAI 62
          L V NL   T   ++  +F KYG + D+ +   PR        G+AF+ F D RDAEDA+
Sbjct: 1  LKVDNLTYRTTPDDLRRVFEKYGEVGDVYI---PRDRYTRESRGFAFVRFYDKRDAEDAM 57

Query: 63 RGRDGYNFDGYRLRV 77
             DG   DG  LRV
Sbjct: 58 DAMDGKELDGRELRV 72

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

>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 53.8 bits (130), Expect = 7e-10
 Identities = 26/72 (36%), Positives = 42/72 (58%), Gaps = 9/72 (12%)

Query: 6  SRTLYVGNLPGD--TRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIR 63
          SR ++VGNL  D  ++  ++E++F KYG I+ I L       GY F++F++  DA  A+ 
Sbjct: 1  SR-VFVGNLNTDKVSK-EDLEEIFSKYGKILGISLH-----KGYGFVQFDNEEDARAAVA 53

Query: 64 GRDGYNFDGYRL 75
          G +G    G +L
Sbjct: 54 GENGREIAGQKL 65

This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes. . Length = 68

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

 Score = 53.3 bits (129), Expect = 1e-09
 Identities = 27/76 (35%), Positives = 39/76 (51%), Gaps = 3/76 (3%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRG 64
          T+ V NL  D    ++ +LF  +GPI  + L   K   +  G+AF+ F    DAE AI  
Sbjct: 1  TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 65 RDGYNFDGYRLRVELA 80
           +G+ +D   L VE A
Sbjct: 61 LNGFGYDNLILSVEWA 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|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 53.4 bits (128), Expect = 1e-09
 Identities = 30/74 (40%), Positives = 45/74 (60%), Gaps = 5/74 (6%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          +Y+G L    R ++++  F  YG +++IDLK      GY F+EFED RDA+DA+   +G 
Sbjct: 2  VYIGRLSYHVREKDIQRFFGGYGKLLEIDLK-----NGYGFVEFEDSRDADDAVYELNGK 56

Query: 69 NFDGYRLRVELAHG 82
          +  G R+ VE A G
Sbjct: 57 DLCGERVIVEHARG 70

This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides. . Length = 70

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

 Score = 53.0 bits (128), Expect = 2e-09
 Identities = 14/68 (20%), Positives = 30/68 (44%), Gaps = 4/68 (5%)

Query: 111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMT----GIVDYTSYDDMKYAIRK 166
            + V  LP   + ++L++   + G V   ++ RD+          V++ S +D + A+  
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 167 LDRSEFRN 174
           L+  E   
Sbjct: 61  LNGKELDG 68

Length = 73

>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 53.4 bits (128), Expect = 2e-09
 Identities = 31/81 (38%), Positives = 50/81 (61%), Gaps = 3/81 (3%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRG 64
          +L+V N+  DTR  ++   F +YGPIVD+ + +     RP G+A+++FED RDAEDA+  
Sbjct: 2  SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN 61

Query: 65 RDGYNFDGYRLRVELAHGGRR 85
           D     G ++ ++ A G R+
Sbjct: 62 LDRKWICGRQIEIQFAQGDRK 82

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

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

 Score = 53.0 bits (128), Expect = 2e-09
 Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 4/77 (5%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVD---IDLKIPPRPPGYAFLEFEDYRDAEDAIR 63
            ++VG LP  T    +   F ++G I +   I  +   +  GY F+ F+D   AE A +
Sbjct: 1  TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 64 GRDGYNFDGYRLRVELA 80
            +    DG +  V LA
Sbjct: 61 DPNP-IIDGRKANVNLA 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|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 52.6 bits (127), Expect = 2e-09
 Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 3/72 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP---GYAFLEFEDYRDAEDAIRGR 65
          LYVG L  +   + +   F  +G I DI + +        G+AF+EFE+  DA  AI   
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 66 DGYNFDGYRLRV 77
          +     G  +RV
Sbjct: 61 NESELFGRTIRV 72

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

 Score = 52.6 bits (127), Expect = 2e-09
 Identities = 31/79 (39%), Positives = 42/79 (53%), Gaps = 15/79 (18%)

Query: 9  LYVGNLPGDTR------MREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAE 59
          L+VG L   TR      ++E+   F  YG + D+DL   +    P GYA++EFE   DAE
Sbjct: 1  LHVGKL---TRNVNKDHLKEI---FSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAE 54

Query: 60 DAIRGRDGYNFDGYRLRVE 78
           AI+  DG   DG  + VE
Sbjct: 55 KAIKHMDGGQIDGQEVTVE 73

This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain. . Length = 73

>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 52.7 bits (127), Expect = 2e-09
 Identities = 22/57 (38%), Positives = 35/57 (61%), Gaps = 3/57 (5%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAI 62
          S TL++G+L       ++++LF +YG I  ID+ IPPR  G A++  E  +DA  A+
Sbjct: 2  STTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDM-IPPR--GCAYVCMETRQDAHRAL 55

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

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

 Score = 53.0 bits (128), Expect = 3e-09
 Identities = 32/79 (40%), Positives = 44/79 (55%), Gaps = 3/79 (3%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIR 63
          +TL+V  L  DT   ++   F +YGPI  I L   K   +P GYAF+EFE  RD + A +
Sbjct: 2  KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61

Query: 64 GRDGYNFDGYRLRVELAHG 82
            DG   DG R+ V++  G
Sbjct: 62 YADGKKIDGRRVLVDVERG 80

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 52.2 bits (125), Expect = 3e-09
 Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 5/70 (7%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          L+VGNLP +   +E+  LF +YG +++ D+        Y F+  +D   A++AIR    Y
Sbjct: 3  LFVGNLPPEATEQEIRSLFEQYGKVLECDII-----KNYGFVHMDDKTAADEAIRNLHHY 57

Query: 69 NFDGYRLRVE 78
             G  + VE
Sbjct: 58 KLHGVAINVE 67

This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 52.3 bits (126), Expect = 3e-09
 Identities = 17/75 (22%), Positives = 36/75 (48%), Gaps = 1/75 (1%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL-KIPPRPPGYAFLEFEDYRDAEDAIRG 64
            +++VG L  D    E+ + F ++G I++++L K       +AF++FE  + A  A+  
Sbjct: 3  KYSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVES 62

Query: 65 RDGYNFDGYRLRVEL 79
           +        + V+ 
Sbjct: 63 ENHSMLKNKTMHVQY 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|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 52.1 bits (125), Expect = 3e-09
 Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 5/72 (6%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          ++VGN+  DT   E+  LF  YG ++   +        +AF+       A+ AI   +G 
Sbjct: 3  IFVGNVDEDTSQEELRALFEAYGAVLSCAVM-----RQFAFVHLRGEAAADRAIEELNGR 57

Query: 69 NFDGYRLRVELA 80
             G +L VE +
Sbjct: 58 ELHGRKLVVEHS 69

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative RNA exonuclease NEF-sp

 Score = 52.0 bits (125), Expect = 4e-09
 Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 3/72 (4%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRP-PGYAFLEFEDYRDAEDAIRGRD 66
          T+Y G  P    + +V+ LF   GP+    + +  R    +AF+ FE+   A+ AI   +
Sbjct: 1  TVYAGPFPTSFCLSDVKRLFETCGPVRK--VTMLSRTVQPHAFITFENLEAAQLAIETLN 58

Query: 67 GYNFDGYRLRVE 78
          G + DG  ++V+
Sbjct: 59 GASVDGNCIKVQ 70

This subfamily corresponds to the RRM1 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities. . Length = 71

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 51.5 bits (123), Expect = 6e-09
 Identities = 34/77 (44%), Positives = 47/77 (61%), Gaps = 5/77 (6%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          +Y+G L    R R+VE  F  YG I+++DLK      GY F+EF+D RDA+DA+   +G 
Sbjct: 2  VYIGRLSYQARERDVERFFKGYGKILEVDLK-----NGYGFVEFDDLRDADDAVYELNGK 56

Query: 69 NFDGYRLRVELAHGGRR 85
          +  G R+ VE A G RR
Sbjct: 57 DLCGERVIVEHARGPRR 73

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

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

 Score = 50.7 bits (122), Expect = 1e-08
 Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 5/74 (6%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRD 66
          + LYV NLP  T   ++ +LF +YG +  +          YAF+ FE+  DA  A+   +
Sbjct: 2  KVLYVRNLPLSTTEEQLRELFSEYGEVERVKK-----IKDYAFVHFEERDDAVKAMEEMN 56

Query: 67 GYNFDGYRLRVELA 80
          G   +G  + V LA
Sbjct: 57 GKELEGSPIEVSLA 70

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

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 3/75 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRP---PGYAFLEFEDYRDAEDAIRGR 65
          ++V  +  + +  +V D F ++G I ++ L +  R     GYA +E+E  ++A+ AI G 
Sbjct: 9  IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 66 DGYNFDGYRLRVELA 80
          +G    G  + V+ A
Sbjct: 69 NGKELLGQTISVDWA 83

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

>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast pre-mRNA-splicing factor Srp1p and similar proteins

 Score = 50.6 bits (121), Expect = 1e-08
 Identities = 31/78 (39%), Positives = 42/78 (53%), Gaps = 6/78 (7%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPG---YAFLEFEDYRDAEDAIRG 64
          TLYV     +TR R++   F +YG +V  D+  PPR      +AF+E+E +RDAEDA   
Sbjct: 1  TLYVTGFGAETRARDLAYEFERYGRLVRCDIP-PPRTFQSRPFAFVEYESHRDAEDAYEE 59

Query: 65 RDGYNF--DGYRLRVELA 80
            G  F   G  L V+ A
Sbjct: 60 MHGRRFPDTGDTLHVQWA 77

This subgroup corresponds to the RRM domain in Srp1p encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but not essential for growth. Srp1p is closely related to the SR protein family found in metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. Some family members also contain another RRM domain. Length = 78

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

 Score = 49.2 bits (118), Expect = 3e-08
 Identities = 22/64 (34%), Positives = 31/64 (48%), Gaps = 3/64 (4%)

Query: 112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGM---TGIVDYTSYDDMKYAIRKLD 168
           + V  LP S +WQDLKD  R  G+V  + V  D  G     G V + S +D + AI   +
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 169 RSEF 172
             + 
Sbjct: 61  GYDL 64

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|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 48.9 bits (116), Expect = 4e-08
 Identities = 25/70 (35%), Positives = 38/70 (54%), Gaps = 5/70 (7%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          L+VGN+      +E+   F +YGP+++ D+        YAF+  E   DA +AIRG D  
Sbjct: 3  LHVGNISSSCTNQELRAKFEEYGPVIECDIV-----KDYAFVHMERAEDAVEAIRGLDNT 57

Query: 69 NFDGYRLRVE 78
           F G R+ V+
Sbjct: 58 EFQGKRMHVQ 67

This subgroup corresponds to the RRM2 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>gnl|CDD|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 = 49.0 bits (117), Expect = 4e-08
 Identities = 26/75 (34%), Positives = 45/75 (60%), Gaps = 3/75 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          ++VGN+P +    +++D+F + GP+V   L   +   +P GY F E++D   A  A+R  
Sbjct: 1  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 66 DGYNFDGYRLRVELA 80
          +GY  +G +LRV+ A
Sbjct: 61 NGYELNGRQLRVDNA 75

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

>gnl|CDD|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 = 49.1 bits (117), Expect = 5e-08
 Identities = 26/75 (34%), Positives = 45/75 (60%), Gaps = 3/75 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          L++G L  DT  + +E +F KYG I ++ +   +   R  G+ F+ FE+  DA+DA+   
Sbjct: 3  LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 66 DGYNFDGYRLRVELA 80
          +G + DG ++RV+ A
Sbjct: 63 NGKSVDGRQIRVDQA 77

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

>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)

 Score = 48.8 bits (116), Expect = 5e-08
 Identities = 29/72 (40%), Positives = 41/72 (56%), Gaps = 5/72 (6%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          +++G L    R ++VE  F  YG I DIDLK      G+ F+EF+D RDA+DA+   DG 
Sbjct: 2  VFIGRLNPAAREKDVERFFKGYGRIRDIDLK-----RGFGFVEFDDPRDADDAVYELDGK 56

Query: 69 NFDGYRLRVELA 80
               R+ +E A
Sbjct: 57 ELCNERVTIEHA 68

This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 70

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

 Score = 48.5 bits (116), Expect = 6e-08
 Identities = 15/66 (22%), Positives = 32/66 (48%), Gaps = 3/66 (4%)

Query: 112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGM---TGIVDYTSYDDMKYAIRKLD 168
           + V  LP   + +DL++   + G++   ++ RD+ G       V++ S +D + A+  L+
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 169 RSEFRN 174
             E   
Sbjct: 61  GKELDG 66

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|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 = 48.4 bits (116), Expect = 6e-08
 Identities = 26/72 (36%), Positives = 34/72 (47%), Gaps = 3/72 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          L+V NLP  T   E+ +LF  +G I ++ L   K   R  G+AF+ F     A  A    
Sbjct: 2  LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 66 DGYNFDGYRLRV 77
          DG  F G  L V
Sbjct: 62 DGSIFQGRLLHV 73

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|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 48.6 bits (116), Expect = 8e-08
 Identities = 22/52 (42%), Positives = 33/52 (63%), Gaps = 2/52 (3%)

Query: 5  SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPG--YAFLEFED 54
          ++RTL+VGNL       E+   F +YG + D+D+K PPR  G  YAF++F +
Sbjct: 1  ATRTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLN 52

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 47.9 bits (114), Expect = 8e-08
 Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 5/71 (7%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          ++VGN+       E+  LF ++G +V+ D         YAF+  E   +A  AI   +G 
Sbjct: 3  IFVGNVSATCTSDELRGLFEEFGRVVECDKVK-----DYAFVHMEREEEALAAIEALNGK 57

Query: 69 NFDGYRLRVEL 79
             G R+ VEL
Sbjct: 58 EVKGRRINVEL 68

This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 68

>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 47.7 bits (113), Expect = 1e-07
 Identities = 29/81 (35%), Positives = 49/81 (60%), Gaps = 3/81 (3%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRG 64
          +L+V N+   TR  ++   F +YGPIVD+ + +     RP G+A+++FED RDAEDA+  
Sbjct: 2  SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 65 RDGYNFDGYRLRVELAHGGRR 85
           +     G ++ ++ A G R+
Sbjct: 62 LNRKWVCGRQIEIQFAQGDRK 82

This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 46.8 bits (112), Expect = 2e-07
 Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 2/67 (2%)

Query: 112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTG--IVDYTSYDDMKYAIRKLDR 169
           + V  LP S + +DL++     G V   ++ R++    G   V++ S +D + A++KL+ 
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 170 SEFRNAF 176
                  
Sbjct: 61  LVLDGRT 67

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

>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 27/71 (38%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDG 67
          TL V NL      +E+  LF ++G + DI  +  P  P   F+EF D R AE A+   +G
Sbjct: 3  TLLVFNLDSPISDQELRSLFSQFGEVKDI--RETPLRPSQKFVEFYDIRAAEAALDALNG 60

Query: 68 YNFDGYRLRVE 78
            F G RL+V+
Sbjct: 61 RPFLGGRLKVK 71

This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

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

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 25/69 (36%), Positives = 37/69 (53%), Gaps = 3/69 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          L+VGNLP D    E ++LF KYG + ++ L    +  G+ F+  +   +AE A    DG 
Sbjct: 4  LFVGNLPNDITEEEFKELFSKYGEVSEVFL---NKEKGFGFIRLDTRTNAEKAKAELDGI 60

Query: 69 NFDGYRLRV 77
             G +LRV
Sbjct: 61 MRKGRQLRV 69

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

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

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 3/77 (3%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          LYVGNL   T   ++ +LF + G I  I +   +    P G+ F+E+    DAE+A++  
Sbjct: 1  LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 66 DGYNFDGYRLRVELAHG 82
          +G   D   +RV+   G
Sbjct: 61 NGTKLDDRIIRVDWDAG 77

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

 Score = 46.6 bits (111), Expect = 3e-07
 Identities = 25/77 (32%), Positives = 36/77 (46%), Gaps = 3/77 (3%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIR 63
            L V  LP D    E+  LF   GPI    +   +I  +  GY F+++ D  DA+ AI 
Sbjct: 1  TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 64 GRDGYNFDGYRLRVELA 80
            +G+     RL+V  A
Sbjct: 61 TLNGFEIRNKRLKVSYA 77

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

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

 Score = 46.5 bits (111), Expect = 4e-07
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 6/76 (7%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP----GYAFLEFEDYRDAEDAIRG 64
          L V NLP      +++ LF  +G + ++   IP +P     G+AF++F    DAE AI+G
Sbjct: 2  LIVRNLPFKCTEADLKKLFSPFGFVWEV--TIPRKPDGKKKGFAFVQFTSKADAEKAIKG 59

Query: 65 RDGYNFDGYRLRVELA 80
           +G    G  + V+ 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|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 46.2 bits (110), Expect = 4e-07
 Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 4/74 (5%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRG 64
           L+VGNLP DT   ++   F   G    + L   K   +  G AF+EF+       A++ 
Sbjct: 2  ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK- 60

Query: 65 RDGYNFDGYRLRVE 78
                 G ++ VE
Sbjct: 61 LHHTLLKGRKINVE 74

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

>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 46.3 bits (110), Expect = 4e-07
 Identities = 20/68 (29%), Positives = 39/68 (57%), Gaps = 4/68 (5%)

Query: 111 RVLVTGLPSSASWQDLKDHMRR-AGDVCFSQVFRDRGGMT---GIVDYTSYDDMKYAIRK 166
           RV ++ +P    WQDLKD  R   G+V + ++F+D  G +   G+V++   + ++ A+  
Sbjct: 1   RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALET 60

Query: 167 LDRSEFRN 174
           ++R E + 
Sbjct: 61  MNRYELKG 68

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

 Score = 46.5 bits (111), Expect = 4e-07
 Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 3/76 (3%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRG 64
          TL+V NLP DT   ++E+ F + GPI    +   K   +  G+ ++ F    DA+ A+  
Sbjct: 1  TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 65 RDGYNFDGYRLRVELA 80
          +    F G ++ VE A
Sbjct: 61 KKKTKFGGRKIHVEFA 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|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 45.7 bits (109), Expect = 5e-07
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 2/71 (2%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDAEDAIRGRD 66
          ++V NLP     ++++DLF + G ++  D+K     R  G+  + FE   DA+ AI   +
Sbjct: 1  IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 67 GYNFDGYRLRV 77
          GY+ +G  L V
Sbjct: 61 GYDLEGRELEV 71

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

>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 46.4 bits (111), Expect = 5e-07
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 4/50 (8%)

Query: 26 LFYKYGPIVDIDLKIPPRPP----GYAFLEFEDYRDAEDAIRGRDGYNFD 71
          +F K+G    + + +P        GYAF+EF    +A++A++  +GY  D
Sbjct: 27 IFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNGYKLD 76

This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain. . Length = 84

>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 45.6 bits (109), Expect = 7e-07
 Identities = 26/67 (38%), Positives = 36/67 (53%), Gaps = 8/67 (11%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDI----DLKIPPRPPGYAFLEFEDYRDAEDAIRG 64
          LYVG+L  D     + ++F   GP++ I    DL I  R  GYA++ F++  DAE   R 
Sbjct: 2  LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDL-ITRRSLGYAYVNFQNPADAE---RA 57

Query: 65 RDGYNFD 71
           D  NFD
Sbjct: 58 LDTLNFD 64

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|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 45.0 bits (107), Expect = 1e-06
 Identities = 27/78 (34%), Positives = 42/78 (53%), Gaps = 10/78 (12%)

Query: 7  RTLYVGNLPGDTRMRE--VEDLFYKYGPIVDIDLKIP----PRPPGYAFLEFEDYRDAED 60
          RTL+VGNL  D R+ E  + +LF + GP+  +  KIP     +P  +AF+ F+       
Sbjct: 2  RTLFVGNL--DARVTEEILYELFLQAGPLEGV--KIPKDPNGKPKSFAFVTFKHEVSVPY 57

Query: 61 AIRGRDGYNFDGYRLRVE 78
          AI+  +G    G  LR++
Sbjct: 58 AIQLLNGIRLFGRELRIK 75

This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 44.8 bits (107), Expect = 1e-06
 Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 4/78 (5%)

Query: 8  TLYVGNLPGDTRMREVED----LFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIR 63
          TLY+ NL    +  E++     LF ++GP++DI      +  G AF+ F+D   A +A+R
Sbjct: 1  TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNALR 60

Query: 64 GRDGYNFDGYRLRVELAH 81
             G+ F    +R++ A 
Sbjct: 61 ALQGFPFYDKPMRIQYAK 78

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

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

 Score = 45.1 bits (107), Expect = 1e-06
 Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 4/70 (5%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAEDAIRGR 65
          L+V NLP   +  ++E LF K+G + ++ + I  +     G+A++ F D  DA  A +  
Sbjct: 5  LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 66 DGYNFDGYRL 75
          DG  F G RL
Sbjct: 65 DGKVFQG-RL 73

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|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins

 Score = 44.7 bits (106), Expect = 1e-06
 Identities = 19/69 (27%), Positives = 29/69 (42%), Gaps = 5/69 (7%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          LYV   P DT    + ++F  YG + ++ +        +AF+EFE    A  A     G 
Sbjct: 2  LYVRPFPPDTSESAIREIFSPYGAVKEVKMI-----SNFAFVEFESLESAIRAKDSVHGK 56

Query: 69 NFDGYRLRV 77
            +   L V
Sbjct: 57 VLNNNPLYV 65

This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 67

>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 44.6 bits (106), Expect = 2e-06
 Identities = 26/74 (35%), Positives = 38/74 (51%), Gaps = 4/74 (5%)

Query: 9  LYVGNLPGDTRMRE--VEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRD 66
          LYVGNL  D  + E  + +LF + GPI    L        YAF+E+ D+R A  A++  +
Sbjct: 1  LYVGNL--DRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMN 58

Query: 67 GYNFDGYRLRVELA 80
          G    G  ++V  A
Sbjct: 59 GRLILGQEIKVNWA 72

This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 72

>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

 Score = 44.1 bits (105), Expect = 2e-06
 Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 3/70 (4%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDG 67
          T+YVGNLP      E++  F  +G I ++  ++     GYAF+ F+ +  A  AI   +G
Sbjct: 2  TVYVGNLPHGLTEEELQRTFSPFGAIEEV--RVFKD-KGYAFVRFDTHEAAATAIVAVNG 58

Query: 68 YNFDGYRLRV 77
           + +G  ++ 
Sbjct: 59 TSINGQTVKC 68

This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 73

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

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 8/82 (9%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPI--VDIDL-KIPPRPPGYAFLEFEDYRDAEDAIR 63
          RT+++ NLP D    E+++LF ++G +    I   K+     G AF++F+    A+  + 
Sbjct: 1  RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

Query: 64 -----GRDGYNFDGYRLRVELA 80
                  G + DG RL V LA
Sbjct: 61 AADNAEDSGLSLDGRRLIVTLA 82

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

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

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 3/75 (4%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGR 65
          TL+VGNL       ++E+ F + G +VD+ +      R  G+  +EF     A+ A+  +
Sbjct: 1  TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALE-K 59

Query: 66 DGYNFDGYRLRVELA 80
           G    G  +RV+LA
Sbjct: 60 SGEELLGREIRVDLA 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|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 43.5 bits (103), Expect = 3e-06
 Identities = 23/81 (28%), Positives = 34/81 (41%), Gaps = 13/81 (16%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP-----GYAFLEFEDYRDAEDAIR 63
          LY+GNL  D    ++  LF         + KIP         GYAF++  D   A+ AI 
Sbjct: 1  LYIGNLSSDVNESDLRQLFE--------EHKIPVSSVLVKKGGYAFVDCPDQSWADKAIE 52

Query: 64 GRDGYNFDGYRLRVELAHGGR 84
            +G    G  + VE +   +
Sbjct: 53 KLNGKILQGKVIEVEHSVPKK 73

Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. Length = 73

>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 43.8 bits (104), Expect = 3e-06
 Identities = 24/77 (31%), Positives = 35/77 (45%), Gaps = 10/77 (12%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP-PRPP-------GYAFLEFEDYRDAED 60
          LYVGNL        +   F ++GP+  +  KI  PR            F+ F +  DAE 
Sbjct: 4  LYVGNLNPKVTEEVLCQEFGRFGPLASV--KIMWPRTEEERRRNRNCGFVAFMNRADAER 61

Query: 61 AIRGRDGYNFDGYRLRV 77
          A+   DG +  GY L++
Sbjct: 62 ALDELDGKDVMGYELKL 78

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 43.4 bits (103), Expect = 4e-06
 Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 7/60 (11%)

Query: 9  LYVGNLPGDTRMRE--VEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIR 63
          +YVGNL  D ++ E  + +LF + GP+V++ +   ++     GY F+EF    DA+ AI+
Sbjct: 1  VYVGNL--DEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIK 58

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 74

>gnl|CDD|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 5/60 (8%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGP-----IVDIDLKIPPRPPGYAFLEFEDYRDAEDAIR 63
          L+VG +P      E+ + F K        IV        +  G+AF+E+E +R A  A R
Sbjct: 4  LFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAMARR 63

This subfamily corresponds to the RRM2 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains); DND1 harbors only two RRMs. . Length = 82

>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 43.8 bits (103), Expect = 4e-06
 Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 3/62 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          LYV  LP     +E+E LF +YG I+   +   ++     G  F+ F+   +AE+AI+G 
Sbjct: 3  LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 66 DG 67
          +G
Sbjct: 63 NG 64

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

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 25/76 (32%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIR 63
           TL+VG L   T    + ++F +YG I  + L    +     GYAF+E+E  RDA  A R
Sbjct: 4  LTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYR 63

Query: 64 GRDGYNFDGYRLRVEL 79
                 DG  + V+ 
Sbjct: 64 DAHKLVIDGSEIFVDF 79

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

 Score = 43.5 bits (103), Expect = 5e-06
 Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 9/63 (14%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP------GYAFLEFEDYRDAEDA 61
          T+YV  LP +     ++ +F KYG +V + L   PR        G+AF+EFE   +A+ A
Sbjct: 1  TVYVECLPKNATHEWLKAVFSKYGTVVYVSL---PRYKHTGDIKGFAFIEFETPEEAQKA 57

Query: 62 IRG 64
           + 
Sbjct: 58 CKH 60

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

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

 Score = 43.0 bits (102), Expect = 5e-06
 Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 3/57 (5%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAI 62
          L+VG L  D    ++ + F +YG +  +++   K   +  G+AF+ F+DY   +  +
Sbjct: 2  LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIV 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|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 43.0 bits (102), Expect = 6e-06
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 11/81 (13%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP--------GYAFLEFEDYRDA 58
          R +YV NL       ++  +F K+G +  I  +IP +          G+AF+ F+D   A
Sbjct: 1  REIYVRNLDFKLDEDDLRGIFSKFGEVESI--RIPKKQDEKQGRLNNGFAFVTFKDASSA 58

Query: 59 EDAIRGRDGYNFDGYRLRVEL 79
          E+A++  +G    G ++ V L
Sbjct: 59 ENALQ-LNGTELGGRKISVSL 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|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 42.9 bits (102), Expect = 6e-06
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDAEDAIRGRD 66
          +YV NL  D    ++++LF KYG I    +      +  G+ F+ FE++  A+ A+   +
Sbjct: 4  VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELN 63

Query: 67 GYNFDGYRLRV 77
          G   +G +L V
Sbjct: 64 GKEVNGKKLYV 74

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

>gnl|CDD|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding protein with multiple splicing (RBP-MS)-like proteins

 Score = 43.0 bits (102), Expect = 7e-06
 Identities = 24/79 (30%), Positives = 34/79 (43%), Gaps = 7/79 (8%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPG----YAFLEFEDYRDAEDAI 62
          RTL+V  LP D + RE+  LF  +       L    +  G      F++F   + A  A+
Sbjct: 1  RTLFVSGLPSDVKERELAHLFRPFPGYEASRLVFKEKKGGEKQPVGFVDFSSAQCAAAAM 60

Query: 63 RGRDGYNFDG---YRLRVE 78
              GY FD      LR+E
Sbjct: 61 DALQGYRFDPDTSSVLRLE 79

This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. It has also been shown to physically interact with Smad2, Smad3 and Smad4, and stimulates Smad-mediated transactivation. Cpo may play an important role in regulating normal function of the nervous system, whereas mutations in Mec-8 affect mechanosensory and chemosensory neuronal function. All members contain a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Some uncharacterized family members contain two RRMs; this subfamily includes their RRM1. Their RRM2 shows high sequence homology to the RRM of yeast proteins scw1, Whi3, and Whi4. Length = 79

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

 Score = 43.0 bits (101), Expect = 8e-06
 Identities = 23/67 (34%), Positives = 32/67 (47%), Gaps = 3/67 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          LYV NLP      E+  +F  YG IV  +L   K    P G AF+ ++   +A+ AI   
Sbjct: 3  LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 66 DGYNFDG 72
          +G    G
Sbjct: 63 NGTIPPG 69

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

>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 42.5 bits (101), Expect = 1e-05
 Identities = 26/84 (30%), Positives = 36/84 (42%), Gaps = 17/84 (20%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP----------GYAFLEFEDY 55
          +R LYVGNLP      E+ D F +   ++   L   P  P           +AF+EF   
Sbjct: 1  ARRLYVGNLPPGITEEELVDFFNQA--MLAAGLNQAPGNPVLSVQINPEKNFAFVEF--- 55

Query: 56 RDAEDAIRG--RDGYNFDGYRLRV 77
          R  E+A      DG  F G  L++
Sbjct: 56 RTVEEATAALALDGIIFKGQPLKI 79

The subfamily corresponds to the RRM1 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 = 82

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

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 5/77 (6%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPI----VDIDLKIPPRPPGYAFLEFEDYRDAEDAIR 63
          TL+V NL       ++ D F    PI    V  D +      GY F+ F    DA++A+ 
Sbjct: 1  TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETG-ESRGYGFVTFAMLEDAQEALA 59

Query: 64 GRDGYNFDGYRLRVELA 80
                  G  LR+++A
Sbjct: 60 KLKNKKLHGRILRLDIA 76

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|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 2/72 (2%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDG 67
          T+ V NLP DT   ++   F   G I ++ +         A +EFE   +A  A+  +D 
Sbjct: 2  TVKVKNLPKDTTENKIRQFFKDCGEIREVKIVESEGGL-VAVIEFETEDEALAALT-KDH 59

Query: 68 YNFDGYRLRVEL 79
              G  + V  
Sbjct: 60 KRLGGNEISVSR 71

This subfamily corresponds to the RRM1 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 = 71

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 3/78 (3%)

Query: 4  RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAED 60
          + S  +Y+G LP +    ++  +F +YG IVDI+L   K   +  G+AFL +ED R    
Sbjct: 7  KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTIL 66

Query: 61 AIRGRDGYNFDGYRLRVE 78
          A+   +G    G  +RV+
Sbjct: 67 AVDNLNGIKLLGRTIRVD 84

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

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 41.9 bits (99), Expect = 1e-05
 Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
           TLYVG L      +++ D FY++G I  I   + PR    AF+ F     AE A
Sbjct: 2  TTLYVGGLGERVTEKDLRDHFYQFGEIRSI--TVVPR-QQCAFVTFTTREAAEKA 53

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 41.9 bits (99), Expect = 1e-05
 Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 3/73 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPG---YAFLEFEDYRDAEDAIRGR 65
          L+V  L   T+  +++ LF KYG +V   +    R PG   + F+      +A   I+  
Sbjct: 2  LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 66 DGYNFDGYRLRVE 78
                G  + VE
Sbjct: 62 HRTELHGRVISVE 74

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 28/79 (35%), Positives = 37/79 (46%), Gaps = 3/79 (3%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRD 66
          R +YVG +P DT   E+   F  +G I +I L        Y F+    YR A DA R  +
Sbjct: 3  RVIYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDNYGFVT---YRYACDAFRAIE 59

Query: 67 GYNFDGYRLRVELAHGGRR 85
            N D    + +L  GGRR
Sbjct: 60 HGNDDPTEPKYDLCFGGRR 78

This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 89

>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal EAR1-like proteins

 Score = 41.7 bits (98), Expect = 2e-05
 Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 2/71 (2%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDG 67
          TL + NL        +  +F  YG + +  L+  P      F+EF D RDA  A+R  +G
Sbjct: 3  TLVIFNLDPTVSSETLRSIFQVYGDVKE--LRETPCKREQRFVEFFDVRDAAKALRAMNG 60

Query: 68 YNFDGYRLRVE 78
              G  + +E
Sbjct: 61 KEISGKPVVIE 71

This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. . Length = 71

>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins

 Score = 41.7 bits (98), Expect = 2e-05
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 6/73 (8%)

Query: 9  LYVGNLPGDT-RMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDG 67
          L++GNLP       ++  +F  YG +  I LK       Y F++F+      +AI    G
Sbjct: 2  LFIGNLPTKRVSKEDLFRIFSTYGELAQIVLK-----NAYGFVQFDSPESCANAINCEQG 56

Query: 68 YNFDGYRLRVELA 80
              G +L +E++
Sbjct: 57 KMIRGRKLHLEVS 69

This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues. . Length = 71

>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins

 Score = 41.8 bits (98), Expect = 2e-05
 Identities = 22/73 (30%), Positives = 37/73 (50%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          S  L+VGNLP D    E+++ F +YG +V++ +    + P + F+ F+D    +  +  R
Sbjct: 3  SHQLFVGNLPHDVDKSELKEFFQQYGNVVELRINSGGKLPNFGFVVFDDSEPVQKILSNR 62

Query: 66 DGYNFDGYRLRVE 78
                  RL VE
Sbjct: 63 PIMFRGDVRLNVE 75

This subgroup corresponds to the RRM of G3BP1, also termed ATP-dependent DNA helicase VIII (DH VIII), or GAP SH3 domain-binding protein 1, which has been identified as a phosphorylation-dependent endoribonuclease that interacts with the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity. The acidic RasGAP binding domain of G3BP1 harbors an arsenite-regulated phosphorylation site and dominantly inhibits stress granule (SG) formation. G3BP1 also contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). The RRM domain and RGG-rich region are canonically associated with RNA binding. G3BP1 co-immunoprecipitates with mRNAs. It binds to and cleaves the 3'-untranslated region (3'-UTR) of the c-myc mRNA in a phosphorylation-dependent manner. Thus, G3BP1 may play a role in coupling extra-cellular stimuli to mRNA stability. It has been shown that G3BP1 is a novel Dishevelled-associated protein that is methylated upon Wnt3a stimulation and that arginine methylation of G3BP1 regulates both Ctnnb1 mRNA and canonical Wnt/beta-catenin signaling. Furthermore, G3BP1 can be associated with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules, demonstrating that G3BP1 may specifically repress the translation of the transcript. Length = 80

>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 41.4 bits (97), Expect = 2e-05
 Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 8/77 (10%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAI 62
          S+ L V NL        ++++F K   I     +IP    RP GYAF+EFE   DA++A+
Sbjct: 1  SKVLVVNNLSYSASEDSLQEVFEKATSI-----RIPQNNGRPKGYAFVEFESAEDAKEAL 55

Query: 63 RGRDGYNFDGYRLRVEL 79
             +    +G  +R+E 
Sbjct: 56 NSCNNTEIEGRSIRLEF 72

This subfamily corresponds to the RRM3 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 = 72

>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2)

 Score = 41.5 bits (97), Expect = 2e-05
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 10/75 (13%)

Query: 9  LYVGNLPGDTRM---REVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          +++GNL  +T +    +VE +F KYG IV   +       G+AF+++ + R+A  A+ G 
Sbjct: 4  VFIGNL--NTLVVKKSDVEAIFSKYGKIVGCSVH-----KGFAFVQYVNERNARAAVAGE 56

Query: 66 DGYNFDGYRLRVELA 80
          DG    G  L + LA
Sbjct: 57 DGRMIAGQVLDINLA 71

This subgroup corresponds to the RRM of heterogeneous nuclear ribonucleoprotein C (hnRNP) proteins C1 and C2, produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex. They are involved in the packaging of hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. hnRNP C proteins contain two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes the variable region, the basic region and the KSG box rich in repeated Lys-Ser-Gly sequences, the leucine zipper, and the acidic region. The RRM is capable of binding poly(U). The KSG box may bind to RNA. The leucine zipper may be involved in dimer formation. The acidic and hydrophilic C-teminus harbors a putative nucleoside triphosphate (NTP)-binding fold and a protein kinase phosphorylation site. . Length = 71

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 6/64 (9%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP----RPPGYAFLEFEDYRDAEDAIRG 64
          ++VG +P D    E+  LF K GPI ++ L +      R  GYAF+ + +   A+ A++ 
Sbjct: 4  VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNR--GYAFVTYTNKEAAQRAVKQ 61

Query: 65 RDGY 68
             Y
Sbjct: 62 LHNY 65

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|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins

 Score = 41.2 bits (97), Expect = 2e-05
 Identities = 15/73 (20%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYA-FLEFEDYRDAEDAIRGR 65
          R + + N+P   R  +++ L   YG + + + ++P +       + +E    A+ A+   
Sbjct: 1  RKIQISNIPPHVRWEDLDSLLSTYGTVKNCE-QVPTKSETATVNVTYESPEQAQQAVNKL 59

Query: 66 DGYNFDGYRLRVE 78
          +G+ ++G +L+V 
Sbjct: 60 NGHEYEGSKLKVS 72

This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. . Length = 76

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

 Score = 41.1 bits (96), Expect = 2e-05
 Identities = 17/61 (27%), Positives = 35/61 (57%), Gaps = 3/61 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRGR 65
          +++G L  DT  ++++D F K+G +VD  LK+ P   R  G+ F+ F++    +  +  +
Sbjct: 1  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 66 D 66
          +
Sbjct: 61 E 61

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|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 24/91 (26%), Positives = 46/91 (50%), Gaps = 21/91 (23%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLK-IPPRPPGY------------------ 47
          RT++VGNLP  T+ ++++ LF ++GPI  +  + +P +                      
Sbjct: 1  RTVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNV 60

Query: 48 -AFLEFEDYRDAEDAIRGRDGYNFDGYRLRV 77
           A++ F++   AE A+   +G  F+G+ +RV
Sbjct: 61 NAYVVFKEEESAEKAL-KLNGTEFEGHHIRV 90

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|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 41.2 bits (96), Expect = 4e-05
 Identities = 24/66 (36%), Positives = 40/66 (60%), Gaps = 3/66 (4%)

Query: 18 TRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYR 74
          T  R++ ++F KYGPI D+ +   +   R  G+AF+ FE+  DA++A    +G   DG R
Sbjct: 21 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 80

Query: 75 LRVELA 80
          +RV+ +
Sbjct: 81 IRVDFS 86

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

 Score = 40.7 bits (96), Expect = 4e-05
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 3/72 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRP---PGYAFLEFEDYRDAEDAIRGR 65
          +YV ++  D    +++ +F  +G I    L   P      GY F+E+E+ + A+DAI   
Sbjct: 3  IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 66 DGYNFDGYRLRV 77
          + ++  G +LRV
Sbjct: 63 NLFDLGGQQLRV 74

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

 Score = 40.6 bits (95), Expect = 4e-05
 Identities = 18/49 (36%), Positives = 31/49 (63%), Gaps = 3/49 (6%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFED 54
          ++VG L  DT  +++++ F K+G +VD  +KI P   R  G+ F+ F+D
Sbjct: 1  MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKD 49

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

 Score = 40.9 bits (96), Expect = 4e-05
 Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 3/72 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          L++ NL       ++E LF KYGP+ ++ L   K+  +P G+AF+ +     A  A    
Sbjct: 5  LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 66 DGYNFDGYRLRV 77
          DG  F G  L +
Sbjct: 65 DGTVFQGRLLHL 76

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|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins

 Score = 40.5 bits (95), Expect = 5e-05
 Identities = 19/77 (24%), Positives = 39/77 (50%), Gaps = 5/77 (6%)

Query: 5  SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPG-YAFLEFEDYRDAEDAIR 63
          + R+++V      T   ++ D F  +GP++++   I  +  G YA +EF+  ++  D + 
Sbjct: 1  AERSVFVSGFKRGTSEEQLMDYFSAFGPVMNV---IMDKDKGVYAIVEFDS-KEGVDKVL 56

Query: 64 GRDGYNFDGYRLRVELA 80
              +  +G+RLRV   
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|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 40.4 bits (95), Expect = 6e-05
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 5/76 (6%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRG 64
          T +VGNLP +T   +++ +F     +  + L   K   +  G+ ++EFED    ++A+  
Sbjct: 3  TAFVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALE- 60

Query: 65 RDGYNFDGYRLRVELA 80
           DG  FD   LRV++A
Sbjct: 61 YDGALFDDRSLRVDIA 76

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 40.2 bits (94), Expect = 6e-05
 Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 2/71 (2%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDG 67
          TL V NL       ++  +F  YG I +I  +  P    + F+EF D R AE A++  + 
Sbjct: 3  TLVVFNLDPSVSNDDLHQIFGAYGEIKEI--RETPNKRHHKFIEFYDVRSAEAALKALNR 60

Query: 68 YNFDGYRLRVE 78
              G R+++E
Sbjct: 61 SEIAGKRIKLE 71

This subgroup corresponds to the RRM2 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 is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 71

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

 Score = 40.3 bits (95), Expect = 6e-05
 Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 7/61 (11%)

Query: 8  TLYVGNLPGDTRMRE--VEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAI 62
          TL++G+L  +  M E  +   F + G +  + +   K   +  GY F+EF  +  AE A+
Sbjct: 1  TLWMGDL--EPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQAL 58

Query: 63 R 63
          +
Sbjct: 59 Q 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|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate

 Score = 40.3 bits (94), Expect = 7e-05
 Identities = 25/67 (37%), Positives = 39/67 (58%), Gaps = 5/67 (7%)

Query: 4  RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPG--YAFLEFEDY---RDA 58
          R++R L++GNL  +    E+   F KYG I ++ +K P R  G  YAFL+F++      A
Sbjct: 6  RATRNLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAHRA 65

Query: 59 EDAIRGR 65
          + A+ GR
Sbjct: 66 KVAMSGR 72

This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 85

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

 Score = 40.1 bits (94), Expect = 7e-05
 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 3/72 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRGR 65
          +YVG++  +     +   F  +GPI  ID+   P   +  G+AF+E+E    A+ A+   
Sbjct: 3  VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 66 DGYNFDGYRLRV 77
          +G    G  ++V
Sbjct: 63 NGVMLGGRNIKV 74

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

>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 39.9 bits (93), Expect = 8e-05
 Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 3/63 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRGR 65
          ++VG +P D    E+  LF K GPI D+ L + P   +  GYAF+ F     A++A++  
Sbjct: 4  VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKLC 63

Query: 66 DGY 68
          D Y
Sbjct: 64 DNY 66

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

 Score = 39.9 bits (94), Expect = 9e-05
 Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 8/81 (9%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPP-----GYAFLEFEDYRDA 58
           TL+V NL   T    ++  F K G +  + +   K P  P      GY F+EF+    A
Sbjct: 1  TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 59 EDAIRGRDGYNFDGYRLRVEL 79
          + A++   G   DG+ L ++L
Sbjct: 61 QKALKRLQGTVLDGHALELKL 81

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

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 17/73 (23%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRG 64
           +Y+G+LP     +E++  F ++G + ++ +   K       Y F++F +   A  A + 
Sbjct: 1  VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKS 60

Query: 65 RDGYNFDGYRLRV 77
           + Y   G  L+V
Sbjct: 61 MNNYLLMGKVLQV 73

This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

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

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 3/72 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRGR 65
          LYVGNL  +    ++  +F  +G I  + L+  P   R  GY F++F D  DA+ A+   
Sbjct: 1  LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 66 DGYNFDGYRLRV 77
          +G+   G  ++V
Sbjct: 61 NGFELAGRPIKV 72

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

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

 Score = 39.4 bits (92), Expect = 1e-04
 Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDL--KIPPRPPGYAFLEFEDYRDAEDAIRGRD 66
          + V NLP +   ++V  LF  YG +  + +  K      G+AF+EF   ++A +A+    
Sbjct: 3  ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALK 62

Query: 67 GYNFDGYRLRVELA 80
            +  G RL ++ A
Sbjct: 63 DTHLLGRRLVLQYA 76

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

>gnl|CDD|241101 cd12657, RRM1_hnRNPM, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 39.2 bits (91), Expect = 1e-04
 Identities = 18/79 (22%), Positives = 41/79 (51%), Gaps = 8/79 (10%)

Query: 111 RVLVTGLPSSASWQDLKDHMR-RAGDVCFSQVFRDRGGMT---GIVDYTSYDDMKYAIRK 166
           R  ++ +P    WQ LKD ++ + G+V + ++  D  G +    +V++   + MK A+  
Sbjct: 1   RAFISNIPFDVKWQSLKDLVKEKVGEVTYVELLMDAEGKSRGCAVVEFKMEESMKKAVEV 60

Query: 167 LDRSEFRNAFSRSYVRVRE 185
           L+    ++  +   ++V+E
Sbjct: 61  LN----KHVLNGRPLKVKE 75

This subgroup corresponds to the RRM1 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 25/69 (36%), Positives = 34/69 (49%), Gaps = 3/69 (4%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDG 67
          T++VG L       E+  LF  +G IV +  KIPP   G  F++F     AE AI+   G
Sbjct: 3  TVFVGGLDPAVTEDELRSLFGPFGEIVYV--KIPP-GKGCGFVQFVHRAAAEAAIQQLQG 59

Query: 68 YNFDGYRLR 76
              G R+R
Sbjct: 60 TIIGGSRIR 68

This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 72

>gnl|CDD|241102 cd12658, RRM1_MYEF2, RNA recognition motif 1 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 39.2 bits (91), Expect = 1e-04
 Identities = 18/66 (27%), Positives = 39/66 (59%), Gaps = 4/66 (6%)

Query: 111 RVLVTGLPSSASWQDLKDHMR-RAGDVCFSQVFRDRGGMT---GIVDYTSYDDMKYAIRK 166
           RV ++ +P    WQ +KD MR + G+V + ++F+D  G +   G+V++   + +K A+  
Sbjct: 1   RVFISNIPYDMKWQAIKDLMREKVGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALEV 60

Query: 167 LDRSEF 172
           +++ + 
Sbjct: 61  MNKYDL 66

This subgroup corresponds to the RRM1 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 39.1 bits (91), Expect = 2e-04
 Identities = 25/69 (36%), Positives = 33/69 (47%), Gaps = 3/69 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          L+VGNLP D    E+  LF KYG   +I +    +  G+ F+  E    AE A    D  
Sbjct: 4  LFVGNLPPDITEEEMRKLFEKYGKAGEIFIH---KDKGFGFIRLETRTLAEIAKAELDNM 60

Query: 69 NFDGYRLRV 77
             G +LRV
Sbjct: 61 PLRGKQLRV 69

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional 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. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 42.2 bits (99), Expect = 2e-04
 Identities = 34/98 (34%), Positives = 39/98 (39%), Gaps = 9/98 (9%)

Query: 165 RKLDRSEFRNAFSRSYVRVREYDSR-----RSYSRSPSRSPYYSRSRSRSPYYSRSRSPS 219
           R  DRS FR+   RS  R    DSR     R  SRSP    Y S  RSR     RSRS  
Sbjct: 27  RSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSVR 86

Query: 220 RSWSYSPRSRSYSPRGKYSRRSPSLSPARSASQRSPSG 257
               +  R R  SP  ++ +        RS     P G
Sbjct: 87  SIEQHRRRLRDRSPSNQWRKDDKK----RSLWDIKPPG 120

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

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

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR-PPGYAFLEFEDYRDAEDAIRGR 65
          + L+V N+P   R  ++  +F ++GPI+D+++    R   G+ F+ F +  DA+ A    
Sbjct: 1  KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKL 60

Query: 66 DGYNFDGYRLRVELA 80
           G   +G ++ V  A
Sbjct: 61 HGTVVEGRKIEVNNA 75

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

>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 3/69 (4%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDG 67
          T+YVGN+P  T   ++  LF  +G I++   +  P   G+AF++ + +  A  AI    G
Sbjct: 2  TVYVGNIPPYTTQADLIPLFQNFGYILEF--RHQPD-RGFAFVKLDTHEQAAMAIVQLQG 58

Query: 68 YNFDGYRLR 76
          +   G  LR
Sbjct: 59 FPVHGRPLR 67

This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

>gnl|CDD|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 = 38.8 bits (91), Expect = 2e-04
 Identities = 15/73 (20%), Positives = 39/73 (53%), Gaps = 3/73 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRGR 65
          L++ +LP +   +++  LF  +G ++   + +     +   + F+ +++   A+ AI+  
Sbjct: 1  LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 66 DGYNFDGYRLRVE 78
          +G+   G RL+V+
Sbjct: 61 NGFQVGGKRLKVQ 73

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

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 5/76 (6%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRGR 65
          L V  LP  T  ++++D F  +G ++ + +K  P   +  G+ F+ F DY D    +  R
Sbjct: 2  LIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQR 61

Query: 66 DGYNFDGYRLRVELAH 81
            +  DG    V++ +
Sbjct: 62 --HMIDGRWCDVKIPN 75

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|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 5/74 (6%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          L+VG L   T + E+E  F ++G I  ID         YA++E+E    A+ A     G+
Sbjct: 1  LWVGGLGPWTSLAELEREFDRFGAIRRIDY---DPGRNYAYIEYESIEAAQAAKEALRGF 57

Query: 69 NF--DGYRLRVELA 80
               G RLRV+ A
Sbjct: 58 PLGGPGRRLRVDFA 71

This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 72

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

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 5/70 (7%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVD----IDLKIPPRPPGYAFLEFEDYRDAEDAI 62
            +Y+  LP +T   ++E L   +G I+     +D K      GY F++F+    A  AI
Sbjct: 1  TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNK-CKGYGFVDFDSPEAALKAI 59

Query: 63 RGRDGYNFDG 72
           G +G     
Sbjct: 60 EGLNGRGVQA 69

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

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 3/73 (4%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRP---PGYAFLEFEDYRDAEDAIRG 64
           ++V NLP D     +  LF  +G + ++ +          GY F+   +Y +A  AI  
Sbjct: 3  CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62

Query: 65 RDGYNFDGYRLRV 77
           +GY   G  L+V
Sbjct: 63 LNGYRLGGRVLQV 75

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

>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 38.3 bits (89), Expect = 3e-04
 Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 9/73 (12%)

Query: 4  RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP----PRPPGYAFLEFEDYRDAE 59
          R +RTL+V NLP +  + E++++F        +D+++P        G A++EF+   +AE
Sbjct: 1  RDARTLFVKNLPYNITVDELKEVFED-----AVDIRLPSGKDGSSKGIAYIEFKTEAEAE 55

Query: 60 DAIRGRDGYNFDG 72
           A+  + G   DG
Sbjct: 56 KALEEKQGAEVDG 68

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

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

 Score = 38.1 bits (89), Expect = 3e-04
 Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 3/76 (3%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVD---IDLKIPPRPPGYAFLEFEDYRDAEDAIRG 64
          TL+VGNL        ++  F K+G +V    I  +   R  G+ +++FE   DA+ AI  
Sbjct: 1  TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 65 RDGYNFDGYRLRVELA 80
           DG   DG  + V+ +
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|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 38.1 bits (88), Expect = 3e-04
 Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 3/58 (5%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRP---PGYAFLEFEDYRDAEDAIR 63
          ++VG +P D    E+  LF K GPI D+ L + P      GYAF+ F     A++A++
Sbjct: 4  IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVK 61

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|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 38.1 bits (88), Expect = 4e-04
 Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 11/79 (13%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGP------IVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
          TLYVGNL  D     +  LF + GP      I+D     P     Y F+EF ++R A  +
Sbjct: 1  TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDP-----YCFVEFFEHRHAAAS 55

Query: 62 IRGRDGYNFDGYRLRVELA 80
          +   +G    G  ++V  A
Sbjct: 56 LAAMNGRKIMGKEVKVNWA 74

This subgroup corresponds to the RRM1 of 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 functions 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 = 74

>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 = 37.9 bits (89), Expect = 4e-04
 Identities = 21/68 (30%), Positives = 32/68 (47%), Gaps = 4/68 (5%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          L+VG LP      +V  LF +YG I ++ +   K   +  G AF++F    +A+ AI   
Sbjct: 2  LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 66 DG-YNFDG 72
           G     G
Sbjct: 62 HGKVTMPG 69

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|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 37.9 bits (89), Expect = 4e-04
 Identities = 17/81 (20%), Positives = 37/81 (45%), Gaps = 12/81 (14%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          L+VG L       ++E+ F ++G + D+++   K      G+A+++        +A   +
Sbjct: 2  LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLR----TSEAQLKK 57

Query: 66 -----DGYNFDGYRLRVELAH 81
               +G  + G  L++E A 
Sbjct: 58 CKSTLNGTKWKGSVLKIEEAK 78

This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. Length = 78

>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 38.1 bits (88), Expect = 4e-04
 Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 3/62 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          LYV  LP     +E+E LF +YG I+   +   ++     G  F+ F+   +AE+AI+G 
Sbjct: 4  LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63

Query: 66 DG 67
          +G
Sbjct: 64 NG 65

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|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 37.6 bits (88), Expect = 4e-04
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 4/74 (5%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRD 66
          R ++VG L  D    ++   F ++G + D+ +  P R   +AF+ F D   A+      +
Sbjct: 1  RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFR--AFAFVTFADPEVAQSLC--GE 56

Query: 67 GYNFDGYRLRVELA 80
           +   G  + V  A
Sbjct: 57 DHIIKGVSVHVSNA 70

This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 71

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

 Score = 37.7 bits (88), Expect = 4e-04
 Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 4/75 (5%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          ++VG LP D    E ++ F ++G +VD  L       R  G+ F+ F+    A + +   
Sbjct: 2  IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDS-ESAVERVFSA 60

Query: 66 DGYNFDGYRLRVELA 80
                G ++ V+ A
Sbjct: 61 GMLELGGKQVEVKRA 75

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 75

>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 37.7 bits (88), Expect = 5e-04
 Identities = 19/80 (23%), Positives = 33/80 (41%), Gaps = 8/80 (10%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPI--------VDIDLKIPPRPPGYAFLEFEDYRDAE 59
           +Y+ NL   +   ++E+    + P+        V        RP G A+ EF     AE
Sbjct: 1  RVYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAE 60

Query: 60 DAIRGRDGYNFDGYRLRVEL 79
            ++  +G  F   +L V+L
Sbjct: 61 KVVKDLNGKVFKNRKLFVKL 80

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate RNA-binding protein 26 (RBM26) and similar proteins

 Score = 37.5 bits (88), Expect = 5e-04
 Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 4/59 (6%)

Query: 6  SRTLYVGNLPGDT-RMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIR 63
          + TL V N+P +   + ++ + F K+G IV+I +   P     A ++F    +A+ A R
Sbjct: 1  NTTLEVRNIPPELNNITKLNEHFSKFGTIVNIQVNYNPES---ALVQFSTSEEAKKAYR 56

This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear. . Length = 72

>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 37.9 bits (88), Expect = 5e-04
 Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 8/82 (9%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP--------GYAFLEFEDYRDAE 59
          TL+V NL   T  + + D F      V   +K  P P         G+ F+ F+    A+
Sbjct: 2  TLFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQ 61

Query: 60 DAIRGRDGYNFDGYRLRVELAH 81
           A++  DG+  DG+ L V+ +H
Sbjct: 62 AALKAMDGFVLDGHTLVVKFSH 83

This subfamily corresponds to the RRM4 of MRD1which 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 = 84

>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 37.5 bits (88), Expect = 5e-04
 Identities = 22/80 (27%), Positives = 37/80 (46%), Gaps = 14/80 (17%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPG--------YAFLEFEDYRDAE 59
          TL+V N P      ++ DLF +YG I+ I      R P         + +++F     A 
Sbjct: 2  TLWVTNFPPSFDQSDIRDLFEQYGEILSI------RFPSLRFNKTRRFCYVQFTSPESAA 55

Query: 60 DAIRGRDGYNFDGYRLRVEL 79
           A+   +G   +GY+L V++
Sbjct: 56 AAVALLNGKLGEGYKLVVKI 75

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 37.8 bits (87), Expect = 5e-04
 Identities = 25/75 (33%), Positives = 36/75 (48%), Gaps = 3/75 (4%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDL--KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          TLYVGNL  D     +  LF + GP     +  +     P Y F+EF ++RDA  A+   
Sbjct: 1  TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-YCFVEFYEHRDAAAALAAM 59

Query: 66 DGYNFDGYRLRVELA 80
          +G    G  ++V  A
Sbjct: 60 NGRKILGKEVKVNWA 74

This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and 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 = 81

>gnl|CDD|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins

 Score = 37.9 bits (89), Expect = 5e-04
 Identities = 23/97 (23%), Positives = 35/97 (36%), Gaps = 39/97 (40%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPI-VDID-----LKIPPRPPGYAFLEFEDYRDAEDAI 62
          +YV  LP D  + E  ++F K G I  D +     +K+              YRD    +
Sbjct: 4  VYVSGLPLDITVEEFVEVFSKCGIIKEDPETGKPKIKL--------------YRDENGNL 49

Query: 63 RGR------------------DGYN-FDGYRLRVELA 80
          +G                   DG     GY+++VE A
Sbjct: 50 KGDALCCYLKEESVELAIQLLDGTEIGRGYKMKVERA 86

This subfamily corresponds to the RRM1 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well. . Length = 92

>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 = 37.7 bits (88), Expect = 5e-04
 Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRG 64
          T+YV NLP      ++  +F KYG +V + +   K   +  G AF+ F D  DA   ++ 
Sbjct: 3  TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62

Query: 65 RDGYNFDGYRLRVELA 80
           +     G  L+  +A
Sbjct: 63 LNNKELFGRTLKCSIA 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|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 37.5 bits (88), Expect = 5e-04
 Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 3/63 (4%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          ++ L++ NLP +T    +E LF ++    ++ L +P R  G AF+EFE    A  A++  
Sbjct: 2  NKILFLQNLPEETTKEMLEMLFNQFPGFKEVRL-VPRR--GIAFVEFETEEQATVALQAL 58

Query: 66 DGY 68
           G+
Sbjct: 59 QGF 61

This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding. . Length = 72

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

 Score = 37.6 bits (88), Expect = 5e-04
 Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 8/78 (10%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP-----GYAFLEFEDYRDAEDAI 62
           L V N+P +   +E+ +LF  +G +  + L   P+       G+AF+EF   ++A++A+
Sbjct: 2  KLIVRNVPFEATKKELRELFSPFGQVKSVRL---PKKFDGSHRGFAFVEFVTKQEAQNAM 58

Query: 63 RGRDGYNFDGYRLRVELA 80
                +  G  L +E A
Sbjct: 59 EALKSTHLYGRHLVLEYA 76

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

>gnl|CDD|240977 cd12533, RRM_EWS, RNA recognition motif in vertebrate Ewing Sarcoma Protein (EWS)

 Score = 38.0 bits (88), Expect = 5e-04
 Identities = 26/83 (31%), Positives = 40/83 (48%), Gaps = 11/83 (13%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYG----------PIVDIDL-KIPPRPPGYAFLEFEDYR 56
          T+YV  L  +  + E+ D F   G          P+V+I   K   +P G A + +ED  
Sbjct: 2  TIYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPP 61

Query: 57 DAEDAIRGRDGYNFDGYRLRVEL 79
           A+ A+   DG +F G +L+V L
Sbjct: 62 SAKAAVEWFDGKDFQGSKLKVSL 84

This subgroup corresponds to the RRM of EWS, also termed Ewing sarcoma breakpoint region 1 protein, 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 multifunctional protein and may play roles in transcription and RNA processing. EWS is involved in transcriptional regulation by interacting with the preinitiation complex TFIID and the RNA polymerase II (RNAPII) complexes. It is also associated with splicing factors, such as the U1 snRNP protein U1C, suggesting its implication in pre-mRNA splicing. Additionally, EWS has been shown to regulate DNA damage-induced alternative splicing (AS). Like other members in the FET family, EWS contains 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. EWS specifically binds to poly G and poly U RNA. It also binds to the proximal-element DNA of the macrophage-specific promoter of the CSF-1 receptor gene. . Length = 84

>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 37.6 bits (87), Expect = 6e-04
 Identities = 20/64 (31%), Positives = 39/64 (60%), Gaps = 3/64 (4%)

Query: 18 TRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYR 74
          T  R++ ++F +YGP+  +++   +   R  G+AF+ FE   D+++A+   +G   DG R
Sbjct: 11 TTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRR 70

Query: 75 LRVE 78
          +RV+
Sbjct: 71 IRVD 74

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

 Score = 37.2 bits (87), Expect = 6e-04
 Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 3/73 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRGR 65
          L V  L   T  R++ ++F +YGPI  + +       R  G+ F+ FE   DA++A    
Sbjct: 2  LGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61

Query: 66 DGYNFDGYRLRVE 78
          +G   DG R+RV+
Sbjct: 62 NGMEIDGRRIRVD 74

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|240907 cd12461, RRM_SCAF4, RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins

 Score = 37.3 bits (86), Expect = 7e-04
 Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 3/61 (4%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAI 62
          S  S TL+VG L   T  ++V  L  ++GPI  I++ IPPR  G A++     +DA  A+
Sbjct: 1  SVCSTTLWVGQLDKRTTQQDVTSLLEEFGPIESINM-IPPR--GCAYIVMVHRQDAYRAL 57

Query: 63 R 63
          +
Sbjct: 58 Q 58

The CD corresponds to the RRM of SCAF4 (also termed splicing factor, arginine/serine-rich 15 or SFR15, or CTD-binding SR-like protein RA4) that belongs to a new class of SCAFs (SR-like CTD-associated factors). Although its biological function remains unclear, SCAF4 shows high sequence similarity to SCAF8 that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II) and may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF4 and SCAF8 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 81

>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 = 37.3 bits (87), Expect = 7e-04
 Identities = 16/57 (28%), Positives = 32/57 (56%), Gaps = 7/57 (12%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAI 62
          ++VG L  +T   ++ + F K+G IV+I+L +     +  G+ F+ F    D+E+ +
Sbjct: 2  IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITF----DSEEPV 54

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

 Score = 40.6 bits (95), Expect = 7e-04
 Identities = 50/279 (17%), Positives = 100/279 (35%), Gaps = 31/279 (11%)

Query: 9   LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDAEDAIRGRD 66
           LYV NL       ++ +LF K+G I    +      R  G+AF+ FE + DA  A+   +
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMN 240

Query: 67  GYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSG-GSRGVSRRSDYRVL---VTGLPSSAS 122
           G      +   +L  G  R     +R +            R+   + +   V  L  + +
Sbjct: 241 GKKIGLAKEGKKLYVG--RAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVT 298

Query: 123 WQDLKDHMRRAGDVCFSQVFRDRGGMT---GIVDYTSYDDMKYAIRKLD------RSEFR 173
            + L++     G++  ++V  D  G++   G V +++ ++   A+ ++       +  + 
Sbjct: 299 DEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYV 358

Query: 174 NAFSRSYVRVREYDSRRSYSRSPSRSPYYSR----SRSRSPYYSRSRSPSRSWSYSPRSR 229
               R   R      +    +   R          +  + PYY +           P+ +
Sbjct: 359 ALAQRKEQRRAHLQDQFMQLQPRMRQLPMGSPMGGAMGQPPYYGQ----------GPQQQ 408

Query: 230 SYSPRGKYSRRSPSLSPARSASQRSPSGSPPRSFSRSGS 268
                  + R S   +P        P+G  P +  R+ S
Sbjct: 409 FNGQPLGWPRMSMMPTPMGPGGPLRPNGLAPMNAVRAPS 447

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

 Score = 37.3 bits (86), Expect = 7e-04
 Identities = 20/67 (29%), Positives = 37/67 (55%), Gaps = 4/67 (5%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRGR 65
          ++VG L  DT  ++++D F K+G + D  +K+ P   R  G+ F+ F+D    E  +  +
Sbjct: 2  MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQK 61

Query: 66 DGYNFDG 72
          + +  DG
Sbjct: 62 E-HRLDG 67

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

 Score = 36.9 bits (86), Expect = 8e-04
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 4/71 (5%)

Query: 10 YVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRD 66
          +VGN+   T   E+++ F   G I  I +   K   +P G+A++EF D    E+A+   +
Sbjct: 3  FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LLN 61

Query: 67 GYNFDGYRLRV 77
             F G +++V
Sbjct: 62 ESEFRGRQIKV 72

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 37.2 bits (86), Expect = 8e-04
 Identities = 19/54 (35%), Positives = 32/54 (59%), Gaps = 2/54 (3%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR--PPGYAFLEFED 54
           R++RTL++GNL       ++   F ++G I ++D+K P R     Y FL+FE+
Sbjct: 4  QRANRTLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFEN 57

This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 87

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

 Score = 36.8 bits (86), Expect = 8e-04
 Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 3/58 (5%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAI 62
          T++V  L    R R++ + F K G + D+ +   +   R  G A++EF D      A+
Sbjct: 1  TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL 58

This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 39.5 bits (92), Expect = 0.001
 Identities = 26/98 (26%), Positives = 33/98 (33%)

Query: 169 RSEFRNAFSRSYVRVREYDSRRSYSRSPSRSPYYSRSRSRSPYYSRSRSPSRSWSYSPRS 228
             E   +  R   R  E   RRS  RS  R  +           SR R   R  S SPRS
Sbjct: 6   DREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRS 65

Query: 229 RSYSPRGKYSRRSPSLSPARSASQRSPSGSPPRSFSRS 266
             YS   +   R    S +  + ++       RS S  
Sbjct: 66  LRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQ 103

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

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

 Score = 37.2 bits (86), Expect = 0.001
 Identities = 19/75 (25%), Positives = 38/75 (50%), Gaps = 3/75 (4%)

Query: 9  LYVGNLPGDTRMRE-VEDLFYKYGPIVDIDL--KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          L + NLP   +    ++ +F +YG + +  +  K   +  G+AF+  +  ++AE A+   
Sbjct: 3  LIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENT 62

Query: 66 DGYNFDGYRLRVELA 80
          +G   DG  + V+ A
Sbjct: 63 NGLEIDGRPVAVDWA 77

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

>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 3/67 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          LYV  LP     +E+E LF +YG I+   +   ++     G  F+ F+   +AE+AI+G 
Sbjct: 5  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64

Query: 66 DGYNFDG 72
          +G    G
Sbjct: 65 NGQKPSG 71

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|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 36.8 bits (85), Expect = 0.001
 Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 6/76 (7%)

Query: 9  LYVGNLPGDTRMRE--VEDLFYKYGPIVDIDLKIPPRPPG--YAFLEFEDYRDAEDAIRG 64
          LYVGNL  D R+ E  ++ +F   GP+ ++ +       G  Y F+E+    DAE A++ 
Sbjct: 1  LYVGNL--DPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQT 58

Query: 65 RDGYNFDGYRLRVELA 80
           +G   +   +RV  A
Sbjct: 59 LNGRQIENNEIRVNWA 74

This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

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

 Score = 38.1 bits (88), Expect = 0.001
 Identities = 28/98 (28%), Positives = 41/98 (41%), Gaps = 3/98 (3%)

Query: 6   SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAI 62
           S  L++G L   T    + D F  +G +VD  + +     R  G+ F+ F D   A  AI
Sbjct: 34  STKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAI 93

Query: 63  RGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGG 100
              DG   +G  +RV  A+       +      YS GG
Sbjct: 94  SEMDGKELNGRHIRVNPANDRPSAPRAYGGGGGYSGGG 131

Length = 144

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 36.4 bits (84), Expect = 0.001
 Identities = 21/53 (39%), Positives = 33/53 (62%), Gaps = 10/53 (18%)

Query: 7  RTLYVGNLPGDTRMRE--VEDLFYKYGPIVDIDLKIPP----RPPGYAFLEFE 53
          RTL+VGNL  D ++ E  + +LF + GP+  I +KIP     +P  +AF+ F+
Sbjct: 2  RTLFVGNL--DPKVTEELIFELFLQAGPV--IKVKIPKDKDGKPKQFAFVNFK 50

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 12/82 (14%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI-PPR----------PPGYAFLEFEDYRD 57
          +Y+  LP D     + +LF   G I+  D +  PP           P G A + ++D   
Sbjct: 1  IYISGLPDDVTEDSLAELFGGIG-IIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSA 59

Query: 58 AEDAIRGRDGYNFDGYRLRVEL 79
          A+ AI   +GY F G +++V L
Sbjct: 60 AQAAIEWFNGYEFRGNKIKVSL 81

This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15. . Length = 81

>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 7/79 (8%)

Query: 3  SRSSRTLYV-GNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
           R   TLYV G    +  +++    F  +G I++I ++         F+ FE    A+ A
Sbjct: 1  PRKGNTLYVHGYGLTEEILKKA---FSPFGNIINISMEKEK---NCGFVTFEKMESADRA 54

Query: 62 IRGRDGYNFDGYRLRVELA 80
          I   +G    G +L+V LA
Sbjct: 55 IAELNGTTVQGVQLKVSLA 73

This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif. . Length = 75

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

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 2/58 (3%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIR 63
          SRTL+V N+  +    E+  LF ++G I  +      R  G+  + + D R A  A R
Sbjct: 1  SRTLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHR--GFIMVSYYDIRAARRAKR 56

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|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen B (HuB)

 Score = 36.7 bits (84), Expect = 0.002
 Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 3/62 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          LYV  LP     +E+E LF +YG I+   +   ++     G  F+ F+   +AE+AI+G 
Sbjct: 8  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 67

Query: 66 DG 67
          +G
Sbjct: 68 NG 69

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|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 4/67 (5%)

Query: 8  TLYVGNLPGDTRMREVED----LFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIR 63
          T+Y+ NL    +  E++     +F ++G I+DI      +  G AF+ F+D   A +A+R
Sbjct: 1  TIYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVVFKDISSATNALR 60

Query: 64 GRDGYNF 70
             G+ F
Sbjct: 61 SMQGFPF 67

This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently. . Length = 78

>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating protein-binding protein 2 (G3BP2) and similar proteins

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 3/52 (5%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLK---IPPRPPGYAFLEFED 54
          S  L+VGNLP D    E+++ F  +G +V++ +    +  + P + F+ F+D
Sbjct: 5  SHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDD 56

This subgroup corresponds to the RRM of G3BP2, also termed GAP SH3 domain-binding protein 2, a cytoplasmic protein that interacts with both IkappaBalpha and IkappaBalpha/NF-kappaB complexes, indicating that G3BP2 may play a role in the control of nucleocytoplasmic distribution of IkappaBalpha and cytoplasmic anchoring of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing five PXXP motifs, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). It binds to the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity, through its N-terminal NTF2-like domain. The acidic domain is sufficient for the interaction of G3BP2 with the IkappaBalpha cytoplasmic retention sequence. Furthermore, G3BP2 might influence stability or translational efficiency of particular mRNAs by binding to RNA-containing structures within the cytoplasm through its RNA-binding domain. Length = 83

>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 = 36.0 bits (84), Expect = 0.002
 Identities = 18/73 (24%), Positives = 28/73 (38%), Gaps = 4/73 (5%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYG-PIVDIDLKIPP--RPPGYAFLEFEDYRDAEDAIRG 64
           + +  LP      ++ D F     P   I +      RP G A++EF    DA  A+R 
Sbjct: 1  VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALR- 59

Query: 65 RDGYNFDGYRLRV 77
          +      G  + V
Sbjct: 60 KHNNKMGGRYIEV 72

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

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 26/84 (30%), Positives = 40/84 (47%), Gaps = 4/84 (4%)

Query: 5  SSRTLYVGNLPG----DTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
           S  ++V +LP     D     V + F KYG +V + +    R   YAF++F +  DA++
Sbjct: 1  PSACVFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQRPYAFVQFTNDDDAKN 60

Query: 61 AIRGRDGYNFDGYRLRVELAHGGR 84
          A+    G   DG  +R E A   R
Sbjct: 61 ALAKGQGTILDGRHIRCERAKVNR 84

This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 86

>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 19/53 (35%), Positives = 24/53 (45%), Gaps = 12/53 (22%)

Query: 29 KYGPIVDIDLKIPPRPP---------GYAFLEFEDYRDAEDAIRGRDGYNFDG 72
          KYG ++ +   IP RP          G  F+EF D  DA+ A     G  FDG
Sbjct: 34 KYGKVLSV--VIP-RPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFDG 83

This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 89

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

 Score = 38.8 bits (90), Expect = 0.002
 Identities = 42/171 (24%), Positives = 69/171 (40%), Gaps = 28/171 (16%)

Query: 6   SRT-LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDA 61
           S+T L V  LP      E+  LF   G I    L   K+  +  GY F+ +    DAE A
Sbjct: 2   SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKA 61

Query: 62  IRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSA 121
           +   +G       ++V  A           R SS S  G+          + V+GLP + 
Sbjct: 62  VNSLNGLRLQNKTIKVSYA-----------RPSSDSIKGA---------NLYVSGLPKTM 101

Query: 122 SWQDLKDHMRRAGDVCFSQVFRDRG-GMT---GIVDYTSYDDMKYAIRKLD 168
           +  +L+      G +  S++  D   G++   G + +   D+   AI+ L+
Sbjct: 102 TQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLN 152

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|241108 cd12664, RRM1_RAVER2, RNA recognition motif 1 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 35.7 bits (82), Expect = 0.002
 Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 4/69 (5%)

Query: 11 VGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNF 70
          + NLP D+  +EV DL   Y    ++      R    AF+   +   A+DAIR     + 
Sbjct: 4  IKNLPQDSTNQEVHDLLKDY----ELKYCYVDRNKRTAFVTLLNGEQAQDAIRTFHQTSV 59

Query: 71 DGYRLRVEL 79
           G  + V+L
Sbjct: 60 RGKDINVQL 68

This subgroup corresponds to the RRM1 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 = 70

>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 7/79 (8%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP----RPPGYAFLEFEDYRDAEDA 61
          SR L V NLP   +  ++  LF  +G I D+ LK       R   + F+ ++   +A+ A
Sbjct: 1  SR-LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFR--KFGFVGYKTEEEAQKA 57

Query: 62 IRGRDGYNFDGYRLRVELA 80
          ++  +    D  ++ VE+ 
Sbjct: 58 LKHFNNSFIDTSKITVEIC 76

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 23/69 (33%), Positives = 31/69 (44%), Gaps = 7/69 (10%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI-----PPRPPGYAFLEFEDYRDAEDAIR 63
          LYV  LP     +E+E LF  YG I  I  +I          G  F+ F+   +AE AI+
Sbjct: 3  LYVSGLPKTMTQQELEALFSPYGRI--ITSRILCDNVTGLSRGVGFIRFDKRIEAERAIK 60

Query: 64 GRDGYNFDG 72
            +G    G
Sbjct: 61 ALNGTIPPG 69

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 5/73 (6%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAEDAIRG 64
           ++VG +P DT   E+ D F ++G + D+ + I  R     GY F+ FE   DAE  +  
Sbjct: 4  RIFVGGIPPDTTEEELRDFFSRFGSVKDVKI-ITDRAGVSKGYGFVTFETQEDAEKILAM 62

Query: 65 RDGYNFDGYRLRV 77
           +  NF G +L +
Sbjct: 63 GN-LNFRGKKLNI 74

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|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 = 0.002
 Identities = 15/57 (26%), Positives = 22/57 (38%), Gaps = 3/57 (5%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAEDA 61
           L VGNLP +    +  +L   +G +    L          GY F+E+     A  A
Sbjct: 1  LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKA 57

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

>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 6/70 (8%)

Query: 11 VGNLPGDTRMREVEDLFYKYGPIV--DIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          V  LP     ++++D   + G +   D+D        G   +EF    D E A+R  DG 
Sbjct: 5  VSGLPEGASWQDLKDFGRQAGDVTYADVD----RDQEGEGVVEFTSQEDMERALRKLDGT 60

Query: 69 NFDGYRLRVE 78
           F G R+RVE
Sbjct: 61 EFRGRRVRVE 70

This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C) and plant pre-mRNA-splicing factor SF2 (SR1). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 71

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

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 8/64 (12%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDI-----DLKIPPRPPGYAFLEFEDYRDAEDAIR 63
          L+VG L      +EVE++F  YG + DI     ++K      G AF+++     A+ AI+
Sbjct: 2  LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQ---SRGCAFVKYSSKEMAQAAIK 58

Query: 64 GRDG 67
            +G
Sbjct: 59 ALNG 62

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

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

 Score = 35.9 bits (83), Expect = 0.003
 Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 5/61 (8%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGP-IVDIDLKIPPR----PPGYAFLEFEDYRDAEDA 61
          R ++VG LP D    E+   F ++GP +VD   K   +    P GYAFL F++    +  
Sbjct: 1  RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 60

Query: 62 I 62
          I
Sbjct: 61 I 61

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

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

 Score = 35.3 bits (81), Expect = 0.003
 Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 4/77 (5%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIR 63
          + ++VG +  DT    + D F KYG I  I++   +   +  G+AF+ F+D+ D  D I 
Sbjct: 1  KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDH-DTVDKIV 59

Query: 64 GRDGYNFDGYRLRVELA 80
           +  +  +G+   V+ A
Sbjct: 60 VQKYHTINGHNCEVKKA 76

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|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein MRN1 and similar proteins

 Score = 35.1 bits (81), Expect = 0.004
 Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 3/59 (5%)

Query: 5  SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIR 63
          +SR +Y+GNLP      E+ +   K+GPI  I  KI  +    AF+ F    +A   + 
Sbjct: 2  ASRNVYIGNLPESYSEEELREDLEKFGPIDQI--KI-VKEKNIAFVHFLSIANAIKVVT 57

This subgroup corresponds to the RRM2 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 = 78

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

 Score = 34.9 bits (81), Expect = 0.004
 Identities = 25/74 (33%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDAEDAIRGR 65
           L V NL  D    ++E+LF + G +  + +      R  G A + FE   DAE AI+  
Sbjct: 2  RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQF 61

Query: 66 DGYNFDGYRLRVEL 79
          +G   DG  ++VEL
Sbjct: 62 NGVLLDGQPMQVEL 75

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	277
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.97
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	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
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.96
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.96
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.96
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.95
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.95
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.95
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.95
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.95
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.95
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.94
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.94
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.94
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.94
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.94
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.94
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.93
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.92
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.91
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.91
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.9
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.89
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.89
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	99.89
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.88
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.87
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.87
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.86
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.85
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.84
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.83
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.83
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.83
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.82
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.82
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.81
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.81
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.8
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.78
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.77
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.76
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.75
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.73
PLN03120	260	nucleic acid binding protein; Provisional	99.72
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.71
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.71
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.71
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.71
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.7
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.68
PLN03121	243	nucleic acid binding protein; Provisional	99.67
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.67
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.66
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.65
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.65
KOG0122	270	consensus Translation initiation factor 3, subunit	99.63
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.63
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.62
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.61
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.61
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.61
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.6
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.59
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.59
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.58
PLN03213	759	repressor of silencing 3; Provisional	99.58
smart00362	72	RRM_2 RNA recognition motif.	99.57
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.54
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.5
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.49
smart00360	71	RRM RNA recognition motif.	99.49
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.48
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.44
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.42
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.42
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.41
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.41
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.4
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.38
PLN03120	260	nucleic acid binding protein; Provisional	99.38
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.38
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.37
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.35
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.34
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.33
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.32
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.32
smart00361	70	RRM_1 RNA recognition motif.	99.31
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.29
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	99.29
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.29
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	99.28
PLN03121	243	nucleic acid binding protein; Provisional	99.28
KOG0122	270	consensus Translation initiation factor 3, subunit	99.28
PLN03213	759	repressor of silencing 3; Provisional	99.27
smart00362	72	RRM_2 RNA recognition motif.	99.25
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.22
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.19
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.14
smart00360	71	RRM RNA recognition motif.	99.12
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.12
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.12
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.11
KOG4660	549	consensus Protein Mei2, essential for commitment t	99.09
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.06
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.04
KOG0533	243	consensus RRM motif-containing protein [RNA proces	99.04
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.03
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.0
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.99
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.94
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.92
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.92
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.9
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.89
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.87
KOG4210	285	consensus Nuclear localization sequence binding pr	98.87
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.83
smart00361	70	RRM_1 RNA recognition motif.	98.83
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.81
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.8
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.8
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.79
KOG0151	877	consensus Predicted splicing regulator, contains R	98.78
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.7
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.61
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.57
KOG0226	290	consensus RNA-binding proteins [General function p	98.54
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.53
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.52
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.51
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.49
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.47
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.41
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.39
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.38
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	98.38
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.3
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.29
KOG0226	290	consensus RNA-binding proteins [General function p	98.25
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.24
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.22
KOG3152	278	consensus TBP-binding protein, activator of basal	98.21
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.18
KOG0151	877	consensus Predicted splicing regulator, contains R	98.14
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.12
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.09
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	98.09
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	98.07
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.03
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.99
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.98
KOG4210	285	consensus Nuclear localization sequence binding pr	97.95
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.95
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.93
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.77
KOG2314	698	consensus Translation initiation factor 3, subunit	97.77
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.69
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.64
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.63
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.62
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.57
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.51
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	97.48
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.39
KOG1996	378	consensus mRNA splicing factor [RNA processing and	97.37
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.33
KOG3152	278	consensus TBP-binding protein, activator of basal	97.29
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.24
KOG2314	698	consensus Translation initiation factor 3, subunit	97.16
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.04
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	97.03
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	97.01
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.96
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.96
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.91
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.91
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.86
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.71
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.49
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.43
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.39
KOG2068	327	consensus MOT2 transcription factor [Transcription	96.28
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	96.24
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	96.11
KOG2591	684	consensus c-Mpl binding protein, contains La domai	96.06
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	96.03
KOG2135	526	consensus Proteins containing the RNA recognition	95.95
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	95.92
KOG2591	684	consensus c-Mpl binding protein, contains La domai	95.9
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	95.66
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	95.39
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	95.29
KOG2318	650	consensus Uncharacterized conserved protein [Funct	95.29
KOG0835	367	consensus Cyclin L [General function prediction on	95.26
KOG0835	367	consensus Cyclin L [General function prediction on	95.08
KOG2135	526	consensus Proteins containing the RNA recognition	94.92
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	94.74
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.62
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	94.57
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	94.34
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	94.05
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	93.93
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	93.63
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	93.49
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	93.46
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	93.27
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	92.86
KOG2888	453	consensus Putative RNA binding protein [General fu	91.8
KOG2891	445	consensus Surface glycoprotein [General function p	90.08
KOG2068	327	consensus MOT2 transcription factor [Transcription	89.95
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	89.59
KOG4019	193	consensus Calcineurin-mediated signaling pathway i	89.54
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	88.23
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	88.21
KOG4483	528	consensus Uncharacterized conserved protein [Funct	87.57
PRK14548	84	50S ribosomal protein L23P; Provisional	87.36
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	87.34
TIGR03636	77	L23_arch archaeal ribosomal protein L23. This mode	86.95
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	86.56
PF03468	116	XS: XS domain; InterPro: IPR005380 The XS (rice ge	85.0
KOG2146	354	consensus Splicing coactivator SRm160/300, subunit	83.47
PF14893	331	PNMA: PNMA	82.3

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=1.1e-32  Score=233.00  Aligned_cols=162  Identities=26%  Similarity=0.366  Sum_probs=140.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      ...++|||+|||+++|+++|+++|+.||+|+.|.|+.   ++.++|||||+|.++++|..|++.||+..|.++.|.|.++
T Consensus       105 ~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a  184 (346)
T TIGR01659       105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYA  184 (346)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecc
Confidence            3578999999999999999999999999999999954   5678899999999999999999999999999999999998


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEec
Q 023765           81 HGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTS  156 (277)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~  156 (277)
                      .+....                    ...++|||.|||..+++++|+++|.+||+|..+.|+.+..+    +||||+|.+
T Consensus       185 ~p~~~~--------------------~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~  244 (346)
T TIGR01659       185 RPGGES--------------------IKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNK  244 (346)
T ss_pred             cccccc--------------------cccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECC
Confidence            643211                    12468999999999999999999999999999999877543    599999999


Q ss_pred             hhHHHHHHHhcCCCeecccceeeEEEEeecC
Q 023765          157 YDDMKYAIRKLDRSEFRNAFSRSYVRVREYD  187 (277)
Q Consensus       157 ~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~  187 (277)
                      .++|++||+.||+..+.+...  .|.|..++
T Consensus       245 ~e~A~~Ai~~lng~~~~g~~~--~l~V~~a~  273 (346)
T TIGR01659       245 REEAQEAISALNNVIPEGGSQ--PLTVRLAE  273 (346)
T ss_pred             HHHHHHHHHHhCCCccCCCce--eEEEEECC
Confidence            999999999999999977433  44444443

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).

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.97  E-value=2.6e-29  Score=184.95  Aligned_cols=187  Identities=60%  Similarity=1.020  Sum_probs=160.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            1 MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         1 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      |+++.+++|||+|||.++.+.+|+.||-+||.|.+|.|+....+..||||+|+++.+|+.||..-+|..++|..|.|+++
T Consensus         1 ~~gr~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    1 MSGRNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             CCCcccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            78999999999999999999999999999999999999887778899999999999999999999999999999999999


Q ss_pred             cCCCCCCCCCCCCCCC------CCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEE
Q 023765           81 HGGRRHSSSMDRYSSY------SSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDY  154 (277)
Q Consensus        81 ~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f  154 (277)
                      ............+..-      ......++.......|.|.+||+..+++||++++.+.|.|.+..+.++.   ++.|+|
T Consensus        81 rggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rDg---~GvV~~  157 (241)
T KOG0105|consen   81 RGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRDG---VGVVEY  157 (241)
T ss_pred             cCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeeccc---ceeeee
Confidence            9876333221111111      1112235566778899999999999999999999999999999999885   789999


Q ss_pred             echhHHHHHHHhcCCCeecccceeeEEEEeecCCCC
Q 023765          155 TSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDSRR  190 (277)
Q Consensus       155 ~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~~~r  190 (277)
                      ...++++.|+.+|+...+.....+..|.+.......
T Consensus       158 ~r~eDMkYAvr~ld~~~~~seGe~~yirv~~~~~~~  193 (241)
T KOG0105|consen  158 LRKEDMKYAVRKLDDQKFRSEGETAYIRVRGDENRD  193 (241)
T ss_pred             eehhhHHHHHHhhccccccCcCcEeeEEecccCCCc
Confidence            999999999999999998877778888888776553

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.97  E-value=1.1e-29  Score=225.37  Aligned_cols=170  Identities=20%  Similarity=0.317  Sum_probs=142.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      ..++|||+|||+.+++++|+++|.+||+|..|.|+.   +++++|||||+|.+.++|..|++.|||..|.|+.|.|.+..
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            467999999999999999999999999999999954   57889999999999999999999999999999999998654


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEech
Q 023765           82 GGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSY  157 (277)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~  157 (277)
                      .........         ...........+|||+||+..+++++|+++|+.||.|..+.+..+..    .|||||+|.+.
T Consensus       186 ~~p~a~~~~---------~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~  256 (612)
T TIGR01645       186 NMPQAQPII---------DMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNL  256 (612)
T ss_pred             ccccccccc---------ccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCH
Confidence            322111000         00011122357999999999999999999999999999999998754    46999999999


Q ss_pred             hHHHHHHHhcCCCeecccceeeEEEEeecC
Q 023765          158 DDMKYAIRKLDRSEFRNAFSRSYVRVREYD  187 (277)
Q Consensus       158 ~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~  187 (277)
                      ++|.+|+..||+..++|    ..|+|...-
T Consensus       257 e~A~kAI~amNg~elgG----r~LrV~kAi  282 (612)
T TIGR01645       257 QSQSEAIASMNLFDLGG----QYLRVGKCV  282 (612)
T ss_pred             HHHHHHHHHhCCCeeCC----eEEEEEecC
Confidence            99999999999999999    566665443

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.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.97  E-value=1.5e-29  Score=218.19  Aligned_cols=161  Identities=22%  Similarity=0.363  Sum_probs=140.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      +.++|||+|||+.+|+++|+++|+.||+|.+|.|+.   ++.++|||||+|.++++|.+|+..|||..|.|+.|.|.++.
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            578999999999999999999999999999999964   56789999999999999999999999999999999999987


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC----CCcEEEEEEech
Q 023765           82 GGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR----GGMTGIVDYTSY  157 (277)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~----~~~~~fv~f~~~  157 (277)
                      +....                    ....+|||+|||..+++++|.++|.+||.|..+.+..+.    ..+||||+|.+.
T Consensus        82 ~~~~~--------------------~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~  141 (352)
T TIGR01661        82 PSSDS--------------------IKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKR  141 (352)
T ss_pred             ccccc--------------------cccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCH
Confidence            53321                    124689999999999999999999999999999988764    346999999999


Q ss_pred             hHHHHHHHhcCCCeecccceeeEEEEeecC
Q 023765          158 DDMKYAIRKLDRSEFRNAFSRSYVRVREYD  187 (277)
Q Consensus       158 ~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~  187 (277)
                      ++|+.|++.|||..+.|...  .|.+....
T Consensus       142 ~~A~~ai~~l~g~~~~g~~~--~i~v~~a~  169 (352)
T TIGR01661       142 DEADRAIKTLNGTTPSGCTE--PITVKFAN  169 (352)
T ss_pred             HHHHHHHHHhCCCccCCCce--eEEEEECC
Confidence            99999999999999987433  45555443

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.97  E-value=9.8e-29  Score=220.07  Aligned_cols=172  Identities=20%  Similarity=0.282  Sum_probs=142.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      +++.++|||+|||+.+++++|+++|+.||.|.+|.|+.   ++.++|||||+|.+.++|.+|+. |+|..|.|+.|.|.+
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQS  164 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEee
Confidence            35688999999999999999999999999999999965   56789999999999999999998 999999999999998


Q ss_pred             ccCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEe
Q 023765           80 AHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYT  155 (277)
Q Consensus        80 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~  155 (277)
                      +............        ......+...+|||+|||..+++++|+++|.+||.|..|.+..+..+    +||||+|.
T Consensus       165 ~~~~~~~~~~~~~--------~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~  236 (457)
T TIGR01622       165 SQAEKNRAAKAAT--------HQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFH  236 (457)
T ss_pred             cchhhhhhhhccc--------ccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEEC
Confidence            7643221110000        00001122689999999999999999999999999999999977654    69999999


Q ss_pred             chhHHHHHHHhcCCCeecccceeeEEEEeecC
Q 023765          156 SYDDMKYAIRKLDRSEFRNAFSRSYVRVREYD  187 (277)
Q Consensus       156 ~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~  187 (277)
                      +.++|..|+..|||..+.|    ..|.|....
T Consensus       237 ~~e~A~~A~~~l~g~~i~g----~~i~v~~a~  264 (457)
T TIGR01622       237 DAEEAKEALEVMNGFELAG----RPIKVGYAQ  264 (457)
T ss_pred             CHHHHHHHHHhcCCcEECC----EEEEEEEcc
Confidence            9999999999999999999    456665543

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.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.96  E-value=1.5e-27  Score=205.66  Aligned_cols=181  Identities=23%  Similarity=0.324  Sum_probs=141.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCC--ceEEEEE
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDG--YRLRVEL   79 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g--~~i~v~~   79 (277)
                      ..++|||+|||+.+++++|.++|++||.|..+.++.   ++.++|||||+|.+.++|..|++.|||..+.|  ..|.|.+
T Consensus        88 ~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~  167 (352)
T TIGR01661        88 KGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKF  167 (352)
T ss_pred             ccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            456899999999999999999999999999999865   45678999999999999999999999999987  5688888


Q ss_pred             ccCCCCCCCC-------------CCC-CCC----------CC---------------------------C---CCCC---
Q 023765           80 AHGGRRHSSS-------------MDR-YSS----------YS---------------------------S---GGSR---  102 (277)
Q Consensus        80 a~~~~~~~~~-------------~~~-~~~----------~~---------------------------~---~~~~---  102 (277)
                      +.........             ... ...          ..                           .   ....   
T Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  247 (352)
T TIGR01661       168 ANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPP  247 (352)
T ss_pred             CCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCc
Confidence            8644311000             000 000          00                           0   0000   


Q ss_pred             ---------------CCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC----CCcEEEEEEechhHHHHH
Q 023765          103 ---------------GVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR----GGMTGIVDYTSYDDMKYA  163 (277)
Q Consensus       103 ---------------~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~----~~~~~fv~f~~~~~a~~a  163 (277)
                                     ......+.+|||+|||..+++++|.++|.+||.|..+.|+.+.    ..|||||+|.+.++|..|
T Consensus       248 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~A  327 (352)
T TIGR01661       248 ATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMA  327 (352)
T ss_pred             cccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHH
Confidence                           0001223479999999999999999999999999999999876    346999999999999999


Q ss_pred             HHhcCCCeecccceeeEEEEeecCCC
Q 023765          164 IRKLDRSEFRNAFSRSYVRVREYDSR  189 (277)
Q Consensus       164 ~~~l~g~~~~g~~~~~~i~~~~~~~~  189 (277)
                      |..|||..++|    ..|.|.....+
T Consensus       328 i~~lnG~~~~g----r~i~V~~~~~~  349 (352)
T TIGR01661       328 ILSLNGYTLGN----RVLQVSFKTNK  349 (352)
T ss_pred             HHHhCCCEECC----eEEEEEEccCC
Confidence            99999999999    67777765443

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.96  E-value=7.6e-28  Score=214.29  Aligned_cols=170  Identities=16%  Similarity=0.184  Sum_probs=139.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHh--cCCcccCCceEEEEEccC
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRG--RDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~--l~~~~~~g~~i~v~~a~~   82 (277)
                      ++++|||+|||+.+|+++|+++|++||+|..|.|+.   .++||||+|.++++|..|++.  +++..|.|+.|.|.++..
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~---~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~   77 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLP---GKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTS   77 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEEC---CCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCC
Confidence            589999999999999999999999999999999974   468999999999999999986  478899999999999976


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHH
Q 023765           83 GRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKY  162 (277)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~  162 (277)
                      ........   .     ...........+|+|.||++.+++++|.++|..||.|..|.++.+...++|||+|.+.++|.+
T Consensus        78 ~~~~~~~~---~-----~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~~~~afVef~~~~~A~~  149 (481)
T TIGR01649        78 QEIKRDGN---S-----DFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNVFQALVEFESVNSAQH  149 (481)
T ss_pred             cccccCCC---C-----cccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCCceEEEEEECCHHHHHH
Confidence            43221110   0     000111223457999999999999999999999999999999888776799999999999999


Q ss_pred             HHHhcCCCeecccceeeEEEEeecC
Q 023765          163 AIRKLDRSEFRNAFSRSYVRVREYD  187 (277)
Q Consensus       163 a~~~l~g~~~~g~~~~~~i~~~~~~  187 (277)
                      |+..|||..+.|..  ..|.+...+
T Consensus       150 A~~~Lng~~i~~~~--~~l~v~~sk  172 (481)
T TIGR01649       150 AKAALNGADIYNGC--CTLKIEYAK  172 (481)
T ss_pred             HHHHhcCCcccCCc--eEEEEEEec
Confidence            99999999997642  345555444

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).

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.96  E-value=5.7e-28  Score=187.97  Aligned_cols=169  Identities=18%  Similarity=0.297  Sum_probs=144.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCCC
Q 023765            8 TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGR   84 (277)
Q Consensus         8 ~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~~   84 (277)
                      -|||+.|.+.++-++|++.|.+||+|.++++..   |++++||+||.|.+.++|+.||..|||..|.++.|.-.||..+.
T Consensus        64 hvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp  143 (321)
T KOG0148|consen   64 HVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKP  143 (321)
T ss_pred             eEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCc
Confidence            489999999999999999999999999999944   78999999999999999999999999999999999999998665


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHH
Q 023765           85 RHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAI  164 (277)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~  164 (277)
                      .......    ..=..-.....+..++|||+|++..+++++|++.|..||.|..|.+..+.  +|+||.|++.|.|..||
T Consensus       144 ~e~n~~~----ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~q--GYaFVrF~tkEaAahAI  217 (321)
T KOG0148|consen  144 SEMNGKP----LTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQ--GYAFVRFETKEAAAHAI  217 (321)
T ss_pred             cccCCCC----ccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEeccc--ceEEEEecchhhHHHHH
Confidence            2111100    00001123345568999999999999999999999999999999999886  49999999999999999


Q ss_pred             HhcCCCeecccceeeEEE
Q 023765          165 RKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       165 ~~l~g~~~~g~~~~~~i~  182 (277)
                      ..+|+.+|.|..+++...
T Consensus       218 v~mNntei~G~~VkCsWG  235 (321)
T KOG0148|consen  218 VQMNNTEIGGQLVRCSWG  235 (321)
T ss_pred             HHhcCceeCceEEEEecc
Confidence            999999999976665443

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.95  E-value=7.3e-27  Score=208.00  Aligned_cols=182  Identities=20%  Similarity=0.261  Sum_probs=141.1

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            4 RSSRTLYVGNLPG-DTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         4 ~~~~~l~V~nL~~-~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      .++++|||+||++ .+|+++|+++|+.||.|..|.++.+.  +|||||+|.+.++|..|+..|||..|.|+.|.|.+++.
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~--~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~  350 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK--KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQ  350 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC--CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccc
Confidence            3678999999998 69999999999999999999997653  69999999999999999999999999999999999876


Q ss_pred             CCCCCCCC----CC---CCCCCCC--CC--------CCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCC--eeEEEEEe
Q 023765           83 GRRHSSSM----DR---YSSYSSG--GS--------RGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGD--VCFSQVFR  143 (277)
Q Consensus        83 ~~~~~~~~----~~---~~~~~~~--~~--------~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~--v~~~~~~~  143 (277)
                      ........    +.   ...+...  ..        ......+..+|||.|||..+++++|+++|..||.  |..+.+..
T Consensus       351 ~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~  430 (481)
T TIGR01649       351 QNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFP  430 (481)
T ss_pred             ccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEec
Confidence            43211110    00   0001000  00        0111245789999999999999999999999998  77777764


Q ss_pred             cC--CCcEEEEEEechhHHHHHHHhcCCCeeccccee--eEEEEeecC
Q 023765          144 DR--GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR--SYVRVREYD  187 (277)
Q Consensus       144 ~~--~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~--~~i~~~~~~  187 (277)
                      ..  ..++|||+|.+.++|.+||..|||..+.++...  ..|++...+
T Consensus       431 ~~~~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~  478 (481)
T TIGR01649       431 KDNERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFST  478 (481)
T ss_pred             CCCCcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEecc
Confidence            43  236999999999999999999999999985422  245555543

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

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

Probab=99.95  E-value=3.6e-27  Score=214.75  Aligned_cols=156  Identities=24%  Similarity=0.383  Sum_probs=136.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCCC
Q 023765            8 TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGR   84 (277)
Q Consensus         8 ~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~~   84 (277)
                      +|||+|||+++|+++|+++|+.||+|..|.|..   +++++|||||+|.+.++|.+|+..||+..|.|+.|.|.|+....
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            799999999999999999999999999999965   46788999999999999999999999999999999999976422


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC---CcEEEEEEechhHHH
Q 023765           85 RHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG---GMTGIVDYTSYDDMK  161 (277)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~---~~~~fv~f~~~~~a~  161 (277)
                      ..                  ......+|||+||+.++++++|.++|..||.|..|.+..+..   .+||||+|.+.++|.
T Consensus        82 ~~------------------~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~  143 (562)
T TIGR01628        82 SL------------------RRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAK  143 (562)
T ss_pred             cc------------------cccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHH
Confidence            11                  011245899999999999999999999999999999987753   469999999999999


Q ss_pred             HHHHhcCCCeecccceeeEEEEee
Q 023765          162 YAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       162 ~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      .|++.|||..+.|+    .|.+..
T Consensus       144 ~Ai~~lng~~~~~~----~i~v~~  163 (562)
T TIGR01628       144 AAIQKVNGMLLNDK----EVYVGR  163 (562)
T ss_pred             HHHHHhcccEecCc----eEEEec
Confidence            99999999999984    555543

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.95  E-value=4.7e-28  Score=190.24  Aligned_cols=145  Identities=28%  Similarity=0.528  Sum_probs=134.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCCCCC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGRRH   86 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~~~~   86 (277)
                      -+|||||||..+++.+|+.||++||+|.+|.|+     |+||||..++...|..|+.+|+|..|+|..|.|+.++.+...
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIv-----KNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKsk~   77 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIV-----KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKSKA   77 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeee-----cccceEEeecccccHHHHhhcccceecceEEEEEeccccCCC
Confidence            379999999999999999999999999999998     789999999999999999999999999999999999876321


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHh
Q 023765           87 SSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRK  166 (277)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~  166 (277)
                                            .++|+|+||.+.++.++|+..|++||.|+.++|.++    |+||.|+..++|..|+..
T Consensus        78 ----------------------stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd----y~fvh~d~~eda~~air~  131 (346)
T KOG0109|consen   78 ----------------------STKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD----YAFVHFDRAEDAVEAIRG  131 (346)
T ss_pred             ----------------------ccccccCCCCccccCHHHhhhhcccCCceeeeeecc----eeEEEEeeccchHHHHhc
Confidence                                  568999999999999999999999999999999999    999999999999999999


Q ss_pred             cCCCeecccceeeEEE
Q 023765          167 LDRSEFRNAFSRSYVR  182 (277)
Q Consensus       167 l~g~~~~g~~~~~~i~  182 (277)
                      ||+.++.|+...+.+.
T Consensus       132 l~~~~~~gk~m~vq~s  147 (346)
T KOG0109|consen  132 LDNTEFQGKRMHVQLS  147 (346)
T ss_pred             ccccccccceeeeeee
Confidence            9999999976555443

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.95  E-value=1.1e-26  Score=206.14  Aligned_cols=176  Identities=22%  Similarity=0.313  Sum_probs=136.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccC-CceEEEEEccC
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFD-GYRLRVELAHG   82 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~-g~~i~v~~a~~   82 (277)
                      .++|||+|||+++++++|+++|++||.|.+|.|+.  ++.++|||||+|.+.++|++||+.||+..|. |+.|.|.++..
T Consensus        58 ~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~~  137 (578)
T TIGR01648        58 GCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISVD  137 (578)
T ss_pred             CCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccccc
Confidence            48999999999999999999999999999999865  5788999999999999999999999998885 67766655431


Q ss_pred             CCC-------CCCC------------------------CCC--CCC------------------C-C------CC-----
Q 023765           83 GRR-------HSSS------------------------MDR--YSS------------------Y-S------SG-----   99 (277)
Q Consensus        83 ~~~-------~~~~------------------------~~~--~~~------------------~-~------~~-----   99 (277)
                      ...       ....                        ...  ...                  + .      +.     
T Consensus       138 ~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~Vd  217 (578)
T TIGR01648       138 NCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVD  217 (578)
T ss_pred             CceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEE
Confidence            100       0000                        000  000                  0 0      00     


Q ss_pred             ----C--CCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCe
Q 023765          100 ----G--SRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRA--GDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSE  171 (277)
Q Consensus       100 ----~--~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~--g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~  171 (277)
                          .  ..........+|||+||+..+++++|+++|.+|  |.|..|.+..+    ||||+|.+.++|++|++.||+.+
T Consensus       218 wA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~rg----fAFVeF~s~e~A~kAi~~lnG~~  293 (578)
T TIGR01648       218 WAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD----YAFVHFEDREDAVKAMDELNGKE  293 (578)
T ss_pred             eecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeecC----eEEEEeCCHHHHHHHHHHhCCCE
Confidence                0  000011235689999999999999999999999  99999988765    99999999999999999999999


Q ss_pred             ecccceeeEEEEeecCCC
Q 023765          172 FRNAFSRSYVRVREYDSR  189 (277)
Q Consensus       172 ~~g~~~~~~i~~~~~~~~  189 (277)
                      |+|    ..|.|....+.
T Consensus       294 i~G----r~I~V~~Akp~  307 (578)
T TIGR01648       294 LEG----SEIEVTLAKPV  307 (578)
T ss_pred             ECC----EEEEEEEccCC
Confidence            999    67777766543

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.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.95  E-value=2.2e-26  Score=207.75  Aligned_cols=176  Identities=19%  Similarity=0.274  Sum_probs=134.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhcc------------CCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCccc
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKY------------GPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNF   70 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~------------G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~   70 (277)
                      +...++|||+|||+.+|+++|.++|.+|            +.|..+.+.   ..+|||||+|.+.++|..||+ |||+.|
T Consensus       172 ~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~---~~kg~afVeF~~~e~A~~Al~-l~g~~~  247 (509)
T TIGR01642       172 TRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNIN---KEKNFAFLEFRTVEEATFAMA-LDSIIY  247 (509)
T ss_pred             CccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEEC---CCCCEEEEEeCCHHHHhhhhc-CCCeEe
Confidence            3567899999999999999999999975            345555443   458999999999999999996 999999


Q ss_pred             CCceEEEEEccCCCCCCCCCCCCC---------CCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEE
Q 023765           71 DGYRLRVELAHGGRRHSSSMDRYS---------SYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQV  141 (277)
Q Consensus        71 ~g~~i~v~~a~~~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~  141 (277)
                      .|..|.|.........+.......         ................+|||+|||..+++++|.++|..||.|..+.+
T Consensus       248 ~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~  327 (509)
T TIGR01642       248 SNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNL  327 (509)
T ss_pred             eCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEE
Confidence            999999986554332111100000         00000011112345679999999999999999999999999999998


Q ss_pred             EecC----CCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          142 FRDR----GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       142 ~~~~----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      +.+.    ..|||||+|.+.++|..|+..|||..+.|+    .|.|...
T Consensus       328 ~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~----~l~v~~a  372 (509)
T TIGR01642       328 IKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDN----KLHVQRA  372 (509)
T ss_pred             EecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCe----EEEEEEC
Confidence            8764    346999999999999999999999999994    5555554

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.95  E-value=2.7e-26  Score=207.11  Aligned_cols=179  Identities=20%  Similarity=0.294  Sum_probs=137.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+.+|+++|.++|+.||.|..+.|+.   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            3467999999999999999999999999999999854   5778999999999999999999999999999999999998


Q ss_pred             cCCCCCCCCCCCC--CCCC-C-C----CCCCCCCCCCceEEEeCCCCCC----------CHHHHHHHHHhcCCeeEEEEE
Q 023765           81 HGGRRHSSSMDRY--SSYS-S-G----GSRGVSRRSDYRVLVTGLPSSA----------SWQDLKDHMRRAGDVCFSQVF  142 (277)
Q Consensus        81 ~~~~~~~~~~~~~--~~~~-~-~----~~~~~~~~~~~~l~v~~l~~~~----------~~~~l~~~f~~~g~v~~~~~~  142 (277)
                      .............  .... . .    ........+..+|+|.||....          ..++|+++|.+||.|..|.|+
T Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~  452 (509)
T TIGR01642       373 CVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIP  452 (509)
T ss_pred             ccCCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEee
Confidence            7544322111100  0000 0 0    0001122356789999986321          236899999999999999998


Q ss_pred             ecC-------CCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          143 RDR-------GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       143 ~~~-------~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      .+.       ..|+|||+|.+.++|++|+..|||.+|+|+    .|.+...
T Consensus       453 ~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr----~v~~~~~  499 (509)
T TIGR01642       453 RPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDR----VVVAAFY  499 (509)
T ss_pred             ccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCe----EEEEEEe
Confidence            652       236899999999999999999999999994    5544443

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.94  E-value=1.3e-26  Score=170.41  Aligned_cols=159  Identities=24%  Similarity=0.346  Sum_probs=137.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      +...||||+||+..++++.|++||-+.|+|..+.++.   +...+|||||+|.++|+|+-|++.||...+.|++|.|..+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            5678999999999999999999999999999999965   5578999999999999999999999999999999999988


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEE-EEEecCC----CcEEEEEEe
Q 023765           81 HGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFS-QVFRDRG----GMTGIVDYT  155 (277)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~-~~~~~~~----~~~~fv~f~  155 (277)
                      ......                   ...+.++||+||.+.+++..|.+.|..||.+... .++.+..    .+||||.|.
T Consensus        87 s~~~~n-------------------l~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~  147 (203)
T KOG0131|consen   87 SAHQKN-------------------LDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYA  147 (203)
T ss_pred             cccccc-------------------ccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEech
Confidence            732211                   1225799999999999999999999999988763 5666554    359999999


Q ss_pred             chhHHHHHHHhcCCCeecccceeeEE
Q 023765          156 SYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       156 ~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      ..+.+.+|+..+||..++++.+++.+
T Consensus       148 sfeasd~ai~s~ngq~l~nr~itv~y  173 (203)
T KOG0131|consen  148 SFEASDAAIGSMNGQYLCNRPITVSY  173 (203)
T ss_pred             hHHHHHHHHHHhccchhcCCceEEEE
Confidence            99999999999999999995444433

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.94  E-value=6.6e-26  Score=187.78  Aligned_cols=174  Identities=22%  Similarity=0.302  Sum_probs=137.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCccc-CCceEEEEEccC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNF-DGYRLRVELAHG   82 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~-~g~~i~v~~a~~   82 (277)
                      +-||||.||.++.|++|.-||+..|+|-++.|+.   ++.++|||||.|.+.+.|+.|++.||+.+| .|+.|.|..+..
T Consensus        84 ~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Sva  163 (506)
T KOG0117|consen   84 CEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSVA  163 (506)
T ss_pred             ceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEeee
Confidence            5799999999999999999999999999999966   578999999999999999999999999988 588888877663


Q ss_pred             CC-------CCCCC------------------------CCC--C-------------------CC-------CCCC----
Q 023765           83 GR-------RHSSS------------------------MDR--Y-------------------SS-------YSSG----   99 (277)
Q Consensus        83 ~~-------~~~~~------------------------~~~--~-------------------~~-------~~~~----   99 (277)
                      +.       +..+.                        .+.  .                   ..       .+..    
T Consensus       164 n~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVd  243 (506)
T KOG0117|consen  164 NCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVD  243 (506)
T ss_pred             cceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcceee
Confidence            31       10000                        000  0                   00       0000    


Q ss_pred             CC------CCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeec
Q 023765          100 GS------RGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFR  173 (277)
Q Consensus       100 ~~------~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~  173 (277)
                      +.      ....+.....|||.||+..+|++.|+++|.+||.|..|..++|    ||||.|.+.++|.+|++.+||++|+
T Consensus       244 WAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD----YaFVHf~eR~davkAm~~~ngkeld  319 (506)
T KOG0117|consen  244 WAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD----YAFVHFAEREDAVKAMKETNGKELD  319 (506)
T ss_pred             ccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc----eeEEeecchHHHHHHHHHhcCceec
Confidence            00      0012234568999999999999999999999999999999988    9999999999999999999999999


Q ss_pred             ccceeeEEEEeecCC
Q 023765          174 NAFSRSYVRVREYDS  188 (277)
Q Consensus       174 g~~~~~~i~~~~~~~  188 (277)
                      |.    .|.+..+++
T Consensus       320 G~----~iEvtLAKP  330 (506)
T KOG0117|consen  320 GS----PIEVTLAKP  330 (506)
T ss_pred             Cc----eEEEEecCC
Confidence            94    444444443

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

Probab=99.94  E-value=1.8e-26  Score=190.32  Aligned_cols=166  Identities=21%  Similarity=0.406  Sum_probs=141.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcc-cCC--ceEEEE
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYN-FDG--YRLRVE   78 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~-~~g--~~i~v~   78 (277)
                      +.-+|||+-||..++|.||+++|++||.|.+|.|+.   ++.++|+|||+|.+.++|++|+..|++.. |.|  .+|.|.
T Consensus        33 ~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk  112 (510)
T KOG0144|consen   33 SAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVK  112 (510)
T ss_pred             hhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeec
Confidence            345799999999999999999999999999999965   57889999999999999999999998854 444  468999


Q ss_pred             EccCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC---cEEEEEEe
Q 023765           79 LAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG---MTGIVDYT  155 (277)
Q Consensus        79 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~fv~f~  155 (277)
                      +|.......                   ....+|||+-|+..++|.+|+++|.+||.|++|.|+++..+   |||||.|.
T Consensus       113 ~Ad~E~er~-------------------~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fs  173 (510)
T KOG0144|consen  113 YADGERERI-------------------VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFS  173 (510)
T ss_pred             ccchhhhcc-------------------ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEe
Confidence            988654321                   22569999999999999999999999999999999998654   79999999


Q ss_pred             chhHHHHHHHhcCCCee-cccceeeEEEEeecCCCCc
Q 023765          156 SYDDMKYAIRKLDRSEF-RNAFSRSYVRVREYDSRRS  191 (277)
Q Consensus       156 ~~~~a~~a~~~l~g~~~-~g~~~~~~i~~~~~~~~r~  191 (277)
                      +.+.|..||+.|||..- .|  +...+-|..++..+.
T Consensus       174 tke~A~~Aika~ng~~tmeG--cs~PLVVkFADtqkd  208 (510)
T KOG0144|consen  174 TKEMAVAAIKALNGTQTMEG--CSQPLVVKFADTQKD  208 (510)
T ss_pred             hHHHHHHHHHhhccceeecc--CCCceEEEecccCCC
Confidence            99999999999999754 44  345777887776543

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

Probab=99.94  E-value=1.5e-25  Score=204.08  Aligned_cols=177  Identities=19%  Similarity=0.303  Sum_probs=142.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccC----CceEEEE
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFD----GYRLRVE   78 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~----g~~i~v~   78 (277)
                      ..++|||+|||+++|+++|+++|+.||+|..+.+..  ++..+|||||+|.+.++|.+|++.|++..|.    |..|.|.
T Consensus       177 ~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~  256 (562)
T TIGR01628       177 KFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVG  256 (562)
T ss_pred             CCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEee
Confidence            457899999999999999999999999999999965  4567899999999999999999999999999    9999998


Q ss_pred             EccCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC---CcEEEEEEe
Q 023765           79 LAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG---GMTGIVDYT  155 (277)
Q Consensus        79 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~---~~~~fv~f~  155 (277)
                      ++.........  ....+..............+|||+||+..+++++|+++|.+||.|..|.++.+..   .+||||+|.
T Consensus       257 ~a~~k~er~~~--~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~  334 (562)
T TIGR01628       257 RAQKRAEREAE--LRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFS  334 (562)
T ss_pred             cccChhhhHHH--HHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeC
Confidence            87654322100  0000000000111223467899999999999999999999999999999988743   369999999


Q ss_pred             chhHHHHHHHhcCCCeecccceeeEEEEeecC
Q 023765          156 SYDDMKYAIRKLDRSEFRNAFSRSYVRVREYD  187 (277)
Q Consensus       156 ~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~  187 (277)
                      +.++|.+|+..|||..+.|+    .|.|..+.
T Consensus       335 ~~~~A~~A~~~~~g~~~~gk----~l~V~~a~  362 (562)
T TIGR01628       335 NPEEANRAVTEMHGRMLGGK----PLYVALAQ  362 (562)
T ss_pred             CHHHHHHHHHHhcCCeeCCc----eeEEEecc
Confidence            99999999999999999994    55555444

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=99.94  E-value=6.2e-26  Score=175.80  Aligned_cols=162  Identities=22%  Similarity=0.342  Sum_probs=142.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      ...+.|.|.-||.++|++||+.||...|+|+.|++..   ++++.||+||-|.+++||++|+..|||..+..+.|+|.+|
T Consensus        39 ~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyA  118 (360)
T KOG0145|consen   39 ESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYA  118 (360)
T ss_pred             cccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEec
Confidence            3456799999999999999999999999999999954   6899999999999999999999999999999999999999


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEec
Q 023765           81 HGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTS  156 (277)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~  156 (277)
                      .+....-                    ....|||.+||..++..+|+++|.+||.|....|..+..+    |.+||.|+.
T Consensus       119 RPSs~~I--------------------k~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDK  178 (360)
T KOG0145|consen  119 RPSSDSI--------------------KDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDK  178 (360)
T ss_pred             cCChhhh--------------------cccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecc
Confidence            8644322                    2679999999999999999999999999988777766544    599999999


Q ss_pred             hhHHHHHHHhcCCCeecccceeeEEEEeecC
Q 023765          157 YDDMKYAIRKLDRSEFRNAFSRSYVRVREYD  187 (277)
Q Consensus       157 ~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~  187 (277)
                      ..+|++||..|||..-.|..  ..|.|..+.
T Consensus       179 r~EAe~AIk~lNG~~P~g~t--epItVKFan  207 (360)
T KOG0145|consen  179 RIEAEEAIKGLNGQKPSGCT--EPITVKFAN  207 (360)
T ss_pred             hhHHHHHHHhccCCCCCCCC--CCeEEEecC
Confidence            99999999999999998853  456666554

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.94  E-value=6.4e-25  Score=195.62  Aligned_cols=174  Identities=21%  Similarity=0.319  Sum_probs=135.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      +++|||+|||+.+|+++|+++|++||.|..|.|+.   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++..
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            58999999999999999999999999999999965   457799999999999999999999999999999999999763


Q ss_pred             CCCCCCCC------------------------------CC---CCCCCCCC-----------------------------
Q 023765           83 GRRHSSSM------------------------------DR---YSSYSSGG-----------------------------  100 (277)
Q Consensus        83 ~~~~~~~~------------------------------~~---~~~~~~~~-----------------------------  100 (277)
                      ........                              ..   .....+..                             
T Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  345 (457)
T TIGR01622       266 STYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALA  345 (457)
T ss_pred             CCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhccccccccccccccccccccccc
Confidence            21110000                              00   00000000                             


Q ss_pred             ----C-CCC---CCCCCceEEEeCCCCCCC----------HHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHH
Q 023765          101 ----S-RGV---SRRSDYRVLVTGLPSSAS----------WQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKY  162 (277)
Q Consensus       101 ----~-~~~---~~~~~~~l~v~~l~~~~~----------~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~  162 (277)
                          . ..+   ...+..+|+|.||....+          .+||++.|.+||.|..|.+......|++||+|.+.++|..
T Consensus       346 ~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~~~~G~~fV~F~~~e~A~~  425 (457)
T TIGR01622       346 IMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTKNSAGKIYLKFSSVDAALA  425 (457)
T ss_pred             cccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCCCCceeEEEEECCHHHHHH
Confidence                0 000   113457888999854433          3689999999999999999877777899999999999999


Q ss_pred             HHHhcCCCeecccceee
Q 023765          163 AIRKLDRSEFRNAFSRS  179 (277)
Q Consensus       163 a~~~l~g~~~~g~~~~~  179 (277)
                      |+..|||..++|+.+..
T Consensus       426 A~~~lnGr~f~gr~i~~  442 (457)
T TIGR01622       426 AFQALNGRYFGGKMITA  442 (457)
T ss_pred             HHHHhcCcccCCeEEEE
Confidence            99999999999954443

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.

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.93  E-value=8.7e-25  Score=185.19  Aligned_cols=178  Identities=20%  Similarity=0.294  Sum_probs=144.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      ..||||++||+.++.++|.++|+.+|+|..+.+..   ++..+||+||.|.-+||+..|++.+++..|.|+.|.|.++..
T Consensus         5 g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~   84 (678)
T KOG0127|consen    5 GATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKK   84 (678)
T ss_pred             CceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccccc
Confidence            38999999999999999999999999999999965   346789999999999999999999999999999999999997


Q ss_pred             CCCCCCCC-CCC----CCCCCCCC-CCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC---cEEEEE
Q 023765           83 GRRHSSSM-DRY----SSYSSGGS-RGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG---MTGIVD  153 (277)
Q Consensus        83 ~~~~~~~~-~~~----~~~~~~~~-~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~fv~  153 (277)
                      ........ ...    ....+..+ ..-...+.+.|+|.|||+.+...+|+.+|..||.|..|.|+....+   |||||+
T Consensus        85 R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~  164 (678)
T KOG0127|consen   85 RARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQ  164 (678)
T ss_pred             cccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEE
Confidence            65443211 100    00111000 0111234789999999999999999999999999999999977655   599999


Q ss_pred             EechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          154 YTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       154 f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      |.+..+|..|++.||+.+|+|+.+-+-+.|
T Consensus       165 fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV  194 (678)
T KOG0127|consen  165 FKEKKDAEKALEFFNGNKIDGRPVAVDWAV  194 (678)
T ss_pred             EeeHHHHHHHHHhccCceecCceeEEeeec
Confidence            999999999999999999999544443333

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.92  E-value=3.2e-24  Score=166.30  Aligned_cols=170  Identities=24%  Similarity=0.348  Sum_probs=138.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCc--eEEEEEc
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGY--RLRVELA   80 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~--~i~v~~a   80 (277)
                      ...|||.+||..+|..||.++|++||.|+.-.+..   ++.++|.+||.|...++|+.|++.|||..-.|.  +|.|+|+
T Consensus       127 ~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFa  206 (360)
T KOG0145|consen  127 DANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFA  206 (360)
T ss_pred             ccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEec
Confidence            35699999999999999999999999988877743   678999999999999999999999999988776  5999999


Q ss_pred             cCCCCCCCCCCCCC-------CCCCC------------------------------------CCCCCCCCCCceEEEeCC
Q 023765           81 HGGRRHSSSMDRYS-------SYSSG------------------------------------GSRGVSRRSDYRVLVTGL  117 (277)
Q Consensus        81 ~~~~~~~~~~~~~~-------~~~~~------------------------------------~~~~~~~~~~~~l~v~~l  117 (277)
                      +.+...........       .+.++                                    ...+......++|||=||
T Consensus       207 nnPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ciFvYNL  286 (360)
T KOG0145|consen  207 NNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGWCIFVYNL  286 (360)
T ss_pred             CCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCCCCeeEEEEEec
Confidence            97643322110000       00000                                    001122345799999999


Q ss_pred             CCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          118 PSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       118 ~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                      .+++++..|+++|.+||.|..|++.++..    .||+||.|.+.++|..||..|||..+.++
T Consensus       287 spd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~r  348 (360)
T KOG0145|consen  287 SPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDR  348 (360)
T ss_pred             CCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccce
Confidence            99999999999999999999999998865    46999999999999999999999999984

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.91  E-value=2.9e-23  Score=176.01  Aligned_cols=178  Identities=21%  Similarity=0.368  Sum_probs=137.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      .-.|+|.|||+.+...+|+.+|++||.|.+|.|+.  ++...|||||+|.+..+|..|++.||+..|+|++|-|.||-++
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~K  196 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDK  196 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeeccc
Confidence            45799999999999999999999999999999965  5667799999999999999999999999999999999999854


Q ss_pred             CCCCCCC---------------------C----------------CC--CC-C----------------CCC---C----
Q 023765           84 RRHSSSM---------------------D----------------RY--SS-Y----------------SSG---G----  100 (277)
Q Consensus        84 ~~~~~~~---------------------~----------------~~--~~-~----------------~~~---~----  100 (277)
                      ..-....                     +                ..  .. +                ...   +    
T Consensus       197 d~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~  276 (678)
T KOG0127|consen  197 DTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKES  276 (678)
T ss_pred             ccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccccccccccccCcc
Confidence            3221100                     0                00  00 0                000   0    


Q ss_pred             -CC------CCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhc--
Q 023765          101 -SR------GVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKL--  167 (277)
Q Consensus       101 -~~------~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l--  167 (277)
                       ..      .....-..+|||.|||+++++++|.++|.+||+|.++.++.++.+    |.|||.|.++.+|..||...  
T Consensus       277 ~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Asp  356 (678)
T KOG0127|consen  277 DKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASP  356 (678)
T ss_pred             cchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCc
Confidence             00      001112479999999999999999999999999999998877655    59999999999999999876  


Q ss_pred             ---CC-CeecccceeeEEEE
Q 023765          168 ---DR-SEFRNAFSRSYVRV  183 (277)
Q Consensus       168 ---~g-~~~~g~~~~~~i~~  183 (277)
                         .| ..++|+.+.+.+.|
T Consensus       357 a~e~g~~ll~GR~Lkv~~Av  376 (678)
T KOG0127|consen  357 ASEDGSVLLDGRLLKVTLAV  376 (678)
T ss_pred             cCCCceEEEeccEEeeeecc
Confidence               33 56677554444433

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.91  E-value=8.7e-24  Score=163.39  Aligned_cols=160  Identities=38%  Similarity=0.625  Sum_probs=131.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCCCCC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGRRH   86 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~~~~   86 (277)
                      ..|||++||+.+.+.+|..||..||.|.++.|+     .+|+||+|.++.+|+.|+..||+..|.|..+.|+++......
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk-----~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~~   76 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK-----NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRRG   76 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee-----cccceeccCchhhhhcccchhcCceecceeeeeecccccccc
Confidence            468999999999999999999999999999998     689999999999999999999999999999999998864322


Q ss_pred             CCCCCCCCCCC-CCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHH
Q 023765           87 SSSMDRYSSYS-SGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIR  165 (277)
Q Consensus        87 ~~~~~~~~~~~-~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~  165 (277)
                      ..... ..... .......+....+.+.|.+++..+.+++|.++|+.+|.+....+..+    ++||+|.+.++|..|+.
T Consensus        77 ~g~~~-~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~~~~----~~~v~Fs~~~da~ra~~  151 (216)
T KOG0106|consen   77 RGRPR-GGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDARRN----FAFVEFSEQEDAKRALE  151 (216)
T ss_pred             cCCCC-CCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhhhcc----ccceeehhhhhhhhcch
Confidence            21000 00000 12223445667889999999999999999999999999966555333    89999999999999999


Q ss_pred             hcCCCeecccc
Q 023765          166 KLDRSEFRNAF  176 (277)
Q Consensus       166 ~l~g~~~~g~~  176 (277)
                      .|++..+.++.
T Consensus       152 ~l~~~~~~~~~  162 (216)
T KOG0106|consen  152 KLDGKKLNGRR  162 (216)
T ss_pred             hccchhhcCce
Confidence            99999999943

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.90  E-value=9.7e-24  Score=170.96  Aligned_cols=165  Identities=22%  Similarity=0.362  Sum_probs=138.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      +.||||.|.+.+.|+-|+..|..||+|+.|+|-+   +++++|||||+|+-+|.|..|++.|||..++|+.|.|....+-
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNm  193 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM  193 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCC
Confidence            5799999999999999999999999999999954   6799999999999999999999999999999999999854332


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhH
Q 023765           84 RRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDD  159 (277)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~  159 (277)
                      ....+..+         ........-+.|||..+.++++++||+..|..||+|..|.+.+++.+    ||+||+|.+...
T Consensus       194 pQAQpiID---------~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs  264 (544)
T KOG0124|consen  194 PQAQPIID---------MVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQS  264 (544)
T ss_pred             cccchHHH---------HHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccc
Confidence            11110000         00001123578999999999999999999999999999999988754    599999999999


Q ss_pred             HHHHHHhcCCCeecccceeeEEEEe
Q 023765          160 MKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       160 a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      ..+|+..||-..++|    ..++|.
T Consensus       265 ~~eAiasMNlFDLGG----QyLRVG  285 (544)
T KOG0124|consen  265 QSEAIASMNLFDLGG----QYLRVG  285 (544)
T ss_pred             hHHHhhhcchhhccc----ceEecc
Confidence            999999999999999    555554

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.89  E-value=2.4e-22  Score=150.86  Aligned_cols=81  Identities=38%  Similarity=0.594  Sum_probs=75.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      ...++|.|.||.+.++.++|+.+|++||.|-+|.|+.   |++++|||||.|.+..+|+.|++.|+|.+|+|+.|.|++|
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            3567899999999999999999999999999999965   6789999999999999999999999999999999999998


Q ss_pred             cCCC
Q 023765           81 HGGR   84 (277)
Q Consensus        81 ~~~~   84 (277)
                      ....
T Consensus        91 rygr   94 (256)
T KOG4207|consen   91 RYGR   94 (256)
T ss_pred             hcCC
Confidence            8644

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.89  E-value=1.5e-21  Score=142.91  Aligned_cols=76  Identities=24%  Similarity=0.266  Sum_probs=68.4

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeecC
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYD  187 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~  187 (277)
                      ..++|||+||+..+++.||+.+|..||.|..|+|..+ +.+||||+|+++.+|+.|+..|+|..|+|    ..|+|+...
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-PPGfAFVEFed~RDA~DAvr~LDG~~~cG----~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-PPGFAFVEFEDPRDAEDAVRYLDGKDICG----SRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-CCCceEEeccCcccHHHHHhhcCCccccC----ceEEEEeec
Confidence            3789999999999999999999999999999999995 44699999999999999999999999999    566666554


Q ss_pred             C
Q 023765          188 S  188 (277)
Q Consensus       188 ~  188 (277)
                      .
T Consensus        84 G   84 (195)
T KOG0107|consen   84 G   84 (195)
T ss_pred             C
Confidence            4

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=99.89  E-value=6.8e-24  Score=173.03  Aligned_cols=169  Identities=16%  Similarity=0.147  Sum_probs=124.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecC------CCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP------PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLR   76 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~------~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~   76 (277)
                      +.....|.|.||.+++|.++|+.||..+|+|.++.|+.+      +.....|||.|.+...+..|.+ |.+++|-++.|.
T Consensus         4 g~~~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdrali   82 (479)
T KOG4676|consen    4 GSSLGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALI   82 (479)
T ss_pred             CCCCceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEE
Confidence            445669999999999999999999999999999999542      2345689999999999999998 777788788777


Q ss_pred             EEEccCCCCCCC----------CCCCCCC----CCCCC------------CCCCCC----------CCCceEEEeCCCCC
Q 023765           77 VELAHGGRRHSS----------SMDRYSS----YSSGG------------SRGVSR----------RSDYRVLVTGLPSS  120 (277)
Q Consensus        77 v~~a~~~~~~~~----------~~~~~~~----~~~~~------------~~~~~~----------~~~~~l~v~~l~~~  120 (277)
                      |........+..          .......    +.+..            -.+|+.          ....+++|++|+..
T Consensus        83 v~p~~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~  162 (479)
T KOG4676|consen   83 VRPYGDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISA  162 (479)
T ss_pred             EEecCCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhh
Confidence            766553322111          0000000    00000            000111          11357999999999


Q ss_pred             CCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeec
Q 023765          121 ASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFR  173 (277)
Q Consensus       121 ~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~  173 (277)
                      +-..++.+.|..+|+|.+..+.......+|.|+|........|+. ++|.++.
T Consensus       163 ~~l~e~~e~f~r~Gev~ya~~ask~~s~~c~~sf~~qts~~halr-~~gre~k  214 (479)
T KOG4676|consen  163 AILPESGESFERKGEVSYAHTASKSRSSSCSHSFRKQTSSKHALR-SHGRERK  214 (479)
T ss_pred             hcchhhhhhhhhcchhhhhhhhccCCCcchhhhHhhhhhHHHHHH-hcchhhh
Confidence            999999999999999999999887777789999999999999986 6665554

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.88  E-value=1.5e-21  Score=166.17  Aligned_cols=147  Identities=25%  Similarity=0.351  Sum_probs=131.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCCCCC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGRRH   86 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~~~~   86 (277)
                      ..||||   +++|+..|.++|+++|+|..+.+..+-.+.|||||.|.++++|.+||..||...+.|++|.|.|+..... 
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~tslgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~~-   77 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDATSLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDPS-   77 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecCCccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCCc-
Confidence            468999   9999999999999999999999944223899999999999999999999999999999999999885331 


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC--cEEEEEEechhHHHHHH
Q 023765           87 SSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG--MTGIVDYTSYDDMKYAI  164 (277)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~--~~~fv~f~~~~~a~~a~  164 (277)
                                              .+||.||++.++..+|.++|..||.|+.|.+..+..+  +| ||+|+++++|.+|+
T Consensus        78 ------------------------~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai  132 (369)
T KOG0123|consen   78 ------------------------LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAI  132 (369)
T ss_pred             ------------------------eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHH
Confidence                                    2999999999999999999999999999999988765  58 99999999999999


Q ss_pred             HhcCCCeecccceeeEEEEeec
Q 023765          165 RKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       165 ~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      ..+||..+.|+    .|.+...
T Consensus       133 ~~~ng~ll~~k----ki~vg~~  150 (369)
T KOG0123|consen  133 EKLNGMLLNGK----KIYVGLF  150 (369)
T ss_pred             HHhcCcccCCC----eeEEeec
Confidence            99999999994    5555433

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.87  E-value=6.2e-21  Score=139.76  Aligned_cols=78  Identities=49%  Similarity=0.802  Sum_probs=72.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCCC
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGR   84 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~~   84 (277)
                      -.++|||+||+..+++.||..+|..||+|..|+|..  .+.|||||||+++.+|+.|+..|+|..|.|..|.|+++....
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvAr--nPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~   86 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVAR--NPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRP   86 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEee--cCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCc
Confidence            468999999999999999999999999999999965  458999999999999999999999999999999999988654

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.87  E-value=1.3e-21  Score=170.89  Aligned_cols=160  Identities=23%  Similarity=0.405  Sum_probs=134.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecC--C----CCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP--P----RPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~--~----~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      ++|||.||++.+|.++|..+|...|.|..+.|..-  +    .+.|||||+|.++++|..|++.|+|+.|+|..|.|.++
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            33999999999999999999999999999988442  2    24599999999999999999999999999999999999


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC----CCcEEEEEEec
Q 023765           81 HGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR----GGMTGIVDYTS  156 (277)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~----~~~~~fv~f~~  156 (277)
                      ........           +..-+.....++|+|.|||+.++..+|+++|..||.+..|.++...    ..|||||+|.+
T Consensus       596 ~~k~~~~~-----------gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t  664 (725)
T KOG0110|consen  596 ENKPASTV-----------GKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLT  664 (725)
T ss_pred             cCcccccc-----------ccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccC
Confidence            82221111           1111222337899999999999999999999999999999998662    23699999999


Q ss_pred             hhHHHHHHHhcCCCeecccce
Q 023765          157 YDDMKYAIRKLDRSEFRNAFS  177 (277)
Q Consensus       157 ~~~a~~a~~~l~g~~~~g~~~  177 (277)
                      +.+|..|++.|....+-|+.+
T Consensus       665 ~~ea~nA~~al~STHlyGRrL  685 (725)
T KOG0110|consen  665 PREAKNAFDALGSTHLYGRRL  685 (725)
T ss_pred             cHHHHHHHHhhcccceechhh
Confidence            999999999999999998533

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.86  E-value=1.8e-20  Score=143.53  Aligned_cols=172  Identities=23%  Similarity=0.354  Sum_probs=139.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHH----HhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEE
Q 023765            1 MSSRSSRTLYVGNLPGDTRMREVED----LFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLR   76 (277)
Q Consensus         1 ~~~~~~~~l~V~nL~~~~t~~~l~~----~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~   76 (277)
                      |+..++.||||.||+..+..++|+.    ||++||.|.+|.+..+.+.+|.|||.|.+.+.|-.|+..|+|..|.|+++.
T Consensus         4 ~~~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mr   83 (221)
T KOG4206|consen    4 MSVNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMR   83 (221)
T ss_pred             cccCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhh
Confidence            3456777999999999999999888    999999999999998999999999999999999999999999999999999


Q ss_pred             EEEccCCCCCCCC-----------------------CCCCCCCC--C-C---CC-CCCCCCCCceEEEeCCCCCCCHHHH
Q 023765           77 VELAHGGRRHSSS-----------------------MDRYSSYS--S-G---GS-RGVSRRSDYRVLVTGLPSSASWQDL  126 (277)
Q Consensus        77 v~~a~~~~~~~~~-----------------------~~~~~~~~--~-~---~~-~~~~~~~~~~l~v~~l~~~~~~~~l  126 (277)
                      |.+|..+...-..                       .+....+.  . .   .. .....++...+++.|||..++.+.|
T Consensus        84 iqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l  163 (221)
T KOG4206|consen   84 IQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEML  163 (221)
T ss_pred             eecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHH
Confidence            9999854321110                       00000000  0 0   00 0223567789999999999999999


Q ss_pred             HHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeec
Q 023765          127 KDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFR  173 (277)
Q Consensus       127 ~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~  173 (277)
                      ..+|.+|.....+.+...... .|||+|.+...|..|...++|..+.
T Consensus       164 ~~lf~qf~g~keir~i~~~~~-iAfve~~~d~~a~~a~~~lq~~~it  209 (221)
T KOG4206|consen  164 SDLFEQFPGFKEIRLIPPRSG-IAFVEFLSDRQASAAQQALQGFKIT  209 (221)
T ss_pred             HHHHhhCcccceeEeccCCCc-eeEEecchhhhhHHHhhhhccceec
Confidence            999999999888887765443 7999999999999999999998876

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.85  E-value=3.2e-19  Score=159.10  Aligned_cols=78  Identities=23%  Similarity=0.444  Sum_probs=72.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      ..++|||+||++++++++|+++|+.||+|..+.|..   ++.++|||||+|.+.++|..|+..||+..|+|+.|.|.++.
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            457999999999999999999999999999999965   45789999999999999999999999999999999999977


Q ss_pred             C
Q 023765           82 G   82 (277)
Q Consensus        82 ~   82 (277)
                      .
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.

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.84  E-value=3.6e-20  Score=157.88  Aligned_cols=174  Identities=21%  Similarity=0.326  Sum_probs=132.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCCC
Q 023765            8 TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGR   84 (277)
Q Consensus         8 ~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~~   84 (277)
                      .|||+||.+++++++|+.+|++||.|..|.++.   ++.++||+||+|.+.++|.+|+..|||..|.|+.|.|.......
T Consensus       280 rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~  359 (549)
T KOG0147|consen  280 RLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERV  359 (549)
T ss_pred             hhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeec
Confidence            389999999999999999999999999999954   68999999999999999999999999999999999998866443


Q ss_pred             CCCCC------CC----CCCCCCCCC------------------------------------------CCCCCC------
Q 023765           85 RHSSS------MD----RYSSYSSGG------------------------------------------SRGVSR------  106 (277)
Q Consensus        85 ~~~~~------~~----~~~~~~~~~------------------------------------------~~~~~~------  106 (277)
                      .....      .+    .+..+...+                                          ....+.      
T Consensus       360 ~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~  439 (549)
T KOG0147|consen  360 DTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADASPAF  439 (549)
T ss_pred             ccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCcccccccc
Confidence            33221      00    000000000                                          000011      


Q ss_pred             -CCCceEEEeCCC--CCCC--------HHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          107 -RSDYRVLVTGLP--SSAS--------WQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       107 -~~~~~l~v~~l~--~~~~--------~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                       .+..++.+.|+=  ...|        .++|.+.+.++|.|+.|.+..+.. |+.||.|.+.+.|..|+..|||.||.|+
T Consensus       440 ~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~ns~-g~VYvrc~s~~~A~~a~~alhgrWF~gr  518 (549)
T KOG0147|consen  440 DIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKNSA-GCVYVRCPSAEAAGTAVKALHGRWFAGR  518 (549)
T ss_pred             CCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccCCC-ceEEEecCcHHHHHHHHHHHhhhhhccc
Confidence             334556666652  1122        478899999999998888877765 7999999999999999999999999998


Q ss_pred             ceeeEEE
Q 023765          176 FSRSYVR  182 (277)
Q Consensus       176 ~~~~~i~  182 (277)
                      .++..+-
T Consensus       519 ~Ita~~~  525 (549)
T KOG0147|consen  519 MITAKYL  525 (549)
T ss_pred             eeEEEEe
Confidence            7766543

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.83  E-value=2.1e-19  Score=136.70  Aligned_cols=170  Identities=22%  Similarity=0.328  Sum_probs=129.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCC----CcEEEEEEcChHHHHHHHHhcCCcccC---CceEEE
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRP----PGYAFLEFEDYRDAEDAIRGRDGYNFD---GYRLRV   77 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~----~g~afV~f~~~~~a~~a~~~l~~~~~~---g~~i~v   77 (277)
                      .-+||||.+||.++...+|+.||..|--.+...|+.+.+.    +.+|||.|.+..+|.+|+..|||+.|+   +..|++
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            4689999999999999999999999966777777665433    489999999999999999999999996   788999


Q ss_pred             EEccCCCCCCCCCCCCCC---------------C-----------------CCCCCC-----------------------
Q 023765           78 ELAHGGRRHSSSMDRYSS---------------Y-----------------SSGGSR-----------------------  102 (277)
Q Consensus        78 ~~a~~~~~~~~~~~~~~~---------------~-----------------~~~~~~-----------------------  102 (277)
                      ++++.............+               +                 ...+..                       
T Consensus       113 ElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P~  192 (284)
T KOG1457|consen  113 ELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAPS  192 (284)
T ss_pred             eehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCCc
Confidence            999865432211000000               0                 000000                       


Q ss_pred             -----------CCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCe
Q 023765          103 -----------GVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSE  171 (277)
Q Consensus       103 -----------~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~  171 (277)
                                 ........+|||.||..++++++|+++|..|.....+.|.....--.||++|++.+.|..|+..|+|..
T Consensus       193 a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~~~~at~am~~lqg~~  272 (284)
T KOG1457|consen  193 ANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEEIEQATDAMNHLQGNL  272 (284)
T ss_pred             ccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHHHHHHHHHHHHhhcce
Confidence                       000012348999999999999999999999988777777655444489999999999999999999988


Q ss_pred             ecc
Q 023765          172 FRN  174 (277)
Q Consensus       172 ~~g  174 (277)
                      +..
T Consensus       273 ~s~  275 (284)
T KOG1457|consen  273 LSS  275 (284)
T ss_pred             ecc
Confidence            854

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.83  E-value=4.3e-20  Score=152.01  Aligned_cols=163  Identities=19%  Similarity=0.310  Sum_probs=136.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEE
Q 023765            2 SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVE   78 (277)
Q Consensus         2 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~   78 (277)
                      ...+.++|||++|+++++++.|++.|.+||+|.++.++.   ++.+++|+||+|.+++.+.+++. .....|+|+.|.+.
T Consensus         2 ~~~~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k   80 (311)
T KOG4205|consen    2 ESGESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPK   80 (311)
T ss_pred             CccCCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccce
Confidence            445789999999999999999999999999999999965   56889999999999999999987 55678999999999


Q ss_pred             EccCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEE
Q 023765           79 LAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDY  154 (277)
Q Consensus        79 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f  154 (277)
                      .|.+.........              .....+|||++||.++++++|++.|.+||.|..+.++.+...    +|+||.|
T Consensus        81 ~av~r~~~~~~~~--------------~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~  146 (311)
T KOG4205|consen   81 RAVSREDQTKVGR--------------HLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTF  146 (311)
T ss_pred             eccCccccccccc--------------ccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEe
Confidence            8887654332111              114679999999999999999999999999999888877654    5999999


Q ss_pred             echhHHHHHHHhcCCCeecccceeeE
Q 023765          155 TSYDDMKYAIRKLDRSEFRNAFSRSY  180 (277)
Q Consensus       155 ~~~~~a~~a~~~l~g~~~~g~~~~~~  180 (277)
                      ++.+.+.+++. ..-..++|+.+.+.
T Consensus       147 ~~e~sVdkv~~-~~f~~~~gk~vevk  171 (311)
T KOG4205|consen  147 DSEDSVDKVTL-QKFHDFNGKKVEVK  171 (311)
T ss_pred             ccccccceecc-cceeeecCceeeEe
Confidence            99999998885 67777777544433

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.83  E-value=1.4e-19  Score=154.14  Aligned_cols=167  Identities=22%  Similarity=0.354  Sum_probs=140.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecC-CCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP-PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~-~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      ++...|||.||+++++..+|..+|+.||+|..|++..+ ..++|| ||+|.+++.|.+|+..|||..+.|+.|.|.....
T Consensus        74 rd~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~  152 (369)
T KOG0123|consen   74 RDPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFER  152 (369)
T ss_pred             cCCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccc
Confidence            45566999999999999999999999999999999663 347899 9999999999999999999999999999999886


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC---CcEEEEEEechhH
Q 023765           83 GRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG---GMTGIVDYTSYDD  159 (277)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~---~~~~fv~f~~~~~  159 (277)
                      ........           .. .......++|.+++.+++++.|.++|..+|.|..+.++.+..   .+|+||+|++.++
T Consensus       153 ~~er~~~~-----------~~-~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~  220 (369)
T KOG0123|consen  153 KEEREAPL-----------GE-YKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPED  220 (369)
T ss_pred             hhhhcccc-----------cc-hhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhH
Confidence            54322211           01 223356899999999999999999999999999999987644   4699999999999


Q ss_pred             HHHHHHhcCCCeecccceeeEEEEeecC
Q 023765          160 MKYAIRKLDRSEFRNAFSRSYVRVREYD  187 (277)
Q Consensus       160 a~~a~~~l~g~~~~g~~~~~~i~~~~~~  187 (277)
                      |..|+..|++..+.+    ..+.|..+.
T Consensus       221 a~~av~~l~~~~~~~----~~~~V~~aq  244 (369)
T KOG0123|consen  221 AKKAVETLNGKIFGD----KELYVGRAQ  244 (369)
T ss_pred             HHHHHHhccCCcCCc----cceeecccc
Confidence            999999999999986    445554443

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.82  E-value=1.1e-20  Score=161.05  Aligned_cols=171  Identities=19%  Similarity=0.273  Sum_probs=139.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      +++.+|||+.-|+..+++.+|.++|+.+|.|.+|.++.   ++.++|.|||+|.+.+.+-.|+. |.|..+.|.+|.|+.
T Consensus       176 ERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq~  254 (549)
T KOG0147|consen  176 ERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQL  254 (549)
T ss_pred             HHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEecc
Confidence            35678899999999999999999999999999999965   56789999999999999999997 999999999999998


Q ss_pred             ccCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC----CCcEEEEEEe
Q 023765           80 AHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR----GGMTGIVDYT  155 (277)
Q Consensus        80 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~----~~~~~fv~f~  155 (277)
                      ....+.....  ....+..    .....+...|||+||..++++++|..+|..||.|..|.+..+.    ..||+||+|.
T Consensus       255 sEaeknr~a~--~s~a~~~----k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~  328 (549)
T KOG0147|consen  255 SEAEKNRAAN--ASPALQG----KGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFV  328 (549)
T ss_pred             cHHHHHHHHh--ccccccc----cccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEe
Confidence            7754322110  0000110    1111223339999999999999999999999999999998775    3469999999


Q ss_pred             chhHHHHHHHhcCCCeecccceeeE
Q 023765          156 SYDDMKYAIRKLDRSEFRNAFSRSY  180 (277)
Q Consensus       156 ~~~~a~~a~~~l~g~~~~g~~~~~~  180 (277)
                      +.++|.+|+..|||.++.|+.+.+-
T Consensus       329 ~~~~ar~a~e~lngfelAGr~ikV~  353 (549)
T KOG0147|consen  329 NKEDARKALEQLNGFELAGRLIKVS  353 (549)
T ss_pred             cHHHHHHHHHHhccceecCceEEEE
Confidence            9999999999999999999766543

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.82  E-value=4.8e-19  Score=133.20  Aligned_cols=75  Identities=19%  Similarity=0.115  Sum_probs=68.3

Q ss_pred             CCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccce
Q 023765          103 GVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFS  177 (277)
Q Consensus       103 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  177 (277)
                      ++...+...|.|.||.+.++.++|..+|++||.|.+|.|.++..+    |||||.|....+|+.|++.|+|..++|+++
T Consensus         7 PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRel   85 (256)
T KOG4207|consen    7 PPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGREL   85 (256)
T ss_pred             CCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeecccee
Confidence            455567889999999999999999999999999999999988755    599999999999999999999999999544

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.81  E-value=1.7e-19  Score=140.90  Aligned_cols=135  Identities=23%  Similarity=0.349  Sum_probs=110.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            1 MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         1 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      |++...+||||+||...+||+-|..||.+.|.|..++|..+                                .|.|.++
T Consensus         1 ~~~~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~--------------------------------e~~v~wa   48 (321)
T KOG0148|consen    1 NGSDEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD--------------------------------ELKVNWA   48 (321)
T ss_pred             CCCCCCceEEeeccChhhHHHHHHHHHHhccccccceeehh--------------------------------hhccccc
Confidence            56788999999999999999999999999999999988743                                4555565


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEec
Q 023765           81 HGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTS  156 (277)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~  156 (277)
                      ..+...+               .+.......+||+.|...++-++|++.|.+||+|..+.|++|.++    ||+||.|.+
T Consensus        49 ~~p~nQs---------------k~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~  113 (321)
T KOG0148|consen   49 TAPGNQS---------------KPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPN  113 (321)
T ss_pred             cCcccCC---------------CCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccc
Confidence            5431111               111122568999999999999999999999999999999988765    599999999


Q ss_pred             hhHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          157 YDDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       157 ~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      .++|+.||..|||.+|.+    +.|+.-.+
T Consensus       114 k~dAEnAI~~MnGqWlG~----R~IRTNWA  139 (321)
T KOG0148|consen  114 KEDAENAIQQMNGQWLGR----RTIRTNWA  139 (321)
T ss_pred             hHHHHHHHHHhCCeeecc----ceeecccc
Confidence            999999999999999998    45554443

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

Probab=99.81  E-value=2.5e-19  Score=148.31  Aligned_cols=181  Identities=22%  Similarity=0.313  Sum_probs=142.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCc-ccCCc--eEEEEE
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGY-NFDGY--RLRVEL   79 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~-~~~g~--~i~v~~   79 (277)
                      +.++|||+-|++.+||.+|+++|.+||.|++|.|+.  ++.++|+|||+|.+.|.|..||+.|||. .+.|+  +|.|+|
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkF  202 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKF  202 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEe
Confidence            368899999999999999999999999999999976  5688999999999999999999999995 45554  699999


Q ss_pred             ccCCCCCCCC-----------------------------------------CC---------------------------
Q 023765           80 AHGGRRHSSS-----------------------------------------MD---------------------------   91 (277)
Q Consensus        80 a~~~~~~~~~-----------------------------------------~~---------------------------   91 (277)
                      |...+.....                                         ..                           
T Consensus       203 ADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~g~~~L~~l~a~~~qq~~~~~~  282 (510)
T KOG0144|consen  203 ADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLGGLPPLGPLNATQLQQAAALAA  282 (510)
T ss_pred             cccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccccccCCCCcchhHHHHHHHhhh
Confidence            9844321100                                         00                           


Q ss_pred             ------------CC------CCCCCC--C--------------------------------CCC----------------
Q 023765           92 ------------RY------SSYSSG--G--------------------------------SRG----------------  103 (277)
Q Consensus        92 ------------~~------~~~~~~--~--------------------------------~~~----------------  103 (277)
                                  ..      .++...  .                                ...                
T Consensus       283 ~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t~~~~n~~~~~a~a~~~sp~aa  362 (510)
T KOG0144|consen  283 AATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGTPANYNLAGGMAGAGTTSPVAA  362 (510)
T ss_pred             hcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCCchhcccccccccccccCcccc
Confidence                        00      000000  0                                000                


Q ss_pred             -----------C---------------------------------------------CCCCCceEEEeCCCCCCCHHHHH
Q 023765          104 -----------V---------------------------------------------SRRSDYRVLVTGLPSSASWQDLK  127 (277)
Q Consensus       104 -----------~---------------------------------------------~~~~~~~l~v~~l~~~~~~~~l~  127 (277)
                                 +                                             .-+.+..+||.+||.+.-+.+|-
T Consensus       363 ~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eGpeGanlfiyhlPqefgdq~l~  442 (510)
T KOG0144|consen  363 SLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEGPEGANLFIYHLPQEFGDQDLI  442 (510)
T ss_pred             cccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccCCCccceeeeeCchhhhhHHHH
Confidence                       0                                             00124589999999999999999


Q ss_pred             HHHHhcCCeeEEEEEecCCCc----EEEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          128 DHMRRAGDVCFSQVFRDRGGM----TGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       128 ~~f~~~g~v~~~~~~~~~~~~----~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      ..|..||.|+..++..++.++    |+||.|++..+|..||..|||..+..+..++.+..+.
T Consensus       443 ~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk~~~  504 (510)
T KOG0144|consen  443 ATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLKRDR  504 (510)
T ss_pred             HHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEeeecc
Confidence            999999999999999998876    8999999999999999999999999976665555443

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.80  E-value=5.8e-19  Score=131.44  Aligned_cols=83  Identities=29%  Similarity=0.490  Sum_probs=76.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      ..+++|||+|||+++|+++|+++|++||+|..|.|+.   ++++++||||+|.+.++|+.|++.||+..|.|+.|.|.++
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            4578999999999999999999999999999999964   5678999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 023765           81 HGGRRH   86 (277)
Q Consensus        81 ~~~~~~   86 (277)
                      ......
T Consensus       112 ~~~~~~  117 (144)
T PLN03134        112 NDRPSA  117 (144)
T ss_pred             CcCCCC
Confidence            865443

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.78  E-value=2.3e-17  Score=133.31  Aligned_cols=178  Identities=20%  Similarity=0.241  Sum_probs=136.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeE--------EEee--cCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVD--------IDLK--IPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGY   73 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~--------v~~~--~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~   73 (277)
                      .-++.|||.|||.++|.+++.++|++||-|..        |+|.  ..|+.+|=|++.|...+++..|+..|++..|.|+
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~  211 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGK  211 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCc
Confidence            34677999999999999999999999997654        3442  2578899999999999999999999999999999


Q ss_pred             eEEEEEccCCCCCCCCCCCC----------------CCCCCCCCC--CCCCCCCceEEEeCCCC----CCC-------HH
Q 023765           74 RLRVELAHGGRRHSSSMDRY----------------SSYSSGGSR--GVSRRSDYRVLVTGLPS----SAS-------WQ  124 (277)
Q Consensus        74 ~i~v~~a~~~~~~~~~~~~~----------------~~~~~~~~~--~~~~~~~~~l~v~~l~~----~~~-------~~  124 (277)
                      .|+|+.|+-.....-....-                ..+.-.+..  +.-.....+|.+.|+-.    ..+       .+
T Consensus       212 ~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlke  291 (382)
T KOG1548|consen  212 KLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKE  291 (382)
T ss_pred             EEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHHH
Confidence            99999998543222110000                000000111  12233467888888732    122       46


Q ss_pred             HHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          125 DLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       125 ~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      +|.+.+.+||.|..|.|....+.|.+.|.|.+.++|..+|..|+|.+++|+.+...|
T Consensus       292 dl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i  348 (382)
T KOG1548|consen  292 DLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASI  348 (382)
T ss_pred             HHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEE
Confidence            788889999999999999888889999999999999999999999999996555444

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.77  E-value=1e-18  Score=121.50  Aligned_cols=79  Identities=37%  Similarity=0.565  Sum_probs=73.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEe---ecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~---~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      +.++||||+||+..++|++|++||+.+|+|..|.|   ..+..+.|||||+|...++|..|+..+++..++.++|.|.|.
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            67899999999999999999999999999999999   335678999999999999999999999999999999999996


Q ss_pred             cC
Q 023765           81 HG   82 (277)
Q Consensus        81 ~~   82 (277)
                      ..
T Consensus       114 ~G  115 (153)
T KOG0121|consen  114 AG  115 (153)
T ss_pred             cc
Confidence            64

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.76  E-value=1e-17  Score=130.89  Aligned_cols=171  Identities=20%  Similarity=0.308  Sum_probs=133.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCc-ccCCc--eEEEEE
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGY-NFDGY--RLRVEL   79 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~-~~~g~--~i~v~~   79 (277)
                      +.++||||-|...-.|+|++.+|..||+|.+|.+..  ++.++|+|||+|.+..+|..||..|+|. .+.|.  .|.|++
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~   97 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKF   97 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEe
Confidence            568999999999999999999999999999999965  6788999999999999999999999995 44444  589999


Q ss_pred             ccCCCCC-------------------------------------------------------------------------
Q 023765           80 AHGGRRH-------------------------------------------------------------------------   86 (277)
Q Consensus        80 a~~~~~~-------------------------------------------------------------------------   86 (277)
                      +...+..                                                                         
T Consensus        98 ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~angl~A~  177 (371)
T KOG0146|consen   98 ADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNANGLAAA  177 (371)
T ss_pred             ccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhcccccC
Confidence            8722100                                                                         


Q ss_pred             ---CCCCCCC------------------CCCCC--------C----------CC-------------------------C
Q 023765           87 ---SSSMDRY------------------SSYSS--------G----------GS-------------------------R  102 (277)
Q Consensus        87 ---~~~~~~~------------------~~~~~--------~----------~~-------------------------~  102 (277)
                         +......                  ..+..        +          ..                         +
T Consensus       178 Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y~Aay  257 (371)
T KOG0146|consen  178 PVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQYAAAY  257 (371)
T ss_pred             CcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHHhhhc
Confidence               0000000                  00000        0          00                         0


Q ss_pred             ------------CC---------CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCc----EEEEEEech
Q 023765          103 ------------GV---------SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGM----TGIVDYTSY  157 (277)
Q Consensus       103 ------------~~---------~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~----~~fv~f~~~  157 (277)
                                  .+         .-+.+++|||=.||.+..+.+|.++|-.||.|+..++..|..+.    |+||.|+++
T Consensus       258 paays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp  337 (371)
T KOG0146|consen  258 PAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNP  337 (371)
T ss_pred             chhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCc
Confidence                        00         01247899999999999999999999999999999988776654    999999999


Q ss_pred             hHHHHHHHhcCCCeeccc
Q 023765          158 DDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       158 ~~a~~a~~~l~g~~~~g~  175 (277)
                      ..|+.||..|||..|+=+
T Consensus       338 ~SaQaAIqAMNGFQIGMK  355 (371)
T KOG0146|consen  338 ASAQAAIQAMNGFQIGMK  355 (371)
T ss_pred             hhHHHHHHHhcchhhhhh
Confidence            999999999999999764

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.75  E-value=7.4e-17  Score=127.97  Aligned_cols=83  Identities=36%  Similarity=0.589  Sum_probs=76.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      +++=+||||+-|+.+++|..|+..|+.||+|+.|.|+.   +++++|||||+|.++.+...|++..+|.+|+|+.|.|.+
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            46789999999999999999999999999999999954   789999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 023765           80 AHGGRR   85 (277)
Q Consensus        80 a~~~~~   85 (277)
                      -.....
T Consensus       178 ERgRTv  183 (335)
T KOG0113|consen  178 ERGRTV  183 (335)
T ss_pred             cccccc
Confidence            775443

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.73  E-value=8.2e-17  Score=141.22  Aligned_cols=177  Identities=19%  Similarity=0.234  Sum_probs=136.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      ...+.|+|+|||..+..++|..+|..||+|..|.|+..   -.-++|+|.++.+|..|+..|....+...+|.+.|+...
T Consensus       383 rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~~---G~~aiv~fl~p~eAr~Afrklaysr~k~~plyle~aP~d  459 (725)
T KOG0110|consen  383 RSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPPG---GTGAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWAPED  459 (725)
T ss_pred             hhcceeeeccCccccccHHHHHHhhcccccceeecCcc---cceeeeeecCccchHHHHHHhchhhhccCccccccChhh
Confidence            35688999999999999999999999999999977632   235899999999999999999999999999999998754


Q ss_pred             CCCCC--CCCC-----CC----------CCCCCC---CC----------CCCCCCCceEEEeCCCCCCCHHHHHHHHHhc
Q 023765           84 RRHSS--SMDR-----YS----------SYSSGG---SR----------GVSRRSDYRVLVTGLPSSASWQDLKDHMRRA  133 (277)
Q Consensus        84 ~~~~~--~~~~-----~~----------~~~~~~---~~----------~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~  133 (277)
                      .-...  ..+.     ..          ...+..   ..          .......++|||.||++.++.++|..+|...
T Consensus       460 vf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~F~k~  539 (725)
T KOG0110|consen  460 VFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLEDLFSKQ  539 (725)
T ss_pred             hccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHHHHHhc
Confidence            33211  0000     00          000000   00          0011223449999999999999999999999


Q ss_pred             CCeeEEEEEecCCC-------cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          134 GDVCFSQVFRDRGG-------MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       134 g~v~~~~~~~~~~~-------~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      |.|..+.|......       |||||+|.+.++|+.|+..|+|..++|+.+.+.|..
T Consensus       540 G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  540 GTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             CeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            99999988755433       799999999999999999999999999766665544

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.72  E-value=5.1e-17  Score=129.26  Aligned_cols=80  Identities=20%  Similarity=0.279  Sum_probs=74.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCCC
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGR   84 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~~   84 (277)
                      ..++|||+|||+.+|+++|+++|+.||+|.+|.|..++..+|||||+|.++++|..|+. |||..|.|+.|.|.++....
T Consensus         3 ~~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~~~   81 (260)
T PLN03120          3 QVRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAEDYQ   81 (260)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccCCC
Confidence            36899999999999999999999999999999998877678999999999999999996 99999999999999988654


Q ss_pred             C
Q 023765           85 R   85 (277)
Q Consensus        85 ~   85 (277)
                      .
T Consensus        82 ~   82 (260)
T PLN03120         82 L   82 (260)
T ss_pred             C
Confidence            4

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.71  E-value=6.4e-16  Score=127.51  Aligned_cols=175  Identities=18%  Similarity=0.212  Sum_probs=139.3

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCCC
Q 023765            6 SRTLYVGNLPG-DTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGR   84 (277)
Q Consensus         6 ~~~l~V~nL~~-~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~~   84 (277)
                      +.+|.|.||.. .+|.+-|..+|.-||+|..|+|...+  +..|+|+|.+..+|..|++.|+|..|.|+.|+|.+++...
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk--kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~  374 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK--KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTN  374 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC--CcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCcc
Confidence            68899999965 58999999999999999999997755  4789999999999999999999999999999999999765


Q ss_pred             CCCCCCC-----CCCCCCCC----------CCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcE
Q 023765           85 RHSSSMD-----RYSSYSSG----------GSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMT  149 (277)
Q Consensus        85 ~~~~~~~-----~~~~~~~~----------~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~  149 (277)
                      ...+...     ....+...          ..+..-.++..++++.|+|..+++++|+++|...|..........+...+
T Consensus       375 vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~kd~km  454 (492)
T KOG1190|consen  375 VQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQKDRKM  454 (492)
T ss_pred             ccCCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecCCCcce
Confidence            4433211     11111111          11122336678999999999999999999999999877766666666669


Q ss_pred             EEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          150 GIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       150 ~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      |++++++.++|..|+-.+|...+++.   -.++|..
T Consensus       455 al~q~~sveeA~~ali~~hnh~lgen---~hlRvSF  487 (492)
T KOG1190|consen  455 ALPQLESVEEAIQALIDLHNHYLGEN---HHLRVSF  487 (492)
T ss_pred             eecccCChhHhhhhccccccccCCCC---ceEEEEe
Confidence            99999999999999999999888763   3455544

>PF00076 RRM_1: RNA recognition motif

Probab=99.71  E-value=2.9e-17  Score=107.61  Aligned_cols=68  Identities=41%  Similarity=0.748  Sum_probs=63.9

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEE
Q 023765            9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLR   76 (277)
Q Consensus         9 l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~   76 (277)
                      |||+|||+++|+++|+++|++||.|..+.+..  ++..+++|||+|.+.++|..|++.|||..|.|+.|+
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 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            79999999999999999999999999999965  467789999999999999999999999999999874

(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 ....

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.71  E-value=3.9e-16  Score=131.82  Aligned_cols=164  Identities=24%  Similarity=0.322  Sum_probs=126.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec-CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI-PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~-~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      ....|.+.+|||++|++||.++|+.++ |+.+.+.. +++..|-|||+|.++|++++|++ .+...+..+-|.|-.+...
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~~   86 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGGA   86 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-eeEEEEeccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCCc
Confidence            456789999999999999999999995 78877765 58999999999999999999999 8888899999999888765


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeE-EEEE---ecCCCcEEEEEEechhH
Q 023765           84 RRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCF-SQVF---RDRGGMTGIVDYTSYDD  159 (277)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~-~~~~---~~~~~~~~fv~f~~~~~  159 (277)
                      .....-       ...+  +........|.+.+||+.++++||.++|.-.-.|.. +.+.   ..+.++-|||+|++++.
T Consensus        87 e~d~~~-------~~~g--~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~  157 (510)
T KOG4211|consen   87 EADWVM-------RPGG--PNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQES  157 (510)
T ss_pred             cccccc-------cCCC--CCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHH
Confidence            432211       0000  001134678999999999999999999997655544 2222   34556799999999999


Q ss_pred             HHHHHHhcCCCeecccceeeEEEEe
Q 023765          160 MKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       160 a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      |+.||. -|...|..    ..|.|.
T Consensus       158 ae~Al~-rhre~iGh----RYIEvF  177 (510)
T KOG4211|consen  158 AEIALG-RHRENIGH----RYIEVF  177 (510)
T ss_pred             HHHHHH-HHHHhhcc----ceEEee
Confidence            999996 55666655    555554

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.71  E-value=1.5e-15  Score=126.39  Aligned_cols=170  Identities=24%  Similarity=0.349  Sum_probs=132.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhh-ccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFY-KYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~-~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      -.+.+||+|||+++.+.+|+.||. +.|+|+.|.|..  .++++|+|.|+|+++|.+++|++.||...+.|++|.|+-..
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            345699999999999999999997 579999999976  57899999999999999999999999999999999998765


Q ss_pred             CCCCCC-----------------------------------------CCCCCCC-------------------CCCCC--
Q 023765           82 GGRRHS-----------------------------------------SSMDRYS-------------------SYSSG--   99 (277)
Q Consensus        82 ~~~~~~-----------------------------------------~~~~~~~-------------------~~~~~--   99 (277)
                      ......                                         ...++..                   .|...  
T Consensus       123 d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~  202 (608)
T KOG4212|consen  123 DEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSAS  202 (608)
T ss_pred             chhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccchhh
Confidence            311000                                         0000000                   00000  


Q ss_pred             ---CCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC---CcEEEEEEechhHHHHHHHhcCCCeec
Q 023765          100 ---GSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG---GMTGIVDYTSYDDMKYAIRKLDRSEFR  173 (277)
Q Consensus       100 ---~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~  173 (277)
                         ......++-..++||.||.+.+....|.+.|.-.|.|+.+.+-.++.   .++|.++|.++-+|.+||..|++.-+.
T Consensus       203 Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~~~g~~  282 (608)
T KOG4212|consen  203 FLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLDRQGLF  282 (608)
T ss_pred             hhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHHHHHHhhccCCCc
Confidence               00111234467899999999999999999999999999998876653   369999999999999999999875544


Q ss_pred             c
Q 023765          174 N  174 (277)
Q Consensus       174 g  174 (277)
                      .
T Consensus       283 ~  283 (608)
T KOG4212|consen  283 D  283 (608)
T ss_pred             c
Confidence            4

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.70  E-value=1.1e-16  Score=142.76  Aligned_cols=128  Identities=22%  Similarity=0.271  Sum_probs=99.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcc--CCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKY--GPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~--G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      ..++|||+||++++|+++|+++|+.|  |+|+.|.+.     ++||||+|.+.++|.+|++.||+..|.|+.|.|.++.+
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~-----rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp  306 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI-----RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKP  306 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee-----cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            45789999999999999999999999  999999876     67999999999999999999999999999999999986


Q ss_pred             CCCCCCCC-CCCCCC-------CCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCee
Q 023765           83 GRRHSSSM-DRYSSY-------SSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVC  137 (277)
Q Consensus        83 ~~~~~~~~-~~~~~~-------~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~  137 (277)
                      .....-.. .+....       ..........+...++++.|+++.++++.+.++|...|.|.
T Consensus       307 ~~~~~~~~~~rg~gg~~~~~~~~~~~~g~~~sp~s~~~~~g~~~~~~~~~~~~~~f~~~g~~~  369 (578)
T TIGR01648       307 VDKKSYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAYEDYYYHPPYAPSLHFPRMPGPIR  369 (578)
T ss_pred             CCcccccccccccCCCcccccccccccCcccCccccccccccccccccccchhhccccCcccc
Confidence            54321100 000000       00000111223578999999999999999999999988754

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.

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.68  E-value=5.3e-18  Score=125.09  Aligned_cols=84  Identities=30%  Similarity=0.516  Sum_probs=78.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEee---cCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLK---IPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~---~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      +++..|||||||+.+||.||.-+|++||+|.+|.|.   .||+++||||+.|+++.+...|+.+|||..|.|+.|.|.+.
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            577889999999999999999999999999999995   48899999999999999999999999999999999999998


Q ss_pred             cCCCCCC
Q 023765           81 HGGRRHS   87 (277)
Q Consensus        81 ~~~~~~~   87 (277)
                      .....+.
T Consensus       113 ~~Yk~pk  119 (219)
T KOG0126|consen  113 SNYKKPK  119 (219)
T ss_pred             ccccCCc
Confidence            8766543

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.67  E-value=5.3e-16  Score=121.45  Aligned_cols=80  Identities=20%  Similarity=0.201  Sum_probs=74.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCCC
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGR   84 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~~   84 (277)
                      ...+|||+||++.+|+++|+++|+.||+|.+|.|..++...+||||+|.++++|..|+. |+|..|.++.|.|..+....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~~y~   82 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWGQYE   82 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCcccc
Confidence            45899999999999999999999999999999999888888999999999999999997 99999999999999988654


Q ss_pred             C
Q 023765           85 R   85 (277)
Q Consensus        85 ~   85 (277)
                      .
T Consensus        83 ~   83 (243)
T PLN03121         83 D   83 (243)
T ss_pred             c
Confidence            4

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.67  E-value=3.9e-15  Score=121.33  Aligned_cols=77  Identities=23%  Similarity=0.449  Sum_probs=70.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      =+.|||..+.++++++||+.+|+.||+|..|.+..   ...++||+||+|.+..+...|+..||-..++|+.|.|..+..
T Consensus       210 fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vT  289 (544)
T KOG0124|consen  210 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  289 (544)
T ss_pred             hheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccC
Confidence            46799999999999999999999999999999943   457899999999999999999999999999999999987663

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.66  E-value=6.7e-16  Score=103.46  Aligned_cols=80  Identities=36%  Similarity=0.468  Sum_probs=74.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCCC
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGR   84 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~~   84 (277)
                      -+..|||.|||+++|.+++.+||..||.|..|.+-.++..+|.|||.|++..+|.+|+..|+|..+.++.|.|-+.++..
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~~   96 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPED   96 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHHH
Confidence            35779999999999999999999999999999997778889999999999999999999999999999999999987543

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.65  E-value=1.1e-15  Score=132.07  Aligned_cols=173  Identities=21%  Similarity=0.289  Sum_probs=129.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      ...+.|||++||..++++++.++...||++..+.+..   ++.++||||.+|.++..++.|++.|||+.+.+..|.|+.|
T Consensus       287 ~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A  366 (500)
T KOG0120|consen  287 DSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRA  366 (500)
T ss_pred             cccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehh
Confidence            3467899999999999999999999999999999844   5688999999999999999999999999999999999998


Q ss_pred             cCCCCCCCCCCC--CCCCCCCCC--CCCCCCCCceEEEeCCC--CCC-C-------HHHHHHHHHhcCCeeEEEEEec-C
Q 023765           81 HGGRRHSSSMDR--YSSYSSGGS--RGVSRRSDYRVLVTGLP--SSA-S-------WQDLKDHMRRAGDVCFSQVFRD-R  145 (277)
Q Consensus        81 ~~~~~~~~~~~~--~~~~~~~~~--~~~~~~~~~~l~v~~l~--~~~-~-------~~~l~~~f~~~g~v~~~~~~~~-~  145 (277)
                      -...........  ......-..  ....-.+...|.+.|+-  .++ .       .++|+..|.+||.|..|.+.+. .
T Consensus       367 ~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~  446 (500)
T KOG0120|consen  367 IVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYP  446 (500)
T ss_pred             hccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCC
Confidence            865543322111  000111000  11122233444444431  111 1       2456677789999999999877 2


Q ss_pred             ------CCcEEEEEEechhHHHHHHHhcCCCeecccc
Q 023765          146 ------GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAF  176 (277)
Q Consensus       146 ------~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  176 (277)
                            ..|..||+|.+.++++.|+..|+|.+++|+.
T Consensus       447 ~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRt  483 (500)
T KOG0120|consen  447 DENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRT  483 (500)
T ss_pred             CCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcE
Confidence                  2358999999999999999999999999953

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.65  E-value=5e-15  Score=123.39  Aligned_cols=141  Identities=28%  Similarity=0.459  Sum_probs=109.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      ..+|||+|||+.+|+++|.++|..||.|..+.+..   ++.++|||||+|.++++|..|+..|++..|.|+.|.|.++..
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            48999999999999999999999999999998855   468899999999999999999999999999999999999764


Q ss_pred             -CCCCCCCCCC-CCC--CCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC
Q 023765           83 -GRRHSSSMDR-YSS--YSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG  146 (277)
Q Consensus        83 -~~~~~~~~~~-~~~--~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~  146 (277)
                       .......... ...  ................+++.+++..+...++...|..+|.+..+.+.....
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  262 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKD  262 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCCC
Confidence             1111110000 000  000111223345678899999999999999999999999996666654443

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

Probab=99.63  E-value=1.5e-15  Score=117.36  Aligned_cols=80  Identities=38%  Similarity=0.602  Sum_probs=75.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEe---ecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~---~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .++++|-|.||+.++++++|++||.+||.|..|.|   +.+|.++|||||.|.+.++|.+||..|||.-++.-.|.|+|+
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEws  266 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWS  266 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEec
Confidence            57899999999999999999999999999999999   448899999999999999999999999999999999999999


Q ss_pred             cCC
Q 023765           81 HGG   83 (277)
Q Consensus        81 ~~~   83 (277)
                      ++.
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            863

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.63  E-value=1.2e-15  Score=99.85  Aligned_cols=68  Identities=32%  Similarity=0.664  Sum_probs=61.0

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeeEEEeecC--CCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEE
Q 023765            9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP--PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLR   76 (277)
Q Consensus         9 l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~--~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~   76 (277)
                      |||+|||+.+++++|.++|+.||.|..+.+...  +..+++|||+|.++++|..|+..+++..|.|+.|.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            799999999999999999999999999999654  45689999999999999999999999999999874

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 ....

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.62  E-value=2.3e-15  Score=124.29  Aligned_cols=175  Identities=17%  Similarity=0.180  Sum_probs=133.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCC--cccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDG--YNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~--~~~~g~~i~v~~a~   81 (277)
                      .+++.|.++|||++++|++|..++.+||.|..+.+..   .+..|||+|.++++|...+..+..  -.+.|++|.|+++.
T Consensus        26 ~pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lk---GknQAflem~d~~sAvtmv~~y~~~~p~lr~~~~yiq~sn  102 (492)
T KOG1190|consen   26 EPSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLK---GKNQAFLEMADEESAVTMVNYYTSVTPVLRGQPIYIQYSN  102 (492)
T ss_pred             CCcceeEeccCCccccHHHHHHhcccccceeeeeeec---cchhhhhhhcchhhhhheeecccccCccccCcceeehhhh
Confidence            5899999999999999999999999999999998873   356899999999999885554444  34678999999877


Q ss_pred             CCCCCCCCCC-----------------CCCCCCC-CCC--CCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEE
Q 023765           82 GGRRHSSSMD-----------------RYSSYSS-GGS--RGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQV  141 (277)
Q Consensus        82 ~~~~~~~~~~-----------------~~~~~~~-~~~--~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~  141 (277)
                      ...-......                 ....... ...  ....+.+.-.++|+++-+.++.+.|.++|.+||.|..|..
T Consensus       103 ~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~VlKIiT  182 (492)
T KOG1190|consen  103 HSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVLKIIT  182 (492)
T ss_pred             HHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcceeEEEEE
Confidence            4322211100                 0000000 000  1112223456788999999999999999999999999988


Q ss_pred             EecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          142 FRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       142 ~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      ....++..|+|+|.+.+.|..|...|+|..|-+..++..|
T Consensus       183 F~Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrI  222 (492)
T KOG1190|consen  183 FTKNNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRI  222 (492)
T ss_pred             EecccchhhhhhccchhhHHHHHHhccCCcccCceeEEEe
Confidence            8888888899999999999999999999999765554443

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.61  E-value=3.9e-15  Score=126.35  Aligned_cols=81  Identities=31%  Similarity=0.495  Sum_probs=72.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCC--ceEEEEE
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDG--YRLRVEL   79 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g--~~i~v~~   79 (277)
                      ..++|||+|||+.+|+++|+++|++||+|+.+.|+.   ++++++||||+|.+.++|++||+.||+..|.+  ++|.|.+
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            467899999999999999999999999999999854   56778999999999999999999999999876  6899999


Q ss_pred             ccCCCC
Q 023765           80 AHGGRR   85 (277)
Q Consensus        80 a~~~~~   85 (277)
                      +.....
T Consensus       272 a~~~~~  277 (346)
T TIGR01659       272 AEEHGK  277 (346)
T ss_pred             CCcccc
Confidence            886543

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).

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.61  E-value=6.8e-14  Score=114.45  Aligned_cols=178  Identities=15%  Similarity=0.159  Sum_probs=138.8

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            4 RSSRTLYVGNLPGD-TRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         4 ~~~~~l~V~nL~~~-~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      -+...+.|.+|... ++.+.|.++|..||.|+.|+++.++  .|.|+|++.+...++.|+..||+..+.|.+|.|.+++.
T Consensus       285 ~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk--~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ  362 (494)
T KOG1456|consen  285 APGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK--PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQ  362 (494)
T ss_pred             CCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc--cceeEEEcCcHHHHHHHHHHhccCccccceEEEeeccc
Confidence            35688999999764 7888999999999999999998876  68999999999999999999999999999999999886


Q ss_pred             CCCCCCC---------------CCCCCCCCCCCCC--CCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCC-eeEEEEEec
Q 023765           83 GRRHSSS---------------MDRYSSYSSGGSR--GVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGD-VCFSQVFRD  144 (277)
Q Consensus        83 ~~~~~~~---------------~~~~~~~~~~~~~--~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~-v~~~~~~~~  144 (277)
                      ....+..               ......|..+.+.  ..-..+.++|+.-|.|..+||+.|.++|...+. ...+.+...
T Consensus       363 ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~svkvFp~  442 (494)
T KOG1456|consen  363 NFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTSVKVFPL  442 (494)
T ss_pred             cccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCCCcceEEeecc
Confidence            6543321               0111122222222  223467899999999999999999999998774 455666655


Q ss_pred             CCC--cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          145 RGG--MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       145 ~~~--~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      +..  .-+++||++..+|.+||..+|...+.+........+
T Consensus       443 kserSssGllEfe~~s~Aveal~~~NH~pi~~p~gs~Pfil  483 (494)
T KOG1456|consen  443 KSERSSSGLLEFENKSDAVEALMKLNHYPIEGPNGSFPFIL  483 (494)
T ss_pred             cccccccceeeeehHHHHHHHHHHhccccccCCCCCCCeee
Confidence            443  278999999999999999999999987544333333

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.61  E-value=1.6e-15  Score=116.78  Aligned_cols=76  Identities=26%  Similarity=0.423  Sum_probs=69.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      -++||||+|+|.++.+.|+++|++||+|++..|..   +++++||+||+|.+.+.|.+|++.- +-.|+|+...|.+|.-
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp-~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDP-NPIIDGRKANCNLASL   90 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCC-CCcccccccccchhhh
Confidence            36899999999999999999999999999988844   7899999999999999999999944 4689999999999876

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.60  E-value=2.5e-15  Score=120.79  Aligned_cols=80  Identities=24%  Similarity=0.448  Sum_probs=74.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec-CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI-PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~-~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      ...+.|+|.|||+..-+-||..+|++||.|.+|.|+. +..+||||||+|++.+||++|-+.|||..+.|++|.|..+..
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATa  173 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATA  173 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccch
Confidence            4567899999999999999999999999999999976 457899999999999999999999999999999999999885


Q ss_pred             C
Q 023765           83 G   83 (277)
Q Consensus        83 ~   83 (277)
                      .
T Consensus       174 r  174 (376)
T KOG0125|consen  174 R  174 (376)
T ss_pred             h
Confidence            4

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.59  E-value=3e-15  Score=105.22  Aligned_cols=79  Identities=24%  Similarity=0.452  Sum_probs=73.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      -.|||+++...+|+++|.+.|..||+|+.|.|..   ++..+|||+|+|++.++|++|+..|||..|.|+.|.|.|+-..
T Consensus        73 wIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv~  152 (170)
T KOG0130|consen   73 WIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFVK  152 (170)
T ss_pred             EEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEec
Confidence            3699999999999999999999999999999965   6788999999999999999999999999999999999998864


Q ss_pred             CC
Q 023765           84 RR   85 (277)
Q Consensus        84 ~~   85 (277)
                      .+
T Consensus       153 gp  154 (170)
T KOG0130|consen  153 GP  154 (170)
T ss_pred             CC
Confidence            43

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.59  E-value=8.8e-14  Score=103.63  Aligned_cols=80  Identities=25%  Similarity=0.365  Sum_probs=70.2

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      ....++|||+|||..+++++|+++|.+||.|..+.++.+..    .+||||+|.+.++|+.|++.||+..|+|    ..|
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~G----r~l  106 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNG----RHI  106 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECC----EEE
Confidence            34577999999999999999999999999999999987754    4699999999999999999999999999    566


Q ss_pred             EEeecCCC
Q 023765          182 RVREYDSR  189 (277)
Q Consensus       182 ~~~~~~~~  189 (277)
                      .|.....+
T Consensus       107 ~V~~a~~~  114 (144)
T PLN03134        107 RVNPANDR  114 (144)
T ss_pred             EEEeCCcC
Confidence            77666543

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.58  E-value=1.3e-13  Score=109.62  Aligned_cols=75  Identities=19%  Similarity=0.217  Sum_probs=67.0

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      .+-.+|||.-|++++++..|+..|..||+|..|.|+.+.-    .|||||+|++..++..|.+..+|.+|+|+    .|-
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgr----ri~  174 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGR----RIL  174 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCc----EEE
Confidence            5678999999999999999999999999999999987743    46999999999999999999999999995    455


Q ss_pred             Eee
Q 023765          183 VRE  185 (277)
Q Consensus       183 ~~~  185 (277)
                      |+.
T Consensus       175 VDv  177 (335)
T KOG0113|consen  175 VDV  177 (335)
T ss_pred             EEe
Confidence            543

>PLN03213 repressor of silencing 3; Provisional

Probab=99.58  E-value=8.9e-15  Score=123.65  Aligned_cols=79  Identities=19%  Similarity=0.328  Sum_probs=72.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcCh--HHHHHHHHhcCCcccCCceEEEEEc
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDY--RDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~--~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      +....+||||||++.+|+++|..+|..||.|..|.|+... .+|||||+|...  .++.+||..|||..+.|+.|.|..|
T Consensus         7 ~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRET-GRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKA   85 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTK-GRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKA   85 (759)
T ss_pred             CCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeccc-CCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeec
Confidence            3467899999999999999999999999999999998532 399999999987  7899999999999999999999999


Q ss_pred             cC
Q 023765           81 HG   82 (277)
Q Consensus        81 ~~   82 (277)
                      ++
T Consensus        86 KP   87 (759)
T PLN03213         86 KE   87 (759)
T ss_pred             cH
Confidence            84

>smart00362 RRM_2 RNA recognition motif

Probab=99.57  E-value=2e-14  Score=94.16  Aligned_cols=70  Identities=43%  Similarity=0.772  Sum_probs=64.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecC-CCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEE
Q 023765            8 TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP-PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV   77 (277)
Q Consensus         8 ~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~-~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v   77 (277)
                      +|+|+|||+.+++++|+++|.+||+|..+.+..+ +.+.++|||+|.+.++|..|+..|++..|.|+.|.|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence            5899999999999999999999999999988654 456799999999999999999999999999999886

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.54  E-value=9e-15  Score=111.35  Aligned_cols=84  Identities=31%  Similarity=0.551  Sum_probs=78.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      ...+|||||+|...+|+.-|...|=+||.|.+|.++.   +++++|||||+|...|+|..||.+||+..+.|+.|.|.+|
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            4578999999999999999999999999999999976   5688999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 023765           81 HGGRRHS   87 (277)
Q Consensus        81 ~~~~~~~   87 (277)
                      .+.+...
T Consensus        88 kP~kike   94 (298)
T KOG0111|consen   88 KPEKIKE   94 (298)
T ss_pred             CCccccC
Confidence            9876543

>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=99.50  E-value=2.3e-13  Score=89.48  Aligned_cols=72  Identities=40%  Similarity=0.739  Sum_probs=66.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCC--CCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            8 TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         8 ~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~--~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      +|+|+|||+.+++++|.++|+.||.|..+.+....  .+.++|||+|.+.++|..|+..+++..+.|..|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            58999999999999999999999999999997543  4589999999999999999999999999999998864

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).

>PF00076 RRM_1: RNA recognition motif

Probab=99.49  E-value=2.2e-13  Score=89.03  Aligned_cols=64  Identities=20%  Similarity=0.379  Sum_probs=59.1

Q ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC---CcEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG---GMTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       112 l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                      |||+|||..+++++|.++|.+||.|..+.+..+..   .++|||+|.+.++|+.|+..|||..+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~   67 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGR   67 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECcc
Confidence            79999999999999999999999999999988622   25999999999999999999999999994

(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 ....

>smart00360 RRM RNA recognition motif

Probab=99.49  E-value=1.7e-13  Score=89.35  Aligned_cols=68  Identities=41%  Similarity=0.710  Sum_probs=62.3

Q ss_pred             EcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEE
Q 023765           11 VGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVE   78 (277)
Q Consensus        11 V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~   78 (277)
                      |+|||..+++++|+++|++||.|..+.+..   ++.++++|||+|.+.++|..|+..|++..+.|+.|.|.
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            689999999999999999999999999965   35678999999999999999999999999999998873

>PF13893 RRM_5: RNA recognition motif

Probab=99.48  E-value=2.2e-13  Score=84.85  Aligned_cols=56  Identities=36%  Similarity=0.622  Sum_probs=51.2

Q ss_pred             HHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765           23 VEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus        23 l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      |+++|++||+|..+.+....  .++|||+|.+.++|..|+..|||..|.|+.|.|.|+
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            68999999999999997654  699999999999999999999999999999999985

(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 ....

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.44  E-value=4e-13  Score=115.77  Aligned_cols=79  Identities=33%  Similarity=0.644  Sum_probs=74.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      ..|||||||+++++++|..+|+..|.|..++++.   +|.++||||++|.++++|..|++.|||..+.|+.|.|.|+...
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            8999999999999999999999999999999955   6899999999999999999999999999999999999998865


Q ss_pred             CC
Q 023765           84 RR   85 (277)
Q Consensus        84 ~~   85 (277)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            43

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=99.42  E-value=4.8e-12  Score=108.10  Aligned_cols=163  Identities=22%  Similarity=0.311  Sum_probs=114.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEee--c----CCCCCc---EEEEEEcChHHHHHHHHhcCCcccCCceE
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLK--I----PPRPPG---YAFLEFEDYRDAEDAIRGRDGYNFDGYRL   75 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~--~----~~~~~g---~afV~f~~~~~a~~a~~~l~~~~~~g~~i   75 (277)
                      =+++||||+||++++|++|...|..||.+.- .++  .    --.++|   |+|+.|+++.++...+..+.-   ....+
T Consensus       258 ~S~KVFvGGlp~dise~~i~~~F~~FGs~~V-dWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~---~~~~~  333 (520)
T KOG0129|consen  258 YSRKVFVGGLPWDITEAQINASFGQFGSVKV-DWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE---GEGNY  333 (520)
T ss_pred             cccceeecCCCccccHHHHHhhcccccceEe-ecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh---cccce
Confidence            4678999999999999999999999997543 332  1    013456   999999999998887654432   33444


Q ss_pred             EEEEccCCCCCCCCCCCCC-----CCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHH-hcCCeeEEEEEecCC---
Q 023765           76 RVELAHGGRRHSSSMDRYS-----SYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMR-RAGDVCFSQVFRDRG---  146 (277)
Q Consensus        76 ~v~~a~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~-~~g~v~~~~~~~~~~---  146 (277)
                      .+....+.........+..     .+...  ...+.++..+|||++||-.++.++|..+|. .||.|..+.|.+|+.   
T Consensus       334 yf~vss~~~k~k~VQIrPW~laDs~fv~d--~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KY  411 (520)
T KOG0129|consen  334 YFKVSSPTIKDKEVQIRPWVLADSDFVLD--HNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKY  411 (520)
T ss_pred             EEEEecCcccccceeEEeeEeccchhhhc--cCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCC
Confidence            4444333332221111100     01111  234456688999999999999999999999 799999999998843   


Q ss_pred             -CcEEEEEEechhHHHHHHHh----cCCCeec
Q 023765          147 -GMTGIVDYTSYDDMKYAIRK----LDRSEFR  173 (277)
Q Consensus       147 -~~~~fv~f~~~~~a~~a~~~----l~g~~~~  173 (277)
                       .|-|-|.|.+...-.+||..    |+..+++
T Consensus       412 PkGaGRVtFsnqqsYi~AIsarFvql~h~d~~  443 (520)
T KOG0129|consen  412 PKGAGRVTFSNQQAYIKAISARFVQLDHTDID  443 (520)
T ss_pred             CCCcceeeecccHHHHHHHhhheEEEeccccc
Confidence             35788999999999999864    4444444

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.42  E-value=3.5e-13  Score=112.80  Aligned_cols=78  Identities=28%  Similarity=0.505  Sum_probs=71.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCCC
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGR   84 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~~   84 (277)
                      .-+.|||.||+.++|++.|+++|++||.|+.|+.+     +.||||.|.+-++|.+||+.|||.+|.|..|.|.+|++..
T Consensus       258 ~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~-----rDYaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~  332 (506)
T KOG0117|consen  258 KVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKP-----RDYAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVD  332 (506)
T ss_pred             heeeeeeeccchhhhHHHHHHHHHhccceEEeecc-----cceeEEeecchHHHHHHHHHhcCceecCceEEEEecCChh
Confidence            35789999999999999999999999999999877     5699999999999999999999999999999999999765


Q ss_pred             CCC
Q 023765           85 RHS   87 (277)
Q Consensus        85 ~~~   87 (277)
                      ...
T Consensus       333 k~k  335 (506)
T KOG0117|consen  333 KKK  335 (506)
T ss_pred             hhc
Confidence            443

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.41  E-value=1e-12  Score=92.55  Aligned_cols=76  Identities=22%  Similarity=0.320  Sum_probs=69.1

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCc----EEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGM----TGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~----~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      ..++.|||.++...+++++|.+.|..||+|..+++..+..+|    ||+|+|++.++|++|+..+||..+.|    ..|.
T Consensus        70 VEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~----q~v~  145 (170)
T KOG0130|consen   70 VEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLG----QNVS  145 (170)
T ss_pred             eeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhC----Ccee
Confidence            458999999999999999999999999999999999887664    99999999999999999999999999    5666


Q ss_pred             Eeec
Q 023765          183 VREY  186 (277)
Q Consensus       183 ~~~~  186 (277)
                      |+.+
T Consensus       146 VDw~  149 (170)
T KOG0130|consen  146 VDWC  149 (170)
T ss_pred             EEEE
Confidence            6654

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.41  E-value=7.3e-12  Score=102.72  Aligned_cols=166  Identities=15%  Similarity=0.217  Sum_probs=125.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHH--hcCCcccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIR--GRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~--~l~~~~~~g~~i~v~~a~   81 (277)
                      .++-.|.|.+|-..+++.+|.+-++.||+|..|.++..   +..|+|+|++.+.|+.++.  .-+...+.|+.--+.++.
T Consensus        29 ~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~---~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~NySt  105 (494)
T KOG1456|consen   29 NPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPH---KRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNYST  105 (494)
T ss_pred             CCCceEEEeccccccchhHHHHHHhcCCceEEEEeccc---cceeeeeeccccchhhheehhccCcccccCchhhcccch
Confidence            45678999999999999999999999999999988642   5689999999999999875  234466677777777764


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCceEE--EeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhH
Q 023765           82 GGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVL--VTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDD  159 (277)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~--v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~  159 (277)
                      .......           +  .....+...|.  |-|--+.+|.+.|-.++...|+|..|.|++. ++-.|.|||++.+.
T Consensus       106 sq~i~R~-----------g--~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk-ngVQAmVEFdsv~~  171 (494)
T KOG1456|consen  106 SQCIERP-----------G--DESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK-NGVQAMVEFDSVEV  171 (494)
T ss_pred             hhhhccC-----------C--CCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec-cceeeEEeechhHH
Confidence            3322111           0  11112233443  4455567899999999999999999998877 44579999999999


Q ss_pred             HHHHHHhcCCCeecccceeeEEEEeecCC
Q 023765          160 MKYAIRKLDRSEFRNAFSRSYVRVREYDS  188 (277)
Q Consensus       160 a~~a~~~l~g~~~~g~~~~~~i~~~~~~~  188 (277)
                      |++|...|||..|-...+  .+.++.+++
T Consensus       172 AqrAk~alNGADIYsGCC--TLKIeyAkP  198 (494)
T KOG1456|consen  172 AQRAKAALNGADIYSGCC--TLKIEYAKP  198 (494)
T ss_pred             HHHHHhhcccccccccce--eEEEEecCc
Confidence            999999999999865444  455555554

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.40  E-value=2e-11  Score=102.09  Aligned_cols=74  Identities=23%  Similarity=0.369  Sum_probs=63.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      ..++||+||...+..+.|++.|.-.|.|+.|.+-.  .+.++|||.|+|.++-.|..||..|++.-++.++..+.+
T Consensus       215 ~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~~~g~~~~~~~~Rl  290 (608)
T KOG4212|consen  215 HNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLDRQGLFDRRMTVRL  290 (608)
T ss_pred             cceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHHHHHHhhccCCCccccceeec
Confidence            35799999999999999999999999999988844  457889999999999999999999997666666666555

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.38  E-value=5.6e-13  Score=108.45  Aligned_cols=79  Identities=27%  Similarity=0.412  Sum_probs=74.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      -|.++|||..|.|-+|+++|..+|+.||.|..|.+..   ++.+..||||+|.+.++|++|+-.|++..|+++.|+|.|+
T Consensus       237 PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFS  316 (479)
T KOG0415|consen  237 PPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFS  316 (479)
T ss_pred             CCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehh
Confidence            3789999999999999999999999999999999954   7788899999999999999999999999999999999998


Q ss_pred             cC
Q 023765           81 HG   82 (277)
Q Consensus        81 ~~   82 (277)
                      +.
T Consensus       317 QS  318 (479)
T KOG0415|consen  317 QS  318 (479)
T ss_pred             hh
Confidence            85

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.38  E-value=4.4e-12  Score=101.28  Aligned_cols=73  Identities=15%  Similarity=0.220  Sum_probs=65.1

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC-CCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR-GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~-~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      ..+|||+||++.+++++|+++|..||+|..|.|..+. ..+||||+|.+.++|..||. |+|..|.|+    .|.|...
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr----~V~Vt~a   77 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQ----SVTITPA   77 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCc----eEEEEec
Confidence            5699999999999999999999999999999998876 35799999999999999995 999999994    5555544

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.38  E-value=8.8e-13  Score=104.70  Aligned_cols=77  Identities=38%  Similarity=0.658  Sum_probs=72.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      ++++++|+|+||.+.++..||++.|++||+|+++.+.     ++|+||.|.-.++|..|+..|||.+|.|+.++|+++..
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv-----kdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~sts  149 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV-----KDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTS  149 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeee-----cceeEEEEeeccchHHHHhcccccccccceeeeeeecc
Confidence            3588999999999999999999999999999999998     78999999999999999999999999999999999886


Q ss_pred             CC
Q 023765           83 GR   84 (277)
Q Consensus        83 ~~   84 (277)
                      .-
T Consensus       150 rl  151 (346)
T KOG0109|consen  150 RL  151 (346)
T ss_pred             cc
Confidence            54

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.37  E-value=6.4e-12  Score=93.47  Aligned_cols=78  Identities=19%  Similarity=0.247  Sum_probs=70.2

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC-CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeecC
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG-GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYD  187 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~-~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~  187 (277)
                      ...|||+|||.++.+.+|+++|-+||.|..|.+...+. ..||||+|+++.+|+.||..-+|..++|    ..++|+...
T Consensus         6 ~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg----~rLRVEfpr   81 (241)
T KOG0105|consen    6 SRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDG----CRLRVEFPR   81 (241)
T ss_pred             cceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCc----ceEEEEecc
Confidence            67899999999999999999999999999999876654 3599999999999999999999999999    688888776


Q ss_pred             CCC
Q 023765          188 SRR  190 (277)
Q Consensus       188 ~~r  190 (277)
                      ..+
T Consensus        82 ggr   84 (241)
T KOG0105|consen   82 GGR   84 (241)
T ss_pred             CCC
Confidence            654

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.35  E-value=3.8e-12  Score=102.69  Aligned_cols=73  Identities=18%  Similarity=0.164  Sum_probs=65.9

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC--CcEEEEEEechhHHHHHHHhcCCCeecccce
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG--GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFS  177 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~--~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  177 (277)
                      .......|+|.|||+...+.||..+|.+||.|.+|.|+.+..  +|||||+|++.++|++|-.+|||..+.|+.+
T Consensus        92 s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkI  166 (376)
T KOG0125|consen   92 SKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKI  166 (376)
T ss_pred             CCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEE
Confidence            345678999999999999999999999999999999987754  4799999999999999999999999999433

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.34  E-value=6.3e-12  Score=109.10  Aligned_cols=170  Identities=21%  Similarity=0.293  Sum_probs=132.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcc-----------C-CeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCC
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKY-----------G-PIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDG   72 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~-----------G-~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g   72 (277)
                      ....++|++||+.++++.+..+|..-           | .|..+.+.   ..++||||+|.+.+.|..|+. +++..+.|
T Consensus       174 q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n---~~~nfa~ie~~s~~~at~~~~-~~~~~f~g  249 (500)
T KOG0120|consen  174 QARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLN---LEKNFAFIEFRSISEATEAMA-LDGIIFEG  249 (500)
T ss_pred             hhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeec---ccccceeEEecCCCchhhhhc-ccchhhCC
Confidence            45679999999999999999999753           3 35556554   347899999999999999998 99999999


Q ss_pred             ceEEEEEccCCCCCCCCCCCC---CCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC---
Q 023765           73 YRLRVELAHGGRRHSSSMDRY---SSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG---  146 (277)
Q Consensus        73 ~~i~v~~a~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~---  146 (277)
                      .++.+.-.......+......   ..+...............++|++||..+++.++.|+...||.+....+..+..   
T Consensus       250 ~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~  329 (500)
T KOG0120|consen  250 RPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGN  329 (500)
T ss_pred             CCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeeccccccc
Confidence            998887655544333221111   11222233344456678999999999999999999999999998887776654   


Q ss_pred             -CcEEEEEEechhHHHHHHHhcCCCeeccccee
Q 023765          147 -GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       147 -~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  178 (277)
                       .+|||.+|.+......|+..|||..+.+..+.
T Consensus       330 skg~af~ey~dpsvtd~A~agLnGm~lgd~~lv  362 (500)
T KOG0120|consen  330 SKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLV  362 (500)
T ss_pred             ccceeeeeeeCCcchhhhhcccchhhhcCceeE
Confidence             46999999999999999999999999985443

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.33  E-value=6.1e-12  Score=82.18  Aligned_cols=64  Identities=25%  Similarity=0.425  Sum_probs=57.5

Q ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC---CcEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG---GMTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       112 l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                      |+|+|||..+++++|.++|..+|.|..+.+..+..   .++|||+|.+.++|..|+..+++..++|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~   67 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGR   67 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCE
Confidence            78999999999999999999999999999998764   35999999999999999999999999984

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 ....

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.32  E-value=9.1e-12  Score=102.49  Aligned_cols=174  Identities=18%  Similarity=0.200  Sum_probs=117.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhcc----CCeeEEEe-ec-CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKY----GPIVDIDL-KI-PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~----G~v~~v~~-~~-~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      -.|-+.+||+++|+.|+.++|.+-    |.++.|.+ .. +++..|-|||.|..+++|+.|+. -|...|+-+.|.+-.+
T Consensus       162 vivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~-khrq~iGqRYIElFRS  240 (508)
T KOG1365|consen  162 VIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALR-KHRQNIGQRYIELFRS  240 (508)
T ss_pred             eEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHH-HHHHHHhHHHHHHHHH
Confidence            356788999999999999999632    23444444 33 78889999999999999999986 3333444443333222


Q ss_pred             cC--------CCCCCC-CCCCCCCCC--CCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCC-eeE--EEEEecC-
Q 023765           81 HG--------GRRHSS-SMDRYSSYS--SGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGD-VCF--SQVFRDR-  145 (277)
Q Consensus        81 ~~--------~~~~~~-~~~~~~~~~--~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~-v~~--~~~~~~~-  145 (277)
                      ..        ...... .........  .+....++.....+|.+.+||+.++.++|.++|..|.. |..  |++..+. 
T Consensus       241 TaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~q  320 (508)
T KOG1365|consen  241 TAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQ  320 (508)
T ss_pred             hHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCC
Confidence            10        000000 000011111  12223344455789999999999999999999999984 544  6776554 


Q ss_pred             --CCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          146 --GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       146 --~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                        ..|-|||+|.+.++|..|..+.+.+.+..    ++|.|..
T Consensus       321 GrPSGeAFIqm~nae~a~aaaqk~hk~~mk~----RYiEvfp  358 (508)
T KOG1365|consen  321 GRPSGEAFIQMRNAERARAAAQKCHKKLMKS----RYIEVFP  358 (508)
T ss_pred             CCcChhhhhhhhhhHHHHHHHHHHHHhhccc----ceEEEee
Confidence              34689999999999999999998888866    5565543

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.32  E-value=6.6e-12  Score=87.78  Aligned_cols=77  Identities=19%  Similarity=0.192  Sum_probs=68.3

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      .+++|||+||..-+++++|.++|.++|+|..|.+-.+..+    |||||+|-..++|+.|+..++|..++.    ..|++
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLdd----r~ir~  110 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDD----RPIRI  110 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccc----cceee
Confidence            4789999999999999999999999999999887666544    599999999999999999999999998    67777


Q ss_pred             eecCC
Q 023765          184 REYDS  188 (277)
Q Consensus       184 ~~~~~  188 (277)
                      +.+..
T Consensus       111 D~D~G  115 (153)
T KOG0121|consen  111 DWDAG  115 (153)
T ss_pred             ecccc
Confidence            76654

>smart00361 RRM_1 RNA recognition motif

Probab=99.31  E-value=9.5e-12  Score=81.11  Aligned_cols=58  Identities=28%  Similarity=0.462  Sum_probs=51.5

Q ss_pred             HHHHHHHhh----ccCCeeEEE-eec---C--CCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEE
Q 023765           20 MREVEDLFY----KYGPIVDID-LKI---P--PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV   77 (277)
Q Consensus        20 ~~~l~~~F~----~~G~v~~v~-~~~---~--~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v   77 (277)
                      +++|+++|+    .||.|..|. +..   +  +.++|||||+|.+.++|.+|+..|||..+.|+.|.+
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            678999998    999999985 322   3  678999999999999999999999999999999976

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.29  E-value=3.1e-11  Score=81.25  Aligned_cols=79  Identities=19%  Similarity=0.222  Sum_probs=68.5

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC-cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG-MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~-~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ++.....|||.|||+.+|.+++-++|.+||.|..|.|-..+.+ |.|||.|++..+|.+|++.|+|..+++    ..+.|
T Consensus        14 ppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~----ryl~v   89 (124)
T KOG0114|consen   14 PPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDN----RYLVV   89 (124)
T ss_pred             ChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCC----ceEEE
Confidence            3344678999999999999999999999999999998766554 699999999999999999999999999    56666


Q ss_pred             eecC
Q 023765          184 REYD  187 (277)
Q Consensus       184 ~~~~  187 (277)
                      ..+.
T Consensus        90 lyyq   93 (124)
T KOG0114|consen   90 LYYQ   93 (124)
T ss_pred             EecC
Confidence            5443

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.29  E-value=2.5e-12  Score=116.03  Aligned_cols=158  Identities=20%  Similarity=0.278  Sum_probs=133.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecC--CCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP--PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~--~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      .++.|||++||+..+++.+|+..|..+|.|..|.|+.+  +....||||.|.+.+.+-.|...+.+..|..-.+.+.+.+
T Consensus       370 ~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~  449 (975)
T KOG0112|consen  370 RATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQ  449 (975)
T ss_pred             hhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCcccccccc
Confidence            46899999999999999999999999999999999653  4556799999999999999999899888766666666554


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHH
Q 023765           82 GGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMK  161 (277)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~  161 (277)
                      +.                      ....+.++|++|+..+....|..+|..||.|..|.+-.+..  ||+|+|++...|+
T Consensus       450 ~k----------------------st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq~--yayi~yes~~~aq  505 (975)
T KOG0112|consen  450 PK----------------------STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQP--YAYIQYESPPAAQ  505 (975)
T ss_pred             cc----------------------cccceeeccCCCCCCChHHHHHHHhhccCcceeeecccCCc--ceeeecccCccch
Confidence            31                      12256899999999999999999999999999987766544  9999999999999


Q ss_pred             HHHHhcCCCeecccceeeEEEEeecC
Q 023765          162 YAIRKLDRSEFRNAFSRSYVRVREYD  187 (277)
Q Consensus       162 ~a~~~l~g~~~~g~~~~~~i~~~~~~  187 (277)
                      .|+..|-|..+++....  ++|+.+.
T Consensus       506 ~a~~~~rgap~G~P~~r--~rvdla~  529 (975)
T KOG0112|consen  506 AATHDMRGAPLGGPPRR--LRVDLAS  529 (975)
T ss_pred             hhHHHHhcCcCCCCCcc--ccccccc
Confidence            99999999999885433  6665444

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.29  E-value=1.1e-11  Score=110.39  Aligned_cols=80  Identities=30%  Similarity=0.507  Sum_probs=74.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCCC
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGR   84 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~~   84 (277)
                      -++|||||.|+.++++.||.++|+.||+|..|.|..   ++++|||.+..-.+|.+|+.+|.+..+.++.|+|.|+.+..
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~---~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G  496 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP---PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKG  496 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeecc---CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCC
Confidence            478999999999999999999999999999999974   48999999999999999999999999999999999998765


Q ss_pred             CCC
Q 023765           85 RHS   87 (277)
Q Consensus        85 ~~~   87 (277)
                      ...
T Consensus       497 ~ks  499 (894)
T KOG0132|consen  497 PKS  499 (894)
T ss_pred             cch
Confidence            443

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=99.28  E-value=9e-13  Score=100.52  Aligned_cols=140  Identities=19%  Similarity=0.264  Sum_probs=113.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      ...+||||+||...|+++-|.+||-+.|+|..|.|+.  +++.+ ||||.|.++..+..|+..|||..+.+..|+|++-.
T Consensus         7 e~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    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRC   85 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhccccc
Confidence            3568999999999999999999999999999999965  34545 99999999999999999999999999999998855


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC---cEEEEEEechh
Q 023765           82 GGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG---MTGIVDYTSYD  158 (277)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~fv~f~~~~  158 (277)
                      +..-.+                             |...++++.+.+.|...|.+..+.+..+..+   .++|+.+.-..
T Consensus        86 G~shap-----------------------------ld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~  136 (267)
T KOG4454|consen   86 GNSHAP-----------------------------LDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLC  136 (267)
T ss_pred             CCCcch-----------------------------hhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhh
Confidence            432111                             4556778888888999998888887766542   37888888777


Q ss_pred             HHHHHHHhcCCCeec
Q 023765          159 DMKYAIRKLDRSEFR  173 (277)
Q Consensus       159 ~a~~a~~~l~g~~~~  173 (277)
                      ..-.++...++....
T Consensus       137 ~~P~~~~~y~~l~~~  151 (267)
T KOG4454|consen  137 AVPFALDLYQGLELF  151 (267)
T ss_pred             cCcHHhhhhcccCcC
Confidence            777777766665443

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.28  E-value=3.7e-11  Score=94.51  Aligned_cols=74  Identities=19%  Similarity=0.284  Sum_probs=65.0

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC-cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG-MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~-~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      .+++|+|+||++.+++++|+++|..||+|..|.|..+... ++|||+|+++++|+.|+ .|+|..|.+.    .|.+...
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~----~I~It~~   78 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAV-LLSGATIVDQ----RVCITRW   78 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHH-hcCCCeeCCc----eEEEEeC
Confidence            3689999999999999999999999999999999988644 59999999999999999 5999999994    4555443

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

Probab=99.28  E-value=3.1e-11  Score=93.75  Aligned_cols=79  Identities=27%  Similarity=0.298  Sum_probs=71.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCc----EEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGM----TGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~----~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      ....++|.|.||+.++++.+|+++|.+||.|..+.+..++.+|    ||||.|...++|.+||+.|||.-+++    .-+
T Consensus       186 R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~----LIL  261 (270)
T KOG0122|consen  186 RDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDN----LIL  261 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccce----EEE
Confidence            3456789999999999999999999999999999999998764    99999999999999999999999988    777


Q ss_pred             EEeecCC
Q 023765          182 RVREYDS  188 (277)
Q Consensus       182 ~~~~~~~  188 (277)
                      +|+..++
T Consensus       262 rvEwskP  268 (270)
T KOG0122|consen  262 RVEWSKP  268 (270)
T ss_pred             EEEecCC
Confidence            7776654

>PLN03213 repressor of silencing 3; Provisional

Probab=99.27  E-value=2.4e-11  Score=103.25  Aligned_cols=76  Identities=17%  Similarity=0.289  Sum_probs=69.1

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEech--hHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSY--DDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~--~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      ...|||+||++.+++++|..+|..||.|..|.|++....|||||+|.+.  .++.+||..|||..+.|    ..|+|..+
T Consensus        10 gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKG----R~LKVNKA   85 (759)
T PLN03213         10 GVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKG----GRLRLEKA   85 (759)
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecC----ceeEEeec
Confidence            5799999999999999999999999999999999777778999999987  78999999999999999    67777766


Q ss_pred             CC
Q 023765          187 DS  188 (277)
Q Consensus       187 ~~  188 (277)
                      ++
T Consensus        86 KP   87 (759)
T PLN03213         86 KE   87 (759)
T ss_pred             cH
Confidence            54

>smart00362 RRM_2 RNA recognition motif

Probab=99.25  E-value=8.4e-11  Score=76.60  Aligned_cols=65  Identities=22%  Similarity=0.356  Sum_probs=59.3

Q ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC--CCcEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR--GGMTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       111 ~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~--~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                      +|+|.|||..++.++|.++|.+||.+..+.+..+.  ..++|||+|.+.++|+.|+..+++..+.|.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~   67 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGR   67 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCE
Confidence            48999999999999999999999999999888765  346999999999999999999999999883

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.22  E-value=3.3e-11  Score=98.28  Aligned_cols=76  Identities=18%  Similarity=0.269  Sum_probs=69.7

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCc----EEEEEEechhHHHHHHHhcCCCeecccceeeE
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGM----TGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSY  180 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~----~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  180 (277)
                      ..++.++|||..|.+.++.++|+-+|..||.|..|.|+++..+|    ||||+|++.+++++|.-+|++..|+.+    .
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDr----R  310 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDR----R  310 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccc----e
Confidence            35678999999999999999999999999999999999998886    999999999999999999999999994    5


Q ss_pred             EEEe
Q 023765          181 VRVR  184 (277)
Q Consensus       181 i~~~  184 (277)
                      |.|+
T Consensus       311 IHVD  314 (479)
T KOG0415|consen  311 IHVD  314 (479)
T ss_pred             EEee
Confidence            5554

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=99.19  E-value=8.2e-11  Score=89.34  Aligned_cols=79  Identities=24%  Similarity=0.349  Sum_probs=72.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcc-CCeeEEEe---ecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKY-GPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~-G~v~~v~~---~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      ....++|..||.-+-+.+|..+|.+| |.|..+.|   ..||.++|||||+|++++.|.-|.+.||+..|.|+.|.|.+-
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            44578999999999999999999998 78888888   458999999999999999999999999999999999999997


Q ss_pred             cCC
Q 023765           81 HGG   83 (277)
Q Consensus        81 ~~~   83 (277)
                      .+.
T Consensus       128 ppe  130 (214)
T KOG4208|consen  128 PPE  130 (214)
T ss_pred             Cch
Confidence            654

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.14  E-value=1.6e-10  Score=89.56  Aligned_cols=75  Identities=13%  Similarity=0.181  Sum_probs=64.6

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      -++|||++|++.+..++|..+|++||+|+.+.|+.|+.+    ||+||+|.+.+.|..|++. -.-.|+|+...+.|-..
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLASL   90 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhhh
Confidence            579999999999999999999999999999999988765    5999999999999999974 44567887666666544

>smart00360 RRM RNA recognition motif

Probab=99.12  E-value=4.8e-10  Score=72.66  Aligned_cols=62  Identities=21%  Similarity=0.388  Sum_probs=56.5

Q ss_pred             EeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          114 VTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       114 v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                      |.|||..+++++|.++|.+||.|..+.+..+..    .++|||+|.+.++|..|+..|++..+.|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~   66 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGR   66 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCc
Confidence            578999999999999999999999999987754    46999999999999999999999999884

>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=99.12  E-value=9.7e-10  Score=71.90  Aligned_cols=65  Identities=22%  Similarity=0.395  Sum_probs=59.9

Q ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC---CcEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG---GMTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       111 ~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                      +|+|.|||..+++++|.++|..+|.|..+.+.....   .++|||+|.+.++|..|+..+++..+.|.
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~   68 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGR   68 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            478999999999999999999999999999987764   56999999999999999999999998884

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).

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.12  E-value=1.5e-10  Score=86.10  Aligned_cols=78  Identities=24%  Similarity=0.321  Sum_probs=67.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC----CCcEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR----GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      .....+|||+||+..++++.|.++|-+.|+|..+++.++.    ..|||||+|.+.++|+.|++.||...+-|+    .|
T Consensus         6 rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgr----pI   81 (203)
T KOG0131|consen    6 RNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGR----PI   81 (203)
T ss_pred             cCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCc----ee
Confidence            3457899999999999999999999999999999998764    457999999999999999999999999994    55


Q ss_pred             EEeecC
Q 023765          182 RVREYD  187 (277)
Q Consensus       182 ~~~~~~  187 (277)
                      ++....
T Consensus        82 rv~kas   87 (203)
T KOG0131|consen   82 RVNKAS   87 (203)
T ss_pred             EEEecc
Confidence            554443

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.11  E-value=1.2e-11  Score=91.72  Aligned_cols=75  Identities=16%  Similarity=0.225  Sum_probs=68.8

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCc----EEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGM----TGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~----~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      ..-|||+|||+++|+.||.-+|.+||+|..|.++++..+|    |||+.|++.....-|+..|||..|.|    +.|+|+
T Consensus        35 sA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~g----RtirVD  110 (219)
T KOG0126|consen   35 SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILG----RTIRVD  110 (219)
T ss_pred             ceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecc----eeEEee
Confidence            5689999999999999999999999999999999987764    99999999999999999999999999    677777


Q ss_pred             ecC
Q 023765          185 EYD  187 (277)
Q Consensus       185 ~~~  187 (277)
                      ...
T Consensus       111 Hv~  113 (219)
T KOG0126|consen  111 HVS  113 (219)
T ss_pred             ecc
Confidence            543

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=99.09  E-value=6.8e-11  Score=101.99  Aligned_cols=164  Identities=21%  Similarity=0.184  Sum_probs=102.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      -++.+|+|.|||..|+.++|..+|+.||+|..|.+  +....+.+||+|.|..+|+.|++.|++..|.|+.|........
T Consensus        73 ~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~--t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~~~~~~~  150 (549)
T KOG4660|consen   73 MNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE--TPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIKRPGGARR  150 (549)
T ss_pred             CccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc--ccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcCCCcccc
Confidence            36789999999999999999999999999999666  3345799999999999999999999999999999882111100


Q ss_pred             CCCCCCC-CCCCCCCCCCCCCCCCCCCc--eEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHH
Q 023765           84 RRHSSSM-DRYSSYSSGGSRGVSRRSDY--RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDM  160 (277)
Q Consensus        84 ~~~~~~~-~~~~~~~~~~~~~~~~~~~~--~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a  160 (277)
                      ....... .-...+..+  ....+++++  --.++.|++..+...++.++.-+|.+..-.......  .-|++|.+..++
T Consensus       151 ~~~~~~~~~~~~~~~~p--~a~s~pgg~~~~~~~g~l~P~~s~~~~~~~~~~~~~~~~~~~~~~~h--q~~~~~~~~~s~  226 (549)
T KOG4660|consen  151 AMGLQSGTSFLNHFGSP--LANSPPGGWPRGQLFGMLSPTRSSILLEHISSVDGSSPGRETPLLNH--QRFVEFADNRSY  226 (549)
T ss_pred             cchhcccchhhhhccch--hhcCCCCCCcCCcceeeeccchhhhhhhcchhccCccccccccchhh--hhhhhhccccch
Confidence            0000000 000001111  111111111  111222888888877777777777665411111111  456778777777


Q ss_pred             HHHHHhcCCCeecc
Q 023765          161 KYAIRKLDRSEFRN  174 (277)
Q Consensus       161 ~~a~~~l~g~~~~g  174 (277)
                      ..++..+ |..+.+
T Consensus       227 a~~~~~~-G~~~s~  239 (549)
T KOG4660|consen  227 AFSEPRG-GFLISN  239 (549)
T ss_pred             hhcccCC-ceecCC
Confidence            5555433 444444

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.06  E-value=2.4e-10  Score=90.02  Aligned_cols=81  Identities=22%  Similarity=0.440  Sum_probs=73.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      -+.|.|||..||....+.||.++|-.||.|+..++..   |.+++-|+||.|.++.+|..||..|||..|+=+.|+|.+.
T Consensus       283 PeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLK  362 (371)
T KOG0146|consen  283 PEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLK  362 (371)
T ss_pred             CCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhc
Confidence            3678999999999999999999999999999988844   6788999999999999999999999999999999999886


Q ss_pred             cCCC
Q 023765           81 HGGR   84 (277)
Q Consensus        81 ~~~~   84 (277)
                      .++.
T Consensus       363 RPkd  366 (371)
T KOG0146|consen  363 RPKD  366 (371)
T ss_pred             Cccc
Confidence            6543

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.04  E-value=3.8e-10  Score=93.52  Aligned_cols=84  Identities=24%  Similarity=0.515  Sum_probs=74.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      .+.+|||++||.++++++|++.|++||.|..+.++.   +...++|+||.|.+++.+++++. ..-+.|.|+.+.|..|.
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~  174 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAI  174 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeecc
Confidence            467999999999999999999999999999988866   45778999999999999999988 78889999999999999


Q ss_pred             CCCCCCCC
Q 023765           82 GGRRHSSS   89 (277)
Q Consensus        82 ~~~~~~~~   89 (277)
                      +.......
T Consensus       175 pk~~~~~~  182 (311)
T KOG4205|consen  175 PKEVMQST  182 (311)
T ss_pred             chhhcccc
Confidence            87655543

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=99.04  E-value=1e-09  Score=87.39  Aligned_cols=80  Identities=25%  Similarity=0.436  Sum_probs=72.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      -+++|+|.|||..|+++||++||+.||.++.+.|..  .+.+.|.|-|.|...++|..||+.||+..++|..|.+.....
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~  161 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISS  161 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecC
Confidence            357899999999999999999999999988888865  578889999999999999999999999999999999988775


Q ss_pred             CC
Q 023765           83 GR   84 (277)
Q Consensus        83 ~~   84 (277)
                      ..
T Consensus       162 ~~  163 (243)
T KOG0533|consen  162 PS  163 (243)
T ss_pred             cc
Confidence            44

>PF13893 RRM_5: RNA recognition motif

Probab=99.03  E-value=1.8e-09  Score=67.06  Aligned_cols=54  Identities=22%  Similarity=0.405  Sum_probs=46.6

Q ss_pred             HHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          126 LKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       126 l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      |.++|++||+|..+.+..+. .++|||+|.+.++|..|+..|||..+.|    ..|.|.
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-~~~a~V~f~~~~~A~~a~~~l~~~~~~g----~~l~V~   54 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-RGFAFVEFASVEDAQKAIEQLNGRQFNG----RPLKVS   54 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-TTEEEEEESSHHHHHHHHHHHTTSEETT----EEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-CCEEEEEECCHHHHHHHHHHhCCCEECC----cEEEEE
Confidence            67899999999999998776 5699999999999999999999999999    455554

(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 ....

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.00  E-value=1.2e-09  Score=89.13  Aligned_cols=76  Identities=30%  Similarity=0.576  Sum_probs=67.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHH-HhcCCcccCCceEEEEEccC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAI-RGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~l~~~~~~g~~i~v~~a~~   82 (277)
                      +..++|||++|...+++.+|++.|.+||+|..+.+...   ++.|||+|.+-+.|+.|. +.+|...|.|..|.|.|..+
T Consensus       226 ~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~---~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  226 TSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR---KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             cceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc---cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            45679999999999999999999999999999999643   679999999999999876 55666788999999999887

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.99  E-value=1.5e-09  Score=93.87  Aligned_cols=81  Identities=26%  Similarity=0.436  Sum_probs=72.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecC---CCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP---PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~---~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      .+.|||.+|...+-..+|++||++||.|+..+|+.+   +..+-|+||++.+.++|.+||..|+.+.|+|+.|.|+.+++
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            467999999999999999999999999999999653   34466999999999999999999999999999999999987


Q ss_pred             CCCC
Q 023765           83 GRRH   86 (277)
Q Consensus        83 ~~~~   86 (277)
                      ....
T Consensus       485 Ep~G  488 (940)
T KOG4661|consen  485 EPGG  488 (940)
T ss_pred             Cccc
Confidence            6543

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.94  E-value=1e-10  Score=97.62  Aligned_cols=142  Identities=24%  Similarity=0.371  Sum_probs=116.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhcc--CCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCc-ccCCceEEEEEccCC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKY--GPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY-NFDGYRLRVELAHGG   83 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~--G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~-~~~g~~i~v~~a~~~   83 (277)
                      +.+||+||.+.++..+|..+|...  +--..+.|+     .||+||.+.++..|.+|++.|+|. .+.|..+.|.+.-+.
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k-----~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~k   76 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK-----SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPK   76 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee-----cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhH
Confidence            479999999999999999999754  322333333     689999999999999999999995 678999999887754


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEE-EecCCCcEEEEEEechhHHHH
Q 023765           84 RRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQV-FRDRGGMTGIVDYTSYDDMKY  162 (277)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~-~~~~~~~~~fv~f~~~~~a~~  162 (277)
                      ...                      ...+.|.|+|+...++.|..++.+||.+..|.. +.+..+...-|+|...+.+..
T Consensus        77 kqr----------------------srk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~etavvnvty~~~~~~~~  134 (584)
T KOG2193|consen   77 KQR----------------------SRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETAVVNVTYSAQQQHRQ  134 (584)
T ss_pred             HHH----------------------hhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHHHHHHHHHHHHHHHH
Confidence            422                      456889999999999999999999999998854 444444345578899999999


Q ss_pred             HHHhcCCCeeccc
Q 023765          163 AIRKLDRSEFRNA  175 (277)
Q Consensus       163 a~~~l~g~~~~g~  175 (277)
                      ||.+|+|..+.+.
T Consensus       135 ai~kl~g~Q~en~  147 (584)
T KOG2193|consen  135 AIHKLNGPQLENQ  147 (584)
T ss_pred             HHHhhcchHhhhh
Confidence            9999999998873

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.92  E-value=1.1e-10  Score=105.24  Aligned_cols=134  Identities=21%  Similarity=0.269  Sum_probs=112.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEee---cCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLK---IPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~---~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      +..++||.||++.+.+.+|...|..+|.+..+++.   ..+..+|+|||+|..++++.+|+. ++...+.|+        
T Consensus       666 ~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~-f~d~~~~gK--------  736 (881)
T KOG0128|consen  666 DLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVA-FRDSCFFGK--------  736 (881)
T ss_pred             HHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhh-hhhhhhhhh--------
Confidence            34578999999999999999999999988887773   467889999999999999999999 555555552        


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEec---CCCcEEEEEEechh
Q 023765           82 GGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD---RGGMTGIVDYTSYD  158 (277)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~---~~~~~~fv~f~~~~  158 (277)
                                                  ..|+|.|+|+..|.++|+.+|..+|.+..+.+...   .+.|.|+|.|.+..
T Consensus       737 ----------------------------~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea  788 (881)
T KOG0128|consen  737 ----------------------------ISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEA  788 (881)
T ss_pred             ----------------------------hhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcc
Confidence                                        26789999999999999999999999888766544   44579999999999


Q ss_pred             HHHHHHHhcCCCeeccc
Q 023765          159 DMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       159 ~a~~a~~~l~g~~~~g~  175 (277)
                      ++..++...++..+.-+
T Consensus       789 ~~s~~~~s~d~~~~rE~  805 (881)
T KOG0128|consen  789 DASRKVASVDVAGKREN  805 (881)
T ss_pred             hhhhhcccchhhhhhhc
Confidence            99999988877666553

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.92  E-value=1.5e-09  Score=83.11  Aligned_cols=79  Identities=22%  Similarity=0.239  Sum_probs=69.9

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC----CCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR----GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ...+|||++|..++++..|...|-.||.|..|.++.+-    ..+||||+|+..++|..||..||+.++.|    ..|+|
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~G----rtirV   84 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFG----RTIRV   84 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcc----eeEEE
Confidence            36799999999999999999999999999999998663    34699999999999999999999999999    67777


Q ss_pred             eecCCCC
Q 023765          184 REYDSRR  190 (277)
Q Consensus       184 ~~~~~~r  190 (277)
                      -.+.+-+
T Consensus        85 N~AkP~k   91 (298)
T KOG0111|consen   85 NLAKPEK   91 (298)
T ss_pred             eecCCcc
Confidence            7766543

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.90  E-value=4.5e-08  Score=83.70  Aligned_cols=167  Identities=20%  Similarity=0.237  Sum_probs=111.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeE-EEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVD-IDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~-v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      +..+|-+.+||+.||++||.++|+..-.|.+ |.|+.  .+.+.|-|||+|++++.|+.|+. -|...|..+-|.|-.+.
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 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALG-RHRENIGHRYIEVFRSS  180 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHH-HHHHhhccceEEeehhH
Confidence            4568999999999999999999998765555 33333  34678999999999999999998 56667777777776544


Q ss_pred             CCC------------CCCCCCCC-----C---------------------------------C---CCC---CC--CCCC
Q 023765           82 GGR------------RHSSSMDR-----Y---------------------------------S---SYS---SG--GSRG  103 (277)
Q Consensus        82 ~~~------------~~~~~~~~-----~---------------------------------~---~~~---~~--~~~~  103 (277)
                      ...            ..+.+-+.     .                                 .   .+.   ..  ...+
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            100            00000000     0                                 0   000   00  0000


Q ss_pred             C---------------CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC---CCcEEEEEEechhHHHHHHH
Q 023765          104 V---------------SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR---GGMTGIVDYTSYDDMKYAIR  165 (277)
Q Consensus       104 ~---------------~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~---~~~~~fv~f~~~~~a~~a~~  165 (277)
                      .               .......++..+||+..++.++..+|...-.+ .|+|...+   .++-|+|+|.+.++|..|+.
T Consensus       261 ~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~-~v~i~ig~dGr~TGEAdveF~t~edav~Ams  339 (510)
T KOG4211|consen  261 VSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPY-RVHIEIGPDGRATGEADVEFATGEDAVGAMG  339 (510)
T ss_pred             CCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCce-eEEEEeCCCCccCCcceeecccchhhHhhhc
Confidence            0               01123678889999999999999999976554 56665443   44689999999999999985


Q ss_pred             hcCCCeecc
Q 023765          166 KLDRSEFRN  174 (277)
Q Consensus       166 ~l~g~~~~g  174 (277)
                       -++..+..
T Consensus       340 -kd~anm~h  347 (510)
T KOG4211|consen  340 -KDGANMGH  347 (510)
T ss_pred             -cCCcccCc
Confidence             45555554

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=98.89  E-value=1.1e-08  Score=84.87  Aligned_cols=74  Identities=24%  Similarity=0.394  Sum_probs=66.1

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC----CCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR----GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      ..+|||+|||..+++++|.++|.+||.|..+.+..+.    ..+||||+|.+.++|..|+..++|..+.|    ..|.|.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~----~~~~v~  190 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEG----RPLRVQ  190 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECC----ceeEee
Confidence            6899999999999999999999999999999888774    33699999999999999999999999999    455555


Q ss_pred             ec
Q 023765          185 EY  186 (277)
Q Consensus       185 ~~  186 (277)
                      ..
T Consensus       191 ~~  192 (306)
T COG0724         191 KA  192 (306)
T ss_pred             cc
Confidence            53

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.87  E-value=6.1e-09  Score=90.20  Aligned_cols=76  Identities=26%  Similarity=0.342  Sum_probs=69.1

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      ..+||+|+|+++++++|.++|..+|.|..+.++.|..+    ||||++|.+.++|..|++.|||.++.|    +.|+|..
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~g----r~l~v~~   94 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNG----RKLRVNY   94 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCC----ceEEeec
Confidence            79999999999999999999999999999999988665    499999999999999999999999999    6777776


Q ss_pred             cCCC
Q 023765          186 YDSR  189 (277)
Q Consensus       186 ~~~~  189 (277)
                      ....
T Consensus        95 ~~~~   98 (435)
T KOG0108|consen   95 ASNR   98 (435)
T ss_pred             cccc
Confidence            6544

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.87  E-value=4.7e-09  Score=86.73  Aligned_cols=171  Identities=19%  Similarity=0.221  Sum_probs=128.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEee---cCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLK---IPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~---~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      ...++|++++...+.+.++..+|..+|.+....+.   .....+++++|.|...+.+..|+.......+.+..+...+..
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            46789999999999999999999999977776662   245678999999999999999999444346666666655544


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCceEE-EeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEec
Q 023765           82 GGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVL-VTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTS  156 (277)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~  156 (277)
                      ........          ........+..+++ |.+|+..++.++|..+|..+|.|..+.+......    +||+|.|.+
T Consensus       167 ~~~~~~~n----------~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~  236 (285)
T KOG4210|consen  167 RRGLRPKN----------KLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSA  236 (285)
T ss_pred             cccccccc----------hhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhh
Confidence            33311110          00011112234455 9999999999999999999999999999877665    489999999


Q ss_pred             hhHHHHHHHhcCCCeecccceeeEEEEeecCCCC
Q 023765          157 YDDMKYAIRKLDRSEFRNAFSRSYVRVREYDSRR  190 (277)
Q Consensus       157 ~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~~~r  190 (277)
                      ...+..++.. +...+.+    ..+.+++.+++.
T Consensus       237 ~~~~~~~~~~-~~~~~~~----~~~~~~~~~~~~  265 (285)
T KOG4210|consen  237 GNSKKLALND-QTRSIGG----RPLRLEEDEPRP  265 (285)
T ss_pred             chhHHHHhhc-ccCcccC----cccccccCCCCc
Confidence            9999999987 7777777    566666665553

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.83  E-value=3e-08  Score=67.80  Aligned_cols=75  Identities=19%  Similarity=0.236  Sum_probs=63.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhcc--CCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccC----CceEEE
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKY--GPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFD----GYRLRV   77 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~--G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~----g~~i~v   77 (277)
                      +||.|.|||...|.++|.+++...  |...-+.|+.   ++...|||||-|.+++.|...++.++|..+.    .+...|
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            699999999999999999998753  7777777765   4567899999999999999999999998875    455677


Q ss_pred             EEcc
Q 023765           78 ELAH   81 (277)
Q Consensus        78 ~~a~   81 (277)
                      .+|.
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            6665

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>smart00361 RRM_1 RNA recognition motif

Probab=98.83  E-value=3e-08  Score=64.48  Aligned_cols=54  Identities=17%  Similarity=0.198  Sum_probs=45.1

Q ss_pred             HHHHHHHHH----hcCCeeEEE-EEecC------CCcEEEEEEechhHHHHHHHhcCCCeecccc
Q 023765          123 WQDLKDHMR----RAGDVCFSQ-VFRDR------GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAF  176 (277)
Q Consensus       123 ~~~l~~~f~----~~g~v~~~~-~~~~~------~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  176 (277)
                      +++|.++|.    +||.|..+. +..++      ..|+|||+|.+.++|.+|+..|||..+.|+.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~   66 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRT   66 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            467888888    999999985 54433      3469999999999999999999999999943

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.81  E-value=1.2e-08  Score=87.96  Aligned_cols=75  Identities=29%  Similarity=0.568  Sum_probs=65.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      .+|||.|||+++++++|.++|..||+|+...|..   .+....||||+|.+.+.+..|+. .+-..++++.|.|+--..
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~-Asp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIE-ASPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhh-cCccccCCeeEEEEeccc
Confidence            4599999999999999999999999999988833   23334899999999999999998 568889999999998664

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.80  E-value=4e-10  Score=93.16  Aligned_cols=63  Identities=17%  Similarity=0.169  Sum_probs=54.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFD   71 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~   71 (277)
                      +||+|++|+..+...++.++|..+|+|....+.. +....+|.|+|....+...|+. ++|..+.
T Consensus       152 Rt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~as-k~~s~~c~~sf~~qts~~halr-~~gre~k  214 (479)
T KOG4676|consen  152 RTREVQSLISAAILPESGESFERKGEVSYAHTAS-KSRSSSCSHSFRKQTSSKHALR-SHGRERK  214 (479)
T ss_pred             hhhhhhcchhhhcchhhhhhhhhcchhhhhhhhc-cCCCcchhhhHhhhhhHHHHHH-hcchhhh
Confidence            6899999999999999999999999998877743 2335689999999999999999 7777766

>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=98.80  E-value=3.3e-08  Score=64.29  Aligned_cols=71  Identities=27%  Similarity=0.426  Sum_probs=50.1

Q ss_pred             CeEEEcCCCCCCCHHHH----HHHhhccC-CeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            7 RTLYVGNLPGDTRMREV----EDLFYKYG-PIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l----~~~F~~~G-~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      ..|+|.|||.+.+...|    ++|+..|| .|..|.       .+.|+|.|.+++.|..|.+.|+|-.++|..|.|.+..
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~-------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~   75 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS-------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSP   75 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE---------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS-
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe-------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcC
Confidence            46999999999987764    67778885 887762       5789999999999999999999999999999999976


Q ss_pred             CCC
Q 023765           82 GGR   84 (277)
Q Consensus        82 ~~~   84 (277)
                      ...
T Consensus        76 ~~r   78 (90)
T PF11608_consen   76 KNR   78 (90)
T ss_dssp             -S-
T ss_pred             Ccc
Confidence            433

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.79  E-value=1.5e-08  Score=81.10  Aligned_cols=81  Identities=25%  Similarity=0.411  Sum_probs=73.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+...|||+|+.+.+|.++|...|+.||.|..+.|+.   .++++||+||+|.+.+.+..|+. ||+..|.|..|.|.+.
T Consensus        99 ~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~  177 (231)
T KOG4209|consen   99 VDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLK  177 (231)
T ss_pred             cCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeee
Confidence            5778999999999999999999999999998777754   45789999999999999999999 9999999999999998


Q ss_pred             cCCCC
Q 023765           81 HGGRR   85 (277)
Q Consensus        81 ~~~~~   85 (277)
                      .-..+
T Consensus       178 r~~~p  182 (231)
T KOG4209|consen  178 RTNVP  182 (231)
T ss_pred             eeecC
Confidence            76543

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.78  E-value=2e-08  Score=89.13  Aligned_cols=78  Identities=24%  Similarity=0.462  Sum_probs=70.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecC------CCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEE
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP------PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVE   78 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~------~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~   78 (277)
                      .++.|||+||++.++++.|...|..||+|..|+++..      .....++||.|-+-.+|++|++.|+|..+.+..+.+.
T Consensus       173 ~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~g  252 (877)
T KOG0151|consen  173 QTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLG  252 (877)
T ss_pred             cccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeec
Confidence            3678999999999999999999999999999999763      2456899999999999999999999999999999999


Q ss_pred             EccC
Q 023765           79 LAHG   82 (277)
Q Consensus        79 ~a~~   82 (277)
                      |++.
T Consensus       253 Wgk~  256 (877)
T KOG0151|consen  253 WGKA  256 (877)
T ss_pred             cccc
Confidence            9853

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.70  E-value=3.6e-07  Score=75.89  Aligned_cols=159  Identities=19%  Similarity=0.235  Sum_probs=107.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeE---EEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVD---IDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~---v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      .+++..|-..+|||..++.+|-.+|.-.-...-   +-+...+.-.|.|.|.|.++|.-+.|++ -+...+.++.|.|.-
T Consensus        57 ~~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~Rdlalk-Rhkhh~g~ryievYk  135 (508)
T KOG1365|consen   57 ADDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALK-RHKHHMGTRYIEVYK  135 (508)
T ss_pred             cCcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhH-hhhhhccCCceeeec
Confidence            357778889999999999999999975421111   1122244556889999999999999998 666778888899887


Q ss_pred             ccCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHh-----cC--CeeEEEEEecCCCcEEEE
Q 023765           80 AHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRR-----AG--DVCFSQVFRDRGGMTGIV  152 (277)
Q Consensus        80 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~-----~g--~v~~~~~~~~~~~~~~fv  152 (277)
                      +....-..-.    ...........+......|.+.+||+++++.++.++|..     -|  .|.+|.-..+..+|-|||
T Consensus       136 a~ge~f~~ia----gg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFv  211 (508)
T KOG1365|consen  136 ATGEEFLKIA----GGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFV  211 (508)
T ss_pred             cCchhheEec----CCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEE
Confidence            6653321110    000001111122223445667899999999999999962     22  244444445566789999


Q ss_pred             EEechhHHHHHHHh
Q 023765          153 DYTSYDDMKYAIRK  166 (277)
Q Consensus       153 ~f~~~~~a~~a~~~  166 (277)
                      .|..+++|+.||.+
T Consensus       212 lfa~ee~aq~aL~k  225 (508)
T KOG1365|consen  212 LFACEEDAQFALRK  225 (508)
T ss_pred             EecCHHHHHHHHHH
Confidence            99999999999963

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.61  E-value=4e-08  Score=75.70  Aligned_cols=66  Identities=24%  Similarity=0.389  Sum_probs=55.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCccc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNF   70 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~   70 (277)
                      ....||||.||.++|||++|+++|+.|--...++|... .....|||+|.+.+.|..||..|+|..|
T Consensus       208 ~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~-~g~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  208 RACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR-GGMPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             hhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC-CCcceEeecHHHHHHHHHHHHHhhccee
Confidence            56678999999999999999999999966666666432 2356899999999999999999998765

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.57  E-value=7e-08  Score=75.40  Aligned_cols=70  Identities=21%  Similarity=0.286  Sum_probs=62.5

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeecC
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYD  187 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~  187 (277)
                      ..+||++||+.+.+.+|+.+|..||.+..+.+...    |+||+|++..+|..|+..||+..+.|-    .+.++...
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~g----f~fv~fed~rda~Dav~~l~~~~l~~e----~~vve~~r   71 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKNG----FGFVEFEDPRDADDAVHDLDGKELCGE----RLVVEHAR   71 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeecc----cceeccCchhhhhcccchhcCceecce----eeeeeccc
Confidence            36899999999999999999999999999988877    899999999999999999999999994    35555544

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.54  E-value=1.6e-07  Score=73.75  Aligned_cols=154  Identities=16%  Similarity=0.164  Sum_probs=109.8

Q ss_pred             EEEcCCCCCCCHHH-H--HHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            9 LYVGNLPGDTRMRE-V--EDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         9 l~V~nL~~~~t~~~-l--~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      ++++|+-..+..+- |  ...|+.+-.+....+..  .+.-.+++|+.|.....-.++...-++..+.-.+|.+--....
T Consensus        99 p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gtsw  178 (290)
T KOG0226|consen   99 PFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTSW  178 (290)
T ss_pred             ccccccccccCCCCCCcchhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceeecccccc
Confidence            45555555555444 3  56666665555544433  3455789999999888888888767777766665444333322


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhH
Q 023765           84 RRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDD  159 (277)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~  159 (277)
                      .....              ..-......||.+.|..+++.+.|...|.+|-......+.++..+    ||+||.|.+..+
T Consensus       179 edPsl--------------~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad  244 (290)
T KOG0226|consen  179 EDPSL--------------AEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPAD  244 (290)
T ss_pred             CCccc--------------ccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHH
Confidence            22111              111234679999999999999999999999998888888876544    599999999999


Q ss_pred             HHHHHHhcCCCeecccc
Q 023765          160 MKYAIRKLDRSEFRNAF  176 (277)
Q Consensus       160 a~~a~~~l~g~~~~g~~  176 (277)
                      +..|+..|+|+.++.+.
T Consensus       245 ~~rAmrem~gkyVgsrp  261 (290)
T KOG0226|consen  245 YVRAMREMNGKYVGSRP  261 (290)
T ss_pred             HHHHHHhhcccccccch
Confidence            99999999999998843

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.53  E-value=5.3e-07  Score=80.21  Aligned_cols=174  Identities=11%  Similarity=-0.004  Sum_probs=118.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      +.+.+-+.++++++...+++++|..- .|..+.|.+   .+...|.++|+|..+.++.+|++ -|...+..+.++|..+.
T Consensus       310 d~~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~-rn~~~~~~R~~q~~P~g  387 (944)
T KOG4307|consen  310 DKYYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFT-RNPSDDVNRPFQTGPPG  387 (944)
T ss_pred             hhheeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHh-cCchhhhhcceeecCCC
Confidence            45677788999999999999998643 344444422   23347899999999999999998 66677778888887665


Q ss_pred             CCCCCC--CC------CCCCCCCCC-----------CCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeE-EEE
Q 023765           82 GGRRHS--SS------MDRYSSYSS-----------GGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCF-SQV  141 (277)
Q Consensus        82 ~~~~~~--~~------~~~~~~~~~-----------~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~-~~~  141 (277)
                      ......  +.      .......+.           +.....+.....+|||..||..+++.++..+|.....|++ |.+
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            322110  00      000000000           0111123345789999999999999999999998887776 555


Q ss_pred             EecCC---CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          142 FRDRG---GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       142 ~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      ...+.   +..|||+|..++++..|+..-+...+..    ..|+|+
T Consensus       468 t~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~----r~irv~  509 (944)
T KOG4307|consen  468 TRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGH----RIIRVD  509 (944)
T ss_pred             ccCCcccccchhhheeccccccchhhhcccccccCc----eEEEee
Confidence            54443   3589999999999998887555555444    455554

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.52  E-value=4.7e-07  Score=72.39  Aligned_cols=70  Identities=26%  Similarity=0.300  Sum_probs=63.8

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC---cEEEEEEechhHHHHHHHhcCCCeecccce
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG---MTGIVDYTSYDDMKYAIRKLDRSEFRNAFS  177 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  177 (277)
                      ....|+|.||++.+..+||+++|.+||.+..+.+..+..+   +.|-|.|...++|..|++.+||..++|...
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~m  154 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPM  154 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCcee
Confidence            3578999999999999999999999999998888888766   699999999999999999999999999653

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.51  E-value=5.7e-08  Score=74.64  Aligned_cols=77  Identities=16%  Similarity=0.125  Sum_probs=66.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC--cEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG--MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~--~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      .+...+|+|+|+...++++.|.|+|-+.|.|..|.|..+...  .||||+|+++..+.-|++.+||..+.+..+.+.++
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            344789999999999999999999999999999999866543  49999999999999999999999998876655443

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.49  E-value=3.9e-07  Score=79.34  Aligned_cols=75  Identities=23%  Similarity=0.333  Sum_probs=65.5

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC-c---EEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG-M---TGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~-~---~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ...+|||.+|...+...+|+.+|.+||+|+-+.|+++... |   |+||+|.+.++|.++|..||..++.|    .-|.|
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHG----rmISV  479 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHG----RMISV  479 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcc----eeeee
Confidence            3568999999999999999999999999999999887543 2   99999999999999999999999999    45555


Q ss_pred             eec
Q 023765          184 REY  186 (277)
Q Consensus       184 ~~~  186 (277)
                      +..
T Consensus       480 Eka  482 (940)
T KOG4661|consen  480 EKA  482 (940)
T ss_pred             eec
Confidence            543

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.47  E-value=4.3e-07  Score=81.74  Aligned_cols=72  Identities=17%  Similarity=0.230  Sum_probs=63.5

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      ..++|||++|+..++++||..+|+.||+|..|.+....  ++|||.+....+|.+|+.+|+...+.++.++..+
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R--~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~W  491 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPR--GCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAW  491 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeeccCC--ceeEEEEeehhHHHHHHHHHhcccccceeeEEee
Confidence            46899999999999999999999999999998876554  5999999999999999999999999886554433

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.41  E-value=1.5e-06  Score=71.42  Aligned_cols=79  Identities=16%  Similarity=0.257  Sum_probs=63.6

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhc-CCCeecccceeeEEE
Q 023765          104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKL-DRSEFRNAFSRSYVR  182 (277)
Q Consensus       104 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l-~g~~~~g~~~~~~i~  182 (277)
                      +......+|||++|...+++++|.++|.+||+|..+.+.....  +|||+|.+.+.|+.|..++ +...|+|    ..|.
T Consensus       223 PeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~~--CAFv~ftTR~aAE~Aae~~~n~lvI~G----~Rl~  296 (377)
T KOG0153|consen  223 PEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRKG--CAFVTFTTREAAEKAAEKSFNKLVING----FRLK  296 (377)
T ss_pred             CcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecccc--cceeeehhhHHHHHHHHhhcceeeecc----eEEE
Confidence            3345568999999999999999999999999999998876654  9999999999999877664 6566677    5566


Q ss_pred             EeecCC
Q 023765          183 VREYDS  188 (277)
Q Consensus       183 ~~~~~~  188 (277)
                      +....+
T Consensus       297 i~Wg~~  302 (377)
T KOG0153|consen  297 IKWGRP  302 (377)
T ss_pred             EEeCCC
Confidence            654443

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.39  E-value=1.8e-06  Score=67.09  Aligned_cols=74  Identities=15%  Similarity=0.191  Sum_probs=63.0

Q ss_pred             CceEEEeCCCCCCCHHHHHH----HHHhcCCeeEEEEEe-cCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          109 DYRVLVTGLPSSASWQDLKD----HMRRAGDVCFSQVFR-DRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~----~f~~~g~v~~~~~~~-~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ..+|||.||...+..++|+.    +|++||.|..|.... .+-.|-|||.|.+.+.|-.|+..|+|.-+-|+    ++++
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK----~mri   84 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGK----PMRI   84 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCc----hhhe
Confidence            44999999999999998888    999999999987764 44457899999999999999999999999995    4444


Q ss_pred             eec
Q 023765          184 REY  186 (277)
Q Consensus       184 ~~~  186 (277)
                      ..+
T Consensus        85 qyA   87 (221)
T KOG4206|consen   85 QYA   87 (221)
T ss_pred             ecc
Confidence            444

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.38  E-value=1.6e-06  Score=66.34  Aligned_cols=75  Identities=16%  Similarity=0.159  Sum_probs=63.2

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhc-CCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRA-GDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~-g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      .....++|..+|..+-+.++..+|.++ |.|..+.+.++..+    +||||+|++.+.|+-|.+.||+..+.++.+.+..
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            445689999999999999999999998 57777777666544    5999999999999999999999999997666544

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=98.38  E-value=3.8e-07  Score=72.00  Aligned_cols=62  Identities=23%  Similarity=0.348  Sum_probs=52.2

Q ss_pred             HHHHHHhh-ccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765           21 REVEDLFY-KYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus        21 ~~l~~~F~-~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      ++|...|+ +||+|+.+++-.  .....|.+||.|..+++|.+|+..||+..|.|++|.+.+..-
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence            44555555 899999998833  345689999999999999999999999999999999998664

>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=98.30  E-value=1.8e-06  Score=60.47  Aligned_cols=70  Identities=16%  Similarity=0.303  Sum_probs=43.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCc-----ccCCceEEEEE
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY-----NFDGYRLRVEL   79 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~-----~~~g~~i~v~~   79 (277)
                      ..|+|.+++..++.++|+++|++||+|..|.+..   ....|||-|.+++.|..|+..+...     .+.+..+.+..
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~---G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~v   76 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSR---GDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEV   76 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--T---T-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE-
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecC---CCCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEE
Confidence            4689999999999999999999999999999864   2458999999999999998766433     44454444444

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.29  E-value=7.5e-06  Score=70.87  Aligned_cols=76  Identities=17%  Similarity=0.242  Sum_probs=61.8

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC----CCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR----GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      ...|||.|||.+++..+|+++|..||.|....|....    ...||||+|.+.+.++.||..- -..+++    ..+.|+
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As-p~~ig~----~kl~Ve  362 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS-PLEIGG----RKLNVE  362 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC-ccccCC----eeEEEE
Confidence            3459999999999999999999999999997666432    2259999999999999999754 556666    677788


Q ss_pred             ecCCC
Q 023765          185 EYDSR  189 (277)
Q Consensus       185 ~~~~~  189 (277)
                      ++...
T Consensus       363 ek~~~  367 (419)
T KOG0116|consen  363 EKRPG  367 (419)
T ss_pred             ecccc
Confidence            77654

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.25  E-value=1.2e-06  Score=69.03  Aligned_cols=75  Identities=19%  Similarity=0.355  Sum_probs=65.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEe---ecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~---~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .-.||.|.|...++++.|-..|.+|-.....++   ..+++++||+||-|.+++++..|+..|||..++.+.|.+.-+
T Consensus       190 DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  190 DFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             cceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            457999999999999999999999865555555   447899999999999999999999999999999998876543

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.24  E-value=7.5e-06  Score=67.38  Aligned_cols=78  Identities=24%  Similarity=0.445  Sum_probs=66.0

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeE--------EEEEecCCC---cEEEEEEechhHHHHHHHhcCCCeecc
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCF--------SQVFRDRGG---MTGIVDYTSYDDMKYAIRKLDRSEFRN  174 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~--------~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g  174 (277)
                      +..++.|||.|||.++|.+++.++|.++|.|..        |.++.+..+   |-|++.|...+++.-|+..|++..+.|
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            344677999999999999999999999997754        677776654   479999999999999999999999998


Q ss_pred             cceeeEEEEeecC
Q 023765          175 AFSRSYVRVREYD  187 (277)
Q Consensus       175 ~~~~~~i~~~~~~  187 (277)
                          ..|+|..+.
T Consensus       211 ----~~~rVerAk  219 (382)
T KOG1548|consen  211 ----KKLRVERAK  219 (382)
T ss_pred             ----cEEEEehhh
Confidence                677776554

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.22  E-value=1.7e-06  Score=75.32  Aligned_cols=71  Identities=18%  Similarity=0.180  Sum_probs=61.4

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeeccccee
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  178 (277)
                      .+..+|+|.|||..++.++|..+|..||+|..|..-.. ..+.+||+|-+..+|+.|++.|++.++.|+.+.
T Consensus        73 ~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~-~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   73 MNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN-KRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             CccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc-cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            44679999999999999999999999999998554333 335899999999999999999999999996544

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=98.21  E-value=8.8e-07  Score=69.81  Aligned_cols=70  Identities=16%  Similarity=0.251  Sum_probs=59.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCC-----------CCC----cEEEEEEcChHHHHHHHHhcCCcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-----------RPP----GYAFLEFEDYRDAEDAIRGRDGYN   69 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~-----------~~~----g~afV~f~~~~~a~~a~~~l~~~~   69 (277)
                      .+-.|||+|||+.+...-|+++|++||+|-.|.|....           ...    .-|+|+|.+...|..+...|||..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            35689999999999999999999999999999994311           111    127899999999999999999999


Q ss_pred             cCCce
Q 023765           70 FDGYR   74 (277)
Q Consensus        70 ~~g~~   74 (277)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99875

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.18  E-value=1.8e-06  Score=71.41  Aligned_cols=80  Identities=29%  Similarity=0.403  Sum_probs=70.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeE--------EEe---ecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVD--------IDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGY   73 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~--------v~~---~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~   73 (277)
                      ...+|||.+||..+++++|.++|.+||.|..        |++   ++|..+++-|.|.|.+...|+.|+..+++..|.+.
T Consensus        65 ~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn  144 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGN  144 (351)
T ss_pred             ccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccCC
Confidence            4678999999999999999999999998764        222   34778999999999999999999999999999999


Q ss_pred             eEEEEEccCCC
Q 023765           74 RLRVELAHGGR   84 (277)
Q Consensus        74 ~i~v~~a~~~~   84 (277)
                      +|.|-+|....
T Consensus       145 ~ikvs~a~~r~  155 (351)
T KOG1995|consen  145 TIKVSLAERRT  155 (351)
T ss_pred             Cchhhhhhhcc
Confidence            99998887544

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.14  E-value=1e-05  Score=72.44  Aligned_cols=70  Identities=17%  Similarity=0.185  Sum_probs=63.3

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC-------cEEEEEEechhHHHHHHHhcCCCeecc
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG-------MTGIVDYTSYDDMKYAIRKLDRSEFRN  174 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~-------~~~fv~f~~~~~a~~a~~~l~g~~~~g  174 (277)
                      ..+..++|||+||++.++++.|...|..||+|..+.|++....       .++||.|-+..+|+.|++.|+|..+.+
T Consensus       170 gDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~  246 (877)
T KOG0151|consen  170 GDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVME  246 (877)
T ss_pred             CCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeee
Confidence            3456789999999999999999999999999999999876532       499999999999999999999999987

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.12  E-value=8.3e-06  Score=66.86  Aligned_cols=76  Identities=24%  Similarity=0.387  Sum_probs=62.1

Q ss_pred             CCeEEEcCCCCCCCHHHH------HHHhhccCCeeEEEeec-CC---CCCcE--EEEEEcChHHHHHHHHhcCCcccCCc
Q 023765            6 SRTLYVGNLPGDTRMREV------EDLFYKYGPIVDIDLKI-PP---RPPGY--AFLEFEDYRDAEDAIRGRDGYNFDGY   73 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l------~~~F~~~G~v~~v~~~~-~~---~~~g~--afV~f~~~~~a~~a~~~l~~~~~~g~   73 (277)
                      .+-+||-+|++.+..+++      .++|.+||.|..|.+.. +.   ...+.  .||+|...|+|..||+..+|..++|+
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            355899999999988873      47999999999999843 21   11122  49999999999999999999999999


Q ss_pred             eEEEEEcc
Q 023765           74 RLRVELAH   81 (277)
Q Consensus        74 ~i~v~~a~   81 (277)
                      .|.+.+..
T Consensus       194 ~lkatYGT  201 (480)
T COG5175         194 VLKATYGT  201 (480)
T ss_pred             eEeeecCc
Confidence            99998855

>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=98.09  E-value=7.2e-06  Score=57.49  Aligned_cols=59  Identities=22%  Similarity=0.405  Sum_probs=39.6

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCC
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRS  170 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~  170 (277)
                      ..|+|.+++..++.++|++.|.+||.|.+|.+..+..  .|+|.|.+.+.|+.|+..+...
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~--~g~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDT--EGYVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-S--EEEEEESS---HHHHHHHHHHT
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCC--EEEEEECCcchHHHHHHHHHhc
Confidence            4788999999999999999999999999999887655  6999999999999999876544

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=98.09  E-value=1.1e-05  Score=48.92  Aligned_cols=53  Identities=32%  Similarity=0.548  Sum_probs=43.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHH
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAI   62 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~   62 (277)
                      ++.|-|.+.+++..+ +|...|.+||+|..+.+.   ....+.||+|.+..+|+.|+
T Consensus         1 ~~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~---~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    1 STWISVSGFPPDLAE-EVLEHFASFGEIVDIYVP---ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             CcEEEEEeECchHHH-HHHHHHHhcCCEEEEEcC---CCCcEEEEEECCHHHHHhhC
Confidence            367899999988664 455588899999999886   23679999999999999985

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=98.07  E-value=3.2e-06  Score=74.09  Aligned_cols=76  Identities=11%  Similarity=0.217  Sum_probs=65.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhh-ccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCccc---CCceEEEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFY-KYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNF---DGYRLRVEL   79 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~-~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~---~g~~i~v~~   79 (277)
                      ..++.|+|.||-..+|.-+|++|+. .+|.|.+++|-   +-+..|||.|.+.++|.+..++|||..+   +++-|.+.|
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmD---kIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf  518 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMD---KIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADF  518 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCchHHHHHH---HhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeee
Confidence            5789999999999999999999999 67899998662   1267899999999999999999999887   467788888


Q ss_pred             ccC
Q 023765           80 AHG   82 (277)
Q Consensus        80 a~~   82 (277)
                      ...
T Consensus       519 ~~~  521 (718)
T KOG2416|consen  519 VRA  521 (718)
T ss_pred             cch
Confidence            763

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.03  E-value=4.8e-06  Score=68.51  Aligned_cols=75  Identities=19%  Similarity=0.172  Sum_probs=63.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccC--CeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYG--PIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G--~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      -.+|||||-|.+|++||.+.+...|  .+.++++.+   +++++|||+|...+...+++.|+.|....|+|+.-.|...+
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~N  160 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSYN  160 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeeccc
Confidence            4589999999999999999988777  555555533   68999999999999999999999999999999986665544

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.99  E-value=7.2e-05  Score=48.98  Aligned_cols=68  Identities=16%  Similarity=0.218  Sum_probs=46.1

Q ss_pred             ceEEEeCCCCCCCHH----HHHHHHHhcC-CeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          110 YRVLVTGLPSSASWQ----DLKDHMRRAG-DVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~----~l~~~f~~~g-~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      ..|+|.|||.+.+..    -|++++..+| .|..|.      ++.|.|.|.+.+.|..|.+.|+|..+-|    .+|.|.
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------GGTAILRFPNQEFAERAQKRMEGEDVFG----NKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE--------TT-EEEEESSHHHHHHHHHHHTT--SSS----S--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe------CCEEEEEeCCHHHHHHHHHhhccccccc----ceEEEE
Confidence            579999999998854    4667777777 676652      2479999999999999999999999999    577776


Q ss_pred             ecC
Q 023765          185 EYD  187 (277)
Q Consensus       185 ~~~  187 (277)
                      ...
T Consensus        73 ~~~   75 (90)
T PF11608_consen   73 FSP   75 (90)
T ss_dssp             SS-
T ss_pred             EcC
Confidence            553

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=97.98  E-value=8.8e-05  Score=50.86  Aligned_cols=65  Identities=15%  Similarity=0.155  Sum_probs=55.1

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEEecC----CCcEEEEEEechhHHHHHHHhcCCCeecc
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRA--GDVCFSQVFRDR----GGMTGIVDYTSYDDMKYAIRKLDRSEFRN  174 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~--g~v~~~~~~~~~----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g  174 (277)
                      ++|.|.|+|...+.++|.+++...  |....+.++.|-    +.|||||.|.+++.|..-.+.++|.....
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~   72 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPN   72 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCcccc
Confidence            589999999999999999988864  566667776554    34799999999999999999999998865

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.95  E-value=7e-06  Score=68.08  Aligned_cols=81  Identities=22%  Similarity=0.358  Sum_probs=71.5

Q ss_pred             CCCCCeEE-EcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEE
Q 023765            3 SRSSRTLY-VGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVE   78 (277)
Q Consensus         3 ~~~~~~l~-V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~   78 (277)
                      ..++.++| |+||+..++.++|+..|..+|.|..+.++.   ++..++||||+|.....+..|+.. +...+.+.++.+.
T Consensus       181 ~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~  259 (285)
T KOG4210|consen  181 SGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLE  259 (285)
T ss_pred             cCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccc
Confidence            34566777 999999999999999999999999999955   568899999999999999999986 8889999999998


Q ss_pred             EccCCC
Q 023765           79 LAHGGR   84 (277)
Q Consensus        79 ~a~~~~   84 (277)
                      ...+..
T Consensus       260 ~~~~~~  265 (285)
T KOG4210|consen  260 EDEPRP  265 (285)
T ss_pred             cCCCCc
Confidence            877643

>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=97.95  E-value=5.5e-05  Score=52.22  Aligned_cols=75  Identities=19%  Similarity=0.269  Sum_probs=55.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEee----------cCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCce
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLK----------IPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYR   74 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~----------~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~   74 (277)
                      ..+.|.|-+.|+. ....|.+.|++||+|.+..-.          ......+...|+|.++.+|.+|+. .||..|.|..
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcE
Confidence            5677999999988 778889999999999887510          112346789999999999999999 9999998865


Q ss_pred             -EEEEEcc
Q 023765           75 -LRVELAH   81 (277)
Q Consensus        75 -i~v~~a~   81 (277)
                       +-|.+++
T Consensus        83 mvGV~~~~   90 (100)
T PF05172_consen   83 MVGVKPCD   90 (100)
T ss_dssp             EEEEEE-H
T ss_pred             EEEEEEcH
Confidence             5577664

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.

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.93  E-value=3.1e-05  Score=69.32  Aligned_cols=73  Identities=23%  Similarity=0.403  Sum_probs=63.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCee-EEEe--ecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIV-DIDL--KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~v~~--~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      ++|-+.|+|++++.+||.++|.-|-.+- +|.+  ..++...|-|.|.|++.++|..|...|++..|..++|.+.+
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            3889999999999999999999996433 3444  44678899999999999999999999999999999988764

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=97.77  E-value=4.8e-05  Score=61.07  Aligned_cols=71  Identities=20%  Similarity=0.209  Sum_probs=62.1

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeeccccee
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  178 (277)
                      .....+||+|+...++.++++.+|..||.|..+.+..+...    +|+||+|.+.+.++.|+. |||..+.|..+.
T Consensus        99 ~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~  173 (231)
T KOG4209|consen   99 VDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIE  173 (231)
T ss_pred             cCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccce
Confidence            34678999999999999999999999999998888766544    599999999999999998 999999995443

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.77  E-value=6.9e-05  Score=65.65  Aligned_cols=76  Identities=26%  Similarity=0.437  Sum_probs=59.8

Q ss_pred             CCeEEEcCCCCCCC--H----HHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccC-CceEE
Q 023765            6 SRTLYVGNLPGDTR--M----REVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFD-GYRLR   76 (277)
Q Consensus         6 ~~~l~V~nL~~~~t--~----~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~-g~~i~   76 (277)
                      ...|+|.|+|---.  .    .-|..+|+++|+|..+.++.  .+..+||.|++|.+..+|+.|++.|||..|+ ...+.
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~  137 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFF  137 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceEE
Confidence            35789999875322  2    23567899999999999975  4568999999999999999999999998885 45566


Q ss_pred             EEEcc
Q 023765           77 VELAH   81 (277)
Q Consensus        77 v~~a~   81 (277)
                      |..-+
T Consensus       138 v~~f~  142 (698)
T KOG2314|consen  138 VRLFK  142 (698)
T ss_pred             eehhh
Confidence            66544

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.69  E-value=0.00012  Score=58.14  Aligned_cols=100  Identities=28%  Similarity=0.244  Sum_probs=80.4

Q ss_pred             HHHHHHHhcCCcccCCceEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCe
Q 023765           57 DAEDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDV  136 (277)
Q Consensus        57 ~a~~a~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v  136 (277)
                      -|..|...|++....|+.|.|.|+..                           ..|+|.||...++.+.|.+.|..||+|
T Consensus         6 ~ae~ak~eLd~~~~~~~~lr~rfa~~---------------------------a~l~V~nl~~~~sndll~~~f~~fg~~   58 (275)
T KOG0115|consen    6 LAEIAKRELDGRFPKGRSLRVRFAMH---------------------------AELYVVNLMQGASNDLLEQAFRRFGPI   58 (275)
T ss_pred             HHHHHHHhcCCCCCCCCceEEEeecc---------------------------ceEEEEecchhhhhHHHHHhhhhcCcc
Confidence            35566677999999999999999874                           479999999999999999999999999


Q ss_pred             eEEEEEecC---CCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          137 CFSQVFRDR---GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       137 ~~~~~~~~~---~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ....++.+.   .++-++|+|.....|.+|+..+...-+.+........|
T Consensus        59 e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~V  108 (275)
T KOG0115|consen   59 ERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGV  108 (275)
T ss_pred             chheeeecccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCC
Confidence            886655443   34589999999999999999886666665444444444

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=97.64  E-value=0.00035  Score=45.78  Aligned_cols=55  Identities=15%  Similarity=0.256  Sum_probs=43.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDG   67 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~   67 (277)
                      +..+|+ +|..+...||.+||+.||.|.--.+.     -..|||...+.++|..|+..+..
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi~-----dTSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWIN-----DTSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEEEEEEC-----TTEEEEEECCCHHHHHHHHHHTT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEEEEEEc-----CCcEEEEeecHHHHHHHHHHhcc
Confidence            455666 99999999999999999998777665     35899999999999999987753

; 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.

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.63  E-value=5.2e-05  Score=64.26  Aligned_cols=64  Identities=27%  Similarity=0.324  Sum_probs=54.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecC--------CC--------CCcEEEEEEcChHHHHHHHHhcCCc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP--------PR--------PPGYAFLEFEDYRDAEDAIRGRDGY   68 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~--------~~--------~~g~afV~f~~~~~a~~a~~~l~~~   68 (277)
                      ++++|.+.|||.+-.-+.|.+||..+|.|..|.+...        +.        .+-+|||+|...+.|.+|.+.|+..
T Consensus       230 ~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~e  309 (484)
T KOG1855|consen  230 PSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNPE  309 (484)
T ss_pred             ccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhchh
Confidence            6789999999999999999999999999999999543        11        2457999999999999999977553

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.62  E-value=0.00031  Score=51.49  Aligned_cols=56  Identities=25%  Similarity=0.422  Sum_probs=46.4

Q ss_pred             HHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765           22 EVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus        22 ~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      +|.+.|..||+|.-+++.     .+--+|+|.+-+.|.+|+. |+|..+.|+.|.|.+..+.
T Consensus        52 ~ll~~~~~~GevvLvRfv-----~~~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFV-----GDTMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEE-----TTCEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE----
T ss_pred             HHHHHHHhCCceEEEEEe-----CCeEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCcc
Confidence            678889999999988887     3467999999999999999 9999999999999986654

; PDB: 1UFW_A 2DNR_A.

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.57  E-value=0.0004  Score=60.50  Aligned_cols=61  Identities=21%  Similarity=0.377  Sum_probs=55.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhh-ccCCeeEEEeecC---CCCCcEEEEEEcChHHHHHHHH
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFY-KYGPIVDIDLKIP---PRPPGYAFLEFEDYRDAEDAIR   63 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~-~~G~v~~v~~~~~---~~~~g~afV~f~~~~~a~~a~~   63 (277)
                      -++.+|||||+||--++.++|..+|+ -||-|..+-|-.+   +-++|.|=|+|.+..+-.+||.
T Consensus       367 lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIs  431 (520)
T KOG0129|consen  367 IDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAIS  431 (520)
T ss_pred             cCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHh
Confidence            36889999999999999999999999 7999999999554   4678999999999999999987

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.51  E-value=0.00032  Score=42.53  Aligned_cols=52  Identities=19%  Similarity=0.239  Sum_probs=41.0

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHH
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAI  164 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~  164 (277)
                      +.|.|.|.++...+. +..+|..||+|..+.+...  ....+|.|.+..+|+.||
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            467888888766644 5568999999999888722  238999999999999985

>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=97.48  E-value=0.001  Score=46.79  Aligned_cols=68  Identities=18%  Similarity=0.153  Sum_probs=52.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhcc-CCeeEEEeecCCCCCc-EEEEEEcChHHHHHHHHhcCCcccC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKY-GPIVDIDLKIPPRPPG-YAFLEFEDYRDAEDAIRGRDGYNFD   71 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~-G~v~~v~~~~~~~~~g-~afV~f~~~~~a~~a~~~l~~~~~~   71 (277)
                      ..+..+.+...|..++.++|..+.+.+ ..|..+.+..++.+.. .++|+|.++++|+..+..+||..|.
T Consensus        11 ~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   11 RRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             CCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            345566666666667777787777776 4777888877765444 5889999999999999999998875

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.39  E-value=0.00027  Score=64.94  Aligned_cols=79  Identities=18%  Similarity=0.219  Sum_probs=69.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      ...|+|.|+|+..|.++|+.+|..+|.+.++.++.  .++++|.|||.|.++.+|..++...+...+....+.|..+++.
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp~  815 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNPE  815 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCCc
Confidence            35689999999999999999999999999998744  6789999999999999999999989988888888888886653


Q ss_pred             C
Q 023765           84 R   84 (277)
Q Consensus        84 ~   84 (277)
                      .
T Consensus       816 ~  816 (881)
T KOG0128|consen  816 R  816 (881)
T ss_pred             c
Confidence            3

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=97.37  E-value=0.00054  Score=55.46  Aligned_cols=62  Identities=23%  Similarity=0.281  Sum_probs=51.2

Q ss_pred             HHHHHHHhhccCCeeEEEeecCC----CCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765           20 MREVEDLFYKYGPIVDIDLKIPP----RPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus        20 ~~~l~~~F~~~G~v~~v~~~~~~----~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      ++++.+..++||.|..|.+....    .-.--.||+|...++|.+|+-.|||..|+|+.+...|-+
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            56678899999999999885422    113357999999999999999999999999998887754

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.33  E-value=0.00042  Score=57.69  Aligned_cols=70  Identities=20%  Similarity=0.273  Sum_probs=59.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeE--------EEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeec
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCF--------SQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFR  173 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~--------~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~  173 (277)
                      .....+|||.+||..+++++|.++|.++|.|..        |+|.++..    .+-|.|.|++...|+.|+.-++++.+.
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            345679999999999999999999999998743        44444443    358999999999999999999999999


Q ss_pred             cc
Q 023765          174 NA  175 (277)
Q Consensus       174 g~  175 (277)
                      +.
T Consensus       143 gn  144 (351)
T KOG1995|consen  143 GN  144 (351)
T ss_pred             CC
Confidence            94

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.29  E-value=0.00016  Score=57.28  Aligned_cols=67  Identities=15%  Similarity=0.160  Sum_probs=59.0

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC---------c-------EEEEEEechhHHHHHHHhcCCCee
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG---------M-------TGIVDYTSYDDMKYAIRKLDRSEF  172 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---------~-------~~fv~f~~~~~a~~a~~~l~g~~~  172 (277)
                      ...||++++|+.+...-|+++|..||+|-.|.+......         +       -|+|+|.....|..+...||+..|
T Consensus        74 ~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~I  153 (278)
T KOG3152|consen   74 TGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPI  153 (278)
T ss_pred             ceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCcc
Confidence            568999999999999999999999999999988744221         1       489999999999999999999999


Q ss_pred             ccc
Q 023765          173 RNA  175 (277)
Q Consensus       173 ~g~  175 (277)
                      +|+
T Consensus       154 ggk  156 (278)
T KOG3152|consen  154 GGK  156 (278)
T ss_pred             CCC
Confidence            985

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.24  E-value=0.0005  Score=63.66  Aligned_cols=81  Identities=27%  Similarity=0.404  Sum_probs=71.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCC--ceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDG--YRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g--~~i~v~~a~   81 (277)
                      ..++.++|++|.+.+....|...|..||.|..|.+-.   ...||||.|++...|..|++.|-|..|+|  +.|.|.++.
T Consensus       453 t~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h---gq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~  529 (975)
T KOG0112|consen  453 TPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH---GQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLAS  529 (975)
T ss_pred             ccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc---CCcceeeecccCccchhhHHHHhcCcCCCCCccccccccc
Confidence            5788999999999999999999999999999988853   36799999999999999999999999975  458999988


Q ss_pred             CCCCCC
Q 023765           82 GGRRHS   87 (277)
Q Consensus        82 ~~~~~~   87 (277)
                      .....+
T Consensus       530 ~~~~~P  535 (975)
T KOG0112|consen  530 PPGATP  535 (975)
T ss_pred             CCCCCh
Confidence            655443

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.16  E-value=0.0014  Score=57.75  Aligned_cols=66  Identities=26%  Similarity=0.315  Sum_probs=55.0

Q ss_pred             CceEEEeCCCCCCC------HHHHHHHHHhcCCeeEEEEEecCCC---cEEEEEEechhHHHHHHHhcCCCeecc
Q 023765          109 DYRVLVTGLPSSAS------WQDLKDHMRRAGDVCFSQVFRDRGG---MTGIVDYTSYDDMKYAIRKLDRSEFRN  174 (277)
Q Consensus       109 ~~~l~v~~l~~~~~------~~~l~~~f~~~g~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g  174 (277)
                      ...|+|.|+|---.      ...|..+|.++|++..+.++.+..+   ||.|++|.++.+|+.|++.|||..++-
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldk  132 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDK  132 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecc
Confidence            56888999886433      3457789999999999988866544   599999999999999999999999975

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.04  E-value=0.002  Score=53.23  Aligned_cols=74  Identities=15%  Similarity=0.200  Sum_probs=58.2

Q ss_pred             CCCCceEEEeCCCCCCCHHH------HHHHHHhcCCeeEEEEEecCCC-----c--EEEEEEechhHHHHHHHhcCCCee
Q 023765          106 RRSDYRVLVTGLPSSASWQD------LKDHMRRAGDVCFSQVFRDRGG-----M--TGIVDYTSYDDMKYAIRKLDRSEF  172 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~------l~~~f~~~g~v~~~~~~~~~~~-----~--~~fv~f~~~~~a~~a~~~l~g~~~  172 (277)
                      ....+-+||-+|++.+..++      -.++|.+||.|..|.|.+....     +  -.+|.|.+.++|..+|...+|..+
T Consensus       111 VvQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~  190 (480)
T COG5175         111 VVQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLL  190 (480)
T ss_pred             eeecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccc
Confidence            34567899999998876555      3579999999999888754311     1  248999999999999999999999


Q ss_pred             cccceee
Q 023765          173 RNAFSRS  179 (277)
Q Consensus       173 ~g~~~~~  179 (277)
                      +|+.+..
T Consensus       191 DGr~lka  197 (480)
T COG5175         191 DGRVLKA  197 (480)
T ss_pred             cCceEee
Confidence            9965543

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=97.03  E-value=0.0053  Score=52.85  Aligned_cols=68  Identities=22%  Similarity=0.349  Sum_probs=59.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcc-CCeeEEEeecCCCCCcE-EEEEEcChHHHHHHHHhcCCcccCC
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKY-GPIVDIDLKIPPRPPGY-AFLEFEDYRDAEDAIRGRDGYNFDG   72 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~-G~v~~v~~~~~~~~~g~-afV~f~~~~~a~~a~~~l~~~~~~g   72 (277)
                      +++.|+|-.+|..+|..||..|...| -.|.++.+..++.+..| ++|+|.+.++|+..+..+||..|..
T Consensus        73 ~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   73 SSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            37899999999999999999999876 48899999887765554 7899999999999999999988853

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=97.01  E-value=0.0027  Score=46.01  Aligned_cols=72  Identities=19%  Similarity=0.248  Sum_probs=55.5

Q ss_pred             CCCeEEEcCCCCCC----CHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            5 SSRTLYVGNLPGDT----RMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         5 ~~~~l~V~nL~~~~----t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      +-.||.|.=|..++    +...|...++.||+|..|.+.    ++..|.|.|.+..+|.+|+.+++. ...|..+++.|-
T Consensus        85 PMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c----GrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsWq  159 (166)
T PF15023_consen   85 PMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC----GRQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSWQ  159 (166)
T ss_pred             CceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec----CCceEEEEehhhHHHHHHHHhhcC-CCCCceEEeecc
Confidence            34567776554444    444566777899999999885    367899999999999999998876 667888888875


Q ss_pred             c
Q 023765           81 H   81 (277)
Q Consensus        81 ~   81 (277)
                      +
T Consensus       160 q  160 (166)
T PF15023_consen  160 Q  160 (166)
T ss_pred             c
Confidence            4

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=96.96  E-value=0.0034  Score=43.35  Aligned_cols=65  Identities=20%  Similarity=0.211  Sum_probs=46.7

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEE-E----------EecCCCcEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQ-V----------FRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~-~----------~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                      ...|.|-+.|+. ....|.++|++||.|.... +          ..........|.|.+..+|.+||. .||..+.|.
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~   81 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGS   81 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTC
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCc
Confidence            456889899888 5566889999999987764 1          111223488999999999999996 899999885

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.96  E-value=0.0012  Score=56.21  Aligned_cols=63  Identities=14%  Similarity=0.265  Sum_probs=54.5

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEec---CC--------------CcEEEEEEechhHHHHHHHhcCC
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD---RG--------------GMTGIVDYTSYDDMKYAIRKLDR  169 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~---~~--------------~~~~fv~f~~~~~a~~a~~~l~g  169 (277)
                      .+..+|.+.|||.+-..+-|.++|..+|.|..|.|...   +.              .-+|+|+|++.+.|.+|.+.|+.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            45789999999999999999999999999999999876   21              12799999999999999997754

>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=96.91  E-value=0.0011  Score=51.07  Aligned_cols=81  Identities=17%  Similarity=0.129  Sum_probs=51.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhc-cCCe---eEEEeec-----CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCc
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYK-YGPI---VDIDLKI-----PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGY   73 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~-~G~v---~~v~~~~-----~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~   73 (277)
                      .+...+|.|.+||+.+|++++.+.+.. ++..   ..+.-..     ......-|||.|.+.+++...+..++|..|.+.
T Consensus         4 ~~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~   83 (176)
T PF03467_consen    4 EKEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDS   83 (176)
T ss_dssp             -----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-T
T ss_pred             cccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECC
Confidence            356679999999999999999998887 6655   3333111     112235699999999999999999999877433


Q ss_pred             -----eEEEEEccCC
Q 023765           74 -----RLRVELAHGG   83 (277)
Q Consensus        74 -----~i~v~~a~~~   83 (277)
                           ...|++|...
T Consensus        84 kg~~~~~~VE~Apyq   98 (176)
T PF03467_consen   84 KGNEYPAVVEFAPYQ   98 (176)
T ss_dssp             TS-EEEEEEEE-SS-
T ss_pred             CCCCcceeEEEcchh
Confidence                 3567776653

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.

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.91  E-value=0.0034  Score=50.93  Aligned_cols=55  Identities=15%  Similarity=0.179  Sum_probs=47.0

Q ss_pred             HHHHHHHHHhcCCeeEEEEEecCCC-----cEEEEEEechhHHHHHHHhcCCCeecccce
Q 023765          123 WQDLKDHMRRAGDVCFSQVFRDRGG-----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFS  177 (277)
Q Consensus       123 ~~~l~~~f~~~g~v~~~~~~~~~~~-----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  177 (277)
                      ++++.+.+.+||.|..|.|...++.     .--||+|...++|.+|+-.|||..|+|+.+
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v  359 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVV  359 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceee
Confidence            4578899999999999988876543     257999999999999999999999999543

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.86  E-value=0.00062  Score=54.17  Aligned_cols=58  Identities=16%  Similarity=0.218  Sum_probs=45.6

Q ss_pred             HHHHHHHH-hcCCeeEEEEEecCCC---cEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          124 QDLKDHMR-RAGDVCFSQVFRDRGG---MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       124 ~~l~~~f~-~~g~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      ++|...|. +||+|..+.|..+-..   |-++|.|...++|++|+..||+.++.|+.+...+
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~  144 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAEL  144 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeee
Confidence            45555555 8999999877655332   4689999999999999999999999997665543

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.71  E-value=0.0079  Score=44.21  Aligned_cols=52  Identities=17%  Similarity=0.210  Sum_probs=43.0

Q ss_pred             HHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeE
Q 023765          124 QDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSY  180 (277)
Q Consensus       124 ~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  180 (277)
                      .+|.+.|..||++.-+.+..+    .-+|.|.+-+.|.+|+. ++|.+++|..+...
T Consensus        51 ~~ll~~~~~~GevvLvRfv~~----~mwVTF~dg~sALaals-~dg~~v~g~~l~i~  102 (146)
T PF08952_consen   51 DELLQKFAQYGEVVLVRFVGD----TMWVTFRDGQSALAALS-LDGIQVNGRTLKIR  102 (146)
T ss_dssp             HHHHHHHHCCS-ECEEEEETT----CEEEEESSCHHHHHHHH-GCCSEETTEEEEEE
T ss_pred             HHHHHHHHhCCceEEEEEeCC----eEEEEECccHHHHHHHc-cCCcEECCEEEEEE
Confidence            478888999999998888776    58999999999999997 99999999544433

; PDB: 1UFW_A 2DNR_A.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.49  E-value=0.025  Score=35.19  Aligned_cols=54  Identities=13%  Similarity=0.175  Sum_probs=42.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhcc---CCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhc
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKY---GPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGR   65 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~---G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l   65 (277)
                      .+|+|.++. +++.++|+.+|..|   .....|.+..+    ..|-|.|.+.+.|..|+..|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdD----tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDD----TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecC----CcEEEEECCHHHHHHHHHcC
Confidence            578999985 68999999999988   13445555543    46889999999999999764

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.43  E-value=0.016  Score=38.11  Aligned_cols=56  Identities=18%  Similarity=0.241  Sum_probs=41.9

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCC
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDR  169 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g  169 (277)
                      ...++|. +|..+...||.++|..||.|.--.|...    .|||...+.+.|..|+..+..
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi~dT----SAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWINDT----SAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEEEEEECTT----EEEEEECCCHHHHHHHHHHTT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEEEEEEcCC----cEEEEeecHHHHHHHHHHhcc
Confidence            4566676 9999999999999999999864444322    699999999999999887754

; 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.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.39  E-value=0.034  Score=34.60  Aligned_cols=55  Identities=16%  Similarity=0.107  Sum_probs=44.4

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhc---CCeeEEEEEecCCCcEEEEEEechhHHHHHHHhc
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRA---GDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKL  167 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~---g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l  167 (277)
                      ...|+|.|+. +++-++|+.+|..|   .....|.+..+.   .|-|.|.+.+.|..||..|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt---ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT---SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC---cEEEEECCHHHHHHHHHcC
Confidence            4589999985 57888999999998   235567777775   5889999999999999764

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=96.28  E-value=0.0019  Score=53.60  Aligned_cols=76  Identities=29%  Similarity=0.423  Sum_probs=59.5

Q ss_pred             CeEEEcCCCCCCCHHHHH---HHhhccCCeeEEEeecCC------CCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEE
Q 023765            7 RTLYVGNLPGDTRMREVE---DLFYKYGPIVDIDLKIPP------RPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV   77 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~---~~F~~~G~v~~v~~~~~~------~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v   77 (277)
                      +-+||-+|+..+..+.+.   +.|.+||.|..|.+..+.      ...--++|+|...++|..||...+|..++|+.|.+
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            457888898887776664   588899999999885422      11123899999999999999999999999999777


Q ss_pred             EEccC
Q 023765           78 ELAHG   82 (277)
Q Consensus        78 ~~a~~   82 (277)
                      .+...
T Consensus       158 ~~gtt  162 (327)
T KOG2068|consen  158 SLGTT  162 (327)
T ss_pred             hhCCC
Confidence            66553

>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=96.24  E-value=0.14  Score=42.04  Aligned_cols=163  Identities=11%  Similarity=0.107  Sum_probs=98.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCC----------CCCcEEEEEEcChHHHHHHHH----hcCC--cc
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP----------RPPGYAFLEFEDYRDAEDAIR----GRDG--YN   69 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~----------~~~g~afV~f~~~~~a~~a~~----~l~~--~~   69 (277)
                      ++.|.+.||...++...+...|-+||+|+.|.|....          .....+.+-|-+.+.|...+.    .|..  ..
T Consensus        15 TRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsEfK~~   94 (309)
T PF10567_consen   15 TRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSEFKTK   94 (309)
T ss_pred             eHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHHHHHh
Confidence            5678899999999999999999999999999995432          334578999999999987653    2222  34


Q ss_pred             cCCceEEEEEccCCCCCCCC-CCCCCCC----CCCCC-CCCCCCCCceEEEeCCCCCC-CHHHHHHHH---HhcC----C
Q 023765           70 FDGYRLRVELAHGGRRHSSS-MDRYSSY----SSGGS-RGVSRRSDYRVLVTGLPSSA-SWQDLKDHM---RRAG----D  135 (277)
Q Consensus        70 ~~g~~i~v~~a~~~~~~~~~-~~~~~~~----~~~~~-~~~~~~~~~~l~v~~l~~~~-~~~~l~~~f---~~~g----~  135 (277)
                      +.-..|.|.+..-....... .+....+    ...-. .-........|.|.=- ..+ .++.+.+.+   ..-+    .
T Consensus        95 L~S~~L~lsFV~l~y~~~~~~~~~~~~~~~~~~~~L~~~i~~~gATRSl~IeF~-~~~~~~dl~~~kL~fL~~~~n~RYV  173 (309)
T PF10567_consen   95 LKSESLTLSFVSLNYQKKTDPNDEEADFSDYLVASLQYNIINRGATRSLAIEFK-DPVDKDDLIEKKLPFLKNSNNKRYV  173 (309)
T ss_pred             cCCcceeEEEEEEeccccccccccccchhhHHhhhhhheeecCCcceEEEEEec-CccchhHHHHHhhhhhccCCCceEE
Confidence            55667777776532211110 1111111    00001 1122333556666532 334 333333322   2233    2


Q ss_pred             eeEEEEEecC------CCcEEEEEEechhHHHHHHHhcCC
Q 023765          136 VCFSQVFRDR------GGMTGIVDYTSYDDMKYAIRKLDR  169 (277)
Q Consensus       136 v~~~~~~~~~------~~~~~fv~f~~~~~a~~a~~~l~g  169 (277)
                      ++.|.++...      +..||.+.|-+...|.+.++.+.-
T Consensus       174 lEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk~  213 (309)
T PF10567_consen  174 LESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLKS  213 (309)
T ss_pred             EEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHHh
Confidence            4556665332      224999999999999999987763

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.

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=96.11  E-value=0.025  Score=46.32  Aligned_cols=72  Identities=18%  Similarity=0.274  Sum_probs=56.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCce-EEEEEccCC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYR-LRVELAHGG   83 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~-i~v~~a~~~   83 (277)
                      .=|.|-++|+. ....|..+|++||+|......   ..-.+-+|.|.+.-+|.+|+. .||+.|+|.. |-|..+.++
T Consensus       198 ~WVTVfGFppg-~~s~vL~~F~~cG~Vvkhv~~---~ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpCtDk  270 (350)
T KOG4285|consen  198 TWVTVFGFPPG-QVSIVLNLFSRCGEVVKHVTP---SNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPCTDK  270 (350)
T ss_pred             ceEEEeccCcc-chhHHHHHHHhhCeeeeeecC---CCCceEEEEecchhHHHHhhh-hcCeeeccceEEeeeecCCH
Confidence            44777788765 456778899999999987665   335689999999999999998 8999998865 556665544

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=96.06  E-value=0.024  Score=50.19  Aligned_cols=56  Identities=14%  Similarity=0.206  Sum_probs=47.6

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHh--cCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhc
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRR--AGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKL  167 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~--~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l  167 (277)
                      .+.|++..||..+..++|+.+|+-  +-+++.|.+..+.+   =||+|++..||+.|.+.|
T Consensus       175 RcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~n---WyITfesd~DAQqAykyl  232 (684)
T KOG2591|consen  175 RCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDN---WYITFESDTDAQQAYKYL  232 (684)
T ss_pred             eeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCc---eEEEeecchhHHHHHHHH
Confidence            467888999999999999999995  56788888877653   689999999999998765

>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=96.03  E-value=0.033  Score=43.20  Aligned_cols=63  Identities=29%  Similarity=0.355  Sum_probs=46.6

Q ss_pred             CHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcC--CcccCCceEEEEEccCCC
Q 023765           19 RMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRD--GYNFDGYRLRVELAHGGR   84 (277)
Q Consensus        19 t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~--~~~~~g~~i~v~~a~~~~   84 (277)
                      ..+.|.++|..|+.+..+.+..   +-+-..|.|.+.++|..|...|+  +..|.|..|.|.++....
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~---sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLK---SFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEET---TTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----SS
T ss_pred             hHHHHHHHHHhcCCceEEEEcC---CCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccccc
Confidence            4578999999999888887763   24568999999999999999999  999999999999986443

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.

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=95.95  E-value=0.005  Score=53.28  Aligned_cols=75  Identities=15%  Similarity=0.232  Sum_probs=61.7

Q ss_pred             CCCeEEEcCCCCCC-CHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            5 SSRTLYVGNLPGDT-RMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         5 ~~~~l~V~nL~~~~-t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      +.+.|.+--+|+.+ |.++|...|.+||+|..|.+-..   .-.|.|+|.+..+|-.|.. .++..|+++.|+|-|.++.
T Consensus       371 dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~---~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps  446 (526)
T KOG2135|consen  371 DHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS---SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPS  446 (526)
T ss_pred             ccchhhhhccCCCCchHhhhhhhhhhcCccccccccCc---hhhheeeeeccccccchhc-cccceecCceeEEEEecCC
Confidence            44555555556654 57889999999999999999543   4578999999999999988 8999999999999998864

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=95.92  E-value=0.0053  Score=54.59  Aligned_cols=67  Identities=15%  Similarity=0.192  Sum_probs=54.7

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHh-cCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeec
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRR-AGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFR  173 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~-~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~  173 (277)
                      .....+.|||.||--..|.-+|++++.. .|.|...+|-..+.  .|||.|.+.++|.+....|||....
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDkIKS--hCyV~yss~eEA~atr~AlhnV~WP  507 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDKIKS--HCYVSYSSVEEAAATREALHNVQWP  507 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHHHHHHhhc--ceeEecccHHHHHHHHHHHhccccC
Confidence            3456789999999999999999999995 55666664443333  6999999999999999999997763

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=95.90  E-value=0.011  Score=52.22  Aligned_cols=71  Identities=17%  Similarity=0.285  Sum_probs=55.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhc--cCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCC--cccCCceEEEEE
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYK--YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDG--YNFDGYRLRVEL   79 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~--~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~--~~~~g~~i~v~~   79 (277)
                      .-+.|+|.-||..+..++|+.||..  |-++++|.+..+    .-=||+|++..||..|++.|..  ..|-|++|...+
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N----~nWyITfesd~DAQqAykylreevk~fqgKpImARI  248 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHN----DNWYITFESDTDAQQAYKYLREEVKTFQGKPIMARI  248 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeec----CceEEEeecchhHHHHHHHHHHHHHhhcCcchhhhh
Confidence            4467899999999999999999974  778999988542    2349999999999999877754  456666655443

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=95.66  E-value=0.013  Score=46.79  Aligned_cols=75  Identities=28%  Similarity=0.366  Sum_probs=59.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCccc----CCceEEEEEc
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNF----DGYRLRVELA   80 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~----~g~~i~v~~a   80 (277)
                      ..|+|.||..-+.-+.|.+-|+.||+|....++.  .+++.+-++|+|...-.|.+|+..+....|    .+.+..|...
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~  111 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEPM  111 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCChh
Confidence            6799999999999999999999999998866644  356778899999999999999987754333    3444555443


Q ss_pred             c
Q 023765           81 H   81 (277)
Q Consensus        81 ~   81 (277)
                      .
T Consensus       112 e  112 (275)
T KOG0115|consen  112 E  112 (275)
T ss_pred             h
Confidence            3

>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=95.39  E-value=0.093  Score=34.18  Aligned_cols=59  Identities=24%  Similarity=0.349  Sum_probs=36.9

Q ss_pred             CCCCHHHHHHHhhccC-----CeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765           16 GDTRMREVEDLFYKYG-----PIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus        16 ~~~t~~~l~~~F~~~G-----~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      ..++..+|..++...+     .|-.|.+.     ..|+||+.. .+.|..++..|++..+.|+.|.|+.|
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-----DNFSFVEVP-EEVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE------SS-EEEEE--TT-HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEe-----eeEEEEEEC-HHHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            3578889999887663     56667776     569999886 45888999999999999999999875

; PDB: 2G0C_A 3MOJ_B.

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=95.29  E-value=0.01  Score=53.50  Aligned_cols=71  Identities=20%  Similarity=0.183  Sum_probs=62.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      +.-+|||+||...+..+-+..+...||-|..+....      |||.+|.....+..|+..|+...++|..+.+..-.
T Consensus        39 ~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~d~  109 (668)
T KOG2253|consen   39 PRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENVDE  109 (668)
T ss_pred             CCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh------hcccchhhHHHHHHHHHHhcccCCCcchhhccchh
Confidence            457899999999999999999999999988876542      99999999999999999999999999998877643

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.29  E-value=0.082  Score=47.24  Aligned_cols=80  Identities=20%  Similarity=0.346  Sum_probs=62.3

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHhhcc----CCeeEEEeecC-------------CC---------------------
Q 023765            3 SRSSRTLYVGNLPGD-TRMREVEDLFYKY----GPIVDIDLKIP-------------PR---------------------   43 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~-~t~~~l~~~F~~~----G~v~~v~~~~~-------------~~---------------------   43 (277)
                      +..++.|-|.||.|+ +...+|..+|..|    |.|..|.|..+             |.                     
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            457899999999996 8999999999877    58999888221             11                     


Q ss_pred             ----------------CCcEEEEEEcChHHHHHHHHhcCCcccCC--ceEEEEEccC
Q 023765           44 ----------------PPGYAFLEFEDYRDAEDAIRGRDGYNFDG--YRLRVELAHG   82 (277)
Q Consensus        44 ----------------~~g~afV~f~~~~~a~~a~~~l~~~~~~g--~~i~v~~a~~   82 (277)
                                      .--||.|+|.+.+.|.+.+..++|+.|..  ..|-+.|...
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFIPD  307 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFIPD  307 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeeecCC
Confidence                            01378999999999999999999999964  4455555443

>KOG0835 consensus Cyclin L [General function prediction only]

Probab=95.26  E-value=0.037  Score=46.00  Aligned_cols=19  Identities=16%  Similarity=0.076  Sum_probs=12.4

Q ss_pred             CcEEEEEEcChHHHHHHHH
Q 023765           45 PGYAFLEFEDYRDAEDAIR   63 (277)
Q Consensus        45 ~g~afV~f~~~~~a~~a~~   63 (277)
                      +.-.||-|..+.-|.+++.
T Consensus       173 RT~v~vry~pe~iACaciy  191 (367)
T KOG0835|consen  173 RTDVFVRYSPESIACACIY  191 (367)
T ss_pred             ccceeeecCHHHHHHHHHH
Confidence            4456788876666666654

>KOG0835 consensus Cyclin L [General function prediction only]

Probab=95.08  E-value=0.03  Score=46.48  Aligned_cols=12  Identities=0%  Similarity=0.125  Sum_probs=7.1

Q ss_pred             CCCHHHHHHHHH
Q 023765          120 SASWQDLKDHMR  131 (277)
Q Consensus       120 ~~~~~~l~~~f~  131 (277)
                      ++++++|.+++-
T Consensus       212 d~~k~eid~ic~  223 (367)
T KOG0835|consen  212 DTTKREIDEICY  223 (367)
T ss_pred             CCcHHHHHHHHH
Confidence            456666666554

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=94.92  E-value=0.054  Score=47.17  Aligned_cols=65  Identities=17%  Similarity=0.230  Sum_probs=49.2

Q ss_pred             eEEEeCCCCCC-CHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeeccccee
Q 023765          111 RVLVTGLPSSA-SWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       111 ~l~v~~l~~~~-~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  178 (277)
                      .|.+.-.+..+ +..+|..+|.+||+|..|.+-...  .-|.|+|.+..+|-.|.. .++..|+++.+.
T Consensus       374 ~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~--~~a~vTF~t~aeag~a~~-s~~avlnnr~iK  439 (526)
T KOG2135|consen  374 PLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSS--LHAVVTFKTRAEAGEAYA-SHGAVLNNRFIK  439 (526)
T ss_pred             hhhhhccCCCCchHhhhhhhhhhcCccccccccCch--hhheeeeeccccccchhc-cccceecCceeE
Confidence            34444455554 578999999999999999886652  258999999999977764 889999985443

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=94.74  E-value=0.0012  Score=56.22  Aligned_cols=78  Identities=15%  Similarity=0.296  Sum_probs=67.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      ++.+.|.|||+...++.|-.|+.+||.|+.|....+....-..-|+|...+.+..|++.|+|..+....+.|.|....
T Consensus        80 srk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~etavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiPde  157 (584)
T KOG2193|consen   80 SRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIPDE  157 (584)
T ss_pred             hhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCchh
Confidence            567899999999999999999999999999988655433445568899999999999999999999999998886644

>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=94.62  E-value=0.11  Score=40.14  Aligned_cols=68  Identities=12%  Similarity=0.205  Sum_probs=46.4

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHh-cCCe---eEEEEEecCCC------cEEEEEEechhHHHHHHHhcCCCeecccc
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRR-AGDV---CFSQVFRDRGG------MTGIVDYTSYDDMKYAIRKLDRSEFRNAF  176 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~-~g~v---~~~~~~~~~~~------~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  176 (277)
                      ..+|.|.+||+.+|++++.+.+.. ++..   .++.-......      .-|+|.|.+.+++..-...++|..+-+..
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            569999999999999999987776 6655   23321122111      16999999999999999999998775543

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.

>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=94.57  E-value=0.56  Score=33.10  Aligned_cols=65  Identities=9%  Similarity=0.047  Sum_probs=47.6

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcC-CeeEEEEEecCCC--cEEEEEEechhHHHHHHHhcCCCeecc
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRAG-DVCFSQVFRDRGG--MTGIVDYTSYDDMKYAIRKLDRSEFRN  174 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~g-~v~~~~~~~~~~~--~~~fv~f~~~~~a~~a~~~l~g~~~~g  174 (277)
                      ..+.+...|..++.++|..+...+- .|..+.|.++...  ..+.+.|.+.+.|.+-...+||+.++.
T Consensus        14 ~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   14 TLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             eEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            3444444555566667766666555 4666788877554  378999999999999999999999976

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=94.34  E-value=0.057  Score=40.53  Aligned_cols=120  Identities=17%  Similarity=0.130  Sum_probs=79.8

Q ss_pred             EEEcCCC--CCCCHHHHHHHhhc-cCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCCCC
Q 023765            9 LYVGNLP--GDTRMREVEDLFYK-YGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGRR   85 (277)
Q Consensus         9 l~V~nL~--~~~t~~~l~~~F~~-~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~~~   85 (277)
                      ..|+.+.  ...+...|.+.+.. ++....+.+..-  ..++..+.|.+++++..++. .....+.|..|.+....+...
T Consensus        18 ~lVg~~l~~~~~~~~~l~~~l~~~W~~~~~~~i~~l--~~~~fl~~F~~~~d~~~vl~-~~p~~~~~~~~~l~~W~~~~~   94 (153)
T PF14111_consen   18 CLVGRVLSPKPISLSALEQELAKIWKLKGGVKIRDL--GDNLFLFQFESEEDRQRVLK-GGPWNFNGHFLILQRWSPDFN   94 (153)
T ss_pred             EEEEEECCCCCCCHHHHHHHHHHHhCCCCcEEEEEe--CCCeEEEEEEeccceeEEEe-cccccccccchhhhhhccccc
Confidence            4455552  34667777777664 454444444321  26899999999999999987 555667787777777664322


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCC-CCHHHHHHHHHhcCCeeEEEEEecC
Q 023765           86 HSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSS-ASWQDLKDHMRRAGDVCFSQVFRDR  145 (277)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~-~~~~~l~~~f~~~g~v~~~~~~~~~  145 (277)
                      ....              .......-|.|-|||.. .+++.|..+...+|++..++.....
T Consensus        95 ~~~~--------------~~~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~i~vD~~t~~  141 (153)
T PF14111_consen   95 PSEV--------------KFEHIPVWVRIYGLPLHLWSEEILKAIGSKIGEPIEVDENTLK  141 (153)
T ss_pred             cccc--------------ceeccchhhhhccCCHHHhhhHHHHHHHHhcCCeEEEEcCCCC
Confidence            1110              00111345777899988 6788899999999999888876554

>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=94.05  E-value=0.27  Score=31.11  Aligned_cols=55  Identities=25%  Similarity=0.467  Sum_probs=44.2

Q ss_pred             CCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEE
Q 023765           17 DTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV   77 (277)
Q Consensus        17 ~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v   77 (277)
                      .++.++|+..+..|+- ..|....    .|| ||.|.+..+|++++...++..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-~~I~~d~----tGf-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-DRIRDDR----TGF-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-ceEEecC----CEE-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            5789999999999963 4444432    344 89999999999999999999998887765

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=93.93  E-value=0.07  Score=44.63  Aligned_cols=68  Identities=16%  Similarity=0.140  Sum_probs=55.7

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCC--eeEEEEEecC----CCcEEEEEEechhHHHHHHHhcCCCeecccc
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGD--VCFSQVFRDR----GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAF  176 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~--v~~~~~~~~~----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  176 (277)
                      ..++||+||-+.+|.+||.+.+...|-  +..++++.+.    ..|||+|.........+.++.|-.+.|.|..
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~  153 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQS  153 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCC
Confidence            568999999999999999999988773  4445555443    3469999999999999999999999998853

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=93.63  E-value=0.37  Score=41.92  Aligned_cols=66  Identities=11%  Similarity=0.155  Sum_probs=58.3

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcC-CeeEEEEEecCCC--cEEEEEEechhHHHHHHHhcCCCeecc
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAG-DVCFSQVFRDRGG--MTGIVDYTSYDDMKYAIRKLDRSEFRN  174 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g-~v~~~~~~~~~~~--~~~fv~f~~~~~a~~a~~~l~g~~~~g  174 (277)
                      ...|+|-.+|..++..||..++..+- .|..+.++++...  ..++|.|.+.++|..-...+||+.++.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            77899999999999999999999876 5788888887544  378999999999999999999999876

>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=93.49  E-value=0.16  Score=34.16  Aligned_cols=73  Identities=22%  Similarity=0.348  Sum_probs=44.8

Q ss_pred             EEEEEcChHHHHHHHHhcCC-cccCCceEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHH
Q 023765           48 AFLEFEDYRDAEDAIRGRDG-YNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDL  126 (277)
Q Consensus        48 afV~f~~~~~a~~a~~~l~~-~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l  126 (277)
                      |+|+|.++..|+..+..-.. ..+.+..+.|.............           .--......+|.|.|||....+++|
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~-----------qv~~~vs~rtVlvsgip~~l~ee~l   69 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKF-----------QVFSGVSKRTVLVSGIPDVLDEEEL   69 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEE-----------EEEEcccCCEEEEeCCCCCCChhhh
Confidence            68999999999998873222 34456666665543222111000           0001123678999999999999988


Q ss_pred             HHHHH
Q 023765          127 KDHMR  131 (277)
Q Consensus       127 ~~~f~  131 (277)
                      ++.+.
T Consensus        70 ~D~Le   74 (88)
T PF07292_consen   70 RDKLE   74 (88)
T ss_pred             eeeEE
Confidence            77543

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=93.46  E-value=0.057  Score=50.32  Aligned_cols=76  Identities=18%  Similarity=0.208  Sum_probs=61.6

Q ss_pred             CCCeEEEcCC------------CCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCccc--
Q 023765            5 SSRTLYVGNL------------PGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNF--   70 (277)
Q Consensus         5 ~~~~l~V~nL------------~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~--   70 (277)
                      ++.+|-|.|+            +-.++-.-|..+|..||.|.+.++..+   -..|.|+|...+.|..|...|+|+.+  
T Consensus       285 ptn~isisnv~plqp~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~---~N~alvs~~s~~sai~a~dAl~gkevs~  361 (1007)
T KOG4574|consen  285 PTNTISISNVFPLQPKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRD---LNMALVSFSSVESAILALDALQGKEVSV  361 (1007)
T ss_pred             ccCcceecccccCcchhhhhcccccchHHHHHHHHHhhcchhhheeccc---ccchhhhhHHHHHHHHhhhhhcCCcccc
Confidence            4555555555            445677889999999999999988643   56899999999999999999999876  


Q ss_pred             CCceEEEEEccCC
Q 023765           71 DGYRLRVELAHGG   83 (277)
Q Consensus        71 ~g~~i~v~~a~~~   83 (277)
                      -|-+.+|.+|+.-
T Consensus       362 ~g~Ps~V~~ak~~  374 (1007)
T KOG4574|consen  362 TGAPSRVSFAKTL  374 (1007)
T ss_pred             cCCceeEEecccc
Confidence            5888899888743

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=93.27  E-value=0.59  Score=38.57  Aligned_cols=70  Identities=19%  Similarity=0.213  Sum_probs=53.2

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      ..-|.|-++++... .-|..+|.+||+|+.....  .++.+-+|.|.+.-+|.+||. .||..|+|.   .-|.|..
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~--~ngNwMhirYssr~~A~KALs-kng~ii~g~---vmiGVkp  266 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP--SNGNWMHIRYSSRTHAQKALS-KNGTIIDGD---VMIGVKP  266 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeecC--CCCceEEEEecchhHHHHhhh-hcCeeeccc---eEEeeee
Confidence            45677778876644 3467889999999776555  445589999999999999997 899999885   4455544

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=92.86  E-value=0.55  Score=34.38  Aligned_cols=62  Identities=8%  Similarity=0.110  Sum_probs=46.0

Q ss_pred             CCCceEEEeCCCCCCC----HHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCe
Q 023765          107 RSDYRVLVTGLPSSAS----WQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSE  171 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~----~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~  171 (277)
                      ++..+|.|.=|..++.    ...+...+..||+|..|.+.-..   .|.|.|.+...|..|+.+++...
T Consensus        84 pPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGrq---savVvF~d~~SAC~Av~Af~s~~  149 (166)
T PF15023_consen   84 PPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGRQ---SAVVVFKDITSACKAVSAFQSRA  149 (166)
T ss_pred             CCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCCc---eEEEEehhhHHHHHHHHhhcCCC
Confidence            4466787876655543    33455566789999998876443   69999999999999999988743

>KOG2888 consensus Putative RNA binding protein [General function prediction only]

Probab=91.80  E-value=0.084  Score=43.84  Aligned_cols=8  Identities=0%  Similarity=0.198  Sum_probs=3.8

Q ss_pred             EEEEEccC
Q 023765           75 LRVELAHG   82 (277)
Q Consensus        75 i~v~~a~~   82 (277)
                      |.|.+.++
T Consensus       163 mYiRYtqp  170 (453)
T KOG2888|consen  163 MYIRYTQP  170 (453)
T ss_pred             eEEeecCC
Confidence            44555443

>KOG2891 consensus Surface glycoprotein [General function prediction only]

Probab=90.08  E-value=0.12  Score=42.02  Aligned_cols=66  Identities=20%  Similarity=0.458  Sum_probs=45.2

Q ss_pred             CCCeEEEcCCCCCC------------CHHHHHHHhhccCCeeEEEeec--------CCC-----CCcE---------EEE
Q 023765            5 SSRTLYVGNLPGDT------------RMREVEDLFYKYGPIVDIDLKI--------PPR-----PPGY---------AFL   50 (277)
Q Consensus         5 ~~~~l~V~nL~~~~------------t~~~l~~~F~~~G~v~~v~~~~--------~~~-----~~g~---------afV   50 (277)
                      -..||++.+||-.+            +++.|...|+.||.|..|.++.        +++     ..||         |||
T Consensus       148 rpdti~la~ip~kwf~lkedg~~dlpse~rlr~a~eafg~ir~vdipicdplr~~mn~kisgiq~~gfg~g~dlffeayv  227 (445)
T KOG2891|consen  148 RPDTIHLAGIPCKWFALKEDGSEDLPSEDRLRKAFEAFGEIRNVDIPICDPLREEMNGKISGIQFHGFGFGGDLFFEAYV  227 (445)
T ss_pred             CCCceeecCCcceeeeecccccccCChHHHHHHHHHHhccceecCCcccchhHHHhcCccccceeeccccCcchhHHHHH
Confidence            35689999998643            5788999999999999998843        222     2344         345


Q ss_pred             EEcChHHHHHHHHhcCCccc
Q 023765           51 EFEDYRDAEDAIRGRDGYNF   70 (277)
Q Consensus        51 ~f~~~~~a~~a~~~l~~~~~   70 (277)
                      +|...---..||..|.|+.+
T Consensus       228 qfmeykgfa~amdalr~~k~  247 (445)
T KOG2891|consen  228 QFMEYKGFAQAMDALRGMKL  247 (445)
T ss_pred             HHHHHHhHHHHHHHHhcchH
Confidence            55555555667777777554

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=89.95  E-value=0.17  Score=42.28  Aligned_cols=68  Identities=16%  Similarity=0.137  Sum_probs=53.6

Q ss_pred             CceEEEeCCCCCCCHHHHH---HHHHhcCCeeEEEEEecCC----C-c--EEEEEEechhHHHHHHHhcCCCeecccc
Q 023765          109 DYRVLVTGLPSSASWQDLK---DHMRRAGDVCFSQVFRDRG----G-M--TGIVDYTSYDDMKYAIRKLDRSEFRNAF  176 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~---~~f~~~g~v~~~~~~~~~~----~-~--~~fv~f~~~~~a~~a~~~l~g~~~~g~~  176 (277)
                      .+.+||-+|+..+..+.+.   +.|.+||.|..|.+..+..    . +  -++|.|...++|..||...+|..++|+.
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~  154 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRA  154 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhh
Confidence            4567888888776544433   4788999999988887652    1 1  5899999999999999999999999865

>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=89.59  E-value=2.7  Score=27.24  Aligned_cols=56  Identities=11%  Similarity=0.200  Sum_probs=33.9

Q ss_pred             CCCCCHHHHHHHHHhcC-----CeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeeccccee
Q 023765          118 PSSASWQDLKDHMRRAG-----DVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       118 ~~~~~~~~l~~~f~~~g-----~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  178 (277)
                      -..++..+|..++...+     .|-.+.+...    |+||+-.. +.|..++..|++..+.|+.+.
T Consensus        10 ~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~----~S~vev~~-~~a~~v~~~l~~~~~~gk~v~   70 (74)
T PF03880_consen   10 KDGLTPRDIVGAICNEAGIPGRDIGRIDIFDN----FSFVEVPE-EVAEKVLEALNGKKIKGKKVR   70 (74)
T ss_dssp             GGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS-----EEEEE-T-T-HHHHHHHHTT--SSS----
T ss_pred             ccCCCHHHHHHHHHhccCCCHHhEEEEEEeee----EEEEEECH-HHHHHHHHHhcCCCCCCeeEE
Confidence            34678888999888765     3555667666    88888654 478889999999999995443

; PDB: 2G0C_A 3MOJ_B.

>KOG4019 consensus Calcineurin-mediated signaling pathway inhibitor DSCR1 [Signal transduction mechanisms; General function prediction only]

Probab=89.54  E-value=2.2  Score=32.68  Aligned_cols=77  Identities=18%  Similarity=0.238  Sum_probs=57.6

Q ss_pred             CeEEEcCCCCCCCH-----HHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCc-eEEEEEc
Q 023765            7 RTLYVGNLPGDTRM-----REVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGY-RLRVELA   80 (277)
Q Consensus         7 ~~l~V~nL~~~~t~-----~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~-~i~v~~a   80 (277)
                      +++++.+|+..+-.     ....++|.+|-+..-+.+.   .+.+..-|-|.+++.|..|...++...|.|. .+...++
T Consensus        11 ~~~~~c~i~~~VF~~~~~k~~~~~lFrq~n~~~~fq~l---rsfrrvRi~f~~p~~a~~a~i~~~~~~f~~~~~~k~yfa   87 (193)
T KOG4019|consen   11 TAIIACDIHEEVFVNREDKALFENLFRQINEDATFQLL---RSFRRVRINFSNPEAAADARIKLHSTSFNGKNELKLYFA   87 (193)
T ss_pred             ceeeeecccHHhhccHHHHHHHHhHHhhhCcchHHHHH---HhhceeEEeccChhHHHHHHHHhhhcccCCCceEEEEEc
Confidence            45778888776432     2345677777776666665   2356778999999999999999999999988 8999888


Q ss_pred             cCCCCC
Q 023765           81 HGGRRH   86 (277)
Q Consensus        81 ~~~~~~   86 (277)
                      +.....
T Consensus        88 Q~~~~~   93 (193)
T KOG4019|consen   88 QPGHPE   93 (193)
T ss_pred             cCCCcc
Confidence            865443

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=88.23  E-value=0.25  Score=46.32  Aligned_cols=58  Identities=17%  Similarity=0.220  Sum_probs=48.5

Q ss_pred             EeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeec
Q 023765          114 VTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFR  173 (277)
Q Consensus       114 v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~  173 (277)
                      +.|.+-..+-.-|..+|.+||.|..++..++-+  .|.|+|...+.|..|++.|+|+++.
T Consensus       303 ~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N--~alvs~~s~~sai~a~dAl~gkevs  360 (1007)
T KOG4574|consen  303 LENNAVNLTSSSLATLCSDYGSVASAWTLRDLN--MALVSFSSVESAILALDALQGKEVS  360 (1007)
T ss_pred             hhcccccchHHHHHHHHHhhcchhhheeccccc--chhhhhHHHHHHHHhhhhhcCCccc
Confidence            334444556677999999999999999887755  7999999999999999999999874

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=88.21  E-value=0.46  Score=43.36  Aligned_cols=69  Identities=14%  Similarity=0.006  Sum_probs=58.3

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccce
Q 023765          104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFS  177 (277)
Q Consensus       104 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  177 (277)
                      .+.++..++||+|+-..+..+-+..+...+|.|..+....     |||..|.....+..|+..++-..++|...
T Consensus        35 ~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~-----fgf~~f~~~~~~~ra~r~~t~~~~~~~kl  103 (668)
T KOG2253|consen   35 QPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK-----FGFCEFLKHIGDLRASRLLTELNIDDQKL  103 (668)
T ss_pred             cCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh-----hcccchhhHHHHHHHHHHhcccCCCcchh
Confidence            3455678999999999999999999999999887665433     89999999999999999988888877544

>KOG4483 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.57  E-value=1.3  Score=38.00  Aligned_cols=54  Identities=19%  Similarity=0.252  Sum_probs=45.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccC-CeeEEEeecCCCCCcEEEEEEcChHHHHHHHH
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYG-PIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIR   63 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G-~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~   63 (277)
                      .++|-|.++|.....+||..+|+.|+ .--+|+++.    ...||..|.....|..|+.
T Consensus       391 pHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvD----dthalaVFss~~~AaeaLt  445 (528)
T KOG4483|consen  391 PHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVD----DTHALAVFSSVNRAAEALT  445 (528)
T ss_pred             cceeEeccCchhhccHHHHHHHHHhhcCCceeEEee----cceeEEeecchHHHHHHhh
Confidence            47899999999999999999999996 444455543    3489999999999999998

>PRK14548 50S ribosomal protein L23P; Provisional

Probab=87.36  E-value=2.9  Score=27.91  Aligned_cols=56  Identities=11%  Similarity=0.192  Sum_probs=43.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhc-cC-CeeEEEeecCCCCCcEEEEEEcChHHHHHHHH
Q 023765            8 TLYVGNLPGDTRMREVEDLFYK-YG-PIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIR   63 (277)
Q Consensus         8 ~l~V~nL~~~~t~~~l~~~F~~-~G-~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~   63 (277)
                      .-|+--++..++-.+|++.++. || .|..|+.........=|||.+...+.|.....
T Consensus        22 n~y~F~V~~~anK~eIK~AvE~lf~VkV~~VnT~~~~~~~KKA~V~L~~g~~A~~va~   79 (84)
T PRK14548         22 NKLTFIVDRRATKPDIKRAVEELFDVKVEKVNTLITPKGEKKAYVKLAEEYDAEEIAS   79 (84)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcCCCcEEEEEEeCCCCcHHHHHH
Confidence            3455556789999999999997 67 88888886655555679999999888887654

>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=87.34  E-value=2.9  Score=32.50  Aligned_cols=53  Identities=11%  Similarity=0.050  Sum_probs=40.7

Q ss_pred             CHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcC--CCeecccc
Q 023765          122 SWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLD--RSEFRNAF  176 (277)
Q Consensus       122 ~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~--g~~~~g~~  176 (277)
                      ..+.|+++|..++.+....+...-.  -..|.|.+.+.|..|...|+  +..+.|..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sFr--Ri~v~f~~~~~A~~~r~~l~~~~~~~~g~~   62 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSFR--RIRVVFESPESAQRARQLLHWDGTSFNGKR   62 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTTT--EEEEE-SSTTHHHHHHHTST--TSEETTEE
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCCC--EEEEEeCCHHHHHHHHHHhcccccccCCCc
Confidence            4578999999999887766655432  47899999999999999999  99999943

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.

>TIGR03636 L23_arch archaeal ribosomal protein L23

Probab=86.95  E-value=3.4  Score=27.05  Aligned_cols=56  Identities=13%  Similarity=0.191  Sum_probs=43.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhc-cC-CeeEEEeecCCCCCcEEEEEEcChHHHHHHHH
Q 023765            8 TLYVGNLPGDTRMREVEDLFYK-YG-PIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIR   63 (277)
Q Consensus         8 ~l~V~nL~~~~t~~~l~~~F~~-~G-~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~   63 (277)
                      .-|+-.+++.++-.+|++.++. || .|..|+.........=|||.+...+.|...-.
T Consensus        15 n~y~F~V~~~anK~eIK~avE~lf~VkV~~Vnt~~~~~~~KKA~VtL~~g~~a~~va~   72 (77)
T TIGR03636        15 NKLTFIVDRKATKGDIKRAVEKLFDVKVEKVNTLITPRGEKKAYVKLAEEYAAEEIAS   72 (77)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcCCCceEEEEEECCCCcHHHHHH
Confidence            4566667889999999999987 66 88888876554445679999988888877544

This model describes the archaeal ribosomal protein L23P and rigorously excludes the bacterial counterpart L23. In order to capture every known instance of archaeal L23P, the trusted cutoff is set lower than a few of the highest scoring eukaryotic cytosolic ribosomal counterparts.

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=86.56  E-value=2.3  Score=34.87  Aligned_cols=58  Identities=21%  Similarity=0.360  Sum_probs=41.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccC-CeeEEEeecCCCCCcEEEEEEcCh-------HHHHHHHHhcC
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYG-PIVDIDLKIPPRPPGYAFLEFEDY-------RDAEDAIRGRD   66 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G-~v~~v~~~~~~~~~g~afV~f~~~-------~~a~~a~~~l~   66 (277)
                      .+-|+++||+.++...||+..+...| ....+.+.   .+.+-||+.|.+.       +++.+++..+|
T Consensus       330 ~~di~~~nl~rd~rv~dlk~~lr~~~~~pm~iswk---g~~~k~flh~~~~~~~~~~~~~~~~~~~s~~  395 (396)
T KOG4410|consen  330 KTDIKLTNLSRDIRVKDLKSELRKRECTPMSISWK---GHFGKCFLHFGNRKGVPSTQDDMDKVLKSLN  395 (396)
T ss_pred             ccceeeccCccccchHHHHHHHHhcCCCceeEeee---cCCcceeEecCCccCCCCCchHHHHHhccCC
Confidence            34599999999999999999988876 33333333   3478899999753       45555555443

>PF03468 XS: XS domain; InterPro: IPR005380 The XS (rice gene X and SGS3) domain is found in a family of plant proteins including gene X Q9SBW2 from SWISSPROT and SGS3 Q9LDX1 from SWISSPROT

Probab=85.00  E-value=0.78  Score=32.73  Aligned_cols=56  Identities=21%  Similarity=0.329  Sum_probs=30.4

Q ss_pred             eEEEcCCCCC---------CCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHH-HHHHH
Q 023765            8 TLYVGNLPGD---------TRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDA-EDAIR   63 (277)
Q Consensus         8 ~l~V~nL~~~---------~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a-~~a~~   63 (277)
                      ++.|-|++..         ++.++|.+.|..|.+++-..+.....+.|+++|+|..--.. ..|+.
T Consensus        10 mgIi~N~~~~~~~~g~~~g~~~~~l~~~l~~f~p~kv~~l~~~~gh~g~aiv~F~~~w~Gf~~A~~   75 (116)
T PF03468_consen   10 MGIIVNIPTEKDDDGRWVGMSNEELLDKLAEFNPLKVKPLYGKQGHTGFAIVEFNKDWSGFKNAMR   75 (116)
T ss_dssp             EEEEE----EE-TTS-EE---SHHHHHHHHH---SEEEEEEETTEEEEEEEEE--SSHHHHHHHHH
T ss_pred             EEEEEcCccccCCCCceeccCHHHHHHHHHhcCCceeEECcCCCCCcEEEEEEECCChHHHHHHHH
Confidence            4667777553         45678999999998876555544445689999999755433 33544

SGS3 is thought to be involved in post-transcriptional gene silencing (PTGS). This domain contains a conserved aspartate residue that may be functionally important. The XS domain containing proteins contain coiled-coils, which suggests that they will oligomerise. Most coiled-coil proteins form either a dimeric or a trimeric structure. It is possible that different members of the XS domain family could oligomerise via their coiled-coils forming a variety of complexes [].; PDB: 4E8U_C.

>KOG2146 consensus Splicing coactivator SRm160/300, subunit SRm160 (contains PWI domain) [RNA processing and modification; General function prediction only]

Probab=83.47  E-value=6.6  Score=32.34  Aligned_cols=17  Identities=29%  Similarity=0.131  Sum_probs=7.2

Q ss_pred             EEEEcChHHHHHHHHhc
Q 023765           49 FLEFEDYRDAEDAIRGR   65 (277)
Q Consensus        49 fV~f~~~~~a~~a~~~l   65 (277)
                      +|-|++...++-++..|
T Consensus        56 ilgfEDdVViefvynqL   72 (354)
T KOG2146|consen   56 ILGFEDDVVIEFVYNQL   72 (354)
T ss_pred             hhccccchhHHHHHHHH
Confidence            34444444444444333

>PF14893 PNMA: PNMA

Probab=82.30  E-value=1.8  Score=36.95  Aligned_cols=55  Identities=22%  Similarity=0.333  Sum_probs=37.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhhc-cCCeeEEEee---c-CCCCCcEEEEEEcCh
Q 023765            1 MSSRSSRTLYVGNLPGDTRMREVEDLFYK-YGPIVDIDLK---I-PPRPPGYAFLEFEDY   55 (277)
Q Consensus         1 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~-~G~v~~v~~~---~-~~~~~g~afV~f~~~   55 (277)
                      |+-++.+.|.|.+||.++++++|++.+.. +-+.-...|.   . .......|+|+|...
T Consensus        13 m~~~~~r~lLv~giP~dc~~~ei~e~l~~~l~plg~yrvl~~~f~~~~~~~aalve~~e~   72 (331)
T PF14893_consen   13 MGVDPQRALLVLGIPEDCEEAEIEEALQAALSPLGRYRVLGKMFRREENAKAALVEFAED   72 (331)
T ss_pred             cCcChhhhheeecCCCCCCHHHHHHHHHHhhcccccceehhhHhhhhcccceeeeecccc
Confidence            66788899999999999999999988764 3233333331   1 122355788988743

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	277
1x4a_A	109	Solution Structure Of Rrm Domain In Splicing Factor		3e-20
3beg_B	115	Crystal Structure Of Sr Protein Kinase 1 Complexed		2e-16
2o3d_A	113	Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (		2e-16
1x4c_A	108	Solution Structure Of Rrm Domain In Splicing Factor		3e-16
1wg4_A	98	Solution Structure Of Rrm Domain In Protein Bab3198		2e-15
2i2y_A	150	Solution Structure Of The Rrm Of Srp20 Bound To The		7e-12
2i38_A	150	Solution Structure Of The Rrm Of Srp20 Length = 150		7e-12
2hvz_A	101	Solution Structure Of The Rrm Domain Of Sr Rich Fac		2e-11
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		2e-08
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		1e-07
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		2e-07
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		3e-07
2dgt_A	92	Solution Structure Of The Second Rna Binding Domain		3e-07
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		6e-07
2dnq_A	90	Solution Structure Of Rna Binding Domain 1 In Rna-B		1e-06
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		1e-06
2fho_B	87	Nmr Solution Structure Of The Human Spliceosomal Pr		9e-06
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		9e-06
3lqv_A	115	Branch Recognition By Sf3b14 Length = 115		1e-05
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		1e-05
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		1e-05
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		1e-05
2f9d_A	125	2.5 Angstrom Resolution Structure Of The Spliceosom		2e-05
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		2e-05
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		2e-05
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		2e-05
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		4e-05
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		4e-05
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		6e-05
2f9j_A	125	3.0 Angstrom Resolution Structure Of A Y22m Mutant		1e-04
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		1e-04
1wf2_A	98	Solution Structure Of Rrm Domain In Hnrpc Protein L		2e-04
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		2e-04
4a8x_A	88	Structure Of The Core Asap Complex Length = 88		4e-04
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		4e-04
2dnp_A	90	Solution Structure Of Rna Binding Domain 2 In Rna-B		5e-04
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		6e-04
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		6e-04
2do4_A	100	Solution Structure Of The Rna Binding Domain Of Squ		6e-04
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		8e-04
1a9n_B	96	Crystal Structure Of The Spliceosomal U2b''-U2a' Pr		8e-04
2nz4_A	94	Structural Investigation Of The Glms Ribozyme Bound		9e-04
1aud_A	101	U1a-Utrrna, Nmr, 31 Structures Length = 101		9e-04

>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2 Length = 109

Iteration: 1
 Score = 95.5 bits (236), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 48/75 (64%), Positives = 58/75 (77%)
Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          +YVGNLP D R +++ED+FYKYG I DIDLK     P +AF+EFED RDAEDA+ GRDGY
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 84
Query: 69 NFDGYRLRVELAHGG 83
          ++DGYRLRVE    G
Sbjct: 85 DYDGYRLRVEFPRSG 99

>pdb|3BEG|B Chain B, Crystal Structure Of Sr Protein Kinase 1 Complexed To Its Substrate AsfSF2 Length = 115

Iteration: 1
 Score = 82.8 bits (203), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 37/63 (58%), Positives = 50/63 (79%), Gaps = 3/63 (4%)
Query: 112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSE 171
           V+V+GLP S SWQDLKDHMR AGDVC++ V+RD    TG+V++   +DM YA+RKLD ++
Sbjct: 19  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTK 75
Query: 172 FRN 174
           FR+
Sbjct: 76  FRS 78

>pdb|2O3D|A Chain A, Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (RRM2) Length = 113

Iteration: 1
 Score = 82.8 bits (203), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 37/63 (58%), Positives = 50/63 (79%), Gaps = 3/63 (4%)
Query: 112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSE 171
           V+V+GLP S SWQDLKDHMR AGDVC++ V+RD    TG+V++   +DM YA+RKLD ++
Sbjct: 18  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTK 74
Query: 172 FRN 174
           FR+
Sbjct: 75  FRS 77

>pdb|1X4C|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 2 Length = 108

Iteration: 1
 Score = 82.4 bits (202), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 37/63 (58%), Positives = 50/63 (79%), Gaps = 3/63 (4%)
Query: 112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSE 171
           V+V+GLP S SWQDLKDHMR AGDVC++ V+RD    TG+V++   +DM YA+RKLD ++
Sbjct: 18  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTK 74
Query: 172 FRN 174
           FR+
Sbjct: 75  FRS 77

>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986 Length = 98

Iteration: 1
 Score = 79.3 bits (194), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 39/63 (61%), Positives = 51/63 (80%), Gaps = 3/63 (4%)
Query: 112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSE 171
           VLV+GLP S SWQDLKDHMR AGDVC++ V +D  GM G+V+Y   +DM+YA+RKLD ++
Sbjct: 18  VLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD--GM-GMVEYLRKEDMEYALRKLDDTK 74
Query: 172 FRN 174
           FR+
Sbjct: 75  FRS 77

>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna Cauc Length = 150

Iteration: 1
 Score = 67.4 bits (163), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 35/74 (47%), Positives = 47/74 (63%), Gaps = 2/74 (2%)
Query: 9   LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
           +YVGNL  +    E+E  F  YGP+  +   +   PPG+AF+EFED RDA DA+R  DG 
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSV--WVARNPPGFAFVEFEDPRDAADAVRELDGR 133
Query: 69  NFDGYRLRVELAHG 82
              G R+RVEL++G
Sbjct: 134 TLCGCRVRVELSNG 147

>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20 Length = 150

Iteration: 1
 Score = 67.4 bits (163), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 35/74 (47%), Positives = 47/74 (63%), Gaps = 2/74 (2%)
Query: 9   LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
           +YVGNL  +    E+E  F  YGP+  +   +   PPG+AF+EFED RDA DA+R  DG 
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSV--WVARNPPGFAFVEFEDPRDAADAVRDLDGR 133
Query: 69  NFDGYRLRVELAHG 82
              G R+RVEL++G
Sbjct: 134 TLCGCRVRVELSNG 147

>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8 Length = 101

Iteration: 1
 Score = 65.9 bits (159), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 47/74 (63%), Gaps = 2/74 (2%)
Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          +YVGNL       E+E  F  YGP+  +   I   PPG+AF+EFED RDAEDA+RG DG 
Sbjct: 3  VYVGNLGTGAGKGELERAFSYYGPLRTV--WIARNPPGFAFVEFEDPRDAEDAVRGLDGK 60
Query: 69 NFDGYRLRVELAHG 82
             G R+RVEL+ G
Sbjct: 61 VICGSRVRVELSTG 74

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/80 (36%), Positives = 47/80 (58%), Gaps = 3/80 (3%)
Query: 4  RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAED 60
          RS R+++VGN+P +    +++D+F + GP+V   L   +   +P GY F E++D   A  
Sbjct: 6  RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65
Query: 61 AIRGRDGYNFDGYRLRVELA 80
          A+R  +G  F G  LRV+ A
Sbjct: 66 AMRNLNGREFSGRALRVDNA 85

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/75 (36%), Positives = 45/75 (60%), Gaps = 3/75 (4%)
Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          L+VG L  DT  + +E +F KYG I ++ +   +   R  G+ F+ FE+  DA+DA+   
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 66 DGYNFDGYRLRVELA 80
          +G + DG ++RV+ A
Sbjct: 75 NGKSVDGRQIRVDQA 89

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAI 62
          SR +Y+G++P D    ++ DL    GP++++ +   P   R  GYAF+EF D   +  A+
Sbjct: 2  SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 63 RGRDGYNF 70
          R  +GY  
Sbjct: 62 RNLNGYQL 69

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAI 62
          SR +Y+G++P D    ++ DL    GP++++ +   P   R  GYAF+EF D   +  A+
Sbjct: 3  SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 62
Query: 63 RGRDGYNF 70
          R  +GY  
Sbjct: 63 RNLNGYQL 70

>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In Rna- Binding Protein 30 Length = 92

Iteration: 1
 Score = 52.0 bits (123), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 27/77 (35%), Positives = 43/77 (55%), Gaps = 5/77 (6%)
Query: 4  RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIR 63
          ++S  L+VGN+      +E+   F +YGP+++ D+        YAF+  E   DA +AIR
Sbjct: 8  KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-----KDYAFVHMERAEDAVEAIR 62
Query: 64 GRDGYNFDGYRLRVELA 80
          G D   F G R+ V+L+
Sbjct: 63 GLDNTEFQGKRMHVQLS 79

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 51.2 bits (121), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 23/68 (33%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAI 62
          SR +Y+G++P D    ++ DL    GP++++ +   P   R  GYAF+EF D   +  A+
Sbjct: 4  SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 63
Query: 63 RGRDGYNF 70
          R  +GY  
Sbjct: 64 RNLNGYQL 71

>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding Protein 30 Length = 90

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 25/70 (35%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          L++GNLP +   +E+  LF +YG +++ D+        Y F+  ED   AEDAIR    Y
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDII-----KNYGFVHIEDKTAAEDAIRNLHHY 65
Query: 69 NFDGYRLRVE 78
             G  + VE
Sbjct: 66 KLHGVNINVE 75

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 32/79 (40%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAEDAIRG 64
          TL V NL   T    +  +F KYG + D+ +   P    P G+AF+ F D RDA+DA   
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 65 RDGYNFDGYRLRVELAHGG 83
           DG   DG  LRV++A  G
Sbjct: 75 MDGAELDGRELRVQVARYG 93

>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein Complex P14-Sf3b155 Length = 87

Iteration: 1
 Score = 47.4 bits (111), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 25/64 (39%), Positives = 36/64 (56%)
Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          +R LY+ NLP      E+ D+F KYGPI  I +   P   G A++ +ED  DA++A    
Sbjct: 12 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHL 71
Query: 66 DGYN 69
           G+N
Sbjct: 72 SGFN 75

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 47.4 bits (111), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 30/79 (37%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 8   TLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRG 64
           +L V NL   T    +  +F KYG + D+ +   +      G+AF+ F D RDAEDA+  
Sbjct: 72  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
Query: 65  RDGYNFDGYRLRVELAHGG 83
            DG   DG  LRV++A  G
Sbjct: 132 MDGAVLDGRELRVQMARYG 150

>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14 Length = 115

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 40/77 (51%)
Query: 1  MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
          +    +R LY+ NLP      E+ D+F KYGPI  I +   P   G A++ +ED  DA++
Sbjct: 3  LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKN 62
Query: 61 AIRGRDGYNFDGYRLRV 77
          A+    G+N     L V
Sbjct: 63 AVDHLSGFNVSNRYLVV 79

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 40/66 (60%), Gaps = 3/66 (4%)
Query: 18  TRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYR 74
           T  R++ ++F KYGPI D+ +   +   R  G+AF+ FE+  DA++A    +G   DG R
Sbjct: 58  TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 117
Query: 75  LRVELA 80
           +RV+ +
Sbjct: 118 IRVDFS 123

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRG 64
          T+ V NL  DTR  ++++LF  +G I  I L   K   +  G+AF+ F    DA  AI G
Sbjct: 17 TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 76
Query: 65 RDGYNFDGYRLRVELA 80
            G+ +D   L VE A
Sbjct: 77 VSGFGYDHLILNVEWA 92

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 40/66 (60%), Gaps = 3/66 (4%)
Query: 18 TRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYR 74
          T  R++ ++F KYGPI D+ +   +   R  G+AF+ FE+  DA++A    +G   DG R
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 86
Query: 75 LRVELA 80
          +RV+ +
Sbjct: 87 IRVDFS 92

>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal Protein P14 Bound To Region Of Sf3b155 Length = 125

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/64 (39%), Positives = 36/64 (56%)
Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          +R LY+ NLP      E+ D+F KYGPI  I +   P   G A++ +ED  DA++A    
Sbjct: 18 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHL 77
Query: 66 DGYN 69
           G+N
Sbjct: 78 SGFN 81

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 39/69 (56%), Gaps = 3/69 (4%)
Query: 18 TRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYR 74
          T  R++ ++F KYGPI D+ +   +   R  G+AF+ FE+  DA++A    +G   DG R
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 86
Query: 75 LRVELAHGG 83
          +RV     G
Sbjct: 87 IRVSGPSSG 95

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 3/80 (3%)
Query: 7   RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIR 63
           R L V  +P      ++  LF +YGPI  + +   +   +  GY F++F+    A+ AI 
Sbjct: 43  RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
Query: 64  GRDGYNFDGYRLRVELAHGG 83
           G +G+N    RL+V LA  G
Sbjct: 103 GLNGFNILNKRLKVALAASG 122

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 40/66 (60%), Gaps = 3/66 (4%)
Query: 18 TRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYR 74
          T  R++ ++F KYGPI D+ +   +   R  G+AF+ FE+  DA++A    +G   DG R
Sbjct: 24 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 83
Query: 75 LRVELA 80
          +RV+ +
Sbjct: 84 IRVDFS 89

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 41/76 (53%), Gaps = 3/76 (3%)
Query: 8   TLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRG 64
           +L V NL   T    +  +F KYG + D+ +   +      G+AF+ F D RDAEDA+  
Sbjct: 49  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108
Query: 65  RDGYNFDGYRLRVELA 80
            DG   DG  LRV++A
Sbjct: 109 MDGAVLDGRELRVQMA 124

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 7   RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIR 63
           +TL+V  +  DT   ++   F  YGPI  I +   K   +P GYAF+E+E  RD   A +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 64  GRDGYNFDGYRLRVELAHG 82
             DG   DG R+ V++  G
Sbjct: 163 HADGKKIDGRRVLVDVERG 181

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 44.7 bits (104), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 45/75 (60%), Gaps = 4/75 (5%)
Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP---GYAFLEFEDYRDAEDAIRGR 65
          L++G L  +T  + ++ +F K+GPI ++ L I  R     G+AF+ FE+  DA++A +  
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEV-LLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 66 DGYNFDGYRLRVELA 80
          +G +  G  ++VE A
Sbjct: 69 NGKSLHGKAIKVEQA 83

>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The Spliceosomal Protein P14 Bound To A Region Of Sf3b155 Length = 125

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/64 (37%), Positives = 35/64 (54%)
Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          +R L + NLP      E+ D+F KYGPI  I +   P   G A++ +ED  DA++A    
Sbjct: 18 NRILMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHL 77
Query: 66 DGYN 69
           G+N
Sbjct: 78 SGFN 81

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 7   RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIR 63
           +TL+V  +  DT   ++   F  YGPI  I +   K   +P GYAF+E+E  RD   A +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 64  GRDGYNFDGYRLRVELAHG 82
             DG   DG R+ V++  G
Sbjct: 163 HADGKKIDGRRVLVDVERG 181

>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein Length = 98

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/81 (33%), Positives = 43/81 (53%), Gaps = 10/81 (12%)
Query: 1  MSSRSSRTLYVGNLPG-DTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAE 59
          M+SR    +++GNL     +  +VE +F KYG IV   +       G+AF+++ + R+A 
Sbjct: 14 MNSR----VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-----KGFAFVQYVNERNAR 64
Query: 60 DAIRGRDGYNFDGYRLRVELA 80
           A+ G DG    G  L + LA
Sbjct: 65 AAVAGEDGRMIAGQVLDINLA 85

>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc) In Complex With A Cap Analogue M7gpppg Length = 156

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 38/71 (53%), Gaps = 3/71 (4%)
Query: 4   RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAED 60
           + S TLYVGNL   T   ++ +LF K G I  I +   K+     G+ F+E+    DAE+
Sbjct: 37  KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 96
Query: 61  AIRGRDGYNFD 71
           A+R  +G   D
Sbjct: 97  AMRYINGTRLD 107

>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex Length = 88

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 4/68 (5%)
Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI----PPRPPGYAFLEFEDYRDAEDAIRG 64
          +++G L  +     + ++F  YG I  ID+ +    P    GYA++EFE+  +AE A++ 
Sbjct: 7  VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 65 RDGYNFDG 72
           DG   DG
Sbjct: 67 MDGGQIDG 74

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 3/81 (3%)
Query: 3   SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAE 59
           + + R LYVG L  +   + +   F  +G I DI + +     +  G+AF+EFE   DA 
Sbjct: 60  ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 119
Query: 60  DAIRGRDGYNFDGYRLRVELA 80
            AI   +     G  +RV LA
Sbjct: 120 AAIDNMNESELFGRTIRVNLA 140

>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding Protein 14 Length = 90

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 25/82 (30%), Positives = 42/82 (51%), Gaps = 5/82 (6%)
Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
          SS ++  ++VGN+      +E+  LF + G +++ D+        YAF+  E   DA+ A
Sbjct: 5  SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-----KDYAFVHMEKEADAKAA 59
Query: 62 IRGRDGYNFDGYRLRVELAHGG 83
          I   +G    G R+ VEL+  G
Sbjct: 60 IAQLNGKEVKGKRINVELSTKG 81

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 27/81 (33%), Positives = 41/81 (50%), Gaps = 2/81 (2%)
Query: 4  RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP--GYAFLEFEDYRDAEDA 61
          + S TLYVGNL   T   ++ +LF K G I  I + +       G+ F+E+    DAE+A
Sbjct: 16 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENA 75
Query: 62 IRGRDGYNFDGYRLRVELAHG 82
          +R  +G   D   +R +   G
Sbjct: 76 MRYINGTRLDDRIIRTDWDAG 96

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 4/78 (5%)
Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIR 63
          R +YVGNL       +V++LF ++G + ++ L   +   +P G+ F+E ++     +AI 
Sbjct: 2  RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIA 60
Query: 64 GRDGYNFDGYRLRVELAH 81
            D  +F G  +RV  A+
Sbjct: 61 KLDNTDFMGRTIRVTEAN 78

>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous Cell Carcinoma Antigen Recognized By T Cells 3 Length = 100

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 2/84 (2%)
Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAE 59
          +S     L++  LP      E+E++   +G + D+ L      +P G A++E+E+   A 
Sbjct: 13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQAS 72
Query: 60 DAIRGRDGYNFDGYRLRVELAHGG 83
           A+   DG       ++V +++ G
Sbjct: 73 QAVMKMDGMTIKENIIKVAISNSG 96

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 40.8 bits (94), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 3/81 (3%)
Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAE 59
          + + R LYVG L  +   + +   F  +G I DI + +     +  G+AF+EFE   DA 
Sbjct: 9  ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 68
Query: 60 DAIRGRDGYNFDGYRLRVELA 80
           AI   +     G  +RV LA
Sbjct: 69 AAIDNMNESELFGRTIRVNLA 89

>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein Complex Bound To A Fragment Of U2 Small Nuclear Rna Length = 96

Iteration: 1
 Score = 40.8 bits (94), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 23/84 (27%), Positives = 44/84 (52%), Gaps = 4/84 (4%)
Query: 1  MSSRSSRTLYVGNLPGDTRMREVE----DLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYR 56
          M  R + T+Y+ N+    +  E++     LF ++G +VDI      +  G AF+ F++  
Sbjct: 1  MDIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELG 60
Query: 57 DAEDAIRGRDGYNFDGYRLRVELA 80
           + +A+R   G+ F G  +R++ A
Sbjct: 61 SSTNALRQLQGFPFYGKPMRIQYA 84

>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its Catalytic Cofactor Length = 94

Iteration: 1
 Score = 40.8 bits (94), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 22/82 (26%), Positives = 43/82 (52%), Gaps = 4/82 (4%)
Query: 3  SRSSRTLYVGNL----PGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDA 58
          +R + T+Y+ NL      D   + +  +F ++G I+DI +    +  G AF+ F++   A
Sbjct: 2  TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 61
Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
           +A+R   G+ F    +R++ A
Sbjct: 62 TNALRSMQGFPFYDKPMRIQYA 83

>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures Length = 101

Iteration: 1
 Score = 40.8 bits (94), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 22/82 (26%), Positives = 43/82 (52%), Gaps = 4/82 (4%)
Query: 3  SRSSRTLYVGNL----PGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDA 58
          +R + T+Y+ NL      D   + +  +F ++G I+DI +    +  G AF+ F++   A
Sbjct: 5  TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
           +A+R   G+ F    +R++ A
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA 86

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	277
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	9e-33
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-32
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	7e-07
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-31
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	4e-30
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-05
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	7e-30
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	7e-30
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-29
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-04
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-29
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	4e-28
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	6e-25
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	4e-05
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-24
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	9e-24
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-10
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-23
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	5e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-22
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-11
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	5e-22
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	6e-22
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	8e-09
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-21
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-05
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	1e-21
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	1e-09
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-21
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	7e-13
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	4e-21
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-21
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	9e-11
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-20
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	3e-20
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-20
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-18
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-20
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-19
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	4e-19
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	4e-19
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-18
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-08
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-18
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	8e-06
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-18
2dis_A	109	Unnamed protein product; structural genomics, RRM	4e-04
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-18
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-07
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-18
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	5e-18
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	7e-18
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-18
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-16
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-11
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-17
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-17
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	3e-17
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-04
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-17
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-09
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	3e-17
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-16
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-16
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-05
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-16
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	9e-05
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-16
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-16
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-05
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-16
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	4e-16
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	5e-16
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-11
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	5e-16
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	6e-05
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	5e-16
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	6e-16
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	7e-16
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-15
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-15
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-15
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-11
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-15
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-15
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-15
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-15
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	6e-09
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-15
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	6e-09
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	3e-15
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	8e-05
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-15
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-06
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-15
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	4e-15
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	6e-15
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	5e-05
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	6e-15
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	6e-15
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	7e-15
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	5e-04
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-14
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-14
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-14
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-14
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-08
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	3e-14
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	3e-14
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-14
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	7e-10
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	7e-14
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-13
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-13
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-04
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	1e-13
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-13
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-13
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-13
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-07
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-13
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-13
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	4e-13
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	5e-13
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	6e-13
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	8e-13
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-04
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	9e-13
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-12
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-12
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	1e-12
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-12
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-12
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-12
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-07
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-12
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-12
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-12
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-12
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	3e-12
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-12
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-12
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	5e-12
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	7e-04
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	7e-12
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	4e-07
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	9e-12
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	6e-07
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-11
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-11
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-11
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	3e-11
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	6e-06
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	5e-11
2div_A	99	TRNA selenocysteine associated protein; structural	6e-11
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	8e-11
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	9e-11
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	9e-11
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-10
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-09
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-10
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-10
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-10
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-10
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	4e-10
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	4e-10
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	5e-10
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	4e-09
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-10
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-09
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-09
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	1e-09
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-09
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-09
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-09
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-09
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	6e-06
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-09
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	3e-09
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	3e-09
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	5e-09
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	5e-09
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	8e-09
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	9e-09
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-08
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-08
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-08
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	3e-08
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	6e-08
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	8e-08
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-07
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-07
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-07
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-04
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	2e-07
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	4e-07
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	4e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-07
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	4e-07
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	6e-07
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	8e-07
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	1e-06
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	2e-06
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-06
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	2e-06
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-06
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-06
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	5e-06
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	6e-06
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	7e-06
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	9e-06
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	3e-05
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	6e-05
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	1e-04
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	1e-04
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	5e-04
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	6e-04
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	7e-04
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	9e-06
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-05
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	2e-05
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	5e-05
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	2e-04
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	4e-04
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-05
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	5e-05
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	1e-04
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-04
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-04
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-04
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	3e-04
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	3e-04
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	5e-04
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	7e-04

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score =  115 bits (289), Expect = 9e-33
 Identities = 46/108 (42%), Positives = 56/108 (51%), Gaps = 13/108 (12%)

Query: 9   LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
           +YVGNL       E+E  F  YGP+  +   I   PPG+AF+EFED RDAEDA+RG DG 
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVW--IARNPPGFAFVEFEDPRDAEDAVRGLDGK 60

Query: 69  NFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTG 116
              G R+RVEL+ G  R            S   R  +RR    VL  G
Sbjct: 61  VICGSRVRVELSTGMPR-----------RSRFDRPPARRKLLEVLFNG 97

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score =  114 bits (287), Expect = 2e-32
 Identities = 50/88 (56%), Positives = 62/88 (70%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
           +  +   +YVGNLP D R +++ED+FYKYG I DIDLK     P +AF+EFED RDAEDA
Sbjct: 18  AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDA 77

Query: 62  IRGRDGYNFDGYRLRVELAHGGRRHSSS 89
           + GRDGY++DGYRLRVE    GR   S 
Sbjct: 78  VYGRDGYDYDGYRLRVEFPRSGRGTGSG 105

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 46.2 bits (110), Expect = 7e-07
 Identities = 28/117 (23%), Positives = 44/117 (37%), Gaps = 10/117 (8%)

Query: 83  GRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVF 142
           G   SS M        G  RG +  +D R+ V  LP     +D++D   + G +    + 
Sbjct: 1   GSSGSSGMSG-----GGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLK 55

Query: 143 RDRGGMT-GIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDSRRSYSRSPSR 198
             RGG     V++    D + A+   D  ++        +RV    S R     PS 
Sbjct: 56  NRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDG----YRLRVEFPRSGRGTGSGPSS 108

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score =  112 bits (283), Expect = 1e-31
 Identities = 28/93 (30%), Positives = 43/93 (46%)

Query: 1  MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
          +    +R LY+ NLP      E+ D+F KYGPI  I +   P   G A++ +ED  DA++
Sbjct: 3  LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKN 62

Query: 61 AIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRY 93
          A+    G+N     L V   +  R       + 
Sbjct: 63 AVDHLSGFNVSNRYLVVLYYNANRAFQKMDTKK 95

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score =  109 bits (274), Expect = 4e-30
 Identities = 37/85 (43%), Positives = 50/85 (58%), Gaps = 2/85 (2%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
            S      +YVGNL  +    E+E  F  YGP+  +   +   PPG+AF+EFED RDA D
Sbjct: 68  DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVW--VARNPPGFAFVEFEDPRDAAD 125

Query: 61  AIRGRDGYNFDGYRLRVELAHGGRR 85
           A+R  DG    G R+RVEL++G +R
Sbjct: 126 AVRELDGRTLCGCRVRVELSNGEKR 150

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 42.9 bits (101), Expect = 2e-05
 Identities = 23/130 (17%), Positives = 41/130 (31%), Gaps = 5/130 (3%)

Query: 43  RPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSR 102
              G    E  D   AE   +     N        +        + ++   S +      
Sbjct: 11  TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYD----DATKTFTVTEGSHHHHHHMH 66

Query: 103 GVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKY 162
             S   D +V V  L ++ +  +L+      G +    V R+  G    V++    D   
Sbjct: 67  RDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGF-AFVEFEDPRDAAD 125

Query: 163 AIRKLDRSEF 172
           A+R+LD    
Sbjct: 126 AVRELDGRTL 135

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score =  107 bits (269), Expect = 7e-30
 Identities = 20/95 (21%), Positives = 42/95 (44%), Gaps = 6/95 (6%)

Query: 2  SSRSSRTLYVGNLPG-DTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
          +      L++GNLP  +    ++  +F  YG I+ I++K       + F++F++ +   D
Sbjct: 6  NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-----NAFGFIQFDNPQSVRD 60

Query: 61 AIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSS 95
          AI         G +L +E++    R       + +
Sbjct: 61 AIECESQEMNFGKKLILEVSSSNARPQFDHGDHGT 95

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score =  107 bits (269), Expect = 7e-30
 Identities = 28/90 (31%), Positives = 42/90 (46%), Gaps = 5/90 (5%)

Query: 1  MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
            S     L++GNLP +   +E+  LF +YG +++ D+        Y F+  ED   AED
Sbjct: 3  SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-----KNYGFVHIEDKTAAED 57

Query: 61 AIRGRDGYNFDGYRLRVELAHGGRRHSSSM 90
          AIR    Y   G  + VE +    + SS  
Sbjct: 58 AIRNLHHYKLHGVNINVEASKNKSKASSGP 87

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score =  106 bits (267), Expect = 1e-29
 Identities = 30/88 (34%), Positives = 47/88 (53%), Gaps = 5/88 (5%)

Query: 1  MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
           S ++S  L+VGN+      +E+   F +YGP+++ D+        YAF+  E   DA +
Sbjct: 5  SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-----KDYAFVHMERAEDAVE 59

Query: 61 AIRGRDGYNFDGYRLRVELAHGGRRHSS 88
          AIRG D   F G R+ V+L+    R +S
Sbjct: 60 AIRGLDNTEFQGKRMHVQLSTSRLRTAS 87

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 24/98 (24%), Positives = 41/98 (41%), Gaps = 8/98 (8%)

Query: 100 GSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDD 159
           GS G S ++  ++ V  +  + + Q+L+      G V    + +D       V     +D
Sbjct: 1   GSSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD----YAFVHMERAED 56

Query: 160 MKYAIRKLDRSEFRNAFSRSYVRVREYDSRRSYSRSPS 197
              AIR LD +EF+       + V+   SR   +  PS
Sbjct: 57  AVEAIRGLDNTEFQG----KRMHVQLSTSRLRTASGPS 90

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score =  105 bits (265), Expect = 2e-29
 Identities = 26/88 (29%), Positives = 45/88 (51%), Gaps = 5/88 (5%)

Query: 1  MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
           SS ++  ++VGN+      +E+  LF + G +++ D+        YAF+  E   DA+ 
Sbjct: 4  GSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-----KDYAFVHMEKEADAKA 58

Query: 61 AIRGRDGYNFDGYRLRVELAHGGRRHSS 88
          AI   +G    G R+ VEL+  G++ S 
Sbjct: 59 AIAQLNGKEVKGKRINVELSTKGQKKSG 86

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score =  102 bits (257), Expect = 4e-28
 Identities = 21/85 (24%), Positives = 39/85 (45%), Gaps = 6/85 (7%)

Query: 2  SSRSSRTLYVGNLPGDT-RMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
           S     L++GNLP       ++  +F  YG I+ I++K       + F++F++ +   D
Sbjct: 18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-----NAFGFIQFDNPQSVRD 72

Query: 61 AIRGRDGYNFDGYRLRVELAHGGRR 85
          AI         G +L +E++    R
Sbjct: 73 AIEXESQEMNFGKKLILEVSSSNAR 97

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 94.5 bits (235), Expect = 6e-25
 Identities = 25/85 (29%), Positives = 37/85 (43%), Gaps = 2/85 (2%)

Query: 1  MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
            +  +  +YVGNLP D R+ +++    + G  V + L     P   AFL + D   A+ 
Sbjct: 14 EGAPLAADVYVGNLPRDARVSDLKRALRELGS-VPLRLTWQ-GPRRRAFLHYPDSAAAQQ 71

Query: 61 AIRGRDGYNFDGYRLRVELAHGGRR 85
          A+    G       LRV LA   R 
Sbjct: 72 AVSCLQGLRLGTDTLRVALARQQRD 96

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 41.0 bits (96), Expect = 4e-05
 Identities = 16/76 (21%), Positives = 22/76 (28%), Gaps = 1/76 (1%)

Query: 97  SSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTS 156
             G   G        V V  LP  A   DLK  +R  G V     ++        + Y  
Sbjct: 7   GPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRR-RAFLHYPD 65

Query: 157 YDDMKYAIRKLDRSEF 172
               + A+  L     
Sbjct: 66  SAAAQQAVSCLQGLRL 81

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 94.0 bits (234), Expect = 1e-24
 Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 6/84 (7%)

Query: 6   SRTLYVGNLPGD-TRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRG 64
           +  +++GNL     +  +VE +F KYG +    +       GYAF+++ + R A  A+ G
Sbjct: 27  NSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH-----KGYAFVQYSNERHARAAVLG 81

Query: 65  RDGYNFDGYRLRVELAHGGRRHSS 88
            +G    G  L + +A   +   S
Sbjct: 82  ENGRVLAGQTLDINMAGEPKPDRS 105

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 91.8 bits (228), Expect = 9e-24
 Identities = 31/114 (27%), Positives = 44/114 (38%), Gaps = 5/114 (4%)

Query: 83  GRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAG-DVCFSQV 141
           G  H            G          YR+ +  LP   SWQDLKD  R    +  FS V
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSV 61

Query: 142 FRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDSRRSYSRS 195
                  TG +++ S + +  A+ +L+  EFR     S + V   D+     RS
Sbjct: 62  NTRDFDGTGALEFPSEEILVEALERLNNIEFRG----SVITVERDDNPPPIRRS 111

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 56.0 bits (135), Expect = 2e-10
 Identities = 14/77 (18%), Positives = 25/77 (32%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
                  + + NLP     ++++DL  +                G   LEF       +A
Sbjct: 24  LPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEA 83

Query: 62  IRGRDGYNFDGYRLRVE 78
           +   +   F G  + VE
Sbjct: 84  LERLNNIEFRGSVITVE 100

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 90.2 bits (224), Expect = 2e-23
 Identities = 26/87 (29%), Positives = 37/87 (42%), Gaps = 6/87 (6%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYG-PIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
          S  S  + V NLP D+  +EV DL   Y      +D     R    AF+   +   A++A
Sbjct: 2  SSGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVD-----RNKRTAFVTLLNGEQAQNA 56

Query: 62 IRGRDGYNFDGYRLRVELAHGGRRHSS 88
          I+    Y+F G  L V+L        S
Sbjct: 57 IQMFHQYSFRGKDLIVQLQPTDALLCS 83

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 43.2 bits (102), Expect = 5e-06
 Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 5/71 (7%)

Query: 103 GVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKY 162
           G S  S   +LV  LP  ++ Q++ D ++          + DR   T  V   + +  + 
Sbjct: 1   GSSGSS--GILVKNLPQDSNCQEVHDLLKDYD---LKYCYVDRNKRTAFVTLLNGEQAQN 55

Query: 163 AIRKLDRSEFR 173
           AI+   +  FR
Sbjct: 56  AIQMFHQYSFR 66

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 89.1 bits (221), Expect = 1e-22
 Identities = 54/109 (49%), Positives = 71/109 (65%), Gaps = 5/109 (4%)

Query: 97  SSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTS 156
           S       SRRS+ RV+V+GLP S SWQDLKDHMR AGDVC++ V+RD    TG+V++  
Sbjct: 3   SGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG---TGVVEFVR 59

Query: 157 YDDMKYAIRKLDRSEFRNAFSR-SYVRVREYDSRRSYSRSPSRSPYYSR 204
            +DM YA+RKLD ++FR+     +Y+RV+  D  RS S   SRS   S 
Sbjct: 60  KEDMTYAVRKLDNTKFRSHEGETAYIRVKV-DGPRSPSYGRSRSSGPSS 107

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 59.4 bits (144), Expect = 1e-11
 Identities = 24/102 (23%), Positives = 35/102 (34%), Gaps = 4/102 (3%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
           S RS   + V  LP     ++++D   + G +   D+       G   +EF    D   A
Sbjct: 11  SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV----YRDGTGVVEFVRKEDMTYA 66

Query: 62  IRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRG 103
           +R  D   F  +               S     S SSG S G
Sbjct: 67  VRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSSGPSSG 108

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 86.9 bits (216), Expect = 5e-22
 Identities = 35/92 (38%), Positives = 45/92 (48%), Gaps = 3/92 (3%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDA 58
                 TL V NL   T    +  +F KYG + D+ +   P    P G+AF+ F D RDA
Sbjct: 9   DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDA 68

Query: 59  EDAIRGRDGYNFDGYRLRVELAHGGRRHSSSM 90
           +DA    DG   DG  LRV++A  GRR  S  
Sbjct: 69  QDAEAAMDGAELDGRELRVQVARYGRRDLSGP 100

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 86.7 bits (215), Expect = 6e-22
 Identities = 12/79 (15%), Positives = 29/79 (36%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
            +  R L + N+P   +   ++ L  +YG +   +            + +     A  A
Sbjct: 11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQA 70

Query: 62 IRGRDGYNFDGYRLRVELA 80
          +   +G+  + + L+V   
Sbjct: 71 LDKLNGFQLENFTLKVAYI 89

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 50.9 bits (122), Expect = 8e-09
 Identities = 24/80 (30%), Positives = 35/80 (43%), Gaps = 2/80 (2%)

Query: 97  SSGGSRGVSRRSDYRVL-VTGLPSSASWQDLKDHMRRAGDVC-FSQVFRDRGGMTGIVDY 154
           SSG S  V +R   R L +  +P    W+ L   + + G V    QV  D       V Y
Sbjct: 2   SSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTY 61

Query: 155 TSYDDMKYAIRKLDRSEFRN 174
           +S D  + A+ KL+  +  N
Sbjct: 62  SSKDQARQALDKLNGFQLEN 81

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 85.8 bits (213), Expect = 1e-21
 Identities = 26/87 (29%), Positives = 37/87 (42%), Gaps = 3/87 (3%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
          +      L+VGNLP D    E+  LF KYG   ++ +    +  G+ F+  E    AE A
Sbjct: 11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI---HKDKGFGFIRLETRTLAEIA 67

Query: 62 IRGRDGYNFDGYRLRVELAHGGRRHSS 88
              D     G +LRV  A      +S
Sbjct: 68 KVELDNMPLRGKQLRVRFACHSASLTS 94

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 23/103 (22%), Positives = 40/103 (38%), Gaps = 7/103 (6%)

Query: 97  SSGGSRGVSRRSDY-RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYT 155
           SSG S G    +   R+ V  LP   + ++++    + G      + +D+G   G +   
Sbjct: 2   SSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG--FGFIRLE 59

Query: 156 SYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDSRRSYSRSPSR 198
           +    + A  +LD    R       +RVR      S +  PS 
Sbjct: 60  TRTLAEIAKVELDNMPLRG----KQLRVRFACHSASLTSGPSS 98

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 86.4 bits (214), Expect = 1e-21
 Identities = 61/115 (53%), Positives = 78/115 (67%), Gaps = 5/115 (4%)

Query: 97  SSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTS 156
             G     SRRS+ RV+V+GLP S SWQDLKDHMR AGDVC++ V+RD    TG+V++  
Sbjct: 4   PRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG---TGVVEFVR 60

Query: 157 YDDMKYAIRKLDRSEFRNAFSR-SYVRVREYDSRR-SYSRSPSRSPYYSRSRSRS 209
            +DM YA+RKLD ++FR+     +Y+RV+    R  SY RS SRS   SRSRSRS
Sbjct: 61  KEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRSRSRSRSRSRS 115

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 53.7 bits (129), Expect = 1e-09
 Identities = 24/106 (22%), Positives = 35/106 (33%), Gaps = 4/106 (3%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
           S RS   + V  LP     ++++D   + G +   D+       G   +EF    D   A
Sbjct: 12  SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV----YRDGTGVVEFVRKEDMTYA 67

Query: 62  IRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRR 107
           +R  D   F  +               S     S S   SR  SR 
Sbjct: 68  VRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRSRSRSRSRS 113

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 88.5 bits (220), Expect = 2e-21
 Identities = 36/176 (20%), Positives = 64/176 (36%), Gaps = 13/176 (7%)

Query: 5   SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--------RPPGYAFLEFEDYR 56
            +R LYVGN+P       + D F     +  +              +   +AFLEF    
Sbjct: 3   MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62

Query: 57  DAEDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTG 116
           +   A+   DG  F G  L++   H  +      +  S Y  G    V   S +++ + G
Sbjct: 63  ETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGG 121

Query: 117 LPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMT----GIVDYTSYDDMKYAIRKLD 168
           LP+  +   +K+ +   G +    + +D            +Y   +    AI  L+
Sbjct: 122 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 177

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 64.7 bits (158), Expect = 7e-13
 Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 3/86 (3%)

Query: 5   SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDA 61
           S+  L++G LP      +V++L   +GP+   +L          GYAF E+ D    + A
Sbjct: 113 SAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 172

Query: 62  IRGRDGYNFDGYRLRVELAHGGRRHS 87
           I G +G      +L V+ A  G +++
Sbjct: 173 IAGLNGMQLGDKKLLVQRASVGAKNA 198

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 84.7 bits (210), Expect = 4e-21
 Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 5/81 (6%)

Query: 5   SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRG 64
           S+  L+V   P D +  E+ ++F  +GP+ ++ +       G+AF+EFE+   A  AI  
Sbjct: 30  SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI-----LNGFAFVEFEEAESAAKAIEE 84

Query: 65  RDGYNFDGYRLRVELAHGGRR 85
             G +F    L V  +    +
Sbjct: 85  VHGKSFANQPLEVVYSKLPAK 105

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 87.5 bits (216), Expect = 5e-21
 Identities = 31/201 (15%), Positives = 62/201 (30%), Gaps = 24/201 (11%)

Query: 6   SRTLYVGNL-PGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRG 64
           S  L V  L         V ++F  YG +  +  K     PG A +E  D    + AI  
Sbjct: 4   SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKV--KFMKSKPGAAMVEMADGYAVDRAITH 61

Query: 65  RDGYNFDGYRLRVELAH---------------GGRRHSSSMDRYSSYSSGGSRGVSR--R 107
            +     G ++ V ++                       S  R + +S+      +R   
Sbjct: 62  LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQH 121

Query: 108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMT----GIVDYTSYDDMKYA 163
               +     P   + ++  +     G    + V    G       G++++ S  D    
Sbjct: 122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALET 181

Query: 164 IRKLDRSEFRNAFSRSYVRVR 184
           +  L+  + +N        ++
Sbjct: 182 LGFLNHYQMKNPNGPYPYTLK 202

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 58.9 bits (142), Expect = 9e-11
 Identities = 11/80 (13%), Positives = 23/80 (28%), Gaps = 3/80 (3%)

Query: 3   SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAE 59
              S  L+  N P +       ++  + G      +K+            LE++   DA 
Sbjct: 120 QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDAL 179

Query: 60  DAIRGRDGYNFDGYRLRVEL 79
           + +   + Y           
Sbjct: 180 ETLGFLNHYQMKNPNGPYPY 199

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 83.1 bits (206), Expect = 1e-20
 Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 5/86 (5%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAI 62
          +  +  L+VG L  +T +  +   F ++G I  ID     +   +A++++E    A+ A 
Sbjct: 14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDH---VKGDSFAYIQYESLDAAQAAC 70

Query: 63 RGRDGYNFDGY--RLRVELAHGGRRH 86
              G+   G   RLRV+ A  G   
Sbjct: 71 AKMRGFPLGGPDRRLRVDFAKSGPSS 96

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 81.8 bits (203), Expect = 3e-20
 Identities = 23/82 (28%), Positives = 39/82 (47%), Gaps = 4/82 (4%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI----PPRPPGYAFLEFEDYRDA 58
          S     +++G L  +     + ++F  YG I  ID+ +    P    GYA++EFE+  +A
Sbjct: 1  SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA 60

Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
          E A++  DG   DG  +     
Sbjct: 61 EKALKHMDGGQIDGQEITATAV 82

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 86.2 bits (214), Expect = 5e-20
 Identities = 34/216 (15%), Positives = 67/216 (31%), Gaps = 29/216 (13%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRD 57
               +   L V NLP     ++ E+L   +G +    L       +  GY F E+     
Sbjct: 90  QLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDS 149

Query: 58  AEDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGL 117
           A  A     G       L V     G+   + +                       V  L
Sbjct: 150 AARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLC-----------------VDRL 192

Query: 118 PSSAS-WQDLKDHMRRAGDVCFSQVFRDRGGMT---GIVDYTSYDDMKYAIRKLDRSEFR 173
           P   +    L   +       F Q+   + G      +++Y + +  + A ++ D     
Sbjct: 193 PPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLG 252

Query: 174 NAFSRSYVRVREYDSRRSYSRSPSRSPYYSRSRSRS 209
                S++RV  + +     RS   +   +++ + +
Sbjct: 253 G----SHLRVS-FCAPGPPGRSMLAALIAAQATALN 283

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 82.3 bits (204), Expect = 1e-18
 Identities = 34/177 (19%), Positives = 53/177 (29%), Gaps = 34/177 (19%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
             R+ R + +  LPGD   +EV DL   Y  +    +    +  G AF+   +   AE A
Sbjct: 18  QFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD---KYKGTAFVTLLNGEQAEAA 73

Query: 62  IRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSA 121
           I            L V+L                            +D  + V  LP S 
Sbjct: 74  INAFHQSRLRERELSVQLQ--------------------------PTDALLCVANLPPSL 107

Query: 122 SWQDLKDHMRRAGDVCFSQVFRDRGGMT----GIVDYTSYDDMKYAIRKLDRSEFRN 174
           + Q  ++ +R  G +    +            G  +Y   D    A   L       
Sbjct: 108 TQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGP 164

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 84.2 bits (208), Expect = 6e-20
 Identities = 38/197 (19%), Positives = 70/197 (35%), Gaps = 24/197 (12%)

Query: 5   SSRTLYVGNL-PGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIR 63
            +  L V NL P     + +  LF  YG +  +  KI       A ++  D   A+ A+ 
Sbjct: 2   GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRV--KILFNKKENALVQMADGNQAQLAMS 59

Query: 64  GRDGYNFDGYRLRVELAH---------GGRRHSSSMDRYSSYSSGGSRGVSRRSDY---- 110
             +G+   G  +R+ L+          G      + D  +S      +  S+        
Sbjct: 60  HLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPP 119

Query: 111 --RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLD 168
              + ++ +P S S +DLK      G V     F  +     ++   S ++   A+  L 
Sbjct: 120 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLH 179

Query: 169 RSEFRN------AFSRS 179
             +         +FS+S
Sbjct: 180 NHDLGENHHLRVSFSKS 196

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 81.1 bits (200), Expect = 2e-19
 Identities = 16/83 (19%), Positives = 33/83 (39%), Gaps = 4/83 (4%)

Query: 2   SSRSSRTLYVGNLPGDTRMRE----VEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRD 57
            +  S+ + + N+  +    +    +  L    G I+DI + +     G A++ F     
Sbjct: 25  HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQES 84

Query: 58  AEDAIRGRDGYNFDGYRLRVELA 80
           A+  +    GY F G  L +  +
Sbjct: 85  AQAFVEAFQGYPFQGNPLVITFS 107

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 78.8 bits (195), Expect = 4e-19
 Identities = 21/89 (23%), Positives = 33/89 (37%), Gaps = 4/89 (4%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
           S     LY+GNL       ++  LF      +   +       GYAF+++ D   A  A
Sbjct: 4  GSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL---LKSGYAFVDYPDQNWAIRA 60

Query: 62 IRGRDG-YNFDGYRLRVELAHGGRRHSSS 89
          I    G     G  + V+ +   +  SS 
Sbjct: 61 IETLSGKVELHGKIMEVDYSVSKKLRSSG 89

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 79.2 bits (196), Expect = 4e-19
 Identities = 26/84 (30%), Positives = 38/84 (45%), Gaps = 3/84 (3%)

Query: 5  SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRG 64
          S + LYV NL   T    +E  F    P     +K   +   YAF+ F +  DA +A++ 
Sbjct: 14 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK---KIRDYAFVHFSNREDAVEAMKA 70

Query: 65 RDGYNFDGYRLRVELAHGGRRHSS 88
           +G   DG  + V LA    + SS
Sbjct: 71 LNGKVLDGSPIEVTLAKPVDKDSS 94

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 77.9 bits (192), Expect = 1e-18
 Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 3/79 (3%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
          S RS   +   NLP  T   E+++ F ++G +  + L   P     A +EF +  +A  A
Sbjct: 6  SGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL---PEGGITAIVEFLEPLEARKA 62

Query: 62 IRGRDGYNFDGYRLRVELA 80
           R      F    L +E A
Sbjct: 63 FRHLAYSKFHHVPLYLEWA 81

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 50.6 bits (121), Expect = 1e-08
 Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 2/75 (2%)

Query: 100 GSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDD 159
           GS G S RS   +L   LP+     ++++   R G +   +V    GG+T IV++    +
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSL--GRVLLPEGGITAIVEFLEPLE 58

Query: 160 MKYAIRKLDRSEFRN 174
            + A R L  S+F +
Sbjct: 59  ARKAFRHLAYSKFHH 73

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 77.8 bits (192), Expect = 2e-18
 Identities = 16/96 (16%), Positives = 41/96 (42%), Gaps = 3/96 (3%)

Query: 6   SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAI 62
            + +    L  + R   ++D+  KYG + ++++ + P   +  G A + F   R A++ +
Sbjct: 6   LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65

Query: 63  RGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSS 98
           +     +  G  +  +L   G++     +   + S 
Sbjct: 66  KNLHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGSY 101

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 43.2 bits (102), Expect = 8e-06
 Identities = 19/102 (18%), Positives = 34/102 (33%), Gaps = 14/102 (13%)

Query: 111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD------RGGMTGIVDYTSYDDMKYAI 164
            V    L  +     LKD  R+ G+V   ++          G     V +TS    K  +
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLG--LARVLFTSTRGAKETV 65

Query: 165 RKLDRSEFRNAF------SRSYVRVREYDSRRSYSRSPSRSP 200
           + L  +             +   R++ Y+   + S +P   P
Sbjct: 66  KNLHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGSYTPQTVP 107

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 77.5 bits (191), Expect = 2e-18
 Identities = 24/106 (22%), Positives = 41/106 (38%), Gaps = 8/106 (7%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDI-----DLKIPPRPPGYAFLEFEDYR 56
            S  +  L++G +P   +  E+ +   K    V             +  G+AF+E+E +R
Sbjct: 4   GSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHR 63

Query: 57  DAEDAIR--GRDGYNFDGYRLRVELAHGGR-RHSSSMDRYSSYSSG 99
            A  A R          G+++ V+ A          M+  S  SSG
Sbjct: 64  AAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVSGPSSG 109

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 38.2 bits (89), Expect = 4e-04
 Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 7/78 (8%)

Query: 103 GVSR-RSDYRVLVTGLPSSASWQDLKDHMRRAGD------VCFSQVFRDRGGMTGIVDYT 155
           G S    + R+ + G+P     +++ + + +  +      V  S   + +      V+Y 
Sbjct: 1   GSSGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYE 60

Query: 156 SYDDMKYAIRKLDRSEFR 173
           S+     A RKL     +
Sbjct: 61  SHRAAAMARRKLMPGRIQ 78

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 81.3 bits (201), Expect = 2e-18
 Identities = 45/235 (19%), Positives = 72/235 (30%), Gaps = 37/235 (15%)

Query: 5   SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRG 64
               L+VGNLP D    + + LF +YG   ++ +    R  G+ F+  E    AE A   
Sbjct: 21  QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI---NRDRGFGFIRLESRTLAEIAKAE 77

Query: 65  RDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQ 124
            DG       LR+  A                               + V  L    S +
Sbjct: 78  LDGTILKSRPLRIRFA--------------------------THGAALTVKNLSPVVSNE 111

Query: 125 DLKDHMRRAGDVCFSQVFRDRGGMT---GIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV 181
            L+    + G V  + V  D  G     G V++ +    + A+ +     F    +   V
Sbjct: 112 LLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPV 171

Query: 182 RVREYDSRRSYSRSPSRSPYYSRSRSRSPYYSRSRSPSRSWSYSPRSRSYSPRGK 236
            V   +        P +       +    Y+     P R          Y+ R K
Sbjct: 172 IVEPMEQFDDEDGLPEK-----LMQKTQQYHKEREQPPRFAQPGTFEFEYASRWK 221

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 50.5 bits (121), Expect = 1e-07
 Identities = 16/76 (21%), Positives = 25/76 (32%), Gaps = 2/76 (2%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDA 58
             +     L V NL        +E  F ++GP+    + +    R  G  F+EF     A
Sbjct: 91  RFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPA 150

Query: 59  EDAIRGRDGYNFDGYR 74
             A+       F    
Sbjct: 151 RKALERCGDGAFLLTT 166

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 76.2 bits (188), Expect = 5e-18
 Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 3/76 (3%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
          +     T Y+GN+P      ++  LF  +G I+D   K  P   G  F++++ +  A   
Sbjct: 23 APPRVTTAYIGNIPHFATEADLIPLFQNFGFILDF--KHYPE-KGCCFIKYDTHEQAAVC 79

Query: 62 IRGRDGYNFDGYRLRV 77
          I     + F G  LR 
Sbjct: 80 IVALANFPFQGRNLRT 95

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 76.2 bits (188), Expect = 5e-18
 Identities = 23/90 (25%), Positives = 35/90 (38%), Gaps = 11/90 (12%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-----------RPPGYAFL 50
          S   + T++V  L  +  +  V D F + G I        P           +  G A +
Sbjct: 9  SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 68

Query: 51 EFEDYRDAEDAIRGRDGYNFDGYRLRVELA 80
           F+D   A+ AI   DG  F G  ++V  A
Sbjct: 69 SFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 75.7 bits (187), Expect = 7e-18
 Identities = 21/83 (25%), Positives = 43/83 (51%), Gaps = 4/83 (4%)

Query: 2  SSRSSRTLYVGNLPGDTR----MREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRD 57
           +R + T+Y+ NL    +     + +  +F ++G I+DI +    +  G AF+ F++   
Sbjct: 4  ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 63

Query: 58 AEDAIRGRDGYNFDGYRLRVELA 80
          A +A+R   G+ F    +R++ A
Sbjct: 64 ATNALRSMQGFPFYDKPMRIQYA 86

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 80.4 bits (199), Expect = 7e-18
 Identities = 34/174 (19%), Positives = 62/174 (35%), Gaps = 33/174 (18%)

Query: 4   RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL-KIPPRPPGYAFLEFEDYRDAEDAI 62
           R   T+ V NLP      +V   F   GPI+ +D+     +   +A +EF  Y  A  AI
Sbjct: 39  RELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAI 98

Query: 63  RGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSAS 122
             +         + V                              ++  + +T  P S +
Sbjct: 99  T-KTHKVVGQNEIIVS---------------------------HLTECTLWMTNFPPSYT 130

Query: 123 WQDLKDHMRRAGDVCFSQVF-RDRGGMT---GIVDYTSYDDMKYAIRKLDRSEF 172
            ++++D ++    V  S      R   +     +D TS +D +Y + KL+  + 
Sbjct: 131 QRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKI 184

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 75.4 bits (186), Expect = 5e-16
 Identities = 27/183 (14%), Positives = 64/183 (34%), Gaps = 25/183 (13%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP----GYAFLEFEDYRD 57
           S  +  TL++ N P     R + DL      +  + +++P         +A+++     D
Sbjct: 113 SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVA-LSIRLPSLRFNTSRRFAYIDVTSKED 171

Query: 58  AEDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGL 117
           A   +   +G   +GY L  +++           R  S +  G           +++  L
Sbjct: 172 ARYCVEKLNGLKIEGYTLVTKVS----NPLEKSKRTDSATLEGR---------EIMIRNL 218

Query: 118 PSSAS-WQDLKDHMRRAGDVCFSQVFRDRGGM-----TGIVDYTSYDDMKYAIRKLDRSE 171
            +       L++     G +    +   +           + + + D  + A+ +++RS 
Sbjct: 219 STELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSL 277

Query: 172 FRN 174
             N
Sbjct: 278 LGN 280

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 61.2 bits (149), Expect = 4e-11
 Identities = 19/87 (21%), Positives = 33/87 (37%), Gaps = 10/87 (11%)

Query: 1   MSSRSSRTLYVGNLPGDTRM-REVEDLFYKYGPIVDIDLKIPPRPP------GYAFLEFE 53
            ++   R + + NL  +      + + F  +G I  I   IP            AF+ FE
Sbjct: 205 SATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKI--NIPAGQKEHSFNNCCAFMVFE 262

Query: 54  DYRDAEDAIRGRDGYNFDGYRLRVELA 80
           +   AE A++  +        + V LA
Sbjct: 263 NKDSAERALQM-NRSLLGNREISVSLA 288

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 78.5 bits (193), Expect = 1e-17
 Identities = 38/202 (18%), Positives = 73/202 (36%), Gaps = 26/202 (12%)

Query: 1   MSSRSSRTLYVGNL-PGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAE 59
           ++   +  L V NL P     + +  LF  YG +  +  KI       A ++  D   A+
Sbjct: 29  LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRV--KILFNKKENALVQMADGNQAQ 86

Query: 60  DAIRGRDGYNFDGYRLRVELAHGGRRH----------------SSSMDRYSSYSSGGSRG 103
            A+   +G+   G  +R+ L+                      +S + R+    S   + 
Sbjct: 87  LAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQN 146

Query: 104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYA 163
           +   S   + ++ +P S S +DLK      G V     F  +     ++   S ++   A
Sbjct: 147 IFPPSA-TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQA 205

Query: 164 IRKLDRSEFRN------AFSRS 179
           +  L   +         +FS+S
Sbjct: 206 LIDLHNHDLGENHHLRVSFSKS 227

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 74.6 bits (184), Expect = 2e-17
 Identities = 25/94 (26%), Positives = 46/94 (48%), Gaps = 3/94 (3%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAI 62
          SR +Y+G++P D    ++ DL    GP++++ +   P   R  GYAF+EF D   +  A+
Sbjct: 2  SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61

Query: 63 RGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSY 96
          R  +GY      L+   +        S++ +  +
Sbjct: 62 RNLNGYQLGSRFLKCGYSSNSDISGVSLEHHHHH 95

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 73.7 bits (182), Expect = 3e-17
 Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 3/81 (3%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAE 59
          + + R LYVG L  +   + +   F  +G I DI + +     +  G+AF+EFE   DA 
Sbjct: 4  ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63

Query: 60 DAIRGRDGYNFDGYRLRVELA 80
           AI   +     G  +RV LA
Sbjct: 64 AAIDNMNESELFGRTIRVNLA 84

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 39.0 bits (92), Expect = 1e-04
 Identities = 16/76 (21%), Positives = 26/76 (34%), Gaps = 8/76 (10%)

Query: 103 GVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMT------GIVDYTS 156
           G    +   + V GL      + L       GD+   Q+  D    T        V++  
Sbjct: 1   GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY--ETEKHRGFAFVEFEL 58

Query: 157 YDDMKYAIRKLDRSEF 172
            +D   AI  ++ SE 
Sbjct: 59  AEDAAAAIDNMNESEL 74

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 77.4 bits (191), Expect = 3e-17
 Identities = 30/180 (16%), Positives = 66/180 (36%), Gaps = 16/180 (8%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDA 58
           +      +YVG++  +     +   F  +GPI  ID+    +  +  G+AF+E+E    A
Sbjct: 24  ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAA 83

Query: 59  EDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLP 118
           + A+   +     G  ++V       +    +D+ +  +             R+ V  + 
Sbjct: 84  QLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF---------NRIYVASVH 134

Query: 119 SSASWQDLKDHMRRAGDVCFSQVFRDRGGMT----GIVDYTSYDDMKYAIRKLDRSEFRN 174
              S  D+K      G +  + + RD         G ++Y      + A+  ++  +   
Sbjct: 135 QDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGG 194

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 56.2 bits (136), Expect = 1e-09
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 7/84 (8%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-----RPPGYAFLEFEDYR 56
            +R+   +YV ++  D    +++ +F  +G I      +       +  GY F+E+E  +
Sbjct: 121 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSA--TLARDPTTGKHKGYGFIEYEKAQ 178

Query: 57  DAEDAIRGRDGYNFDGYRLRVELA 80
            ++DA+   + ++  G  LRV  A
Sbjct: 179 SSQDAVSSMNLFDLGGQYLRVGKA 202

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 74.4 bits (183), Expect = 3e-17
 Identities = 25/98 (25%), Positives = 39/98 (39%), Gaps = 15/98 (15%)

Query: 6   SRTLYVGNLPGDTRMRE------VEDLFYKYGPIVDIDLKIPP-RPPGYAFLEFEDYRDA 58
              + V N+P     R       +  +F K+G I +        +  GY FLE+     A
Sbjct: 15  DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHA 74

Query: 59  EDAIRGRDGYNFDG-YRLRVELAHGGRRHSSSMDRYSS 95
            DA++  DGY  D  +  RV L        +  D+Y +
Sbjct: 75  VDAVKNADGYKLDKQHTFRVNLF-------TDFDKYMT 105

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 72.3 bits (178), Expect = 1e-16
 Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 3/81 (3%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAE 59
          + S  T+YV NLP      ++  +F KYG +V + +   K   +  G AF+ F D   A+
Sbjct: 13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72

Query: 60 DAIRGRDGYNFDGYRLRVELA 80
          +  R  +     G  ++  +A
Sbjct: 73 NCTRAINNKQLFGRVIKASIA 93

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 73.7 bits (181), Expect = 1e-16
 Identities = 27/82 (32%), Positives = 40/82 (48%), Gaps = 3/82 (3%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDA 58
           S+ + R LYVG L  +   + +   F  +G I DI + +     +  G+AF+EFE   DA
Sbjct: 59  SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 118

Query: 59  EDAIRGRDGYNFDGYRLRVELA 80
             AI   +     G  +RV LA
Sbjct: 119 AAAIDNMNESELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 43.2 bits (102), Expect = 1e-05
 Identities = 18/92 (19%), Positives = 29/92 (31%), Gaps = 8/92 (8%)

Query: 87  SSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG 146
            +           G  G S  +   + V GL      + L       GD+   Q+  D  
Sbjct: 41  CTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY- 99

Query: 147 GMT------GIVDYTSYDDMKYAIRKLDRSEF 172
             T        V++   +D   AI  ++ SE 
Sbjct: 100 -ETEKHRGFAFVEFELAEDAAAAIDNMNESEL 130

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 72.7 bits (179), Expect = 2e-16
 Identities = 28/113 (24%), Positives = 53/113 (46%), Gaps = 2/113 (1%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDA 58
           + +     L++G L  +T  + ++ +F K+GPI ++ L      +  G+AF+ FE+  DA
Sbjct: 2   VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADA 61

Query: 59  EDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYR 111
           ++A +  +G +  G  ++VE A      S    R  + S   S   S    + 
Sbjct: 62  KNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLEHHHH 114

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 40.0 bits (94), Expect = 9e-05
 Identities = 22/124 (17%), Positives = 43/124 (34%), Gaps = 17/124 (13%)

Query: 104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMT---GIVDYTSYDDM 160
           V      ++ + GL    + + LK    + G +    + +DR   +     + + +  D 
Sbjct: 2   VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADA 61

Query: 161 KYAIRKLDRSEFRNAFSRSYVRVREYDSRRSYSRSPSRSPYYSRSRSRSPYYSRSRSPSR 220
           K A + ++                    +        +  + S  R R P  SR+RSPS 
Sbjct: 62  KNAAKDMNGKSL--------------HGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSG 107

Query: 221 SWSY 224
           S  +
Sbjct: 108 SLEH 111

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 71.9 bits (177), Expect = 2e-16
 Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 1/87 (1%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
           S  S+TL + NL        ++++F K   I         +  GYAF+EF  + DA++A
Sbjct: 11 WSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQ-NQNGKSKGYAFIEFASFEDAKEA 69

Query: 62 IRGRDGYNFDGYRLRVELAHGGRRHSS 88
          +   +    +G  +R+EL       +S
Sbjct: 70 LNSCNKREIEGRAIRLELQGPRGSPNS 96

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 71.5 bits (176), Expect = 3e-16
 Identities = 20/86 (23%), Positives = 40/86 (46%), Gaps = 2/86 (2%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDAE 59
          +S     L++  LP      E+E++   +G + D+ L      +P G A++E+E+   A 
Sbjct: 13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQAS 72

Query: 60 DAIRGRDGYNFDGYRLRVELAHGGRR 85
           A+   DG       ++V +++ G  
Sbjct: 73 QAVMKMDGMTIKENIIKVAISNSGPS 98

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 3/82 (3%)

Query: 94  SSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMT---G 150
           SS SSG  R  +    +++ ++GLP S + ++L++  +  G V   ++  +R G      
Sbjct: 2   SSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLA 61

Query: 151 IVDYTSYDDMKYAIRKLDRSEF 172
            V+Y +      A+ K+D    
Sbjct: 62  YVEYENESQASQAVMKMDGMTI 83

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 73.4 bits (181), Expect = 3e-16
 Identities = 25/188 (13%), Positives = 63/188 (33%), Gaps = 29/188 (15%)

Query: 6   SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP-------PRPPGYAFLEFEDYRDA 58
           +  ++VG +P     +++ +LF +YG + +I   +        P+  G  F+ F   + A
Sbjct: 3   AIKMFVGQVPRTWSEKDLRELFEQYGAVYEI--NVLRDRSQNPPQSKGCCFVTFYTRKAA 60

Query: 59  EDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLP 118
            +A                                   +           D ++ +  + 
Sbjct: 61  LEAQNALHNMKVLPGMHHP--------------IQMKPADSEKNNAVE--DRKLFIGMIS 104

Query: 119 SSASWQDLKDHMRRAGDVCFSQVFRDRGGMT---GIVDYTSYDDMKYAIRKLDRSEFRNA 175
              +  D++      G +   ++ R   G++     V +T+    + AI+ + +++    
Sbjct: 105 KKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEG 164

Query: 176 FSRS-YVR 182
            S    V+
Sbjct: 165 CSSPMVVK 172

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 71.2 bits (175), Expect = 4e-16
 Identities = 20/102 (19%), Positives = 38/102 (37%), Gaps = 5/102 (4%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
                + L+V NL        +E  F ++G +  +          YAF+ F++   A  A
Sbjct: 7   GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKK-----LKDYAFIHFDERDGAVKA 61

Query: 62  IRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRG 103
           +   +G + +G  + +  A    +           +SG S G
Sbjct: 62  MEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGPSSG 103

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 73.0 bits (180), Expect = 5e-16
 Identities = 34/178 (19%), Positives = 63/178 (35%), Gaps = 37/178 (20%)

Query: 5   SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP--------PRPPGYAFLEFEDYR 56
           S+R LYVGN+P       + D F     +  +              +   +AFLEF    
Sbjct: 3   SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62

Query: 57  DAEDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTG 116
           +   A+   DG  F G  L++   H  +    +                    +++ + G
Sbjct: 63  ETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGA--------------------HKLFIGG 101

Query: 117 LPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGI------VDYTSYDDMKYAIRKLD 168
           LP+  +   +K+ +   G +    + +D    TG+       +Y   +    AI  L+
Sbjct: 102 LPNYLNDDQVKELLTSFGPLKAFNLVKDSA--TGLSKGYAFCEYVDINVTDQAIAGLN 157

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 60.3 bits (147), Expect = 2e-11
 Identities = 22/82 (26%), Positives = 36/82 (43%), Gaps = 3/82 (3%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDA 58
               +  L++G LP      +V++L   +GP+   +L          GYAF E+ D    
Sbjct: 90  PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 149

Query: 59  EDAIRGRDGYNFDGYRLRVELA 80
           + AI G +G      +L V+ A
Sbjct: 150 DQAIAGLNGMQLGDKKLLVQRA 171

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 71.3 bits (175), Expect = 5e-16
 Identities = 26/109 (23%), Positives = 41/109 (37%), Gaps = 17/109 (15%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-----------RPPGYAFL 50
               +  +YV  L     + ++ D F + G +        P           +P G A +
Sbjct: 11  EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 70

Query: 51  EFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSG 99
            +ED   A+ A+   DG +F G +L+V LA             S  SSG
Sbjct: 71  SYEDPPTAKAAVEWFDGKDFQGSKLKVSLAR------KKPPMNSGPSSG 113

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 40.5 bits (95), Expect = 6e-05
 Identities = 19/91 (20%), Positives = 32/91 (35%), Gaps = 16/91 (17%)

Query: 97  SSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQ--------VFRDRGGM 148
           S           +  + V GL  S +  DL D  ++ G V  ++        ++ D+   
Sbjct: 3   SGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDK--E 60

Query: 149 TG------IVDYTSYDDMKYAIRKLDRSEFR 173
           TG       V Y      K A+   D  +F+
Sbjct: 61  TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ 91

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 70.8 bits (174), Expect = 5e-16
 Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 2/79 (2%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
            R++RTL   NL  +    E++++F     I  +      +  G A++EF+   DAE  
Sbjct: 12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSK--GIAYIEFKSEADAEKN 69

Query: 62 IRGRDGYNFDGYRLRVELA 80
          +  + G   DG  + +   
Sbjct: 70 LEEKQGAEIDGRSVSLYYT 88

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 71.3 bits (175), Expect = 6e-16
 Identities = 24/112 (21%), Positives = 41/112 (36%), Gaps = 18/112 (16%)

Query: 3   SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-----------RPPGYAFLE 51
           +  + T++V  L  +  +  V D F + G I        P           +  G A + 
Sbjct: 4   NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63

Query: 52  FEDYRDAEDAIRGRDGYNFDGYRLRVELA-------HGGRRHSSSMDRYSSY 96
           F+D   A+ AI   DG  F G  ++V  A        GG      ++ +  +
Sbjct: 64  FDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRGGLEHHHHH 115

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 70.3 bits (173), Expect = 7e-16
 Identities = 28/85 (32%), Positives = 43/85 (50%), Gaps = 3/85 (3%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDA 58
          +   +  L V  L   T  R++ ++F KYGPI D+ +       R  G+AF+ FE+  DA
Sbjct: 11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 70

Query: 59 EDAIRGRDGYNFDGYRLRVELAHGG 83
          ++A    +G   DG R+RV     G
Sbjct: 71 KEAKERANGMELDGRRIRVSGPSSG 95

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 70.4 bits (173), Expect = 1e-15
 Identities = 25/98 (25%), Positives = 43/98 (43%), Gaps = 9/98 (9%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
           SS  + T+Y G +      + +   F  +G I++I  ++ P   GY+F+ F  +  A  A
Sbjct: 21  SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEI--RVFPE-KGYSFVRFSTHESAAHA 77

Query: 62  IRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSG 99
           I   +G   +G+ ++            S D  S  SSG
Sbjct: 78  IVSVNGTTIEGHVVKCYWGK------ESPDMTSGPSSG 109

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 69.7 bits (171), Expect = 1e-15
 Identities = 21/78 (26%), Positives = 32/78 (41%), Gaps = 8/78 (10%)

Query: 8  TLYVGNLPGDTR------MREVEDLFYKYGPIVDIDLKIPP-RPPGYAFLEFEDYRDAED 60
           + V N+P             +  +F K+G I +        +  GY FLE+     A D
Sbjct: 3  VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVD 62

Query: 61 AIRGRDGYNFDG-YRLRV 77
          A++  DGY  D  +  RV
Sbjct: 63 AVKNADGYKLDKQHTFRV 80

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 72.3 bits (178), Expect = 1e-15
 Identities = 26/177 (14%), Positives = 61/177 (34%), Gaps = 32/177 (18%)

Query: 3   SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP----GYAFLEFEDYRDA 58
           S +   L++GNL  +  + E++    +     D+   +          + +++FE   D 
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDL--AVVDVRTGTNRKFGYVDFESAEDL 67

Query: 59  EDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLP 118
           E A+    G    G  +++E                     G      R+   +L   L 
Sbjct: 68  EKAL-ELTGLKVFGNEIKLEKPK------------------GRDSKKVRAARTLLAKNLS 108

Query: 119 SSASWQDLKDHMRRAGDVCFSQVFRDRGGMT---GIVDYTSYDDMKYAIRKLDRSEF 172
            + +  +LK+    A ++        + G +     +++ S  D +  + +   +E 
Sbjct: 109 FNITEDELKEVFEDALEI----RLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI 161

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 59.2 bits (144), Expect = 5e-11
 Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 2/80 (2%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
              R++RTL   NL  +    E++++F     I  +      +  G A++EF+   DAE 
Sbjct: 94  KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSK--GIAYIEFKSEADAEK 151

Query: 61  AIRGRDGYNFDGYRLRVELA 80
            +  + G   DG  + +   
Sbjct: 152 NLEEKQGAEIDGRSVSLYYT 171

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 70.0 bits (172), Expect = 1e-15
 Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRD 57
             S     L+V  +  +    ++ D F +YG I +I L +        GY  +E+E Y++
Sbjct: 18  QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 77

Query: 58  AEDAIRGRDGYNFDGYRLRVELAH 81
           A+ A+ G +G +  G  + V+   
Sbjct: 78  AQAAMEGLNGQDLMGQPISVDWCF 101

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 70.0 bits (172), Expect = 2e-15
 Identities = 20/84 (23%), Positives = 38/84 (45%), Gaps = 3/84 (3%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRD 57
             S     L+V ++  + +  E+++ F  YG I +I L +        GYA +E+E ++ 
Sbjct: 21  QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQ 80

Query: 58  AEDAIRGRDGYNFDGYRLRVELAH 81
           A  A    +G    G  ++V+   
Sbjct: 81  ALAAKEALNGAEIMGQTIQVDWCF 104

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 69.2 bits (170), Expect = 2e-15
 Identities = 29/82 (35%), Positives = 47/82 (57%), Gaps = 3/82 (3%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDA 58
            RS R+++VGN+P +    +++D+F + GP+V   L   +   +P GY F E++D   A
Sbjct: 4  VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63

Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
            A+R  +G  F G  LRV+ A
Sbjct: 64 LSAMRNLNGREFSGRALRVDNA 85

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 71.1 bits (175), Expect = 3e-15
 Identities = 44/186 (23%), Positives = 67/186 (36%), Gaps = 27/186 (14%)

Query: 5   SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDA 61
           S+  L V  LP D   RE+  LF   GPI    +          GYAF++F    D++ A
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61

Query: 62  IRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSA 121
           I+  +G      RL+V                 SY+  G        D  + VT LP + 
Sbjct: 62  IKVLNGITVRNKRLKV-----------------SYARPGGE---SIKDTNLYVTNLPRTI 101

Query: 122 SWQDLKDHMRRAGDVCFSQVFRDRGGMT----GIVDYTSYDDMKYAIRKLDRSEFRNAFS 177
           +   L     + G +    + RD+          V Y   ++ + AI  L+         
Sbjct: 102 TDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQ 161

Query: 178 RSYVRV 183
              VR+
Sbjct: 162 PLSVRL 167

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 53.0 bits (128), Expect = 6e-09
 Identities = 27/86 (31%), Positives = 38/86 (44%), Gaps = 9/86 (10%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-----RPPGYAFLEFEDYR 56
            S     LYV NLP      +++ +F KYG IV     I       RP G AF+ +    
Sbjct: 85  ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQK--NILRDKLTGRPRGVAFVRYNKRE 142

Query: 57  DAEDAIRGRDGYNFDGY--RLRVELA 80
           +A++AI   +    +G    L V LA
Sbjct: 143 EAQEAISALNNVIPEGGSQPLSVRLA 168

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 70.7 bits (174), Expect = 3e-15
 Identities = 40/171 (23%), Positives = 67/171 (39%), Gaps = 27/171 (15%)

Query: 5   SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDA 61
           S   L V  LP +    E   LF   G I    L   KI  +  GY F+ + D +DAE A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 62  IRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSA 121
           I   +G       ++V                 SY+   S       D  + V+GLP + 
Sbjct: 61  INTLNGLRLQTKTIKV-----------------SYARPSSA---SIRDANLYVSGLPKTM 100

Query: 122 SWQDLKDHMRRAGDVCFSQVFRDRGGMT----GIVDYTSYDDMKYAIRKLD 168
           + ++L+    + G +  S++  D+        G + +    + + AI+ L+
Sbjct: 101 TQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN 151

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 53.0 bits (128), Expect = 6e-09
 Identities = 28/86 (32%), Positives = 43/86 (50%), Gaps = 7/86 (8%)

Query: 2   SSRSSRT--LYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYR 56
           SS S R   LYV  LP     +E+E LF +YG I+   +   ++     G  F+ F+   
Sbjct: 82  SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRI 141

Query: 57  DAEDAIRGRDGYNFDGYR--LRVELA 80
           +AE+AI+G +G    G    + V+ A
Sbjct: 142 EAEEAIKGLNGQKPSGATEPITVKFA 167

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 70.6 bits (173), Expect = 3e-15
 Identities = 35/94 (37%), Positives = 45/94 (47%), Gaps = 7/94 (7%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-----RPPGYAFLEFEDY 55
           M      +L V NL   T    +  +F KYG + D+   IP         G+AF+ F D 
Sbjct: 65  MDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDV--YIPRDRYTKESRGFAFVRFHDK 122

Query: 56  RDAEDAIRGRDGYNFDGYRLRVELAHGGRRHSSS 89
           RDAEDA+   DG   DG  LRV++A  GR   S 
Sbjct: 123 RDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSH 156

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 41.0 bits (96), Expect = 8e-05
 Identities = 21/133 (15%), Positives = 35/133 (26%), Gaps = 15/133 (11%)

Query: 46  GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVS 105
           G    E  D   AE   +     N                 ++     +  S      + 
Sbjct: 14  GETTTEAVDAATAEKVFKQYANDNGVDGEWT-------YDDATKTFTVTEGSHHHHHHMD 66

Query: 106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGI------VDYTSYDD 159
                 + V  L    S   L+    + G V    + RDR   T        V +    D
Sbjct: 67  VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDR--YTKESRGFAFVRFHDKRD 124

Query: 160 MKYAIRKLDRSEF 172
            + A+  +D +  
Sbjct: 125 AEDAMDAMDGAVL 137

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 68.8 bits (169), Expect = 3e-15
 Identities = 21/84 (25%), Positives = 35/84 (41%), Gaps = 6/84 (7%)

Query: 4  RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP----RPPGYAFLEFEDYRDAE 59
           + RT++VGNL    R   + +LF + GP+  +   I      +P  + F+ F+      
Sbjct: 14 EADRTVFVGNLEARVREEILYELFLQAGPLTKV--TICKDREGKPKSFGFVCFKHPESVS 71

Query: 60 DAIRGRDGYNFDGYRLRVELAHGG 83
           AI   +G    G  + V     G
Sbjct: 72 YAIALLNGIRLYGRPINVSGPSSG 95

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 43.4 bits (103), Expect = 4e-06
 Identities = 19/81 (23%), Positives = 31/81 (38%), Gaps = 3/81 (3%)

Query: 95  SYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMT---GI 151
           S  S G       +D  V V  L +    + L +   +AG +    + +DR G     G 
Sbjct: 2   SSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGF 61

Query: 152 VDYTSYDDMKYAIRKLDRSEF 172
           V +   + + YAI  L+    
Sbjct: 62  VCFKHPESVSYAIALLNGIRL 82

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 69.2 bits (170), Expect = 3e-15
 Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 3/86 (3%)

Query: 6   SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAI 62
           ++ LY+ NL      R++  LF ++       ++      R  G AF+ F +   A  A+
Sbjct: 25  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84

Query: 63  RGRDGYNFDGYRLRVELAHGGRRHSS 88
              +GY   G  L +E     ++ SS
Sbjct: 85  HLVNGYKLYGKILVIEFGKNKKQRSS 110

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 68.0 bits (167), Expect = 6e-15
 Identities = 30/91 (32%), Positives = 43/91 (47%), Gaps = 3/91 (3%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDA 58
            +  + T+ V NL  DTR  ++++LF  +G I  I L   K   +  G+AF+ F    DA
Sbjct: 11  RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDA 70

Query: 59  EDAIRGRDGYNFDGYRLRVELAHGGRRHSSS 89
             AI G  G+ +D   L VE A        S
Sbjct: 71  ARAIAGVSGFGYDHLILNVEWAKPSTNSGPS 101

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 19/85 (22%), Positives = 32/85 (37%), Gaps = 9/85 (10%)

Query: 97  SSGGSRGVSRRSD-YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGI---- 151
           SSG S    R  D   + VT L       DL++  R  G +    + +D+   TG     
Sbjct: 2   SSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDK--TTGQSKGF 59

Query: 152 --VDYTSYDDMKYAIRKLDRSEFRN 174
             + +   +D   AI  +    + +
Sbjct: 60  AFISFHRREDAARAIAGVSGFGYDH 84

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 68.1 bits (167), Expect = 6e-15
 Identities = 20/93 (21%), Positives = 38/93 (40%), Gaps = 5/93 (5%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDI----DLKIPPRPPGYAFLEFEDYRD 57
             +++  + V N+P     RE+ +LF  +G +  +     +       G+ F++F   +D
Sbjct: 11  KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70

Query: 58  AEDAIRG-RDGYNFDGYRLRVELAHGGRRHSSS 89
           A+ A        +  G RL +E A       S 
Sbjct: 71  AKKAFNALCHSTHLYGRRLVLEWADSEVTVQSG 103

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 68.0 bits (167), Expect = 6e-15
 Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 3/81 (3%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAE 59
          + + R LYVG L  +   + +   F  +G I DI + +     +  G+AF+EFE   DA 
Sbjct: 9  ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 68

Query: 60 DAIRGRDGYNFDGYRLRVELA 80
           AI   +     G  +RV LA
Sbjct: 69 AAIDNMNESELFGRTIRVNLA 89

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 68.1 bits (167), Expect = 7e-15
 Identities = 22/89 (24%), Positives = 43/89 (48%), Gaps = 1/89 (1%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL-KIPPRPPGYAFLEFEDYRDAED 60
          S  + + L+V N+P   R  ++  +F ++G I+D+++        G+ F+ FE+  DA+ 
Sbjct: 11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADR 70

Query: 61 AIRGRDGYNFDGYRLRVELAHGGRRHSSS 89
          A     G   +G ++ V  A      +S 
Sbjct: 71 AREKLHGTVVEGRKIEVNNATARVMTNSG 99

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 37.6 bits (88), Expect = 5e-04
 Identities = 23/106 (21%), Positives = 38/106 (35%), Gaps = 12/106 (11%)

Query: 98  SGGSRGVSRRSD--YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGI--VD 153
           S GS G S       R+ V+ +P      DL+    + G +   ++  +  G  G   V 
Sbjct: 2   SSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVT 61

Query: 154 YTSYDDMKYAIRKLDRSEF--RNAFSRSYVRVREYDSRRSYSRSPS 197
           + +  D   A  KL  +    R       + V    +R   +  PS
Sbjct: 62  FENSADADRAREKLHGTVVEGRK------IEVNNATARVMTNSGPS 101

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 67.2 bits (165), Expect = 1e-14
 Identities = 28/94 (29%), Positives = 40/94 (42%), Gaps = 3/94 (3%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDA 58
           S  S  L+V NL   +   ++E LF  YGP+ ++   I     +P G+AF+ F     A
Sbjct: 4  GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 59 EDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDR 92
            A    DG  F G  L V  +   +  S S   
Sbjct: 64 VKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPS 97

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 67.0 bits (164), Expect = 1e-14
 Identities = 17/78 (21%), Positives = 35/78 (44%), Gaps = 3/78 (3%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAI 62
          S   R+++V   P      ++ + F  +GP+  +   +      +A +E  D   A +A+
Sbjct: 5  SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGVFAIVEMGDV-GAREAV 61

Query: 63 RGRDGYNFDGYRLRVELA 80
            +  ++  G+RLRV   
Sbjct: 62 LSQSQHSLGGHRLRVRPR 79

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 67.9 bits (166), Expect = 2e-14
 Identities = 35/111 (31%), Positives = 51/111 (45%), Gaps = 7/111 (6%)

Query: 3   SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAE 59
            + S TLYVGNL   T   ++ +LF K G I  I +   K+     G+ F+E+    DAE
Sbjct: 36  LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 95

Query: 60  DAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDY 110
           +A+R  +G   D   +R +   G +       +Y    SGG      R DY
Sbjct: 96  NAMRYINGTRLDDRIIRTDWDAGFK----EGRQYGRGRSGGQVRDEYRQDY 142

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 70.3 bits (171), Expect = 2e-14
 Identities = 22/83 (26%), Positives = 43/83 (51%), Gaps = 4/83 (4%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFY----KYGPIVDIDLKIPPRPPGYAFLEFEDYRD 57
           +R + T+Y+ NL    +  E++   Y    ++G I+DI +    +  G AF+ F++   
Sbjct: 5  ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64

Query: 58 AEDAIRGRDGYNFDGYRLRVELA 80
          A +A+R   G+ F    +R++ A
Sbjct: 65 ATNALRSMQGFPFYDKPMRIQYA 87

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 53.3 bits (127), Expect = 2e-08
 Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 3/74 (4%)

Query: 8   TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDG 67
            L++ NLP +T    +  LF ++    ++  ++ P     AF+EF++   A  A     G
Sbjct: 209 ILFLTNLPEETNELMLSMLFNQFPGFKEV--RLVPGRHDIAFVEFDNEVQAGAARDALQG 266

Query: 68  YNF-DGYRLRVELA 80
           +       +++  A
Sbjct: 267 FKITQNNAMKISFA 280

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 65.8 bits (161), Expect = 3e-14
 Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 4/77 (5%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
            ++  TLYVG L       ++ + FY++G I  I   +  R    AF++F   + AE A
Sbjct: 8  EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTI--TVVQR-QQCAFIQFATRQAAEVA 64

Query: 62 I-RGRDGYNFDGYRLRV 77
            +  +    +G RL V
Sbjct: 65 AEKSFNKLIVNGRRLNV 81

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 65.7 bits (161), Expect = 3e-14
 Identities = 21/93 (22%), Positives = 41/93 (44%), Gaps = 6/93 (6%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIV------DIDLKIPPRPPGYAFLEFEDYR 56
          S  S  L++ NL   T    ++ +F K G I         +        G+ F+E++   
Sbjct: 2  SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61

Query: 57 DAEDAIRGRDGYNFDGYRLRVELAHGGRRHSSS 89
           A+ A++   G+  DG++L V ++    + +S 
Sbjct: 62 QAQKALKQLQGHTVDGHKLEVRISERATKPASG 94

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 64.9 bits (159), Expect = 6e-14
 Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 1/88 (1%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-RPPGYAFLEFEDYRDAED 60
           S  +  ++V NLP D   + ++D F + G ++  D+K+   +  G   ++FE    AE 
Sbjct: 4  GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAER 63

Query: 61 AIRGRDGYNFDGYRLRVELAHGGRRHSS 88
          A R  +G    G  + V +       SS
Sbjct: 64 ACRMMNGMKLSGREIDVRIDRNASGPSS 91

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 53.7 bits (130), Expect = 7e-10
 Identities = 22/96 (22%), Positives = 38/96 (39%), Gaps = 13/96 (13%)

Query: 105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG---GMTGIVDYTSYDDMK 161
                 ++ V  LP   +W+ LKD     G V ++ +  + G   G  G+V + S +  +
Sbjct: 4   GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGC-GVVKFESPEVAE 62

Query: 162 YAIRKLDRSEF--RNAFSRSYVRVREYDSRRSYSRS 195
            A R ++  +   R       + VR  D   S   S
Sbjct: 63  RACRMMNGMKLSGRE------IDVRI-DRNASGPSS 91

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 65.1 bits (159), Expect = 7e-14
 Identities = 19/90 (21%), Positives = 37/90 (41%), Gaps = 11/90 (12%)

Query: 10 YVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRGRD 66
           + +       + +  LF K G +V+++  I     +  G+ F+E     DA+  I+   
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 67 GYNFDG-YRLRVELAHGGRRHSSSMDRYSS 95
          G   D  +RL +            ++RY+S
Sbjct: 76 GKRLDLKHRLFLYTM-------KDVERYNS 98

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 65.5 bits (160), Expect = 1e-13
 Identities = 29/88 (32%), Positives = 46/88 (52%), Gaps = 3/88 (3%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDA 58
           +   +  L V  L   T  R++ ++F KYGPI D+ +       R  G+AF+ FE+  DA
Sbjct: 42  NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 101

Query: 59  EDAIRGRDGYNFDGYRLRVELAHGGRRH 86
           ++A    +G   DG R+RV+ +   R H
Sbjct: 102 KEAKERANGMELDGRRIRVDFSITKRPH 129

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 64.6 bits (158), Expect = 1e-13
 Identities = 20/81 (24%), Positives = 33/81 (40%), Gaps = 3/81 (3%)

Query: 5  SSRTLYVGNLPGDTRMREVEDLFYKYGPIVD-IDLKIPP--RPPGYAFLEFEDYRDAEDA 61
              + V N+P    + E+ D FY Y  I   + LK      P G A + FE   +A  A
Sbjct: 14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73

Query: 62 IRGRDGYNFDGYRLRVELAHG 82
          +   +       ++++ L  G
Sbjct: 74 VIDLNDRPIGSRKVKLVLGSG 94

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 21/94 (22%), Positives = 38/94 (40%), Gaps = 10/94 (10%)

Query: 94  SSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDV--CFSQVFRDRGGMTG- 150
           SS SSG S G        + V  +P + S  ++ D       +       + ++G  TG 
Sbjct: 2   SSGSSGASSGKP--GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGE 59

Query: 151 -IVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV 183
            +V + S D+   A+  L+     +   R  V++
Sbjct: 60  AMVAFESRDEATAAVIDLNDRPIGS---R-KVKL 89

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 64.0 bits (156), Expect = 1e-13
 Identities = 21/82 (25%), Positives = 32/82 (39%), Gaps = 9/82 (10%)

Query: 4  RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVD--------IDLKIPPRPPGYAFLEFEDY 55
           S+R LYVGN+P       + D F     +          +      +   +AFLEF   
Sbjct: 4  GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 63

Query: 56 RDAEDAIRGRDGYNFDGYRLRV 77
           +   A+   DG  F G  L++
Sbjct: 64 DETTQAMA-FDGIIFQGQSLKI 84

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 64.6 bits (158), Expect = 1e-13
 Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 3/82 (3%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDA 58
                T+YVG L        + +LF + GP+V+  +   ++  +  GY F+EF    DA
Sbjct: 11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 70

Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
          + AI+  D     G  +RV  A
Sbjct: 71 DYAIKIMDMIKLYGKPIRVNKA 92

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 64.2 bits (157), Expect = 2e-13
 Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 3/82 (3%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDA 58
            S     LYVG+L  +     +  +F  +G I  I L +     R  GY F+ F D   A
Sbjct: 22  GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECA 81

Query: 59  EDAIRGRDGYNFDGYRLRVELA 80
           + A+   +G+   G  ++V   
Sbjct: 82  KKALEQLNGFELAGRPMKVGHV 103

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 65.6 bits (161), Expect = 2e-13
 Identities = 38/170 (22%), Positives = 65/170 (38%), Gaps = 28/170 (16%)

Query: 7   RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP----RPPGYAFLEFEDYRDAEDAI 62
           R LYVGNL        ++  F   GPI +I  KI      +   YAF+E+    DA  A+
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANI--KIMIDKNNKNVNYAFVEYHQSHDANIAL 58

Query: 63  RGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSAS 122
           +  +G   +   +++  A   ++ SS                     + + V  L  +  
Sbjct: 59  QTLNGKQIENNIVKINWAFQSQQSSSD------------------DTFNLFVGDLNVNVD 100

Query: 123 WQDLKDHMRRAGDVCFSQVFRDRG-GMT---GIVDYTSYDDMKYAIRKLD 168
            + L++  +         V  D   G +   G V +TS DD + A+  + 
Sbjct: 101 DETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQ 150

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 49.1 bits (118), Expect = 2e-07
 Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 7/78 (8%)

Query: 8   TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-----RPPGYAFLEFEDYRDAEDAI 62
            L+VG+L  +     + + F  +   +     +          GY F+ F    DA++A+
Sbjct: 89  NLFVGDLNVNVDDETLRNAFKDFPSYLSG--HVMWDMQTGSSRGYGFVSFTSQDDAQNAM 146

Query: 63  RGRDGYNFDGYRLRVELA 80
               G + +G  LR+  A
Sbjct: 147 DSMQGQDLNGRPLRINWA 164

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 65.6 bits (160), Expect = 2e-13
 Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 3/82 (3%)

Query: 3   SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAE 59
           S     L+V ++  + +  E+++ F  YG I +I L +        GYA +E+E ++ A 
Sbjct: 69  SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 128

Query: 60  DAIRGRDGYNFDGYRLRVELAH 81
            A    +G    G  ++V+   
Sbjct: 129 AAKEALNGAEIMGQTIQVDWCF 150

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 63.9 bits (156), Expect = 3e-13
 Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 1/80 (1%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL-KIPPRPPGYAFLEFEDYRDAED 60
           +    + L+V N+P   R  ++  +F ++G I+D+++        G+ F+ FE+  DA+ 
Sbjct: 25  NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADR 84

Query: 61  AIRGRDGYNFDGYRLRVELA 80
           A     G   +G ++ V  A
Sbjct: 85  AREKLHGTVVEGRKIEVNNA 104

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 63.0 bits (154), Expect = 4e-13
 Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 3/81 (3%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAE 59
          S  S  LYVG+L  +     +  +F  +G I +I L       R  GY F+ F D   A 
Sbjct: 2  SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61

Query: 60 DAIRGRDGYNFDGYRLRVELA 80
           A+   +G+   G  +RV   
Sbjct: 62 RALEQLNGFELAGRPMRVGHV 82

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 63.0 bits (153), Expect = 5e-13
 Identities = 18/82 (21%), Positives = 30/82 (36%), Gaps = 9/82 (10%)

Query: 8  TLYVGNLPGDTRMREV---EDLFYKYGPIVDIDL------KIPPRPPGYAFLEFEDYRDA 58
           ++V  L       EV    + F K+G I  + +           P   A++ +    DA
Sbjct: 17 LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76

Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
            AI+  +    DG  L+  L 
Sbjct: 77 LRAIQCVNNVVVDGRTLKASLG 98

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 63.5 bits (155), Expect = 6e-13
 Identities = 23/105 (21%), Positives = 41/105 (39%), Gaps = 3/105 (2%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRD 57
             S     L+V  +  +    ++ D F +YG I +I L +        GY  +E+E Y++
Sbjct: 17  QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 76

Query: 58  AEDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSR 102
           A+ A+ G +G +  G  + V+                  S    R
Sbjct: 77  AQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRSPDR 121

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 62.3 bits (152), Expect = 8e-13
 Identities = 18/79 (22%), Positives = 31/79 (39%), Gaps = 3/79 (3%)

Query: 5  SSRTLYVGNLPGDTRMREVEDLFYKYGPIVD-IDLKIPP--RPPGYAFLEFEDYRDAEDA 61
              + V N+P    + E+ D FY Y  I   + LK      P G A + FE   +A  A
Sbjct: 14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73

Query: 62 IRGRDGYNFDGYRLRVELA 80
          +   +       ++++   
Sbjct: 74 VIDLNDRPIGSRKVKLSGP 92

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 21/94 (22%), Positives = 38/94 (40%), Gaps = 10/94 (10%)

Query: 94  SSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDV--CFSQVFRDRGGMTG- 150
           SS SSG S G        + V  +P + S  ++ D       +       + ++G  TG 
Sbjct: 2   SSGSSGSSSGKP--GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGE 59

Query: 151 -IVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV 183
            +V + S D+   A+  L+     +   R  V++
Sbjct: 60  AMVAFESRDEATAAVIDLNDRPIGS---R-KVKL 89

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 61.8 bits (151), Expect = 9e-13
 Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 4/80 (5%)

Query: 4  RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAED 60
            +R++YVGN+       E+E  F+  G +  + +   K    P G+A++EF D      
Sbjct: 4  ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 63

Query: 61 AIRGRDGYNFDGYRLRVELA 80
          ++   D   F G +++V   
Sbjct: 64 SLA-LDESLFRGRQIKVIPK 82

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 61.9 bits (151), Expect = 1e-12
 Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 5/79 (6%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
          + R   TLYV     D     +   F  +G I+D+   + P P   AF+ +E    A+ A
Sbjct: 11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDL--SMDP-PRNCAFVTYEKMESADQA 65

Query: 62 IRGRDGYNFDGYRLRVELA 80
          +   +G   +  +L+V +A
Sbjct: 66 VAELNGTQVESVQLKVNIA 84

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 61.6 bits (150), Expect = 1e-12
 Identities = 13/91 (14%), Positives = 31/91 (34%), Gaps = 9/91 (9%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP-----PRPPGYAFLEFEDYR 56
                T+ + N+   T +  +      Y  +   ++++       +  G+AF++     
Sbjct: 5  HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAM 64

Query: 57 DAEDAIRGRDG----YNFDGYRLRVELAHGG 83
          DA   ++           DG  + V+ A   
Sbjct: 65 DASQLLQILQSLHPPLKIDGKTIGVDFAKSA 95

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 61.9 bits (151), Expect = 1e-12
 Identities = 28/93 (30%), Positives = 47/93 (50%), Gaps = 7/93 (7%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-----RPPGYAFLEFEDYR 56
           +     L+VG L  DT  + +E +F KYG I ++   +       R  G+ F+ FE+  
Sbjct: 8  MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEV--VVVKDRETQRSRGFGFVTFENID 65

Query: 57 DAEDAIRGRDGYNFDGYRLRVELAHGGRRHSSS 89
          DA+DA+   +G + DG ++RV+ A     + S 
Sbjct: 66 DAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSG 98

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 62.8 bits (153), Expect = 1e-12
 Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 3/82 (3%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDA 58
                R L V  +P      ++  LF +YGPI  + +   +   +  GY F++F+    A
Sbjct: 38  EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSA 97

Query: 59  EDAIRGRDGYNFDGYRLRVELA 80
           + AI G +G+N    RL+V LA
Sbjct: 98  QQAIAGLNGFNILNKRLKVALA 119

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 62.0 bits (151), Expect = 1e-12
 Identities = 23/93 (24%), Positives = 40/93 (43%), Gaps = 4/93 (4%)

Query: 3   SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAE 59
            R +RT++   L    R R++ED F   G + D+ +   +   R  G A++EF + +   
Sbjct: 22  ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP 81

Query: 60  DAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDR 92
            AI G  G    G  + V+ +   +   S    
Sbjct: 82  LAI-GLTGQRLLGVPIIVQASQAEKNRLSGPSS 113

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 64.2 bits (157), Expect = 1e-12
 Identities = 37/169 (21%), Positives = 65/169 (38%), Gaps = 23/169 (13%)

Query: 5   SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDA 61
              +LYVG+L  D     + + F   GPI+ I +    I  R  GYA++ F+   DAE A
Sbjct: 14  PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 73

Query: 62  IRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSA 121
           +   +     G  +R+                  +S      + +     + +  L  S 
Sbjct: 74  LDTMNFDVIKGKPVRI-----------------MWSQ-RDPSLRKSGVGNIFIKNLDKSI 115

Query: 122 SWQDLKDHMRRAGDVCFSQVFRDRGGMTGI--VDYTSYDDMKYAIRKLD 168
             + L D     G++   +V  D  G  G   V + + +  + AI K++
Sbjct: 116 DNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 164

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 49.6 bits (119), Expect = 2e-07
 Identities = 18/76 (23%), Positives = 31/76 (40%), Gaps = 5/76 (6%)

Query: 8   TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRG 64
            +++ NL      + + D F  +G I+    K+        GY F+ FE    AE AI  
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSC--KVVCDENGSKGYGFVHFETQEAAERAIEK 162

Query: 65  RDGYNFDGYRLRVELA 80
            +G   +  ++ V   
Sbjct: 163 MNGMLLNDRKVFVGRF 178

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 61.3 bits (149), Expect = 2e-12
 Identities = 12/76 (15%), Positives = 32/76 (42%), Gaps = 3/76 (3%)

Query: 4  RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDAEDA 61
            +R++Y+   P D  + ++++     G +++I ++        G  F+ F+    A+  
Sbjct: 9  VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKF 68

Query: 62 IRGRDGYNFDGYRLRV 77
          +    G  +    L +
Sbjct: 69 VE-TPGQKYKETDLLI 83

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 61.1 bits (149), Expect = 2e-12
 Identities = 30/98 (30%), Positives = 43/98 (43%), Gaps = 11/98 (11%)

Query: 5   SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP---GYAFLEFEDYRDAEDA 61
             RTLYVGNL  D     +  LF + GP      K+         Y F+EF ++RDA  A
Sbjct: 14  QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSC--KMITEHTSNDPYCFVEFYEHRDAAAA 71

Query: 62  IRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSG 99
           +   +G    G  ++V  A      ++   + S  SSG
Sbjct: 72  LAAMNGRKILGKEVKVNWA------TTPSSQKSGPSSG 103

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 62.1 bits (151), Expect = 2e-12
 Identities = 32/90 (35%), Positives = 43/90 (47%), Gaps = 3/90 (3%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDA 58
                 +L V NL   T    +  +F KYG + D+ +          G+AF+ F D RDA
Sbjct: 43  DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 102

Query: 59  EDAIRGRDGYNFDGYRLRVELAHGGRRHSS 88
           EDA+   DG   DG  LRV++A  GR   S
Sbjct: 103 EDAMDAMDGAVLDGRELRVQMARYGRPPDS 132

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 62.2 bits (151), Expect = 2e-12
 Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 8/83 (9%)

Query: 6   SRTLYVGNLPGDTRMREVEDLFYKYGPI--------VDIDLKIPPRPPGYAFLEFEDYRD 57
           +  +YV NL    + ++++ +F +Y            DI L    R  G AF+   + + 
Sbjct: 45  NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKA 104

Query: 58  AEDAIRGRDGYNFDGYRLRVELA 80
           A  A++  +GY   G  + V+ A
Sbjct: 105 AAKALKEANGYVLFGKPMVVQFA 127

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 61.0 bits (148), Expect = 3e-12
 Identities = 12/77 (15%), Positives = 27/77 (35%), Gaps = 5/77 (6%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIR-- 63
          S  ++V  L       ++ +   K+G I  + +         A +EFE+   A++ +   
Sbjct: 15 SPVVHVRGLCESVVEADLVEALEKFGTICYVMM---MPFKRQALVEFENIDSAKECVTFA 71

Query: 64 GRDGYNFDGYRLRVELA 80
                  G +     +
Sbjct: 72 ADVPVYIAGQQAFFNYS 88

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 60.6 bits (148), Expect = 3e-12
 Identities = 23/92 (25%), Positives = 44/92 (47%), Gaps = 8/92 (8%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-----RPPGYAFLEFEDYRDAEDA 61
          R +YVGNL       +V++LF ++G + ++  K+       +P G+ F+E ++     +A
Sbjct: 2  RNIYVGNLVYSATSEQVKELFSQFGKVFNV--KLIYDRETKKPKGFGFVEMQE-ESVSEA 58

Query: 62 IRGRDGYNFDGYRLRVELAHGGRRHSSSMDRY 93
          I   D  +F G  +RV  A+  +        +
Sbjct: 59 IAKLDNTDFMGRTIRVTEANPKKSLEHHHHHH 90

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 60.2 bits (147), Expect = 3e-12
 Identities = 19/84 (22%), Positives = 30/84 (35%), Gaps = 3/84 (3%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAE 59
          S  S  LY+  L   T  +++  L   YG IV       K   +  GY F++F+    A+
Sbjct: 2  SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61

Query: 60 DAIRGRDGYNFDGYRLRVELAHGG 83
           A+             +      G
Sbjct: 62 KAVTALKASGVQAQMAKQSGPSSG 85

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 60.4 bits (147), Expect = 5e-12
 Identities = 18/84 (21%), Positives = 38/84 (45%), Gaps = 9/84 (10%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAI 62
           +T+++ NL  D+    + ++  ++G +  + + + P      G AF +F     A+  +
Sbjct: 15 GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74

Query: 63 RGRD------GYNFDGYRLRVELA 80
                    G   DG +L+V+LA
Sbjct: 75 AAASLEAEGGGLKLDGRQLKVDLA 98

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 37.7 bits (88), Expect = 7e-04
 Identities = 16/111 (14%), Positives = 40/111 (36%), Gaps = 13/111 (11%)

Query: 97  SSGGSRGVSRRSDYRVL-VTGLPSSASWQDLKDHMRRAGDVCFSQVFRD------RGGMT 149
           SSG S   S  ++ + + +  L   +  + L + +++ GD+ + +V         +G   
Sbjct: 2   SSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKG--C 59

Query: 150 GIVDYTSYDDMKYAIRKLDRSEFRNAFS---RSYVRVREYDSRRSYSRSPS 197
               + + +  +  +                R  ++V    +R   +  PS
Sbjct: 60  AFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ-LKVDLAVTRDEAASGPS 109

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 60.0 bits (146), Expect = 7e-12
 Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 2/81 (2%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDAE 59
              +   L V NL       ++++LF ++G +    +      R  G A + FE   DA 
Sbjct: 25  GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADAL 84

Query: 60  DAIRGRDGYNFDGYRLRVELA 80
            A++  +G   DG  + ++L 
Sbjct: 85  KAMKQYNGVPLDGRPMNIQLV 105

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 46.5 bits (111), Expect = 4e-07
 Identities = 17/88 (19%), Positives = 35/88 (39%), Gaps = 3/88 (3%)

Query: 84  RRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFR 143
            +      ++  + SG   G    +  ++LV+ L    S  D+++     G +  + V  
Sbjct: 4   PKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHY 63

Query: 144 DRGGM---TGIVDYTSYDDMKYAIRKLD 168
           DR G    T  V +    D   A+++ +
Sbjct: 64  DRSGRSLGTADVHFERKADALKAMKQYN 91

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 60.1 bits (146), Expect = 9e-12
 Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 2/81 (2%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDAE 59
              +   L V NL       ++++LF ++G +    +      R  G A + FE   DA 
Sbjct: 31  GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADAL 90

Query: 60  DAIRGRDGYNFDGYRLRVELA 80
            A++   G   DG  + ++L 
Sbjct: 91  KAMKQYKGVPLDGRPMDIQLV 111

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 46.6 bits (111), Expect = 6e-07
 Identities = 20/97 (20%), Positives = 39/97 (40%), Gaps = 5/97 (5%)

Query: 77  VELAHGGRRHSSSMDRYS--SYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAG 134
           +    GG++     D++    + SG   G    +  ++LV+ L    S  D+++     G
Sbjct: 1   MASMTGGQQMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFG 60

Query: 135 DVCFSQVFRDRGGM---TGIVDYTSYDDMKYAIRKLD 168
            +  + V  DR G    T  V +    D   A+++  
Sbjct: 61  TLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 59.0 bits (143), Expect = 1e-11
 Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 5/75 (6%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIR-- 63
          S  +++  L       ++ +   ++GPI  + + +P +    A +EFED   A +A+   
Sbjct: 21 SPVVHIRGLIDGVVEADLVEALQEFGPISYVVV-MPKK--RQALVEFEDVLGACNAVNYA 77

Query: 64 GRDGYNFDGYRLRVE 78
            +     G+   V 
Sbjct: 78 ADNQIYIAGHPAFVN 92

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 58.4 bits (142), Expect = 1e-11
 Identities = 12/77 (15%), Positives = 27/77 (35%), Gaps = 5/77 (6%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-----RPPGYAFLEFEDYRDAEDAIR 63
          LY+GNL   T   ++ +  +  G    +++K        +  G+A +       ++  + 
Sbjct: 4  LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 64 GRDGYNFDGYRLRVELA 80
                  G    V  +
Sbjct: 64 LLPKRELHGQNPVVTPS 80

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 59.3 bits (144), Expect = 2e-11
 Identities = 28/94 (29%), Positives = 43/94 (45%), Gaps = 4/94 (4%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDA 58
                R++YVGN+   +  +++E  F   G I  I +   K    P GYA++EF + R++
Sbjct: 32  KEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE-RNS 90

Query: 59  EDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDR 92
            DA    D   F G  ++V          SS DR
Sbjct: 91  VDAAVAMDETVFRGRTIKVLPKRTNMPGISSTDR 124

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 58.1 bits (141), Expect = 3e-11
 Identities = 16/86 (18%), Positives = 36/86 (41%), Gaps = 6/86 (6%)

Query: 1  MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRD 57
          M    +  L++G +P +   ++++ LF ++G I ++ +   +      G AFL + +   
Sbjct: 8  MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERES 67

Query: 58 AEDAIRGRDGYN---FDGYRLRVELA 80
          A  A                ++V+ A
Sbjct: 68 ALKAQSALHEQKTLPGMNRPIQVKPA 93

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 43.5 bits (103), Expect = 6e-06
 Identities = 23/106 (21%), Positives = 40/106 (37%), Gaps = 9/106 (8%)

Query: 98  SGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGI------ 151
           S GS G+      ++ +  +P +   +DLK      G +    V +DR   TG+      
Sbjct: 2   SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDR--FTGMHKGCAF 59

Query: 152 VDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDSRRSYSRSPS 197
           + Y   +    A   L   +     +R  ++V+  DS       PS
Sbjct: 60  LTYCERESALKAQSALHEQKTLPGMNRP-IQVKPADSESRGGSGPS 104

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 57.7 bits (140), Expect = 5e-11
 Identities = 19/88 (21%), Positives = 36/88 (40%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
           S+ S+TL+V  L  DT    +++ F        +  +      G+ F++F    DA+ A
Sbjct: 11 RSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAA 70

Query: 62 IRGRDGYNFDGYRLRVELAHGGRRHSSS 89
              +    DG ++ ++ A       S 
Sbjct: 71 KEAMEDGEIDGNKVTLDWAKPKGEGGSG 98

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 56.9 bits (138), Expect = 6e-11
 Identities = 21/83 (25%), Positives = 32/83 (38%), Gaps = 6/83 (7%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-----RPPGYAFLEFEDYR 56
          SS  + +L++G+L        +   F   G  V + +KI        P GY F+EF D  
Sbjct: 5  SSGMAASLWMGDLEPYMDENFISRAFATMGETV-MSVKIIRNRLTGIPAGYCFVEFADLA 63

Query: 57 DAEDAIRGRDGYNFDGYRLRVEL 79
           AE  +   +G    G       
Sbjct: 64 TAEKCLHKINGKPLPGATPAKRF 86

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 56.9 bits (138), Expect = 8e-11
 Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 8/79 (10%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP----RPPGYAFLEFEDYRDAEDA 61
            T++VG +       E+   F +YG + ++  KI         GY F+ F +  D +  
Sbjct: 9  PNTVFVGGIDVRMDETEIRSFFARYGSVKEV--KIITDRTGVSKGYGFVSFYNDVDVQKI 66

Query: 62 IRGRDGYNFDGYRLRVELA 80
          +      NF G +L++  A
Sbjct: 67 V--ESQINFHGKKLKLGPA 83

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 56.5 bits (137), Expect = 9e-11
 Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 6/84 (7%)

Query: 1  MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDI----DLKIPPRPPGYAFLEFEDYR 56
          +      T ++GNLP D     +++ F     I  +    +   P R  G+ + EFED  
Sbjct: 14 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLD 72

Query: 57 DAEDAIRGRDGYNFDGYRLRVELA 80
              A+   +  +    R+RV++A
Sbjct: 73 SLLSALS-LNEESLGNRRIRVDVA 95

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 57.0 bits (138), Expect = 9e-11
 Identities = 25/105 (23%), Positives = 45/105 (42%), Gaps = 3/105 (2%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDA 58
            + +   ++VG+L  +    +++  F  +G I D  +       +  GY F+ F +  DA
Sbjct: 11  DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 70

Query: 59  EDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRG 103
           E+AI+   G    G ++R   A        S    ++  SG S G
Sbjct: 71  ENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGPSSG 115

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 56.9 bits (138), Expect = 1e-10
 Identities = 21/104 (20%), Positives = 39/104 (37%), Gaps = 2/104 (1%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDAE 59
           + R   T++V NL      ++++++F   G +V  D+      +  G   + FE   +A 
Sbjct: 11  AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAV 70

Query: 60  DAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRG 103
            AI   +G       + V++                  SG S G
Sbjct: 71  QAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPSSG 114

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 51.9 bits (125), Expect = 6e-09
 Identities = 27/115 (23%), Positives = 41/115 (35%), Gaps = 8/115 (6%)

Query: 97  SSGGSRGV-SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGM---TGIV 152
           SSG S  + + R    V V  L     W+ LK+    AG V  + +  D+ G     G V
Sbjct: 2   SSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTV 61

Query: 153 DYTSYDDMKYAIRKLDRSEFRNAFSRS-YVRVREYDSRRSYSRSPSRSPYYSRSR 206
            +    +   AI   +       F R  +V++ E    +     P R      S 
Sbjct: 62  TFEQSIEAVQAISMFNGQLL---FDRPMHVKMDERALPKGDFFPPERPQQSGPSS 113

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 56.5 bits (137), Expect = 1e-10
 Identities = 21/93 (22%), Positives = 38/93 (40%), Gaps = 6/93 (6%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDI----DLKIPPRPPGYAFLEFEDYR 56
           +      T ++GNLP D     +++ F     I  +    +   P R  G+ + EFED  
Sbjct: 10  LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLD 68

Query: 57  DAEDAIRGRDGYNFDGYRLRVELAHGGRRHSSS 89
               A+   +  +    R+RV++A   +   S 
Sbjct: 69  SLLSALS-LNEESLGNKRIRVDVADQAQDKDSG 100

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 56.0 bits (135), Expect = 2e-10
 Identities = 14/77 (18%), Positives = 29/77 (37%), Gaps = 5/77 (6%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIR-- 63
          SR +++  LP D    EV  L   +G + ++ +    +    AF+E      A   +   
Sbjct: 16 SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLM---LKGKNQAFIEMNTEEAANTMVNYY 72

Query: 64 GRDGYNFDGYRLRVELA 80
                  G  + ++ +
Sbjct: 73 TSVTPVLRGQPIYIQFS 89

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 56.5 bits (137), Expect = 2e-10
 Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 5/79 (6%)

Query: 5  SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDA 61
           S  +++ NL      + + D F  +G I+    K+        GY F+ FE    AE A
Sbjct: 4  GSGNIFIKNLDKSIDNKALYDTFSAFGNILSC--KVVCDENGSKGYGFVHFETQEAAERA 61

Query: 62 IRGRDGYNFDGYRLRVELA 80
          I   +G   +  ++ V   
Sbjct: 62 IEKMNGMLLNDRKVFVGRF 80

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 55.7 bits (134), Expect = 3e-10
 Identities = 14/81 (17%), Positives = 30/81 (37%), Gaps = 5/81 (6%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
           +   SR +++  LP D    EV  L   +G + ++ +    +    AF+E      A   
Sbjct: 27  AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLM---LKGKNQAFIEMNTEEAANTM 83

Query: 62  IR--GRDGYNFDGYRLRVELA 80
           +           G  + ++ +
Sbjct: 84  VNYYTSVTPVLRGQPIYIQFS 104

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 56.5 bits (136), Expect = 4e-10
 Identities = 14/84 (16%), Positives = 28/84 (33%), Gaps = 5/84 (5%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-----RPPGYAFLEFEDYR 56
                  +YVG+    T  +++  +    G    ++LK        +  GYA +      
Sbjct: 51  LRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASEN 110

Query: 57  DAEDAIRGRDGYNFDGYRLRVELA 80
                +    G   +G ++ V  A
Sbjct: 111 SVHKLLELLPGKVLNGEKVDVRPA 134

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 54.8 bits (132), Expect = 4e-10
 Identities = 16/77 (20%), Positives = 30/77 (38%), Gaps = 5/77 (6%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIR-- 63
          SR L++  LPG+    EV  L   +G + +I +    +    AFLE      A   +   
Sbjct: 15 SRVLHIRKLPGEVTETEVIALGLPFGKVTNILM---LKGKNQAFLELATEEAAITMVNYY 71

Query: 64 GRDGYNFDGYRLRVELA 80
               +     + ++ +
Sbjct: 72 SAVTPHLRNQPIYIQYS 88

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 56.4 bits (137), Expect = 5e-10
 Identities = 32/170 (18%), Positives = 65/170 (38%), Gaps = 33/170 (19%)

Query: 6   SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAI 62
           S  +++G L  DT    + + F KYG + D+ +   P   R  G+ FL FE     ++ +
Sbjct: 3   SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62

Query: 63  RGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSAS 122
           + +  +  DG  +  + A                     R    ++  ++ V G+     
Sbjct: 63  KTQ--HILDGKVIDPKRAI-------------------PRDEQDKTG-KIFVGGIGPDVR 100

Query: 123 WQDLKDHMRRAGDVCFSQVFRDRGGMT------GIVDYTSYDDMKYAIRK 166
            ++ ++   + G +  +Q+  D+   T      G V Y S D +    + 
Sbjct: 101 PKEFEEFFSQWGTIIDAQLMLDKD--TGQSRGFGFVTYDSADAVDRVCQN 148

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 53.7 bits (130), Expect = 4e-09
 Identities = 15/83 (18%), Positives = 38/83 (45%), Gaps = 4/83 (4%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRD 57
                +  ++VG +  D R +E E+ F ++G I+D  L +     +  G+ F+ ++    
Sbjct: 82  DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA 141

Query: 58  AEDAIRGRDGYNFDGYRLRVELA 80
            +   + +   +F   ++ ++ A
Sbjct: 142 VDRVCQNK-FIDFKDRKIEIKRA 163

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 53.7 bits (130), Expect = 7e-10
 Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 7/80 (8%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-----RPPGYAFLEFEDYRDAED 60
          +  L+VG+L  +     + + F  +   +     +          GY F+ F    DA++
Sbjct: 1  TFNLFVGDLNVNVDDETLRNAFKDFPSYLSG--HVMWDMQTGSSRGYGFVSFTSQDDAQN 58

Query: 61 AIRGRDGYNFDGYRLRVELA 80
          A+    G + +G  LR+  A
Sbjct: 59 AMDSMQGQDLNGRPLRINWA 78

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 54.3 bits (131), Expect = 1e-09
 Identities = 16/75 (21%), Positives = 36/75 (48%), Gaps = 3/75 (4%)

Query: 9   LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRGR 65
           L++ +LP +    ++   F  +G ++   + I         + F+ F++   A+ AI+  
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102

Query: 66  DGYNFDGYRLRVELA 80
           +G+     RL+V+L 
Sbjct: 103 NGFQVGTKRLKVQLK 117

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 53.8 bits (130), Expect = 1e-09
 Identities = 24/91 (26%), Positives = 45/91 (49%), Gaps = 5/91 (5%)

Query: 1  MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRD 57
          + +    T YVGNLP +T   +++ +F     I  + L   K   +  G+ ++EF++   
Sbjct: 10 LPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDS 68

Query: 58 AEDAIRGRDGYNFDGYRLRVELAHGGRRHSS 88
           ++A+   DG       LRV++A G ++  S
Sbjct: 69 LKEAL-TYDGALLGDRSLRVDIAEGRKQDKS 98

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 53.0 bits (128), Expect = 1e-09
 Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 4/78 (5%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAI 62
          S  S  ++VG   GD    E+ + F +YG ++D+ +  P R   +AF+ F D + A+   
Sbjct: 2  SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR--AFAFVTFADDQIAQSLC 59

Query: 63 RGRDGYNFDGYRLRVELA 80
             +     G  + +  A
Sbjct: 60 --GEDLIIKGISVHISNA 75

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 53.6 bits (129), Expect = 1e-09
 Identities = 15/106 (14%), Positives = 35/106 (33%), Gaps = 6/106 (5%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP----RPPGYAFLEFEDYRD 57
            + +    ++ N+P      +V         + +  + +      +  G A ++F++  D
Sbjct: 11  VNSAKVCAHITNIPFSITKMDVLQFLEGIP-VDENAVHVLVDNNGQGLGQALVQFKNEDD 69

Query: 58  AEDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRG 103
           A  + R       +G    V +           +  +   SG S G
Sbjct: 70  ARKSER-LHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSGPSSG 114

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 55.0 bits (133), Expect = 2e-09
 Identities = 27/171 (15%), Positives = 59/171 (34%), Gaps = 22/171 (12%)

Query: 3   SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAE 59
               R L++G L  +T    +   F ++G + D  +   P   R  G+ F+ +    + +
Sbjct: 10  PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 69

Query: 60  DAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPS 119
            A+  R  +  DG  +  + A             +                ++ V G+  
Sbjct: 70  AAMNAR-PHKVDGRVVEPKRAVSREDSQRPGAHLTV--------------KKIFVGGIKE 114

Query: 120 SASWQDLKDHMRRAGDVCFSQVFRDRGGMT----GIVDYTSYDDMKYAIRK 166
                 L+D+  + G +   ++  DRG         V +  +D +   + +
Sbjct: 115 DTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 55.0 bits (133), Expect = 2e-09
 Identities = 18/82 (21%), Positives = 40/82 (48%), Gaps = 4/82 (4%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDA 58
           +  + + ++VG +  DT    + D F +YG I  I++   +   +  G+AF+ F+D+   
Sbjct: 100 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 159

Query: 59  EDAIRGRDGYNFDGYRLRVELA 80
           +  +  +  +  +G+   V  A
Sbjct: 160 DKIVIQK-YHTVNGHNCEVRKA 180

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 54.5 bits (131), Expect = 2e-09
 Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 2/81 (2%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDAE 59
              +   L V NL       ++++LF ++G +    +      R  G A + FE   DA 
Sbjct: 84  GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADAL 143

Query: 60  DAIRGRDGYNFDGYRLRVELA 80
            A++   G   DG  + ++L 
Sbjct: 144 KAMKQYKGVPLDGRPMDIQLV 164

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 44.5 bits (105), Expect = 6e-06
 Identities = 20/109 (18%), Positives = 38/109 (34%), Gaps = 5/109 (4%)

Query: 63  RGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSAS 122
           R R      G        +   +      ++  + SG   G    +  ++LV+ L    S
Sbjct: 44  RNRPAIARGGRNRPA--PYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVS 101

Query: 123 WQDLKDHMRRAGDVCFSQVFRDRGGM---TGIVDYTSYDDMKYAIRKLD 168
             D+++     G +  + V  DR G    T  V +    D   A+++  
Sbjct: 102 DADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 53.1 bits (128), Expect = 2e-09
 Identities = 16/75 (21%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 9   LYVGNLPGDTRMREVEDLFYKYGPIVD---IDLKIPPRPPGYAFLEFEDYRDAEDAIRGR 65
           L++ +LP +   +++  +F  +G +V       K       + F+ +++   A+ AI+  
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87

Query: 66  DGYNFDGYRLRVELA 80
           +G+     RL+V+L 
Sbjct: 88  NGFQIGMKRLKVQLK 102

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 52.6 bits (127), Expect = 3e-09
 Identities = 15/81 (18%), Positives = 33/81 (40%), Gaps = 3/81 (3%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDAE 59
           S +   L++GNL  +  + E++    +     D+ +          + +++FE   D E
Sbjct: 13 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLE 72

Query: 60 DAIRGRDGYNFDGYRLRVELA 80
           A+    G    G  +++E  
Sbjct: 73 KAL-ELTGLKVFGNEIKLEKP 92

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 52.2 bits (126), Expect = 3e-09
 Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 3/79 (3%)

Query: 5  SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDA 61
          S   ++VG+L  +     +   F  +G I D  +       +  GY F+ F +  DAE+A
Sbjct: 5  SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64

Query: 62 IRGRDGYNFDGYRLRVELA 80
          I+   G    G ++R   A
Sbjct: 65 IQQMGGQWLGGRQIRTNWA 83

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 52.3 bits (126), Expect = 5e-09
 Identities = 26/106 (24%), Positives = 42/106 (39%), Gaps = 4/106 (3%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRD 57
               +   ++VG LP  T    +   F  +G I +  +       +  GY F+   D   
Sbjct: 12  QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAA 71

Query: 58  AEDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRG 103
           AE A +  +    DG +  V LA+ G +  S    ++   SG S G
Sbjct: 72  AERACKDPNP-IIDGRKANVNLAYLGAKPRSLQTGFAIGVSGPSSG 116

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 54.3 bits (130), Expect = 5e-09
 Identities = 16/112 (14%), Positives = 34/112 (30%), Gaps = 5/112 (4%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-----RPPGYAFLEFEDYR 56
            +     LY+GNL   T   ++ +  +  G    +++K        +  G+A +      
Sbjct: 64  YTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEA 123

Query: 57  DAEDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRS 108
            ++  +         G    V   +        M    +  SG   G  +  
Sbjct: 124 SSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAG 175

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 51.1 bits (123), Expect = 8e-09
 Identities = 22/80 (27%), Positives = 33/80 (41%), Gaps = 5/80 (6%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDAEDAIR 63
           R L+VG L       +V  LF  +G I +  +   P     G AF++F  + +A+ AI 
Sbjct: 15 DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIH 74

Query: 64 GRDG---YNFDGYRLRVELA 80
             G          L V+ A
Sbjct: 75 ALHGSQTMPGASSSLVVKFA 94

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 50.7 bits (122), Expect = 9e-09
 Identities = 18/80 (22%), Positives = 33/80 (41%), Gaps = 4/80 (5%)

Query: 1  MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
                  ++VG    D    E++  F +YG +VD+ +  P R   +AF+ F D + A+ 
Sbjct: 6  HHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFR--AFAFVTFADDKVAQS 63

Query: 61 AIRGRDGYNFDGYRLRVELA 80
               +     G  + +  A
Sbjct: 64 LC--GEDLIIKGISVHISNA 81

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 14/82 (17%), Positives = 25/82 (30%), Gaps = 2/82 (2%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDA 58
              +    LY+ NLP     +E+E++   +G ++   +         G  F   E     
Sbjct: 20  QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKC 79

Query: 59  EDAIRGRDGYNFDGYRLRVELA 80
           E  I   +G             
Sbjct: 80  EAVIGHFNGKFIKTPPGVSAPT 101

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 50.7 bits (122), Expect = 1e-08
 Identities = 20/82 (24%), Positives = 41/82 (50%), Gaps = 4/82 (4%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDA 58
          S   S  ++VG +P +    E+ + F K+G + ++ +       RP G+ F+ FED +  
Sbjct: 6  SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSV 65

Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
          + A+     ++  G ++ V+ A
Sbjct: 66 DQAVNMH-FHDIMGKKVEVKRA 86

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 49.9 bits (120), Expect = 2e-08
 Identities = 21/83 (25%), Positives = 35/83 (42%), Gaps = 6/83 (7%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-----RPPGYAFLEFEDYRD 57
          S  S  +++GNL  +   + + D F  +G I+    KI          GYAF+ F  +  
Sbjct: 2  SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQ-TPKIMRDPDTGNSKGYAFINFASFDA 60

Query: 58 AEDAIRGRDGYNFDGYRLRVELA 80
          ++ AI   +G       + V  A
Sbjct: 61 SDAAIEAMNGQYLCNRPITVSYA 83

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 48.7 bits (117), Expect = 3e-08
 Identities = 14/75 (18%), Positives = 36/75 (48%), Gaps = 4/75 (5%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRGR 65
          ++VG L  DT   ++ + F  +G +  I+L +     +  G+ F+ F++    +  +  +
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 66 DGYNFDGYRLRVELA 80
            +N    +  +++A
Sbjct: 62 -YHNVGLSKCEIKVA 75

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 49.2 bits (117), Expect = 6e-08
 Identities = 13/69 (18%), Positives = 29/69 (42%), Gaps = 5/69 (7%)

Query: 2  SSRSSRTLYVGN--LPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAE 59
           S ++++L V N  L       ++  +  K G +  +   +PP    Y+F  +    +++
Sbjct: 21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDAL--LMPPNK-PYSFARYRTTEESK 77

Query: 60 DAIRGRDGY 68
           A    +G 
Sbjct: 78 RAYVTLNGK 86

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 48.4 bits (116), Expect = 8e-08
 Identities = 20/75 (26%), Positives = 28/75 (37%), Gaps = 5/75 (6%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRGR 65
          LYV NL        +   F  +G I     K+     R  G+ F+ F    +A  A+   
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSA--KVMMEGGRSKGFGFVCFSSPEEATKAVTEM 75

Query: 66 DGYNFDGYRLRVELA 80
          +G       L V LA
Sbjct: 76 NGRIVATKPLYVALA 90

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 46.7 bits (112), Expect = 2e-07
 Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 4/75 (5%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRGR 65
          ++VG L  +T + +V+  F ++G + D  L       R  G+ F+ FE     E      
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 66 DGYNFDGYRLRVELA 80
            +  +   +  + A
Sbjct: 62 -FHEINNKMVECKKA 75

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 47.4 bits (113), Expect = 2e-07
 Identities = 18/101 (17%), Positives = 37/101 (36%), Gaps = 5/101 (4%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDAE 59
            +     + V  +P      +V D F+    +  + L      R  G   ++F   +D  
Sbjct: 12  INPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGRNNGNGLVKFLSPQDTF 70

Query: 60  DAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGG 100
           +A++ R+        + V  A   R+  ++    +S  S G
Sbjct: 71  EALK-RNRMLMIQRYVEVSPAT-ERQWVAAGGHITSGPSSG 109

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 47.4 bits (113), Expect = 2e-07
 Identities = 12/83 (14%), Positives = 29/83 (34%), Gaps = 4/83 (4%)

Query: 1  MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVD---IDLKIPPRPPGYAFLEFEDYRD 57
            + +   + +  LP      E+   F     + +   + +    R  G AF++F     
Sbjct: 10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEI 69

Query: 58 AEDAIRGRDGYNFDGYRLRVELA 80
          AE A++ +         + +  +
Sbjct: 70 AEKALK-KHKERIGHRYIEIFKS 91

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 38.6 bits (90), Expect = 2e-04
 Identities = 20/108 (18%), Positives = 36/108 (33%), Gaps = 10/108 (9%)

Query: 96  YSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDV--CFSQVFRDRGGMTGI-- 151
            S          +D  V + GLP   S +++         V    +     +G  TG   
Sbjct: 2   SSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAF 61

Query: 152 VDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDSRRSYSRSPSRS 199
           V + S +  + A++K  +    +     Y+ +    SR     S   S
Sbjct: 62  VQFASQEIAEKALKK-HKERIGH----RYIEI-FKSSRAEVRTSGPSS 103

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 46.9 bits (111), Expect = 2e-07
 Identities = 22/93 (23%), Positives = 39/93 (41%), Gaps = 8/93 (8%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVE------DLFYKYGPIVDIDLKIPPRPPGYAFLEFEDY 55
          SS +   + V N+  D R+   E      + F ++G +  ++L         A ++ E+ 
Sbjct: 5  SSGNGADVQVSNI--DYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENL 62

Query: 56 RDAEDAIRGRDGYNFDGYRLRVELAHGGRRHSS 88
          +DA  A+     Y     ++ V LA G    SS
Sbjct: 63 QDAIGAVNSLHRYKIGSKKILVSLATGASGPSS 95

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 46.1 bits (110), Expect = 4e-07
 Identities = 13/80 (16%), Positives = 30/80 (37%), Gaps = 2/80 (2%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPI-VDIDLKIPPRPPGYAFLEFEDYRDAED 60
          S  +  T+ +   P +   + V +      P+ + I         GY F++F +  + + 
Sbjct: 6  SGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQ 65

Query: 61 AIRGRDGYNFDGYRLRVELA 80
          A++  +     G  + V   
Sbjct: 66 ALK-CNREYMGGRYIEVFRE 84

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 46.6 bits (111), Expect = 4e-07
 Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 2/80 (2%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPI-VDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
          S +   +++  LP      ++ + F    P+ V I++    R  G A +EF  + DA  A
Sbjct: 12 STTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAA 71

Query: 62 IRGRDGYNFDGYRLRVELAH 81
          +  +D  N     + + L  
Sbjct: 72 MA-KDKANMQHRYVELFLNS 90

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 49.5 bits (117), Expect = 4e-07
 Identities = 51/263 (19%), Positives = 79/263 (30%), Gaps = 6/263 (2%)

Query: 7   RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIR 63
           +TL+V  +  DT   ++   F  YGPI  I +   K   +P GYAF+E+E  RD   A +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162

Query: 64  GRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASW 123
             DG   DG R+ V++  G         R      G        +D  +  +G   ++ +
Sbjct: 163 HADGKKIDGRRVLVDVERGRTVKG---WRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRY 219

Query: 124 QDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV 183
            +                 R+R   +   D         +  +  RS  R+   R   R 
Sbjct: 220 DERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRE 279

Query: 184 REYDSRRSYSRSPSRSPYYSRSRSRSPYYSRSRSPSRSWSYSPRSRSYSPRGKYSRRSPS 243
           R  D  R   R  SRS   +R         R      +                      
Sbjct: 280 RSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDG 339

Query: 244 LSPARSASQRSPSGSPPRSFSRS 266
                   +           S  
Sbjct: 340 PDGPEEKGRDRDRERRRSHRSER 362

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 48.3 bits (114), Expect = 4e-07
 Identities = 12/77 (15%), Positives = 31/77 (40%), Gaps = 3/77 (3%)

Query: 7   RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDAEDAIRG 64
           R++Y+   P D  + ++++     G +++I ++        G  F+ F+    A+  +  
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE- 168

Query: 65  RDGYNFDGYRLRVELAH 81
             G  +    L +    
Sbjct: 169 TPGQKYKETDLLILFKD 185

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3 Length = 104

 Score = 46.0 bits (109), Expect = 6e-07
 Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 2/60 (3%)

Query: 22  EVEDLFYKYGPIVD--IDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL 79
              ++  KYG + +  +   +     G  +++F    DAE A+   +   F+G  +  EL
Sbjct: 43  VFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 46.4 bits (110), Expect = 8e-07
 Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 4/82 (4%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPI---VDIDLKIPPRPPGYAFLEFEDYRDA 58
              +   +Y+  LP +   + V D F K   +   + I      +  G  F+EF +  D 
Sbjct: 21  PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADY 80

Query: 59  EDAIRGRDGYNFDGYRLRVELA 80
           + A+  R         ++V   
Sbjct: 81  KAALC-RHKQYMGNRFIQVHPI 101

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 44.5 bits (106), Expect = 1e-06
 Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 4/78 (5%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAI 62
          +  ++VG L  DT  ++++D F K+G +VD  +K+ P   R  G+ F+ F+D    E  +
Sbjct: 11 AGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVL 70

Query: 63 RGRDGYNFDGYRLRVELA 80
            ++    DG  +  + A
Sbjct: 71 DQKEHR-LDGRVIDPKKA 87

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 112

 Score = 45.1 bits (107), Expect = 2e-06
 Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 1/68 (1%)

Query: 22  EVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH 81
           ++     K+G I  + L     P G A + F D  +A+  I+  DG  F G ++  +   
Sbjct: 42  DLRVECSKFGQIRKLLL-FDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWD 100

Query: 82  GGRRHSSS 89
           G   + S 
Sbjct: 101 GTTDYQSG 108

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 16/82 (19%), Positives = 35/82 (42%), Gaps = 5/82 (6%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDA 58
          + + +  L V  LP  T  +++++ F  +G ++ + +K         G+ F+ F +Y   
Sbjct: 11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 70

Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
             +  R  +  DG     +L 
Sbjct: 71 VKVMSQR--HMIDGRWCDCKLP 90

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 44.9 bits (106), Expect = 2e-06
 Identities = 21/107 (19%), Positives = 39/107 (36%), Gaps = 9/107 (8%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPI------VDIDLKIPPRPPGYAFLEFED 54
           +S  +   + +  LP      EV   F ++ PI      +        RP G AF+ F  
Sbjct: 18  LSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFAC 77

Query: 55  YRDAEDAIRGRDGYNFDGYRLRVELAHGG--RRHSSSMDRYSSYSSG 99
              A++A+R +         + +  +     ++  +     S  SSG
Sbjct: 78  EEYAQNALR-KHKDLLGKRYIELFRSTAAEVQQVLNRFSSASGPSSG 123

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 44.5 bits (105), Expect = 3e-06
 Identities = 13/82 (15%), Positives = 28/82 (34%), Gaps = 4/82 (4%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPI---VDIDLKIPPRPPGYAFLEFEDYRDA 58
            S +   + +  LP      E+   F     +   + + +    +  G AF++F     A
Sbjct: 38  DSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELA 97

Query: 59  EDAIRGRDGYNFDGYRLRVELA 80
           E A+  +         + V  +
Sbjct: 98  EKALG-KHKERIGHRYIEVFKS 118

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 42.9 bits (102), Expect = 4e-06
 Identities = 13/75 (17%), Positives = 31/75 (41%), Gaps = 4/75 (5%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRGR 65
          +++G L   T    + + F ++G + +  +   P   R  G+ F+ F D    +  +   
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 66 DGYNFDGYRLRVELA 80
            +  D   +  ++A
Sbjct: 63 -RHELDSKTIDPKVA 76

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 45.9 bits (108), Expect = 5e-06
 Identities = 15/89 (16%), Positives = 30/89 (33%), Gaps = 12/89 (13%)

Query: 3   SRSSRTLYVGNLPGDTRMREVE---------DLFYKYGPIVDIDLKIPPRPPGYAFLEFE 53
            + ++TLYVG + G    + ++          +F + G I  I  +         F++F+
Sbjct: 131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRI--RYVESK-NCGFVKFK 187

Query: 54  DYRDAEDAIRGRDGYNFDGYRLRVELAHG 82
              +AE A              +      
Sbjct: 188 YQANAEFAKEAMSNQTLLLPSDKEWDDRR 216

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 44.1 bits (104), Expect = 6e-06
 Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 4/81 (4%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDAE 59
            S +   +++  LP      ++ + F    P V + ++I P  R  G A +EF  + +A 
Sbjct: 42  QSTTGHCVHMRGLPYKATENDIYNFFSPLNP-VRVHIEIGPDGRVTGEADVEFATHEEAV 100

Query: 60  DAIRGRDGYNFDGYRLRVELA 80
            A+  +D  N     + + L 
Sbjct: 101 AAMS-KDRANMQHRYIELFLN 120

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 43.9 bits (103), Expect = 7e-06
 Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 3/74 (4%)

Query: 9   LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
           + V NL     +  +  +F K+G ++   +         A L++ D   A+ A    DG 
Sbjct: 31  IIVENLFYPVTLDVLHQIFSKFGTVLK-IITFTKNNQFQALLQYADPVSAQHAKLSLDGQ 89

Query: 69  NF--DGYRLRVELA 80
           N       LR++ +
Sbjct: 90  NIYNACCTLRIDFS 103

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 45.8 bits (108), Expect = 9e-06
 Identities = 36/83 (43%), Positives = 41/83 (49%), Gaps = 6/83 (7%)

Query: 191  SYS-RSPSRSPYYSRSRSRSPYY---SRSRSPSRSWSYSPRSRSYSPRG-KYSRRSPSLS 245
            SYS  SPS SP      + SP Y   S S SP+ S SYSP S SYSP    YS  SPS S
Sbjct: 1591 SYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPT-SPSYSPTSPSYSPTSPSYSPTSPSYS 1649

Query: 246  PARSASQRSPSGSPPRSFSRSGS 268
            P   +   +     P S S S +
Sbjct: 1650 PTSPSYSPTSPSYSPTSPSYSPT 1672

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 44.7 bits (105), Expect = 3e-05
 Identities = 34/77 (44%), Positives = 36/77 (46%), Gaps = 3/77 (3%)

Query: 186  YDSRRSYSRSPSRSPYYSRSRSRSPYYSRSRSPS-RSWSYSPRSRSYSPR-GKYSRRSPS 243
            Y S  S + SP            SP YS S +    S SYSP S SYSP    YS  SPS
Sbjct: 1539 YTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPSSPSYSPTSPSYSPTSPSYSPTSPS 1598

Query: 244  LSPAR-SASQRSPSGSP 259
             SP   S S  SPS SP
Sbjct: 1599 YSPTSPSYSATSPSYSP 1615

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 43.5 bits (102), Expect = 6e-05
 Identities = 38/82 (46%), Positives = 40/82 (48%), Gaps = 14/82 (17%)

Query: 191  SYS-RSPSRSPYYSRSRSRSPYYSRSRSPSRSW---SYSPRSRSYSPRG--------KYS 238
            SYS  SPS SP        SP YS + SPS S    SYSP S SYSP           YS
Sbjct: 1612 SYSPTSPSYSPTSPSYSPTSPSYSPT-SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1670

Query: 239  RRSPSLSPARSA-SQRSPSGSP 259
              SPS SP   + S  SPS SP
Sbjct: 1671 PTSPSYSPTSPSYSPTSPSYSP 1692

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 42.8 bits (100), Expect = 1e-04
 Identities = 33/83 (39%), Positives = 39/83 (46%), Gaps = 13/83 (15%)

Query: 191  SYSRSPSR----SPYYSRSRSRSPYYSRSRSPSRSWSYSPRSRSYSPRG-KYSRRSPSLS 245
            SYS +       SP YS +   SP YS + SP    SYSP S SYSP    YS  SPS S
Sbjct: 1619 SYSPTSPSYSPTSPSYSPT---SPSYSPT-SP----SYSPTSPSYSPTSPSYSPTSPSYS 1670

Query: 246  PARSASQRSPSGSPPRSFSRSGS 268
            P   +   +     P S S S +
Sbjct: 1671 PTSPSYSPTSPSYSPTSPSYSPT 1693

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 42.8 bits (100), Expect = 1e-04
 Identities = 34/84 (40%), Positives = 40/84 (47%), Gaps = 7/84 (8%)

Query: 188  SRRSYSRSPSRSPYYSRSRSRSPYYSRS--RSPSRSWSYSPRSRSYSPRG-KYSRRSPSL 244
            S  S S SP+ SP YS +   SP YS +       S SYSP S SYSP    YS  SPS 
Sbjct: 1635 SPTSPSYSPT-SPSYSPT---SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1690

Query: 245  SPARSASQRSPSGSPPRSFSRSGS 268
            SP   +   +     P S S S +
Sbjct: 1691 SPTSPSYSPTSPSYSPTSPSYSPT 1714

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 40.4 bits (94), Expect = 5e-04
 Identities = 39/92 (42%), Positives = 45/92 (48%), Gaps = 11/92 (11%)

Query: 191  SYSRSPSRSPYYSRSRSRSPYYSRSRSPSR------SWSYSPRSRSYSPR-GKYSRRSPS 243
            S S SP+ SP YS +       S S SP+       S SYSP S SYSP    YS  SPS
Sbjct: 1645 SPSYSPT-SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1703

Query: 244  LSPARSA-SQRSPSGSP--PRSFSRSGSFART 272
             SP   + S  SPS SP  P     S S++ T
Sbjct: 1704 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1735

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 40.1 bits (93), Expect = 6e-04
 Identities = 24/70 (34%), Positives = 31/70 (44%), Gaps = 4/70 (5%)

Query: 191  SYSRSPSRSPYYSRSRSRSPYYSRSRSPSRSWSYSPRSRSYSPRGKYSRRSPSLSPARSA 250
             Y    + SPY      +SP Y+   S + S  Y   S SYSP       SP+  P+  +
Sbjct: 1521 DYGLLGAASPYKG---VQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPSSPS 1577

Query: 251  -SQRSPSGSP 259
             S  SPS SP
Sbjct: 1578 YSPTSPSYSP 1587

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 40.1 bits (93), Expect = 7e-04
 Identities = 33/75 (44%), Positives = 35/75 (46%), Gaps = 7/75 (9%)

Query: 187  DSRRSYSRSPSRSPYYSRSRSRSPYYSRSRSPSRSWSYSPRSRSYSPR-GKYSRRSPSLS 245
             S      SPS SP        SP YS +     S SYSP S SYSP    YS  SPS S
Sbjct: 1679 TSPSYSPTSPSYSPTSPSYSPTSPSYSPT-----SPSYSPTSPSYSPTSPSYSPTSPSYS 1733

Query: 246  PARSA-SQRSPSGSP 259
            P   + S  SPS SP
Sbjct: 1734 PTSPSYSPTSPSYSP 1748

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 43.0 bits (101), Expect = 9e-06
 Identities = 19/107 (17%), Positives = 35/107 (32%), Gaps = 6/107 (5%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPI-----VDIDLKIPPRPPGYAFLEFEDYR 56
                  + +  LP    + +V++             V        R  G AF+E E   
Sbjct: 13  EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESED 72

Query: 57  DAEDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRG 103
           D + A++ +D  +     + V  +H             + +SG S G
Sbjct: 73  DVKLALK-KDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSASGPSSG 118

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 43.9 bits (103), Expect = 1e-05
 Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 3/74 (4%)

Query: 9   LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
           + V NL     +  +  +F K+G ++   +         A L++ D   A+ A    DG 
Sbjct: 49  IIVENLFYPVTLDVLHQIFSKFGTVLK-IITFTKNNQFQALLQYADPVSAQHAKLSLDGQ 107

Query: 69  NF--DGYRLRVELA 80
           N       LR++ +
Sbjct: 108 NIYNACCTLRIDFS 121

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 45.1 bits (106), Expect = 2e-05
 Identities = 33/78 (42%), Positives = 37/78 (47%), Gaps = 5/78 (6%)

Query: 195  SPSRSPYYSRSRSRSPYY---SRSRSPSRSWSYSPRSRSYSPR-GKYSRRSPSLSPARSA 250
            SPS SP        SP Y   S S SP+ S SYSP S SYSP    YS  SPS SP   +
Sbjct: 1574 SPSYSPTSPSYSPTSPSYSPTSPSYSPT-SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1632

Query: 251  SQRSPSGSPPRSFSRSGS 268
               +     P S S S +
Sbjct: 1633 YSPTSPSYSPTSPSYSPT 1650

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 43.9 bits (103), Expect = 5e-05
 Identities = 27/70 (38%), Positives = 37/70 (52%), Gaps = 3/70 (4%)

Query: 191  SYSRSPSRSPYYSRSRSRSPYYSRSRSPSRSWSYSPRSRSYSPRG-KYSRRSPSLSPARS 249
            S S SP+ SP YS +       S S SP+ S +YSP S SYSP    YS  SP+ SP + 
Sbjct: 1665 SPSYSPT-SPSYSPTSPSYSPTSPSYSPT-SPNYSPTSPSYSPTSPGYSPGSPAYSPKQD 1722

Query: 250  ASQRSPSGSP 259
              + + + + 
Sbjct: 1723 EQKHNENENS 1732

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 41.6 bits (97), Expect = 2e-04
 Identities = 33/78 (42%), Positives = 36/78 (46%), Gaps = 5/78 (6%)

Query: 195  SPSRSPYYSRSRSRSPYYSRSRSPS---RSWSYSPRSRSYSPRG-KYSRRSPSLSPARSA 250
            SPS SP        SP YS   SPS    S SYSP S SYSP    YS  SPS SP   +
Sbjct: 1595 SPSYSPTSPSYSPTSPSYS-PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1653

Query: 251  SQRSPSGSPPRSFSRSGS 268
               +     P S S S +
Sbjct: 1654 YSPTSPAYSPTSPSYSPT 1671

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 40.8 bits (95), Expect = 4e-04
 Identities = 36/90 (40%), Positives = 40/90 (44%), Gaps = 6/90 (6%)

Query: 188  SRRSYSRSPSR---SPYYSRSRSRSPYYSRSRSPSRSWSYSPRSRSYSPRG-KYSRRSPS 243
            S      SPS    SP YS +       S S SP+   SYSP S SYSP    YS  SPS
Sbjct: 1560 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP-SYSPTSPSYSPTSPSYSPTSPS 1618

Query: 244  LSPAR-SASQRSPSGSPPRSFSRSGSFART 272
             SP   S S  SPS SP        S + +
Sbjct: 1619 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1648

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 41.8 bits (98), Expect = 2e-05
 Identities = 13/85 (15%), Positives = 25/85 (29%), Gaps = 6/85 (7%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPI-----VDIDLKIPPRPPGYAFLEFEDYR 56
                 +    LP    M +V + F           +   L    +  G A +E E  +
Sbjct: 7  EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQ 66

Query: 57 DAEDAIRGRDGYNFDGYRLRVELAH 81
          D + A+  +         + V   +
Sbjct: 67 DVQKALE-KHRMYMGQRYVEVYEIN 90

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A Length = 105

 Score = 40.6 bits (95), Expect = 5e-05
 Identities = 18/88 (20%), Positives = 31/88 (35%), Gaps = 9/88 (10%)

Query: 1  MSSRSSRTLYVGNL--PGDTRMREVEDLFY---KYGPIVDIDLKIPPRPP----GYAFLE 51
          M    ++ + + N+   G+       +      KYG +    +   P  P       FLE
Sbjct: 3  MGKCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLE 62

Query: 52 FEDYRDAEDAIRGRDGYNFDGYRLRVEL 79
          FE    A  A+   +G  F G  ++   
Sbjct: 63 FERVESAIKAVVDLNGRYFGGRVVKACF 90

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 39.9 bits (93), Expect = 1e-04
 Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 6/83 (7%)

Query: 2   SSRSSRTLYVGNLPGD-TRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
                R +++ NLP        V  L   YG I +  L +  +    AF+E E   DA  
Sbjct: 21  KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL-MRMK--SQAFIEMETREDAMA 77

Query: 61  AIR--GRDGYNFDGYRLRVELAH 81
            +    +    F G  ++V+L+ 
Sbjct: 78  MVDHCLKKALWFQGRCVKVDLSE 100

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 14/83 (16%), Positives = 32/83 (38%), Gaps = 4/83 (4%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRD 57
               S   +++G L   T    + + F ++G + +  +   P   R  G+ F+ F D   
Sbjct: 20  HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG 79

Query: 58  AEDAIRGRDGYNFDGYRLRVELA 80
            +  +     +  D   +  ++A
Sbjct: 80  VDKVLAQS-RHELDSKTIDPKVA 101

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 16/75 (21%), Positives = 35/75 (46%), Gaps = 4/75 (5%)

Query: 9   LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIRGR 65
           L++G L  +T    + + + ++G + D  +   P   R  G+ F+ F    + + A+  R
Sbjct: 30  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89

Query: 66  DGYNFDGYRLRVELA 80
             ++ DG  +  + A
Sbjct: 90  -PHSIDGRVVEPKRA 103

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 14/85 (16%), Positives = 28/85 (32%), Gaps = 6/85 (7%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPI-----VDIDLKIPPRPPGYAFLEFEDYR 56
                  + +  LP    + +V++             V        R  G AF+E     
Sbjct: 40  EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSED 99

Query: 57  DAEDAIRGRDGYNFDGYRLRVELAH 81
           D + A++ +D  +     + V  +H
Sbjct: 100 DVKMALK-KDRESMGHRYIEVFKSH 123

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 38.4 bits (89), Expect = 3e-04
 Identities = 22/77 (28%), Positives = 32/77 (41%), Gaps = 5/77 (6%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-----RPPGYAFLEFEDYR 56
           S  SR ++VG LP D    E+   F ++GP+V              P GYAFL F++  
Sbjct: 4  GSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEES 63

Query: 57 DAEDAIRGRDGYNFDGY 73
            +  I      +   Y
Sbjct: 64 SVQALIDACLEEDGKLY 80

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 4/77 (5%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAIR 63
            L+VG L   T    +   F +YG +VD  +       +  G+ F++F+D       + 
Sbjct: 17 GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLA 76

Query: 64 GRDGYNFDGYRLRVELA 80
           R  +  DG  +  +  
Sbjct: 77 SR-PHTLDGRNIDPKPC 92

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 102

 Score = 37.5 bits (87), Expect = 5e-04
 Identities = 11/58 (18%), Positives = 24/58 (41%), Gaps = 4/58 (6%)

Query: 6  SRTLYVGNLPGDTRMR-EVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAI 62
           R +++ +      +R ++  L   +G I +    +       AF+E     DA+ A+
Sbjct: 15 RRVVHIMDFQRGKNLRYQLLQLVEPFGVISNH---LILNKINEAFIEMATTEDAQAAV 69

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 37.7 bits (87), Expect = 7e-04
 Identities = 16/74 (21%), Positives = 27/74 (36%), Gaps = 4/74 (5%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          L + N      +  +  +    G +  I   I  R    A +EFE    A+ A    +G 
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQRI--VIFKRNGIQAMVEFESVLCAQKAKAALNGA 85

Query: 69 NF--DGYRLRVELA 80
          +       L++E A
Sbjct: 86 DIYAGCCTLKIEYA 99

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	277
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	100.0
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	100.0
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	100.0
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	100.0
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	100.0
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.98
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.98
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.98
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.97
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	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
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
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.91
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.88
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.87
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.87
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.87
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.85
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.85
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.85
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.85
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.85
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.85
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.85
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.84
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.84
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.84
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.84
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.84
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.83
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.83
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.83
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.83
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.83
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.83
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.83
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.83
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.83
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.83
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.83
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.83
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.83
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.83
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.83
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.83
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.82
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.82
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.82
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.82
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.82
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.82
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.82
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.82
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.82
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.82
2div_A	99	TRNA selenocysteine associated protein; structural	99.82
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.82
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.82
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.82
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.82
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.82
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.82
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.82
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.82
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.82
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.81
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.81
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.81
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.81
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.81
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.81
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.81
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.81
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.81
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.81
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.81
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.81
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.81
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.81
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.81
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.81
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.8
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.8
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.8
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.8
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.8
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.8
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.8
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.8
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.8
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.8
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.8
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.8
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.8
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.8
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.8
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.8
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.8
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.8
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.8
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.8
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.8
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.8
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.79
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.79
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.79
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.79
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.79
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.79
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.79
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.79
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.79
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.79
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.79
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.79
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.79
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.79
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.79
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.79
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.78
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.78
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.78
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.78
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.78
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.78
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.78
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.78
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.78
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.78
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.78
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.78
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.78
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.78
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.78
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.77
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.77
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.77
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.77
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.77
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.77
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.77
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.77
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.77
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.77
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.77
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.77
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.77
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.76
1x5p_A	97	Negative elongation factor E; structure genomics,	99.76
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.76
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.76
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.76
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.76
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.76
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.76
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.75
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.75
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.75
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.75
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.75
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.75
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.75
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.74
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.74
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.74
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.74
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.73
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.73
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.73
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.73
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.72
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.56
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.71
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.71
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.71
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.71
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.7
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.7
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.7
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.7
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.7
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.69
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.69
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.67
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.67
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.67
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.67
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.67
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.67
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.67
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.67
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.66
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.66
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.66
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.66
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.66
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.65
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.65
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.65
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.65
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.65
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.65
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.65
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.65
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.65
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.64
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.64
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.64
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.63
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.63
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.63
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.63
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.63
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.63
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.63
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.63
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.63
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.63
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.63
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.63
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.63
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.63
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.63
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.63
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.62
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.62
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.62
2div_A	99	TRNA selenocysteine associated protein; structural	99.62
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.62
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.62
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.62
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.62
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.62
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.62
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.62
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.62
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.61
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.61
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.61
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.61
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.61
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.61
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.61
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.61
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.61
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.6
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.6
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.6
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.6
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.6
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.6
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.6
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.6
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.6
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.6
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.59
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.59
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.59
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.59
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.59
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.59
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.59
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.59
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.59
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.59
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.59
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.59
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.58
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.58
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.58
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.58
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.58
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.58
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.58
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.58
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.58
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.58
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.58
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.57
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.57
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.57
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.57
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.57
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.57
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.56
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.56
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.56
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.56
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.55
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.55
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.55
1x5p_A	97	Negative elongation factor E; structure genomics,	99.55
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.55
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.55
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.55
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.55
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.54
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.54
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.54
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.54
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.54
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.54
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.54
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.54
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.54
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.54
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.54
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.53
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.53
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.53
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.53
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.53
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.53
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.53
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.53
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.53
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.53
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.52
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.52
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.52
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.52
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.51
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.51
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.51
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.51
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.5
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.5
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.5
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.5
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.5
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.49
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.49
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.49
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.49
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.49
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.49
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.48
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.48
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.47
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.47
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.46
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.46
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.46
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.45
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.45
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.45
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.43
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.42
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.42
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.41
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.4
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.39
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.09
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.37
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.37
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.37
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.36
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.33
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.27
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.25
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.24
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.23
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.22
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.21
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.15
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.11
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.11
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.08
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.99
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.93
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.86
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.79
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.75
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.44
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.43
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.22
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	98.18
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	98.09
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.96
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.94
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.67
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.58
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.49
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	97.38
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.37
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.34
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.29
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.25
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	97.11
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.59
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.47
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	94.93
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	94.18
4eyt_A	129	Telomerase associated protein P65; RNA, LA protein	88.8
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	86.94
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	80.82

>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=2.3e-34  Score=229.77  Aligned_cols=163  Identities=23%  Similarity=0.335  Sum_probs=142.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .++++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|.+|+..||+..+.|+.|.|.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            5788999999999999999999999999999999964   5678899999999999999999999999999999999997


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC--cEEEEEEechh
Q 023765           81 HGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG--MTGIVDYTSYD  158 (277)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~--~~~fv~f~~~~  158 (277)
                      .......                  .....+|||+|||..+++++|.++|.+||.|..|.|+.+..+  +||||+|.+.+
T Consensus        93 ~~~~~~~------------------~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~  154 (213)
T 4f02_A           93 QRDPSLR------------------KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQE  154 (213)
T ss_dssp             CCCTHHH------------------HHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHH
T ss_pred             ccccccc------------------ccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHH
Confidence            7532111                  112468999999999999999999999999999999887543  59999999999


Q ss_pred             HHHHHHHhcCCCeecccceeeEEEEeecCC
Q 023765          159 DMKYAIRKLDRSEFRNAFSRSYVRVREYDS  188 (277)
Q Consensus       159 ~a~~a~~~l~g~~~~g~~~~~~i~~~~~~~  188 (277)
                      +|++|+..|||..++|    ..|.|..+..
T Consensus       155 ~a~~Ai~~lng~~~~g----~~i~V~~a~~  180 (213)
T 4f02_A          155 AAERAIEKMNGMLLND----RKVFVGRFKS  180 (213)
T ss_dssp             HHHHHHHHHTTCEETT----EECEEEECCC
T ss_pred             HHHHHHHHhCCCEECC----EEEEEEEcCC
Confidence            9999999999999999    5777776654

>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=100.00  E-value=2.4e-33  Score=221.93  Aligned_cols=179  Identities=16%  Similarity=0.211  Sum_probs=143.7

Q ss_pred             CCCCeEEEcCCC-CCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            4 RSSRTLYVGNLP-GDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         4 ~~~~~l~V~nL~-~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      -++++|||+||| +.+|+++|+++|++||.|..|.|+.+  .+|||||+|.+.++|..|++.|||..|.|+.|.|.++..
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~--~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~   79 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS--KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQ   79 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT--STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC--CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccC
Confidence            378999999999 79999999999999999999999754  379999999999999999999999999999999999975


Q ss_pred             CCCCCCCC----CCC---CCCCCC--CC--------CCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCe--eEEEEEe
Q 023765           83 GRRHSSSM----DRY---SSYSSG--GS--------RGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDV--CFSQVFR  143 (277)
Q Consensus        83 ~~~~~~~~----~~~---~~~~~~--~~--------~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v--~~~~~~~  143 (277)
                      ....+...    ...   ..+...  ..        ......+..+|||+|||..+++++|+++|.+||.|  ..+.++.
T Consensus        80 ~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~  159 (205)
T 3tyt_A           80 PAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFS  159 (205)
T ss_dssp             SCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECS
T ss_pred             CccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEc
Confidence            43211100    000   000000  00        00112456789999999999999999999999998  8888877


Q ss_pred             cCC--CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          144 DRG--GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       144 ~~~--~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      +..  .++|||+|.+.++|.+||..|||..+.|......+.|.
T Consensus       160 ~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk  202 (205)
T 3tyt_A          160 GKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLK  202 (205)
T ss_dssp             CCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECE
T ss_pred             CCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEE
Confidence            642  36999999999999999999999999997766666554

>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=6.2e-33  Score=212.96  Aligned_cols=154  Identities=24%  Similarity=0.364  Sum_probs=138.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      ++++|||+|||+++|+++|+++|+.||+|..+.++.   ++.++|||||+|.++++|..|++.||+..+.|+.|.|.++.
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecC
Confidence            468999999999999999999999999999999964   56677999999999999999999999999999999999987


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEech
Q 023765           82 GGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSY  157 (277)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~  157 (277)
                      +...                    .....+|+|+|||..+++++|.++|.+||.|..+.+..+..    .+||||+|.+.
T Consensus        81 ~~~~--------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~  140 (167)
T 1fxl_A           81 PSSA--------------------SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKR  140 (167)
T ss_dssp             CCCG--------------------GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             CCcc--------------------cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCH
Confidence            5432                    12357899999999999999999999999999999988763    35999999999


Q ss_pred             hHHHHHHHhcCCCeeccccee
Q 023765          158 DDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       158 ~~a~~a~~~l~g~~~~g~~~~  178 (277)
                      ++|.+|+..|||..+.|+.+.
T Consensus       141 ~~A~~A~~~l~g~~~~g~~~~  161 (167)
T 1fxl_A          141 IEAEEAIKGLNGQKPSGATEP  161 (167)
T ss_dssp             HHHHHHHHHHTTCCCTTCSSC
T ss_pred             HHHHHHHHHhcCCccCCCccc
Confidence            999999999999999996433

>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=9.7e-33  Score=212.23  Aligned_cols=150  Identities=27%  Similarity=0.387  Sum_probs=136.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      ++++|||+|||+++|+++|+++|++||+|..|.++.   ++.++|||||+|.++++|..|++.|++..+.|+.|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            679999999999999999999999999999999954   56678999999999999999999999999999999999987


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEech
Q 023765           82 GGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSY  157 (277)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~  157 (277)
                      +....                    ....+|+|+|||..+++++|.++|.+||.|..+.+..+...    +||||+|.+.
T Consensus        82 ~~~~~--------------------~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~  141 (168)
T 1b7f_A           82 PGGES--------------------IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKR  141 (168)
T ss_dssp             CCSST--------------------TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             CCccc--------------------CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCH
Confidence            54321                    23679999999999999999999999999999999887632    5999999999


Q ss_pred             hHHHHHHHhcCCCeecc
Q 023765          158 DDMKYAIRKLDRSEFRN  174 (277)
Q Consensus       158 ~~a~~a~~~l~g~~~~g  174 (277)
                      ++|.+|+..|||..+.|
T Consensus       142 ~~A~~A~~~l~g~~~~g  158 (168)
T 1b7f_A          142 EEAQEAISALNNVIPEG  158 (168)
T ss_dssp             HHHHHHHHHHTTCCCTT
T ss_pred             HHHHHHHHHhcCCEecC
Confidence            99999999999999987

>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=1e-32  Score=211.54  Aligned_cols=158  Identities=23%  Similarity=0.367  Sum_probs=139.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCCC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGR   84 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~~   84 (277)
                      ++|||+|||+++|+++|+++|++||+|..|.++.  ++.++|||||+|.+.++|..|+..|||..+.|+.|.|.++....
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            5899999999999999999999999999999965  35678999999999999999999999999999999999987543


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHH
Q 023765           85 RHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDM  160 (277)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a  160 (277)
                      ..                  ...+..+|+|+|||..+++++|.++|.+||.|..+.+..+..+    +||||+|.+.++|
T Consensus        81 ~~------------------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A  142 (166)
T 3md3_A           81 QS------------------SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDA  142 (166)
T ss_dssp             CC------------------CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHH
T ss_pred             CC------------------CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHH
Confidence            21                  1234679999999999999999999999999999999877443    5999999999999


Q ss_pred             HHHHHhcCCCeecccceeeEEEEeec
Q 023765          161 KYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       161 ~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      .+|+..|||..++|    ..|.|..+
T Consensus       143 ~~A~~~l~g~~~~g----~~i~v~~a  164 (166)
T 3md3_A          143 QNAMDSMQGQDLNG----RPLRINWA  164 (166)
T ss_dssp             HHHHHHHTTCEETT----EECEEEES
T ss_pred             HHHHHHhCCCccCC----cEEEEEec
Confidence            99999999999999    56666554

>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=2.1e-32  Score=215.59  Aligned_cols=167  Identities=17%  Similarity=0.297  Sum_probs=138.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+++|+++|+++|+.||+|..|.|+.   ++.++|||||+|.+.++|.+|+. +++..|.|+.|.|.++
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~l~v~~~   89 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRA   89 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHh-cCCCEECCEEeeeecc
Confidence            4678999999999999999999999999999999965   45678999999999999999998 5999999999999998


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEec
Q 023765           81 HGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTS  156 (277)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~  156 (277)
                      ........              ........+|||+|||..+++++|.++|.+||.|..+.+..+..    .+||||+|.+
T Consensus        90 ~~~~~~~~--------------~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~  155 (196)
T 1l3k_A           90 VSREDSQR--------------PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD  155 (196)
T ss_dssp             CC-------------------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             cCcccccc--------------cccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECC
Confidence            76432211              11223468999999999999999999999999999999998754    3599999999


Q ss_pred             hhHHHHHHHhcCCCeecccceeeEEEEeecCCCC
Q 023765          157 YDDMKYAIRKLDRSEFRNAFSRSYVRVREYDSRR  190 (277)
Q Consensus       157 ~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~~~r  190 (277)
                      .++|.+|+.. +|..++|    ..|.|....++.
T Consensus       156 ~~~A~~A~~~-~~~~~~G----~~i~v~~a~~k~  184 (196)
T 1l3k_A          156 HDSVDKIVIQ-KYHTVNG----HNCEVRKALSKQ  184 (196)
T ss_dssp             HHHHHHHHHC-SCCEETT----EECEEEECC---
T ss_pred             HHHHHHHHHh-CCcEECC----EEEEEEecCChh
Confidence            9999999986 7999999    567776665543

>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=100.00  E-value=9.9e-32  Score=223.69  Aligned_cols=179  Identities=19%  Similarity=0.280  Sum_probs=145.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH----HHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVE----DLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVE   78 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~----~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~   78 (277)
                      ..++++|||+|||+++|+++|+    ++|++||.|..|.++.++.++|||||+|.+.++|..|++.|||..|.|+.|.|.
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   85 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   85 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEEE
Confidence            4789999999999999999966    999999999999998888899999999999999999999999999999999999


Q ss_pred             EccCCCCCCCCCC--------------------------C------------C----------------------CCCC-
Q 023765           79 LAHGGRRHSSSMD--------------------------R------------Y----------------------SSYS-   97 (277)
Q Consensus        79 ~a~~~~~~~~~~~--------------------------~------------~----------------------~~~~-   97 (277)
                      ++...........                          .            .                      ..+. 
T Consensus        86 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~  165 (282)
T 3pgw_A           86 YAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMP  165 (282)
T ss_pred             EeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCCCC
Confidence            9875442100000                          0            0                      0000 


Q ss_pred             ------CCC------------------------CCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC
Q 023765           98 ------SGG------------------------SRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG  147 (277)
Q Consensus        98 ------~~~------------------------~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~  147 (277)
                            ..+                        .......+..+|||+|||..+++++|+++|.+||.|..|.+..+. .
T Consensus       166 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-~  244 (282)
T 3pgw_A          166 PPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-H  244 (282)
T ss_pred             CCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-C
Confidence                  000                        000122356789999999999999999999999999999998665 3


Q ss_pred             cEEEEEEechhHHHHHHHhcCCCeec-ccceeeEEEEeec
Q 023765          148 MTGIVDYTSYDDMKYAIRKLDRSEFR-NAFSRSYVRVREY  186 (277)
Q Consensus       148 ~~~fv~f~~~~~a~~a~~~l~g~~~~-g~~~~~~i~~~~~  186 (277)
                      +||||+|.+.++|.+|+..|||..+. |    ..|.|...
T Consensus       245 g~afV~f~~~~~A~~A~~~l~g~~~~~g----~~l~v~~a  280 (282)
T 3pgw_A          245 DIAFVEFDNEVQAGAARDALQGFKITQN----NAMKISFA  280 (282)
T ss_pred             cEEEEEeCCHHHHHHHHHHcCCcEeCCC----CEEEEEEe
Confidence            69999999999999999999999999 7    56666654

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

Probab=100.00  E-value=1.5e-31  Score=211.15  Aligned_cols=178  Identities=22%  Similarity=0.366  Sum_probs=143.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhcc----C-------CeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKY----G-------PIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDG   72 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~----G-------~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g   72 (277)
                      ..+++|||+|||+++|+++|+++|++|    |       .|..+.+.   .++|||||+|.++++|.+|+ .|||..|.|
T Consensus         2 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~---~~~g~afV~F~~~~~A~~Al-~l~g~~~~g   77 (198)
T 2yh0_A            2 AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN---QDKNFAFLEFRSVDETTQAM-AFDGIIFQG   77 (198)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE---TTTTEEEEEESCSHHHHHHG-GGTTEEETT
T ss_pred             CceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec---CCCCEEEEEeCCHHHHHHHH-HhcCCEEcC
Confidence            468999999999999999999999999    5       66666664   45899999999999999999 799999999


Q ss_pred             ceEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----Cc
Q 023765           73 YRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GM  148 (277)
Q Consensus        73 ~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~  148 (277)
                      +.|.|.++..............................+|||+|||..+++++|.++|.+||.|..+.+..+..    .+
T Consensus        78 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g  157 (198)
T 2yh0_A           78 QSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKG  157 (198)
T ss_dssp             EEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEE
T ss_pred             ceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcce
Confidence            99999998876443322111111111111223345678999999999999999999999999999999998753    35


Q ss_pred             EEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeecCCC
Q 023765          149 TGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDSR  189 (277)
Q Consensus       149 ~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~~~  189 (277)
                      ||||+|.+.++|..|+..|||..++|    ..|.|....++
T Consensus       158 ~afV~f~~~~~a~~A~~~l~g~~~~g----~~l~v~~a~~~  194 (198)
T 2yh0_A          158 YAFCEYVDINVTDQAIAGLNGMQLGD----KKLLVQRASVG  194 (198)
T ss_dssp             EEEEEESSSSHHHHHHHHHTTCEETT----EECEEEESCCC
T ss_pred             EEEEEECCHHHHHHHHHHcCCCEECC----EEEEEEECCCC
Confidence            99999999999999999999999999    67777766544

>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=7e-32  Score=208.75  Aligned_cols=151  Identities=15%  Similarity=0.309  Sum_probs=132.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecC---C--CCCcEEEEEEcChHHHHHHHHhcCCcccC---CceEE
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP---P--RPPGYAFLEFEDYRDAEDAIRGRDGYNFD---GYRLR   76 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~---~--~~~g~afV~f~~~~~a~~a~~~l~~~~~~---g~~i~   76 (277)
                      ++++|||+|||+++|+++|+++|++||+|..|.|+.+   +  .++|||||+|.+.++|..|++.|++..+.   +..+.
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            6789999999999999999999999999999999653   2  56899999999999999999999998876   67788


Q ss_pred             EEEccCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC---cEEEEE
Q 023765           77 VELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG---MTGIVD  153 (277)
Q Consensus        77 v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~fv~  153 (277)
                      +.++......                   .....+|||+|||..+++++|+++|.+||.|..+.+..+..+   +||||+
T Consensus        82 ~~~~~~~~~~-------------------~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~  142 (175)
T 3nmr_A           82 MKPADSEKNN-------------------AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVT  142 (175)
T ss_dssp             EEECGGGCCS-------------------CGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEE
T ss_pred             Eccccccccc-------------------cCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEE
Confidence            8887654321                   123679999999999999999999999999999999887553   599999


Q ss_pred             EechhHHHHHHHhcCCCeecc
Q 023765          154 YTSYDDMKYAIRKLDRSEFRN  174 (277)
Q Consensus       154 f~~~~~a~~a~~~l~g~~~~g  174 (277)
                      |.+.++|.+|+..|||..+.+
T Consensus       143 f~~~~~A~~A~~~l~g~~~~~  163 (175)
T 3nmr_A          143 FTTRAMAQTAIKAMHQAQTME  163 (175)
T ss_dssp             ESSHHHHHHHHHHHTTSCCCT
T ss_pred             ECCHHHHHHHHHHhcCCcccC
Confidence            999999999999999988764

>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=2e-31  Score=213.20  Aligned_cols=172  Identities=19%  Similarity=0.296  Sum_probs=142.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      +.++|||+|||+++|+++|+++|+.||+|..|.|+.   ++.++|||||+|.+.++|.+|++.||+..|.|+.|.|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            457999999999999999999999999999999964   56789999999999999999999999999999999998876


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEech
Q 023765           82 GGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSY  157 (277)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~  157 (277)
                      .........         ...........+|||+|||..+++++|.++|.+||.|..+.+..+..    .+||||+|.+.
T Consensus       107 ~~~~~~~~~---------~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~  177 (216)
T 2qfj_A          107 NIGQAQPII---------DQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKA  177 (216)
T ss_dssp             CCGGGHHHH---------HHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             Cccccchhh---------hhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCH
Confidence            432110000         00000113367999999999999999999999999999999998754    35999999999


Q ss_pred             hHHHHHHHhcCCCeecccceeeEEEEeecCCC
Q 023765          158 DDMKYAIRKLDRSEFRNAFSRSYVRVREYDSR  189 (277)
Q Consensus       158 ~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~~~  189 (277)
                      ++|.+|+..|||..+.|    ..|.|......
T Consensus       178 ~~A~~A~~~l~g~~~~g----~~i~V~~a~~~  205 (216)
T 2qfj_A          178 QSSQDAVSSMNLFDLGG----QYLRVGKAVTP  205 (216)
T ss_dssp             HHHHHHHHHHTTCBCSS----SBCEEEECSSC
T ss_pred             HHHHHHHHHccCCEeCC----cEEEEEEecCC
Confidence            99999999999999999    56667666544

>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=2.7e-31  Score=204.91  Aligned_cols=154  Identities=23%  Similarity=0.414  Sum_probs=135.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhcc----C-------CeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKY----G-------PIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDG   72 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~----G-------~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g   72 (277)
                      +++++|||+|||+++|+++|+++|++|    |       .|..+.+.   ..+|||||+|.++++|.+|+ .||+..|.|
T Consensus         2 r~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~---~~~g~afV~f~~~~~A~~A~-~~~~~~~~g   77 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN---QDKNFAFLEFRSVDETTQAM-AFDGIIFQG   77 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE---TTTTEEEEEESSHHHHHHHG-GGTTCEETT
T ss_pred             CcccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec---CCCCEEEEEeCCHHHHHHHH-HhCCcEecC
Confidence            468999999999999999999999999    6       77777775   34899999999999999999 799999999


Q ss_pred             ceEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----c
Q 023765           73 YRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----M  148 (277)
Q Consensus        73 ~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~  148 (277)
                      +.|.|.++......                    ....+|+|+|||..+++++|.++|.+||.|..+.+..+..+    +
T Consensus        78 ~~i~v~~~~~~~~~--------------------~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g  137 (172)
T 2g4b_A           78 QSLKIRRPHDYQPL--------------------PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKG  137 (172)
T ss_dssp             EECEEECCSSCCCC--------------------TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEE
T ss_pred             ceeeecCCcccCCC--------------------CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcce
Confidence            99999987654321                    22679999999999999999999999999999999988533    5


Q ss_pred             EEEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          149 TGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       149 ~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      ||||+|.+.++|.+|+..|||..++|    ..|.|..
T Consensus       138 ~afV~f~~~~~A~~A~~~l~g~~~~g----~~l~V~~  170 (172)
T 2g4b_A          138 YAFCEYVDINVTDQAIAGLNGMQLGD----KKLLVQR  170 (172)
T ss_dssp             EEEEEESSTTHHHHHHHHHTTCEETT----EECEEEE
T ss_pred             EEEEEeCCHHHHHHHHHHcCCCEECC----eEEEEEe
Confidence            99999999999999999999999999    4555543

>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=99.98  E-value=4e-31  Score=213.37  Aligned_cols=177  Identities=18%  Similarity=0.195  Sum_probs=142.6

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            4 RSSRTLYVGNLPG-DTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         4 ~~~~~l~V~nL~~-~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      .++++|||+|||+ ++|+++|+++|+.||.|..|.|+.+.  +|||||+|.++++|.+|++.||+..|.|+.|.|.++..
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~--~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  109 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK--KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH  109 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT--SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC--CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecC
Confidence            5789999999999 99999999999999999999998654  79999999999999999999999999999999999986


Q ss_pred             CCCCCCCCC-----CCC--------CCCCC--CCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcC-CeeEEEEEecCC
Q 023765           83 GRRHSSSMD-----RYS--------SYSSG--GSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAG-DVCFSQVFRDRG  146 (277)
Q Consensus        83 ~~~~~~~~~-----~~~--------~~~~~--~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g-~v~~~~~~~~~~  146 (277)
                      .........     ...        .+...  ........+..+|||+|||..+++++|+++|.+|| .|..+.+... .
T Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-~  188 (229)
T 2adc_A          110 QNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-D  188 (229)
T ss_dssp             CCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-S
T ss_pred             ccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-C
Confidence            532211100     000        00000  00011234578999999999999999999999999 9999998653 3


Q ss_pred             CcEEEEEEechhHHHHHHHhcCCCeec-ccceeeEEEEeecC
Q 023765          147 GMTGIVDYTSYDDMKYAIRKLDRSEFR-NAFSRSYVRVREYD  187 (277)
Q Consensus       147 ~~~~fv~f~~~~~a~~a~~~l~g~~~~-g~~~~~~i~~~~~~  187 (277)
                      .+||||+|.+.++|.+|+..|||..+. |    ..|.|....
T Consensus       189 ~g~afV~f~~~~~A~~Ai~~l~g~~~~~g----~~l~v~~a~  226 (229)
T 2adc_A          189 RKMALIQMGSVEEAVQALIDLHNHDLGEN----HHLRVSFSK  226 (229)
T ss_dssp             TTCEEEEESSHHHHHHHHHHHTTCBSSSS----CBCEEEECS
T ss_pred             CcEEEEEECCHHHHHHHHHHHCCCccCCC----CeEEEEEec
Confidence            469999999999999999999999998 7    456665543

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

Probab=99.98  E-value=3e-31  Score=209.48  Aligned_cols=168  Identities=17%  Similarity=0.201  Sum_probs=137.8

Q ss_pred             CCCeEEEcCCCC-CCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            5 SSRTLYVGNLPG-DTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         5 ~~~~l~V~nL~~-~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      ++++|||+|||+ ++|+++|+++|++||.|..|.++.+.  +|||||+|.+.++|..|+..|||..|.|+.|.|.++...
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~--~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~   79 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK--KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   79 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC--SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC--CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCC
Confidence            368999999999 99999999999999999999997654  789999999999999999999999999999999999865


Q ss_pred             CCCCCCCC-----CCC--------CCCCC--CCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcC-CeeEEEEEecCCC
Q 023765           84 RRHSSSMD-----RYS--------SYSSG--GSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAG-DVCFSQVFRDRGG  147 (277)
Q Consensus        84 ~~~~~~~~-----~~~--------~~~~~--~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g-~v~~~~~~~~~~~  147 (277)
                      ........     ...        .+...  ........+..+|||+|||..+++++|.++|.+|| .|..+.+..+. .
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~-~  158 (198)
T 1qm9_A           80 NVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD-R  158 (198)
T ss_dssp             SCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT-S
T ss_pred             CcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC-C
Confidence            32211100     000        00000  01112234578999999999999999999999999 99999986543 5


Q ss_pred             cEEEEEEechhHHHHHHHhcCCCeec-cc
Q 023765          148 MTGIVDYTSYDDMKYAIRKLDRSEFR-NA  175 (277)
Q Consensus       148 ~~~fv~f~~~~~a~~a~~~l~g~~~~-g~  175 (277)
                      ++|||+|.+.++|.+|+..|||..+. |+
T Consensus       159 g~afV~f~~~~~A~~A~~~l~g~~~~~g~  187 (198)
T 1qm9_A          159 KMALIQMGSVEEAVQALIDLHNHDLGENH  187 (198)
T ss_dssp             SCEEEECSSHHHHHHHHHHHTSSCCSSCC
T ss_pred             cEEEEEeCCHHHHHHHHHHhcCCccCCCC
Confidence            69999999999999999999999998 74

>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=99.98  E-value=3.7e-32  Score=208.79  Aligned_cols=158  Identities=19%  Similarity=0.374  Sum_probs=137.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      +++++|||+|||+++|+++|+++|++||+|..|.++.   ++.++|||||+|.+.++|..|+..  +..+.|+.|.|.++
T Consensus         1 k~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~   78 (167)
T 2cjk_A            1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRA   78 (167)
T ss_dssp             CGGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEcccccc
Confidence            4689999999999999999999999999999999964   568899999999999999999994  57899999999987


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEec
Q 023765           81 HGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTS  156 (277)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~  156 (277)
                      .....                    .....+|||+|||..+++++|.++|.+||.|..+.+..+..    .|||||+|.+
T Consensus        79 ~~~~~--------------------~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~  138 (167)
T 2cjk_A           79 IPRDE--------------------QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDS  138 (167)
T ss_dssp             CCHHH--------------------HHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESS
T ss_pred             cchhh--------------------ccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECC
Confidence            64321                    12256899999999999999999999999999999987643    3699999999


Q ss_pred             hhHHHHHHHhcCCCeecccceeeEEEEeecCC
Q 023765          157 YDDMKYAIRKLDRSEFRNAFSRSYVRVREYDS  188 (277)
Q Consensus       157 ~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~~  188 (277)
                      .++|.+|++ ++|..+.|    ..|.|..+.+
T Consensus       139 ~~~a~~A~~-~~~~~~~g----~~i~V~~a~p  165 (167)
T 2cjk_A          139 ADAVDRVCQ-NKFIDFKD----RKIEIKRAEP  165 (167)
T ss_dssp             HHHHHHHHH-CSEECSSS----SCEEEEECCC
T ss_pred             HHHHHHHHh-CCCEEeCC----eEEEEeecCC
Confidence            999999998 89999999    5666666544

>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=99.97  E-value=5.2e-32  Score=209.66  Aligned_cols=162  Identities=16%  Similarity=0.241  Sum_probs=138.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEe--ecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL--KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~--~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      ..++++|||+|||+++|+++|+++|..||.|..+.+  ..++.++|||||+|.++++|.+|++ ||+..|.|+.|.|.++
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~~   88 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEecC
Confidence            367899999999999999999999999997766333  3356789999999999999999996 9999999999999998


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHH
Q 023765           81 HGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDM  160 (277)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a  160 (277)
                      ......                  ......+|||+|||..+++++|+++|.+||.|..+ .......+||||+|.+.++|
T Consensus        89 ~~~~~~------------------~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-~~~~~~~g~afV~f~~~~~A  149 (175)
T 1fje_B           89 KGRDSK------------------KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-SQDGKSKGIAYIEFKSEADA  149 (175)
T ss_dssp             CCSSCS------------------TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-CSSSSCCSEEEEECSSHHHH
T ss_pred             CCcccc------------------ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-cCCCCCceEEEEEECCHHHH
Confidence            764321                  12347899999999999999999999999999877 33344567999999999999


Q ss_pred             HHHHHhcCCCeecccceeeEEEEeecCC
Q 023765          161 KYAIRKLDRSEFRNAFSRSYVRVREYDS  188 (277)
Q Consensus       161 ~~a~~~l~g~~~~g~~~~~~i~~~~~~~  188 (277)
                      .+|+..|||..+.|    ..|.|....+
T Consensus       150 ~~A~~~l~g~~~~g----~~i~v~~a~~  173 (175)
T 1fje_B          150 EKNLEEKQGAEIDG----RSVSLYYTGE  173 (175)
T ss_dssp             HHHHHHHTEEEETT----EEEEEEECSS
T ss_pred             HHHHHHhCCCEECC----eEEEEEecCC
Confidence            99999999999999    6777776654

>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=4.2e-30  Score=211.34  Aligned_cols=156  Identities=24%  Similarity=0.320  Sum_probs=135.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      .+.++|||+|||+++|+++|+++|+.||.|..|.|..   .+|||||+|.+.++|..|+..|||..|.|+.|.|.++.+ 
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~~-   95 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR---DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH-   95 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET---TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC-
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC---CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeeccc-
Confidence            3567899999999999999999999999999999964   479999999999999999999999999999999999864 


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC---cEEEEEEechhHH
Q 023765           84 RRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG---MTGIVDYTSYDDM  160 (277)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~fv~f~~~~~a  160 (277)
                                               ..+|||+|||..+++++|.++|..||.|..|.+..+..+   +||||+|.+.++|
T Consensus        96 -------------------------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A  150 (261)
T 3sde_A           96 -------------------------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPA  150 (261)
T ss_dssp             -------------------------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHH
T ss_pred             -------------------------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHH
Confidence                                     468999999999999999999999999999999887543   5999999999999


Q ss_pred             HHHHHhcCCCeecccceeeEEEEeecCC
Q 023765          161 KYAIRKLDRSEFRNAFSRSYVRVREYDS  188 (277)
Q Consensus       161 ~~a~~~l~g~~~~g~~~~~~i~~~~~~~  188 (277)
                      ..|+..||+..+........|.|.....
T Consensus       151 ~~A~~~l~~~~~~~~~~~r~i~v~~~~~  178 (261)
T 3sde_A          151 RKALERCGDGAFLLTTTPRPVIVEPMEQ  178 (261)
T ss_dssp             HHHHHHHHHSCEESSSSCCBCEEEECCC
T ss_pred             HHHHHHhcCCeEEecCCCceEEEeeccc
Confidence            9999999654444212224566665543

>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=1.3e-29  Score=211.07  Aligned_cols=165  Identities=19%  Similarity=0.225  Sum_probs=144.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+++|+++|+++|+.||.|..+.++.   ++.++|||||+|.+.++|..|+..|+|..|.|+.|.|.++
T Consensus        93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a  172 (284)
T 3smz_A           93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT  172 (284)
T ss_dssp             CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            3578999999999999999999999999999998854   5677899999999999999999999999999999999998


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCC-CHHHHHHHHHhcCCeeEEEEEecCCC---cEEEEEEec
Q 023765           81 HGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSA-SWQDLKDHMRRAGDVCFSQVFRDRGG---MTGIVDYTS  156 (277)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~-~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~fv~f~~  156 (277)
                      .......                 ......+|||+|||..+ ++++|.++|..||.|..+.+..+..+   ++|||+|.+
T Consensus       173 ~~~~~~~-----------------~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~  235 (284)
T 3smz_A          173 DAGQLTP-----------------ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYET  235 (284)
T ss_dssp             CGGGCCT-----------------TTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSS
T ss_pred             CCCCCCc-----------------ccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCC
Confidence            8644321                 12346799999999995 99999999999999999999887543   599999999


Q ss_pred             hhHHHHHHHhcCCCeecccceeeEEEEeecCCC
Q 023765          157 YDDMKYAIRKLDRSEFRNAFSRSYVRVREYDSR  189 (277)
Q Consensus       157 ~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~~~  189 (277)
                      .++|.+|+..|||..+.|    ..|.|....+.
T Consensus       236 ~~~A~~A~~~l~g~~~~g----~~l~v~~a~~~  264 (284)
T 3smz_A          236 AEMAEEAQQQADGLSLGG----SHLRVSFCAPG  264 (284)
T ss_dssp             HHHHHHHHHHHTTCEETT----EECEEEECCSS
T ss_pred             HHHHHHHHHHhCCCccCC----eEEEEEEecCC
Confidence            999999999999999999    57777766554

>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=9.8e-30  Score=212.66  Aligned_cols=166  Identities=16%  Similarity=0.278  Sum_probs=139.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccC-CeeEEEeecC--CCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYG-PIVDIDLKIP--PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G-~v~~v~~~~~--~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      +.++|||+|||+.+|+++|+++|+.|| .|..|.++.+  +.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  195 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN  195 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            578999999999999999999999999 9999999653  4678999999999999999999999999999999999988


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCC-CCHHHHHHHHHhcCCeeEEEEEecCC-----CcEEEEEEe
Q 023765           82 GGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSS-ASWQDLKDHMRRAGDVCFSQVFRDRG-----GMTGIVDYT  155 (277)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~-~~~~~l~~~f~~~g~v~~~~~~~~~~-----~~~~fv~f~  155 (277)
                      +.......             ........+|||.|||.. +++++|.++|.+||.|..|.+..+..     .+||||+|.
T Consensus       196 ~~~~~~~~-------------~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~  262 (292)
T 2ghp_A          196 PLEKSKRT-------------DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFE  262 (292)
T ss_dssp             CC----------------------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEES
T ss_pred             CCcccccc-------------cccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeC
Confidence            65432211             122345789999999999 99999999999999999999987654     469999999


Q ss_pred             chhHHHHHHHhcCCCeecccceeeEEEEeecCC
Q 023765          156 SYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDS  188 (277)
Q Consensus       156 ~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~~  188 (277)
                      +.++|..|+ .|||..+.|    ..|.|....+
T Consensus       263 ~~~~A~~A~-~l~g~~~~g----~~i~V~~a~~  290 (292)
T 2ghp_A          263 NKDSAERAL-QMNRSLLGN----REISVSLADK  290 (292)
T ss_dssp             SHHHHHHHG-GGTTEEETT----EEEEEEECCC
T ss_pred             CHHHHHHHH-HhcCCEECC----cEEEEEEecC
Confidence            999999999 999999999    6777776654

>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=2.9e-29  Score=208.95  Aligned_cols=151  Identities=24%  Similarity=0.280  Sum_probs=136.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      .++++|||+|||+++|+++|+++|+.|| |..+.+   +.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.. 
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~---~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~~-   94 (284)
T 3smz_A           20 RNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV---DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPT-   94 (284)
T ss_dssp             HCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE---ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC-
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE---ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecCC-
Confidence            3678999999999999999999999999 999988   45689999999999999999999999999999999998542 


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhH
Q 023765           84 RRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDD  159 (277)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~  159 (277)
                                               ..+|||+|||..+++++|.++|.+||.|..+.+..+..+    +||||+|.+.++
T Consensus        95 -------------------------~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~  149 (284)
T 3smz_A           95 -------------------------DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDS  149 (284)
T ss_dssp             -------------------------SCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHH
T ss_pred             -------------------------CCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHH
Confidence                                     469999999999999999999999999999999877643    599999999999


Q ss_pred             HHHHHHhcCCCeecccceeeEEEEeecCC
Q 023765          160 MKYAIRKLDRSEFRNAFSRSYVRVREYDS  188 (277)
Q Consensus       160 a~~a~~~l~g~~~~g~~~~~~i~~~~~~~  188 (277)
                      |..|+..|+|..+.|    ..|.+.....
T Consensus       150 a~~A~~~l~~~~~~g----~~i~v~~a~~  174 (284)
T 3smz_A          150 AARAKSDLLGKPLGP----RTLYVHWTDA  174 (284)
T ss_dssp             HHHHHHHHTTCEETT----EECEEEECCG
T ss_pred             HHHHHHHhCCCEeCC----cEEEEEECCC
Confidence            999999999999999    5666666543

>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-29  Score=209.55  Aligned_cols=154  Identities=21%  Similarity=0.289  Sum_probs=134.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecC-CCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP-PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~-~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      .++++|||+|||+++|+++|+++|+.||+|..|.|+.+ ...+|||||+|.+.++|..|++ ||+..|.|+.|.|.++. 
T Consensus        39 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~~~~-  116 (292)
T 2ghp_A           39 RELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHLT-  116 (292)
T ss_dssp             ---CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEECC-
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEEECC-
Confidence            56899999999999999999999999999999999663 2348999999999999999996 99999999999999864 


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcC-CeeEEEEEecC---CCcEEEEEEechh
Q 023765           83 GRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAG-DVCFSQVFRDR---GGMTGIVDYTSYD  158 (277)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g-~v~~~~~~~~~---~~~~~fv~f~~~~  158 (277)
                                                ..+|||+|||..+++++|.++|.+|| .|..|.++.+.   ..+||||+|.+.+
T Consensus       117 --------------------------~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~  170 (292)
T 2ghp_A          117 --------------------------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKE  170 (292)
T ss_dssp             --------------------------SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHH
T ss_pred             --------------------------CCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHH
Confidence                                      57999999999999999999999999 99999998765   4579999999999


Q ss_pred             HHHHHHHhcCCCeecccceeeEEEEeecCCC
Q 023765          159 DMKYAIRKLDRSEFRNAFSRSYVRVREYDSR  189 (277)
Q Consensus       159 ~a~~a~~~l~g~~~~g~~~~~~i~~~~~~~~  189 (277)
                      +|..|+..|||..+.|    ..|.+....+.
T Consensus       171 ~a~~A~~~l~g~~~~g----~~l~v~~a~~~  197 (292)
T 2ghp_A          171 DARYCVEKLNGLKIEG----YTLVTKVSNPL  197 (292)
T ss_dssp             HHHHHHHHHTTCEETT----EECEEEECCCC
T ss_pred             HHHHHHHHhCCCEeCC----cEEEEEECCCC
Confidence            9999999999999999    56666665443

>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=99.91  E-value=2.2e-24  Score=154.78  Aligned_cols=109  Identities=18%  Similarity=0.316  Sum_probs=73.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec-CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI-PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~-~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      .+++|||+|||+++|+++|+++|++||+|..|.|+. .+.++|||||+|.+.++|..|++.||+..|.|+.|.|.++...
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~   83 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   83 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCc
Confidence            367899999999999999999999999999999965 3456899999999999999999999999999999999998764


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHH
Q 023765           84 RRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQD  125 (277)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~  125 (277)
                      ......            .........+|||+|||+.+|++.
T Consensus        84 ~~~~~~------------~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           84 KEREAE------------LGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             CC----------------------------------------
T ss_pred             cccccc------------cccccCCCCceEeCCCCCCccccc
Confidence            322110            111122346799999999998763

>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=99.88  E-value=1.5e-22  Score=176.86  Aligned_cols=163  Identities=16%  Similarity=0.166  Sum_probs=102.2

Q ss_pred             CCCCCCCHHHHHHHhhccCCeeEEEe----ecCC-CCCcEE-----EEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765           13 NLPGDTRMREVEDLFYKYGPIVDIDL----KIPP-RPPGYA-----FLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus        13 nL~~~~t~~~l~~~F~~~G~v~~v~~----~~~~-~~~g~a-----fV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      .||++     |.+||.++|+|..|..    +... ...+|+     |+.|....++..++..++.....+..........
T Consensus         4 ~lPp~-----L~~lF~p~pPl~~~~P~~~~p~~~~~~~~~~gia~~~~~f~~~~~~~~~~~~e~~~~~~~~~~~~k~~~~   78 (437)
T 3pgw_S            4 FLPPN-----LLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRAETREERMERKRREKIERR   78 (437)
T ss_pred             cCCcc-----HHHhcCCCCCCcCCCCcccccccccCCCCcccHHHHHHhhcCcccccccccccCHHHHHHHHHHHHHHHH
Confidence            45654     7899999999988733    2111 233444     7888777666555544433322221100000000


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechh
Q 023765           83 GRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYD  158 (277)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~  158 (277)
                      .......   ...+...........+.++|||+|||+.+++++|.++|.+||.|..|.|+.+..    .+||||+|.+.+
T Consensus        79 ~~~~~~~---~~~~~p~~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e  155 (437)
T 3pgw_S           79 QQEVETE---LKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHER  155 (437)
T ss_pred             HHHHHHh---hhhcCCcccccccCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHH
Confidence            0000000   000000001111224467999999999999999999999999999999987643    469999999999


Q ss_pred             HHHHHHHhcCCCeecccceeeEEEEeecC
Q 023765          159 DMKYAIRKLDRSEFRNAFSRSYVRVREYD  187 (277)
Q Consensus       159 ~a~~a~~~l~g~~~~g~~~~~~i~~~~~~  187 (277)
                      +|.+||..|||..|.|    ..|.|..+.
T Consensus       156 ~A~~Ai~~lng~~i~g----r~i~V~~a~  180 (437)
T 3pgw_S          156 DMHSAYKHADGKKIDG----RRVLVDVER  180 (437)
T ss_pred             HHHHHHHHcCCCEECC----EEEEEEEeC
Confidence            9999999999999999    455555443

>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=99.87  E-value=3.2e-21  Score=168.47  Aligned_cols=82  Identities=34%  Similarity=0.583  Sum_probs=75.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+.||+++|.++|++||.|+.|.|+.   ++.++|||||+|.+.++|.+||+.|||..|.|+.|.|.++
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            4568999999999999999999999999999999964   5778999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 023765           81 HGGRR   85 (277)
Q Consensus        81 ~~~~~   85 (277)
                      .+...
T Consensus       180 ~~~~~  184 (437)
T 3pgw_S          180 RGRTV  184 (437)
T ss_pred             CCCCC
Confidence            86543

>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=99.87  E-value=1.8e-22  Score=145.03  Aligned_cols=105  Identities=30%  Similarity=0.437  Sum_probs=94.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      ..++++|||+|||+.+|+++|+++|++||.|..|.|+.++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   84 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNA   84 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecC
Confidence            45789999999999999999999999999999999988888899999999999999999999999999999999999886


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCC
Q 023765           83 GRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGD  135 (277)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~  135 (277)
                      ....                            .+++...++++|+++|.+||.
T Consensus        85 ~~~~----------------------------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           85 NRAF----------------------------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             HHHT----------------------------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             Chhh----------------------------hhhhHhHhHHHHHHHHHHhCC
Confidence            4321                            346667789999999999984

>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=99.87  E-value=3.8e-22  Score=138.95  Aligned_cols=78  Identities=26%  Similarity=0.425  Sum_probs=72.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      ..++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.+|+
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            457899999999999999999999999999999964   56788999999999999999999999999999999999987


Q ss_pred             C
Q 023765           82 G   82 (277)
Q Consensus        82 ~   82 (277)
                      +
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            4

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.85  E-value=1.5e-21  Score=133.88  Aligned_cols=80  Identities=18%  Similarity=0.330  Sum_probs=72.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccC-CeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcC-CcccCCceEEEEEc
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYG-PIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRD-GYNFDGYRLRVELA   80 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G-~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~-~~~~~g~~i~v~~a   80 (277)
                      +++|||+|||+++|+++|+++|++|| +|.+|.|+.   ++.++|||||+|.+.++|.+|++.|+ +..|.|+.|.|.++
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            58999999999999999999999999 899999854   57889999999999999999998774 56799999999999


Q ss_pred             cCCCC
Q 023765           81 HGGRR   85 (277)
Q Consensus        81 ~~~~~   85 (277)
                      .+...
T Consensus        81 ~~~~~   85 (91)
T 2lxi_A           81 DPKPK   85 (91)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            86543

>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=99.85  E-value=6e-21  Score=135.61  Aligned_cols=83  Identities=59%  Similarity=1.050  Sum_probs=78.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      ..+.++|||+|||+++|+++|+++|++||.|..|.|+.++.+++||||+|.+.++|.+|++.||+..|.|+.|.|.++..
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   98 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   98 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEccc
Confidence            46789999999999999999999999999999999988888899999999999999999999999999999999999987


Q ss_pred             CCC
Q 023765           83 GRR   85 (277)
Q Consensus        83 ~~~   85 (277)
                      ...
T Consensus        99 ~~~  101 (109)
T 1x4a_A           99 GRG  101 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            553

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

Probab=99.85  E-value=2.1e-21  Score=136.08  Aligned_cols=100  Identities=41%  Similarity=0.583  Sum_probs=83.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCCCCC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGRRH   86 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~~~~   86 (277)
                      ++|||+|||+++|+++|+++|++||+|..|.++.+  ++|||||+|.+.++|.+|+..||+..|.|+.|.|.++......
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   78 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN--PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRR   78 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS--SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCCS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC--CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCCc
Confidence            58999999999999999999999999999999866  6899999999999999999999999999999999999875532


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCceEEEeCCC
Q 023765           87 SSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLP  118 (277)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~  118 (277)
                      ...          ...........+|||+||+
T Consensus        79 ~~~----------~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           79 SRF----------DRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             SCC----------CSCCCSCCCCSCCCSCCCC
T ss_pred             ccC----------CCCCccccCCCceecCCCC
Confidence            211          1111122346689999986

>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=99.85  E-value=2.4e-20  Score=141.52  Aligned_cols=138  Identities=17%  Similarity=0.062  Sum_probs=101.3

Q ss_pred             CCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCC
Q 023765           42 PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSA  121 (277)
Q Consensus        42 ~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~  121 (277)
                      ..++|||||+|.+.++|++|+..+++....+..+.+...........       ...............+|||+|||..+
T Consensus        10 ~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~l~v~nl~~~~   82 (158)
T 2kn4_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE-------GSHHHHHHMDVEGMTSLKVDNLTYRT   82 (158)
T ss_dssp             SSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEEC-------CCCCSSCCCCCCBCCEEEEESCCTTC
T ss_pred             ccccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccc-------cccccccccCCCCCCEEEEeCCCCCC
Confidence            36789999999999999999988876443333333322111100000       00001112223457899999999999


Q ss_pred             CHHHHHHHHHhcCCeeEEEEEecC----CCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeecCCCC
Q 023765          122 SWQDLKDHMRRAGDVCFSQVFRDR----GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDSRR  190 (277)
Q Consensus       122 ~~~~l~~~f~~~g~v~~~~~~~~~----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~~~r  190 (277)
                      ++++|+++|.+||.|..|.+..+.    ..|||||+|.+.++|+.|+..|||..+.|    ..|.|......+
T Consensus        83 ~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----~~l~v~~a~~~~  151 (158)
T 2kn4_A           83 SPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG----RELRVQMARYGR  151 (158)
T ss_dssp             CHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSS----SEEEEEEECCSS
T ss_pred             CHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECC----eEEEEEECCCCC
Confidence            999999999999999999998764    34699999999999999999999999999    677777776543

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

Probab=99.85  E-value=5.6e-21  Score=126.87  Aligned_cols=75  Identities=17%  Similarity=0.217  Sum_probs=71.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      -.+.-|||+||++.+|+++|+++|.+||+|..+.+..   ++|||||+|.++++|++|++.||+..+.|++|.|.+|.
T Consensus         5 ~~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~---~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            5 WGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL---NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET---TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             CccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC---CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            4578899999999999999999999999999999975   59999999999999999999999999999999999984

>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=9.3e-21  Score=142.49  Aligned_cols=138  Identities=19%  Similarity=0.129  Sum_probs=109.4

Q ss_pred             CCCCcEEEEEEcChHHHHHHHHhc-CCcccCCceEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCC
Q 023765           42 PRPPGYAFLEFEDYRDAEDAIRGR-DGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSS  120 (277)
Q Consensus        42 ~~~~g~afV~f~~~~~a~~a~~~l-~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~  120 (277)
                      ...+|+++|+|.+.++|.+|++.| |+..++| .|.+.++..........    .............+..+|||+|||..
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~----~~~~~~~~~~~~~~~~~l~V~nl~~~   84 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGS----HHHHHHMHRDSCPLDCKVYVGNLGNN   84 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSS----SSCCCCSCSSSSTTSCEEEEESCCSC
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCcccccccc----ccccccccccCCCCCCEEEEeCCCCC
Confidence            366899999999999999999999 9999999 99999876432111000    00011112233455789999999999


Q ss_pred             CCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeecCCC
Q 023765          121 ASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDSR  189 (277)
Q Consensus       121 ~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~~~  189 (277)
                      +++++|+++|.+||.|..|.+..+ ..+||||+|.+.++|..|+..|||..+.|    ..|.|....++
T Consensus        85 ~t~~~l~~~F~~~G~i~~v~i~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g----~~l~v~~a~~~  148 (150)
T 2i2y_A           85 GNKTELERAFGYYGPLRSVWVARN-PPGFAFVEFEDPRDAADAVRELDGRTLCG----CRVRVELSNGE  148 (150)
T ss_dssp             CSCHHHHHHHHHHSCEEEEEECSS-SCSEEEEEESSHHHHHHHHHHHSSSCSSS----SCCEEEECCCC
T ss_pred             CCHHHHHHHHHhhCCEEEEEEeeC-CCcEEEEEECCHHHHHHHHHHcCCCEECC----eEEEEEEcCCC
Confidence            999999999999999999999887 45799999999999999999999999999    46666665443

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

Probab=99.85  E-value=6.6e-21  Score=135.18  Aligned_cols=81  Identities=17%  Similarity=0.303  Sum_probs=75.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      ..+.++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.+
T Consensus         3 ~~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~   82 (110)
T 3s8s_A            3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQL   82 (110)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            45789999999999999999999999999999999965   467899999999999999999999999999999999999


Q ss_pred             ccCC
Q 023765           80 AHGG   83 (277)
Q Consensus        80 a~~~   83 (277)
                      +...
T Consensus        83 a~~~   86 (110)
T 3s8s_A           83 DIKG   86 (110)
T ss_dssp             CSTT
T ss_pred             CCCC
Confidence            8743

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=6e-21  Score=132.78  Aligned_cols=81  Identities=17%  Similarity=0.219  Sum_probs=73.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcC--CcccCCceEEEEEc
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRD--GYNFDGYRLRVELA   80 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~--~~~~~g~~i~v~~a   80 (277)
                      ..+.++|||+|||+++|+++|+++|++||+|.+|.|+.+   +|||||+|.+.++|..|++.|+  +..|.|++|.|.++
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~---kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A   89 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG---KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFS   89 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC---CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEc
Confidence            467899999999999999999999999999999999854   7999999999999999999876  47899999999999


Q ss_pred             cCCCCC
Q 023765           81 HGGRRH   86 (277)
Q Consensus        81 ~~~~~~   86 (277)
                      ......
T Consensus        90 ~~~~~~   95 (105)
T 1sjq_A           90 NHKELK   95 (105)
T ss_dssp             SSSSCC
T ss_pred             CCCCCC
Confidence            875543

>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=99.84  E-value=3e-20  Score=133.30  Aligned_cols=84  Identities=27%  Similarity=0.491  Sum_probs=77.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            2 SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         2 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      ...++++|||+|||+++|+++|+++|++||.|..|.|+.  ++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.+
T Consensus         3 e~~~~~~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            3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TTCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            457889999999999999999999999999999999966  567889999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 023765           80 AHGGRR   85 (277)
Q Consensus        80 a~~~~~   85 (277)
                      +.....
T Consensus        83 a~~~~~   88 (116)
T 2fy1_A           83 AKKPSF   88 (116)
T ss_dssp             CCCSSC
T ss_pred             CCCCCC
Confidence            986554

>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=99.84  E-value=3.5e-20  Score=129.29  Aligned_cols=83  Identities=31%  Similarity=0.476  Sum_probs=77.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      ..++++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|..|+..||+..|.|+.|.|.+
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            46789999999999999999999999999999999965   567889999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 023765           80 AHGGRR   85 (277)
Q Consensus        80 a~~~~~   85 (277)
                      +.....
T Consensus        85 a~~~~~   90 (99)
T 1whw_A           85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             cCCCcc
Confidence            997654

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

Probab=99.84  E-value=1.3e-20  Score=131.19  Aligned_cols=83  Identities=24%  Similarity=0.409  Sum_probs=76.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec------CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI------PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLR   76 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~------~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~   76 (277)
                      +.++++|||+|||+++|+++|+++|++||+|..|.|+.      ++.++|||||+|.+.++|.+|+..||+..|.|+.|.
T Consensus         2 s~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   81 (98)
T 2cpf_A            2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLE   81 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            56899999999999999999999999999999999964      236689999999999999999999999999999999


Q ss_pred             EEEccCCCC
Q 023765           77 VELAHGGRR   85 (277)
Q Consensus        77 v~~a~~~~~   85 (277)
                      |.++.....
T Consensus        82 V~~a~~~~~   90 (98)
T 2cpf_A           82 VRISERATK   90 (98)
T ss_dssp             EECSSCSSC
T ss_pred             EEEccCCCC
Confidence            999987654

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

Probab=99.84  E-value=1.4e-20  Score=129.64  Aligned_cols=78  Identities=18%  Similarity=0.218  Sum_probs=71.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcc--cCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYN--FDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~--~~g~~i~v~~a~   81 (277)
                      .++++|||+|||+++|+++|.++|++||.|..|.|+.   .+|||||+|.+.++|..|+..|++..  |.|++|.|.+++
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~---~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~   95 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP---KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYST   95 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET---TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc---CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEecc
Confidence            5889999999999999999999999999999999974   47999999999999999999999875  789999999998


Q ss_pred             CCC
Q 023765           82 GGR   84 (277)
Q Consensus        82 ~~~   84 (277)
                      ...
T Consensus        96 ~k~   98 (100)
T 3r27_A           96 SQK   98 (100)
T ss_dssp             CSC
T ss_pred             ccc
Confidence            643

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

Probab=99.83  E-value=5.9e-20  Score=127.12  Aligned_cols=83  Identities=29%  Similarity=0.440  Sum_probs=76.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      ..++++|||+|||+++|+++|+++|++||+|..|.++.   ++.++|||||+|.+.++|.+|++.||+..|.|+.|.|.+
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   81 (95)
T 2dnz_A            2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGH   81 (95)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            35789999999999999999999999999999999965   467899999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 023765           80 AHGGRR   85 (277)
Q Consensus        80 a~~~~~   85 (277)
                      +.....
T Consensus        82 a~~~~~   87 (95)
T 2dnz_A           82 VTERLD   87 (95)
T ss_dssp             SSCCCC
T ss_pred             cccccC
Confidence            987554

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

Probab=99.83  E-value=2.4e-20  Score=135.26  Aligned_cols=81  Identities=20%  Similarity=0.382  Sum_probs=75.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVE----DLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~----~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      .++++|||+|||+.+++++|+    ++|++||+|.+|.+..++.++|||||+|.+.++|..|+..|||..|.|+.|.|.+
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~  106 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITF  106 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEE
Confidence            568899999999999999876    7999999999999988888999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 023765           80 AHGGR   84 (277)
Q Consensus        80 a~~~~   84 (277)
                      +....
T Consensus       107 a~~~~  111 (127)
T 2a3j_A          107 SETPQ  111 (127)
T ss_dssp             CCCCC
T ss_pred             ccCcc
Confidence            98643

>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=99.83  E-value=2.8e-20  Score=129.04  Aligned_cols=80  Identities=29%  Similarity=0.625  Sum_probs=74.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      ++++|||+|||+.+++++|+++|++||.|..|.|+.   ++.++|||||+|.+.++|..|++.|||..|.|+.|.|.++.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            578999999999999999999999999999999965   46779999999999999999999999999999999999998


Q ss_pred             CCC
Q 023765           82 GGR   84 (277)
Q Consensus        82 ~~~   84 (277)
                      +..
T Consensus        81 ~~~   83 (96)
T 2x1f_A           81 NSD   83 (96)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            754

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.83  E-value=6.2e-21  Score=131.35  Aligned_cols=79  Identities=19%  Similarity=0.337  Sum_probs=71.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCC--eeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCc----ccCCce
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGP--IVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGY----NFDGYR   74 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~--v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~----~~~g~~   74 (277)
                      ..-+||||+|||+++|+++|+++|++||.  |.+|.++.   ++.++|||||+|.+.++|.+|++.|||.    .|+|+.
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            56689999999999999999999999995  67888854   5788999999999999999999999996    489999


Q ss_pred             EEEEEccC
Q 023765           75 LRVELAHG   82 (277)
Q Consensus        75 i~v~~a~~   82 (277)
                      |.|.+|+.
T Consensus        87 i~V~~Aks   94 (95)
T 2lkz_A           87 IGVDFAKS   94 (95)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEccC
Confidence            99999874

>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=99.83  E-value=7e-20  Score=128.70  Aligned_cols=83  Identities=30%  Similarity=0.442  Sum_probs=76.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecC-CCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP-PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~-~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      ..+.++|||+|||+.+|+++|+++|++||+|..|.|+.+ ..++|||||+|.+.++|.+|+..||+..|.|+.|.|.++.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   91 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   91 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECC
Confidence            367899999999999999999999999999999999763 3468999999999999999999999999999999999998


Q ss_pred             CCCC
Q 023765           82 GGRR   85 (277)
Q Consensus        82 ~~~~   85 (277)
                      ....
T Consensus        92 ~~~~   95 (103)
T 2cqi_A           92 TPSS   95 (103)
T ss_dssp             CTTC
T ss_pred             CCcc
Confidence            7553

>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=99.83  E-value=3.4e-20  Score=128.54  Aligned_cols=81  Identities=20%  Similarity=0.304  Sum_probs=74.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVE----DLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~----~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      .+.++|||+|||+++++++|+    ++|++||+|..|.|+.+...++||||+|.+.++|.+|++.|||..|.|+.|.|.+
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~   86 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSL   86 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            467899999999999999999    9999999999999987554489999999999999999999999999999999999


Q ss_pred             ccCCC
Q 023765           80 AHGGR   84 (277)
Q Consensus        80 a~~~~   84 (277)
                      +.+..
T Consensus        87 a~~~~   91 (96)
T 2dgx_A           87 ATGAS   91 (96)
T ss_dssp             CCCSS
T ss_pred             cCCCC
Confidence            98644

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

Probab=99.83  E-value=3.3e-20  Score=130.41  Aligned_cols=82  Identities=40%  Similarity=0.589  Sum_probs=76.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+++|+++|+++|++||.|..|.|+.   ++.++|||||+|.+.++|.+|+..||+..|.|+.|.|.++
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2dnm_A           11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVA   90 (103)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEC
Confidence            5789999999999999999999999999999999965   4678999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 023765           81 HGGRR   85 (277)
Q Consensus        81 ~~~~~   85 (277)
                      .....
T Consensus        91 ~~~~~   95 (103)
T 2dnm_A           91 RYGRR   95 (103)
T ss_dssp             SSCCS
T ss_pred             CcCCC
Confidence            87554

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

Probab=99.83  E-value=4.6e-20  Score=127.91  Aligned_cols=83  Identities=23%  Similarity=0.419  Sum_probs=76.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEE-Eeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDI-DLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVE   78 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v-~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~   78 (277)
                      ..++++|||+|||+++|+++|+++|++||.|..+ .|+.   ++.++|||||+|.+.++|.+|+..||+..|.|+.|.|.
T Consensus         2 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   81 (96)
T 1x5t_A            2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVS   81 (96)
T ss_dssp             CSCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3578999999999999999999999999999999 8854   56789999999999999999999999999999999999


Q ss_pred             EccCCCC
Q 023765           79 LAHGGRR   85 (277)
Q Consensus        79 ~a~~~~~   85 (277)
                      ++.....
T Consensus        82 ~a~~~~~   88 (96)
T 1x5t_A           82 YAFKKDS   88 (96)
T ss_dssp             ESCCCCC
T ss_pred             EecccCC
Confidence            9987553

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

Probab=99.83  E-value=8.5e-20  Score=130.92  Aligned_cols=84  Identities=24%  Similarity=0.420  Sum_probs=77.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+.+|+++|+++|++||.|..|.|+.   ++.++|||||+|.+.++|.+|++.||+..|.|+.|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   92 (115)
T 2dgo_A           13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   92 (115)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            5788999999999999999999999999999999964   5677899999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 023765           81 HGGRRHS   87 (277)
Q Consensus        81 ~~~~~~~   87 (277)
                      .......
T Consensus        93 ~~~~~~~   99 (115)
T 2dgo_A           93 TRKPPAP   99 (115)
T ss_dssp             SCCCCCS
T ss_pred             cCCCCCC
Confidence            8765543

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

Probab=99.83  E-value=8.7e-20  Score=127.28  Aligned_cols=82  Identities=23%  Similarity=0.492  Sum_probs=75.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      ..++++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|.+|+. ||+..|.|+.|.|.+
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~   85 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKR   85 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEE
Confidence            36789999999999999999999999999999999965   46789999999999999999999 999999999999999


Q ss_pred             ccCCCC
Q 023765           80 AHGGRR   85 (277)
Q Consensus        80 a~~~~~   85 (277)
                      +.....
T Consensus        86 a~~~~~   91 (99)
T 2dgs_A           86 AEPRDS   91 (99)
T ss_dssp             CCCCCC
T ss_pred             CCCCcc
Confidence            987554

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

Probab=99.83  E-value=3.6e-20  Score=129.97  Aligned_cols=83  Identities=33%  Similarity=0.524  Sum_probs=76.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+.+|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|.+|++.||+..|.|+.|.|.++
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            5789999999999999999999999999999999965   4678999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 023765           81 HGGRRH   86 (277)
Q Consensus        81 ~~~~~~   86 (277)
                      .+....
T Consensus        90 ~~~~~~   95 (102)
T 2cqb_A           90 KPMRIK   95 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876543

>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=99.83  E-value=2.8e-20  Score=126.03  Aligned_cols=79  Identities=33%  Similarity=0.564  Sum_probs=73.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      ..+.++|||+|||+++++++|+++|++||+|..|.++.   ++.++|||||+|.+.++|..|++.|||..|.|+.|.|.+
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            45889999999999999999999999999999999954   566799999999999999999999999999999999999


Q ss_pred             cc
Q 023765           80 AH   81 (277)
Q Consensus        80 a~   81 (277)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

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

Probab=99.83  E-value=2.9e-20  Score=127.91  Aligned_cols=83  Identities=25%  Similarity=0.417  Sum_probs=76.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec-CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI-PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~-~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      ..+.++|||+|||+++|+++|+++|++||+|..|.|+. ++.++|||||+|.+.++|.+|+..||+..|.|+.|.|.++.
T Consensus         5 ~~~~~~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            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDR   84 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            46889999999999999999999999999999999965 56778999999999999999999999999999999999998


Q ss_pred             CCCC
Q 023765           82 GGRR   85 (277)
Q Consensus        82 ~~~~   85 (277)
                      +...
T Consensus        85 ~~~~   88 (92)
T 2dgv_A           85 NASG   88 (92)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            7553

>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=99.83  E-value=3.1e-20  Score=125.20  Aligned_cols=78  Identities=22%  Similarity=0.400  Sum_probs=72.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      +.+|||+|||+++++++|+++|++||+|..+.++.   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            47899999999999999999999999999999964   467789999999999999999999999999999999999986


Q ss_pred             C
Q 023765           83 G   83 (277)
Q Consensus        83 ~   83 (277)
                      .
T Consensus        81 ~   81 (83)
T 3md1_A           81 L   81 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.83  E-value=7.3e-20  Score=129.08  Aligned_cols=82  Identities=29%  Similarity=0.447  Sum_probs=76.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|.+|+..||+..|.|+.|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   92 (105)
T 1x5u_A           13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   92 (105)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC
Confidence            5789999999999999999999999999999999965   5678899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 023765           81 HGGRR   85 (277)
Q Consensus        81 ~~~~~   85 (277)
                      .....
T Consensus        93 ~~~~~   97 (105)
T 1x5u_A           93 SAHNK   97 (105)
T ss_dssp             TTTSC
T ss_pred             CCCCc
Confidence            87654

>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=99.83  E-value=3.8e-20  Score=131.97  Aligned_cols=82  Identities=17%  Similarity=0.228  Sum_probs=73.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCC--cccCCceEEEEEc
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDG--YNFDGYRLRVELA   80 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~--~~~~g~~i~v~~a   80 (277)
                      ..++++|||+|||+++|+++|+++|++||.|..|.|+.+   +|||||+|.+.++|.+|++.|++  ..|.|++|.|.++
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~---kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a  104 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG---KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFS  104 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG---GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC---CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEc
Confidence            357899999999999999999999999999999999854   79999999999999999998874  6899999999999


Q ss_pred             cCCCCCC
Q 023765           81 HGGRRHS   87 (277)
Q Consensus        81 ~~~~~~~   87 (277)
                      .......
T Consensus       105 ~~k~~~~  111 (119)
T 2ad9_A          105 NHKELKT  111 (119)
T ss_dssp             SSSSCCC
T ss_pred             cCCCCCc
Confidence            8765433

>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=99.82  E-value=1.4e-19  Score=127.11  Aligned_cols=82  Identities=24%  Similarity=0.447  Sum_probs=75.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecC-CCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP-PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~-~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      .+.++|||+|||+++|+++|+++|++||+|..|.|+.+ ..+++||||+|.+.++|.+|+..||+..|.|+.|.|.++..
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   92 (103)
T 2cq3_A           13 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA   92 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccc
Confidence            57899999999999999999999999999999999763 34789999999999999999999999999999999999987


Q ss_pred             CCC
Q 023765           83 GRR   85 (277)
Q Consensus        83 ~~~   85 (277)
                      ...
T Consensus        93 ~~~   95 (103)
T 2cq3_A           93 RVM   95 (103)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            654

>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=99.82  E-value=7.2e-20  Score=127.40  Aligned_cols=79  Identities=20%  Similarity=0.230  Sum_probs=72.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhc--CCcccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGR--DGYNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l--~~~~~~g~~i~v~~a~   81 (277)
                      .++++|||+|||+.+|+++|+++|++||.|..|.|+..   +|||||+|.+.++|..|++.|  ++..|.|++|.|.++.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~---kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~   89 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG---KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSN   89 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC---CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcC
Confidence            57899999999999999999999999999999998754   899999999999999999976  4678999999999998


Q ss_pred             CCCC
Q 023765           82 GGRR   85 (277)
Q Consensus        82 ~~~~   85 (277)
                      ....
T Consensus        90 ~~~~   93 (101)
T 2cq1_A           90 HKEL   93 (101)
T ss_dssp             CSSC
T ss_pred             cccC
Confidence            6554

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

Probab=99.82  E-value=5.7e-20  Score=129.16  Aligned_cols=83  Identities=23%  Similarity=0.336  Sum_probs=76.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec-CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI-PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~-~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      ..+.++|||+|||+++|+++|+++|++||+|..|.|+. ++.+++||||+|.+.++|.+|+..||+..|.|+.|.|.++.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   91 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQ   91 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEec
Confidence            35789999999999999999999999999999999965 46678999999999999999999999999999999999998


Q ss_pred             CCCC
Q 023765           82 GGRR   85 (277)
Q Consensus        82 ~~~~   85 (277)
                      ....
T Consensus        92 ~~~~   95 (103)
T 2d9p_A           92 RKEE   95 (103)
T ss_dssp             SCCC
T ss_pred             cccc
Confidence            7654

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

Probab=99.82  E-value=6e-20  Score=128.32  Aligned_cols=81  Identities=23%  Similarity=0.466  Sum_probs=74.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      .+.++|||+|||+++|+++|+++|++||+|..|.|+.  ++.++|||||+|.+.++|.+|+..||+..|.|+.|.|.++.
T Consensus        15 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   94 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISN   94 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            5688999999999999999999999999999999965  45667999999999999999999999999999999999998


Q ss_pred             CCC
Q 023765           82 GGR   84 (277)
Q Consensus        82 ~~~   84 (277)
                      +..
T Consensus        95 ~~~   97 (100)
T 2do4_A           95 SGP   97 (100)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            654

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

Probab=99.82  E-value=5.7e-20  Score=126.94  Aligned_cols=78  Identities=27%  Similarity=0.442  Sum_probs=73.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+++++++|+++|++||+|..|.++.   ++.++|||||+|.+.++|.+|++.||+..|.|+.|.|.++
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   93 (94)
T 2e5h_A           14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA   93 (94)
T ss_dssp             CCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEec
Confidence            5678999999999999999999999999999999965   3677899999999999999999999999999999999997


Q ss_pred             c
Q 023765           81 H   81 (277)
Q Consensus        81 ~   81 (277)
                      +
T Consensus        94 k   94 (94)
T 2e5h_A           94 I   94 (94)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.82  E-value=3e-20  Score=126.42  Aligned_cols=79  Identities=27%  Similarity=0.442  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+++|+++|+++|++||.|..|.++.   ++.++|||||+|.+.++|..|+..||+..|.|+.|.|.++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            4678999999999999999999999999999999964   5677899999999999999999999999999999999998


Q ss_pred             cC
Q 023765           81 HG   82 (277)
Q Consensus        81 ~~   82 (277)
                      ..
T Consensus        84 ~~   85 (87)
T 3bs9_A           84 TR   85 (87)
T ss_dssp             C-
T ss_pred             CC
Confidence            75

>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=99.82  E-value=4.9e-20  Score=125.65  Aligned_cols=81  Identities=26%  Similarity=0.481  Sum_probs=73.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCC---C-CCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---R-PPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~---~-~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      ..+++|||+|||+++|+++|+++|++||+|..+.++.+.   . ++|||||+|.+.++|.+|+..|||..|.|+.|.|.+
T Consensus         2 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   81 (88)
T 4a8x_A            2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATA   81 (88)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEE
Confidence            367899999999999999999999999999999996532   2 789999999999999999999999999999999999


Q ss_pred             ccCCC
Q 023765           80 AHGGR   84 (277)
Q Consensus        80 a~~~~   84 (277)
                      +.+..
T Consensus        82 a~~~~   86 (88)
T 4a8x_A           82 VLAPW   86 (88)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            87643

>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=99.82  E-value=1.5e-20  Score=130.66  Aligned_cols=84  Identities=26%  Similarity=0.513  Sum_probs=76.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHH----HHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEE
Q 023765            1 MSSRSSRTLYVGNLPGDTRMREVE----DLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLR   76 (277)
Q Consensus         1 ~~~~~~~~l~V~nL~~~~t~~~l~----~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~   76 (277)
                      |+..++++|||+|||+++++++|+    ++|++||.|..|.++.++.++|||||+|.+.++|..|+..|||..|.|+.|.
T Consensus         3 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             ---CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            356789999999999999999999    9999999999999987667789999999999999999999999999999999


Q ss_pred             EEEccCCC
Q 023765           77 VELAHGGR   84 (277)
Q Consensus        77 v~~a~~~~   84 (277)
                      |.++....
T Consensus        83 v~~a~~~~   90 (97)
T 1nu4_A           83 IQYAKTDS   90 (97)
T ss_dssp             EEECSSCC
T ss_pred             EEEccCCC
Confidence            99998643

>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=99.82  E-value=1.7e-20  Score=130.50  Aligned_cols=79  Identities=18%  Similarity=0.161  Sum_probs=71.7

Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCc--ccCCceEEEEE
Q 023765            3 SRSSRTLYVGNLPG-DTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY--NFDGYRLRVEL   79 (277)
Q Consensus         3 ~~~~~~l~V~nL~~-~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~--~~~g~~i~v~~   79 (277)
                      ..++++|||+|||+ ++|+++|+++|++||.|..|.|+.+   ++||||+|.+.++|..|++.||+.  .|.|++|.|.+
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~---kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~   88 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK---INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHL   88 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS---SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC---CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEE
Confidence            35889999999999 9999999999999999999999753   689999999999999999988864  59999999999


Q ss_pred             ccCCC
Q 023765           80 AHGGR   84 (277)
Q Consensus        80 a~~~~   84 (277)
                      +....
T Consensus        89 a~~~~   93 (102)
T 1x4d_A           89 SQKYK   93 (102)
T ss_dssp             ECCCT
T ss_pred             CCCCC
Confidence            98644

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

Probab=99.82  E-value=5e-20  Score=129.24  Aligned_cols=82  Identities=33%  Similarity=0.579  Sum_probs=76.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .++++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|..|++.||+..|.|+.|.|.++
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            5789999999999999999999999999999999965   4568899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 023765           81 HGGRR   85 (277)
Q Consensus        81 ~~~~~   85 (277)
                      .....
T Consensus        90 ~~~~~   94 (102)
T 1x5s_A           90 GKSSD   94 (102)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            87553

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

Probab=99.82  E-value=3.9e-20  Score=129.08  Aligned_cols=83  Identities=24%  Similarity=0.396  Sum_probs=76.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCee-EEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCce---
Q 023765            2 SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIV-DIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYR---   74 (277)
Q Consensus         2 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~---   74 (277)
                      +..++++|||+|||+++|+++|+++|++||+|. .|.|+.   ++.++|||||+|.+.++|.+|++.||+..|.|+.   
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~   84 (99)
T 2div_A            5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAK   84 (99)
T ss_dssp             CCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCE
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcce
Confidence            356889999999999999999999999999999 999864   4577899999999999999999999999999999   


Q ss_pred             -EEEEEccCCC
Q 023765           75 -LRVELAHGGR   84 (277)
Q Consensus        75 -i~v~~a~~~~   84 (277)
                       |.|.++.+..
T Consensus        85 ~l~v~~a~~~~   95 (99)
T 2div_A           85 RFKLNYATYSG   95 (99)
T ss_dssp             ECCEEETTCCS
T ss_pred             eEEEeecCCCC
Confidence             9999998654

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

Probab=99.82  E-value=1.6e-19  Score=129.32  Aligned_cols=83  Identities=20%  Similarity=0.270  Sum_probs=75.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      ..++++|||+|||+++|+++|+++|++||+|..|.|+.  ++.+++||||+|.+.++|..|+..||+..|.|+.|.|.++
T Consensus        12 ~~~~~~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           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD   91 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEc
Confidence            35789999999999999999999999999999999965  4566899999999999999999999999999999999998


Q ss_pred             cCCCC
Q 023765           81 HGGRR   85 (277)
Q Consensus        81 ~~~~~   85 (277)
                      .....
T Consensus        92 ~~~~~   96 (114)
T 2do0_A           92 ERALP   96 (114)
T ss_dssp             SCCCC
T ss_pred             ccCCC
Confidence            86543

>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=99.82  E-value=7.6e-20  Score=128.06  Aligned_cols=79  Identities=16%  Similarity=0.168  Sum_probs=71.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCC--cccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDG--YNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~--~~~~g~~i~v~~a~   81 (277)
                      .++++|||+|||+++++++|+++|++||.|..|.|+..   +|||||+|.+.++|..|++.|++  ..|.|+.|.|.++.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~---kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~   89 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF---KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYST   89 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC---CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcc
Confidence            57899999999999999999999999999999998753   79999999999999999998865  45999999999998


Q ss_pred             CCCC
Q 023765           82 GGRR   85 (277)
Q Consensus        82 ~~~~   85 (277)
                      ....
T Consensus        90 ~~~~   93 (104)
T 1wex_A           90 SKRI   93 (104)
T ss_dssp             SSSC
T ss_pred             Cccc
Confidence            7554

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

Probab=99.82  E-value=3.9e-20  Score=129.99  Aligned_cols=82  Identities=34%  Similarity=0.555  Sum_probs=76.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .++++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|.+|+..||+..|.|+.|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   92 (103)
T 2cq0_A           13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   92 (103)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEC
Confidence            5689999999999999999999999999999999964   4677899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 023765           81 HGGRR   85 (277)
Q Consensus        81 ~~~~~   85 (277)
                      .....
T Consensus        93 ~~~~~   97 (103)
T 2cq0_A           93 KPSTN   97 (103)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            87553

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

Probab=99.82  E-value=9.6e-20  Score=128.93  Aligned_cols=82  Identities=24%  Similarity=0.445  Sum_probs=76.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec----CCCCCcEEEEEEcChHHHHHHHHhc-CCcccCCceEEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI----PPRPPGYAFLEFEDYRDAEDAIRGR-DGYNFDGYRLRVE   78 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~----~~~~~g~afV~f~~~~~a~~a~~~l-~~~~~~g~~i~v~   78 (277)
                      .++++|||+|||+.+|+++|+++|++||+|..|.|+.    ++.++|||||+|.+.++|.+|+..| |+..|.|+.|.|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~   92 (107)
T 2cph_A           13 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   92 (107)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEEE
Confidence            5789999999999999999999999999999999954    4677999999999999999999999 9999999999999


Q ss_pred             EccCCCC
Q 023765           79 LAHGGRR   85 (277)
Q Consensus        79 ~a~~~~~   85 (277)
                      ++.....
T Consensus        93 ~a~~~~~   99 (107)
T 2cph_A           93 WADSEVT   99 (107)
T ss_dssp             ECCCCCC
T ss_pred             eCCCCCC
Confidence            9987554

>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=99.82  E-value=2.3e-19  Score=126.02  Aligned_cols=79  Identities=20%  Similarity=0.418  Sum_probs=73.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      .++++|||+|||+++|+++|+++|++||.|..|.++     ++||||+|.+.++|.+|++.||+..|.|+.|.|.++...
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~-----~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   83 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-----KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPP   83 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC-----SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-----CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCC
Confidence            467999999999999999999999999999999987     679999999999999999999999999999999999876


Q ss_pred             CCCC
Q 023765           84 RRHS   87 (277)
Q Consensus        84 ~~~~   87 (277)
                      ....
T Consensus        84 ~~~~   87 (103)
T 2dgu_A           84 DQKR   87 (103)
T ss_dssp             CCCC
T ss_pred             cccc
Confidence            5443

>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=99.82  E-value=1.5e-19  Score=128.08  Aligned_cols=78  Identities=23%  Similarity=0.314  Sum_probs=73.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCC-----ceEEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDG-----YRLRVE   78 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g-----~~i~v~   78 (277)
                      ...++|||+|||+++|+++|+++|++||+|..|.|+.+    |||||+|.+.++|.+||+.||+..|.|     +.|.|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~----g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~   88 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   88 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT----TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC----CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEE
Confidence            56789999999999999999999999999999999865    899999999999999999999999999     999999


Q ss_pred             EccCCCC
Q 023765           79 LAHGGRR   85 (277)
Q Consensus        79 ~a~~~~~   85 (277)
                      ++.+...
T Consensus        89 ~a~~~~~   95 (108)
T 1x4c_A           89 VDGPRSP   95 (108)
T ss_dssp             ESSCCSC
T ss_pred             eCCCCCC
Confidence            9987543

>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=4.2e-19  Score=127.50  Aligned_cols=82  Identities=26%  Similarity=0.411  Sum_probs=75.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      ..+.++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|.+|+..|++ .|.|+.|.|.+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~   92 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   92 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEE
Confidence            35789999999999999999999999999999999965   467899999999999999999999998 89999999999


Q ss_pred             ccCCCC
Q 023765           80 AHGGRR   85 (277)
Q Consensus        80 a~~~~~   85 (277)
                      +.....
T Consensus        93 a~~~~~   98 (116)
T 2cqd_A           93 AYLGAK   98 (116)
T ss_dssp             STTTCC
T ss_pred             cccCCC
Confidence            986543

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

Probab=99.82  E-value=1.7e-19  Score=123.53  Aligned_cols=78  Identities=33%  Similarity=0.642  Sum_probs=73.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      ..+.++|||+|||+++|+++|+++|++||+|..|.++     ++||||+|.+.++|.+|+..||+..|.|+.|.|.++..
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   79 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-----KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKN   79 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-----TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-----CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCC
Confidence            4678999999999999999999999999999999998     78999999999999999999999999999999999987


Q ss_pred             CCC
Q 023765           83 GRR   85 (277)
Q Consensus        83 ~~~   85 (277)
                      ...
T Consensus        80 ~~~   82 (90)
T 2dnq_A           80 KSK   82 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            554

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

Probab=99.82  E-value=5.5e-20  Score=129.96  Aligned_cols=81  Identities=25%  Similarity=0.502  Sum_probs=74.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .++++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  100 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC  100 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEee
Confidence            4568899999999999999999999999999999965   4677899999999999999999999999999999999999


Q ss_pred             cCCC
Q 023765           81 HGGR   84 (277)
Q Consensus        81 ~~~~   84 (277)
                      ....
T Consensus       101 ~~~~  104 (106)
T 1p27_B          101 FVRG  104 (106)
T ss_dssp             EESS
T ss_pred             cCCC
Confidence            8643

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

Probab=99.81  E-value=1.9e-19  Score=123.72  Aligned_cols=78  Identities=36%  Similarity=0.635  Sum_probs=73.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      ..++++|||+|||+++|+++|+++|++||.|..|.++     ++||||+|.+.++|.+|+..||+..|.|+.|.|.++..
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~-----~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   81 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-----KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTS   81 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC-----SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE-----CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccC
Confidence            4678999999999999999999999999999999998     56999999999999999999999999999999999987


Q ss_pred             CCC
Q 023765           83 GRR   85 (277)
Q Consensus        83 ~~~   85 (277)
                      ...
T Consensus        82 ~~~   84 (92)
T 2dgt_A           82 RLR   84 (92)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            554

>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=99.81  E-value=2e-19  Score=128.16  Aligned_cols=82  Identities=21%  Similarity=0.438  Sum_probs=76.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcC------CcccCCce
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRD------GYNFDGYR   74 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~------~~~~~g~~   74 (277)
                      .+.++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|.+|+..||      +..|.|+.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~   92 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   92 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEE
Confidence            5688999999999999999999999999999999965   46789999999999999999999999      99999999


Q ss_pred             EEEEEccCCCC
Q 023765           75 LRVELAHGGRR   85 (277)
Q Consensus        75 i~v~~a~~~~~   85 (277)
                      |.|.++.+...
T Consensus        93 l~v~~a~~~~~  103 (111)
T 1x4h_A           93 LKVDLAVTRDE  103 (111)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEECCCCcc
Confidence            99999987544

>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=99.81  E-value=1.3e-19  Score=127.78  Aligned_cols=82  Identities=26%  Similarity=0.355  Sum_probs=75.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCC---ceEEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDG---YRLRVE   78 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g---~~i~v~   78 (277)
                      .++++|||+|||+++|+++|+++|++||.|..|.|+.  ++.++|||||+|.+.++|.+|+..||+..|.|   +.|.|.
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~   92 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVK   92 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEE
Confidence            4689999999999999999999999999999999965  45668999999999999999999999999998   999999


Q ss_pred             EccCCCC
Q 023765           79 LAHGGRR   85 (277)
Q Consensus        79 ~a~~~~~   85 (277)
                      ++.....
T Consensus        93 ~a~~~~~   99 (105)
T 2dnh_A           93 FADTDKE   99 (105)
T ss_dssp             ESCSSCC
T ss_pred             ECccCcc
Confidence            9987554

>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=99.81  E-value=8.7e-20  Score=130.85  Aligned_cols=82  Identities=20%  Similarity=0.426  Sum_probs=75.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+++|+++|+++|+.||.|..|.|+.   ++.++|||||+|.+.++|.+|+..||+..|.|+.|.|.++
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  102 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK  102 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            4668999999999999999999999999999999965   4677899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 023765           81 HGGRR   85 (277)
Q Consensus        81 ~~~~~   85 (277)
                      .....
T Consensus       103 ~~~~~  107 (115)
T 2cpz_A          103 RSKND  107 (115)
T ss_dssp             CCSCC
T ss_pred             CCCCc
Confidence            87554

>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=99.81  E-value=6.7e-20  Score=126.85  Aligned_cols=79  Identities=24%  Similarity=0.429  Sum_probs=73.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      .+.++|||+|||+.+++++|+++|++||+|..|.|+.  ++.++|||||+|.+.++|.+|++.||+..|.|+.|.|.++.
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   93 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS   93 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcC
Confidence            5678999999999999999999999999999999965  35668999999999999999999999999999999999986


Q ss_pred             C
Q 023765           82 G   82 (277)
Q Consensus        82 ~   82 (277)
                      .
T Consensus        94 ~   94 (95)
T 2ywk_A           94 S   94 (95)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.81  E-value=7.3e-20  Score=128.14  Aligned_cols=78  Identities=15%  Similarity=0.403  Sum_probs=72.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecC--CCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP--PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~--~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      .+.++|||+|||+++|+++|.++|++||+|..|.|+.+  +.++|||||+|.+.++|..|+. +++..|.|+.|.|.++.
T Consensus         9 ~~~~~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            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   87 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEch
Confidence            45689999999999999999999999999999999653  6789999999999999999999 99999999999999977


Q ss_pred             C
Q 023765           82 G   82 (277)
Q Consensus        82 ~   82 (277)
                      .
T Consensus        88 ~   88 (103)
T 1s79_A           88 D   88 (103)
T ss_dssp             H
T ss_pred             H
Confidence            5

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

Probab=99.81  E-value=6.6e-20  Score=126.89  Aligned_cols=79  Identities=34%  Similarity=0.549  Sum_probs=73.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .++++|||+|||+++|+++|+++|++||+|..|.++.   ++.++|||||+|.+.++|.+|+..||+..|.|+.|.|.++
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   92 (95)
T 2cqc_A           13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGP   92 (95)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            5678999999999999999999999999999999965   3567899999999999999999999999999999999998


Q ss_pred             cC
Q 023765           81 HG   82 (277)
Q Consensus        81 ~~   82 (277)
                      ..
T Consensus        93 ~~   94 (95)
T 2cqc_A           93 SS   94 (95)
T ss_dssp             SC
T ss_pred             CC
Confidence            74

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.81  E-value=8.5e-20  Score=129.13  Aligned_cols=79  Identities=18%  Similarity=0.192  Sum_probs=72.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccC-CeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYG-PIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G-~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      ...++|||+|||+++|+++|+++|++|| +|..+.+.. ..++|||||+|.+.++|++|++.|||..|.|+.|.|.++..
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~-~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~  104 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT-RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDN  104 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS-CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc-CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCC
Confidence            4567999999999999999999999999 999998853 35789999999999999999999999999999999999875


Q ss_pred             C
Q 023765           83 G   83 (277)
Q Consensus        83 ~   83 (277)
                      .
T Consensus       105 ~  105 (111)
T 2jvr_A          105 P  105 (111)
T ss_dssp             -
T ss_pred             C
Confidence            4

>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=99.81  E-value=1.7e-19  Score=125.30  Aligned_cols=78  Identities=27%  Similarity=0.503  Sum_probs=72.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccC--CceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFD--GYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~--g~~i~v~~a~   81 (277)
                      .++++|||+|||+++|+++|+++|++||+|..|.+...   ++||||+|.+.++|.+|++.||+..|.  |+.|.|.++.
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~   91 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG---DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAK   91 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS---SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC---CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECC
Confidence            57899999999999999999999999999999999753   789999999999999999999999999  9999999998


Q ss_pred             CCC
Q 023765           82 GGR   84 (277)
Q Consensus        82 ~~~   84 (277)
                      +..
T Consensus        92 ~~~   94 (97)
T 1why_A           92 SGP   94 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.81  E-value=1.3e-19  Score=127.47  Aligned_cols=80  Identities=25%  Similarity=0.449  Sum_probs=73.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecC----CCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP----PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~----~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      .+.++|||+|||+++|+++|+++|++|| |..|.|+.+    +.++|||||+|.+.++|.+|+ .||+..|.|+.|.|.+
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            5779999999999999999999999999 999999654    677999999999999999999 8999999999999999


Q ss_pred             ccCCCC
Q 023765           80 AHGGRR   85 (277)
Q Consensus        80 a~~~~~   85 (277)
                      +.....
T Consensus        91 a~~~~~   96 (104)
T 1wi8_A           91 ADQAQD   96 (104)
T ss_dssp             CCCCCC
T ss_pred             ccCCCC
Confidence            987553

>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=99.81  E-value=1.4e-20  Score=128.96  Aligned_cols=79  Identities=16%  Similarity=0.198  Sum_probs=67.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccC--CeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYG--PIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G--~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      .+|||+|||+++|+++|+++|++||  .|..+.++.   ++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.++.
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  999999855   56789999999999999999999999999999999999998


Q ss_pred             CCCC
Q 023765           82 GGRR   85 (277)
Q Consensus        82 ~~~~   85 (277)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            7543

>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=99.81  E-value=1.6e-19  Score=127.55  Aligned_cols=83  Identities=19%  Similarity=0.339  Sum_probs=76.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCccc---CCceEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNF---DGYRLR   76 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~---~g~~i~   76 (277)
                      ..+.++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|.+|+..||+..+   .|+.|.
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            35789999999999999999999999999999999965   467899999999999999999999999987   899999


Q ss_pred             EEEccCCCC
Q 023765           77 VELAHGGRR   85 (277)
Q Consensus        77 v~~a~~~~~   85 (277)
                      |.++.....
T Consensus        90 v~~a~~~~~   98 (106)
T 2dgp_A           90 VKPADSESR   98 (106)
T ss_dssp             EEECCCCSC
T ss_pred             EEECCcccc
Confidence            999987553

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

Probab=99.81  E-value=1.6e-19  Score=123.60  Aligned_cols=77  Identities=30%  Similarity=0.568  Sum_probs=72.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      .+.++|||+|||+++|+++|+++|++||.|..|.++     ++||||+|.+.++|..|+..||+..|.|+.|.|.++...
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~-----~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   81 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-----KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKG   81 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC-----SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCC
Confidence            578999999999999999999999999999999998     569999999999999999999999999999999999876


Q ss_pred             CC
Q 023765           84 RR   85 (277)
Q Consensus        84 ~~   85 (277)
                      ..
T Consensus        82 ~~   83 (90)
T 2dnp_A           82 QK   83 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.81  E-value=8.3e-20  Score=133.34  Aligned_cols=81  Identities=35%  Similarity=0.575  Sum_probs=75.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .++++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|.+|+..||+..|.|+.|.|.++
T Consensus        44 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a  123 (129)
T 2kxn_B           44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS  123 (129)
T ss_dssp             CCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            5788999999999999999999999999999999965   4678999999999999999999999999999999999999


Q ss_pred             cCCC
Q 023765           81 HGGR   84 (277)
Q Consensus        81 ~~~~   84 (277)
                      ....
T Consensus       124 ~~~~  127 (129)
T 2kxn_B          124 ITKR  127 (129)
T ss_dssp             SSSS
T ss_pred             cCCC
Confidence            8654

>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=99.81  E-value=1.3e-19  Score=128.90  Aligned_cols=81  Identities=23%  Similarity=0.417  Sum_probs=74.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .++++|||+|||+.+|+++|+++|++||.|..|.|+.   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  103 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC  103 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEc
Confidence            4678899999999999999999999999999999964   5677999999999999999999999999999999999999


Q ss_pred             cCCC
Q 023765           81 HGGR   84 (277)
Q Consensus        81 ~~~~   84 (277)
                      ....
T Consensus       104 ~~~~  107 (110)
T 1oo0_B          104 FVKG  107 (110)
T ss_dssp             EESS
T ss_pred             ccCC
Confidence            8644

>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=99.81  E-value=2.4e-19  Score=122.44  Aligned_cols=79  Identities=25%  Similarity=0.487  Sum_probs=73.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      +.++|||+|||+++|+++|+++|++||+|..+.++.   ++.++|||||+|.+.++|.+|+ .||+..|.|+.|.|.++.
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            468999999999999999999999999999999954   5678999999999999999999 899999999999999988


Q ss_pred             CCC
Q 023765           82 GGR   84 (277)
Q Consensus        82 ~~~   84 (277)
                      ...
T Consensus        84 ~~~   86 (89)
T 3ucg_A           84 TNR   86 (89)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            643

>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=99.80  E-value=1.4e-19  Score=128.06  Aligned_cols=78  Identities=24%  Similarity=0.404  Sum_probs=73.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      .++++|||+|||+.+|+++|+++|++||.|..|.|+.  ++.++|||||+|.+.++|.+|+..||+..|.|+.|.|.++.
T Consensus        27 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            4688999999999999999999999999999999964  56778999999999999999999999999999999999975

>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=99.80  E-value=6.2e-20  Score=130.68  Aligned_cols=81  Identities=22%  Similarity=0.287  Sum_probs=74.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH---HHhhccCCeeEEEeecCC------CCCcEEEEEEcChHHHHHHHHhcCCcccCCce
Q 023765            4 RSSRTLYVGNLPGDTRMREVE---DLFYKYGPIVDIDLKIPP------RPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYR   74 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~---~~F~~~G~v~~v~~~~~~------~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~   74 (277)
                      ...++|||+|||+++++++|.   ++|++||+|..|.|+.+.      .++|||||+|.+.++|.+|++.||+..|.|+.
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            467899999999999999999   999999999999996532      45699999999999999999999999999999


Q ss_pred             EEEEEccCCC
Q 023765           75 LRVELAHGGR   84 (277)
Q Consensus        75 i~v~~a~~~~   84 (277)
                      |.|.++....
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            9999998754

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

Probab=99.80  E-value=3.3e-20  Score=129.51  Aligned_cols=79  Identities=24%  Similarity=0.378  Sum_probs=73.6

Q ss_pred             CCCCeEEEcCCCC------CCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCC-c
Q 023765            4 RSSRTLYVGNLPG------DTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDG-Y   73 (277)
Q Consensus         4 ~~~~~l~V~nL~~------~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g-~   73 (277)
                      ..+++|||+|||+      ++++++|.++|++||+|..|.|+.   ++.++|||||+|.+.++|.+|++.|||..|.| +
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            4578999999999      999999999999999999999964   47789999999999999999999999999999 9


Q ss_pred             eEEEEEccC
Q 023765           74 RLRVELAHG   82 (277)
Q Consensus        74 ~i~v~~a~~   82 (277)
                      .|.|.++.+
T Consensus        84 ~l~V~~a~~   92 (100)
T 3ns6_A           84 RLFLYTMKD   92 (100)
T ss_dssp             BCEEEESHH
T ss_pred             EEEEEECch
Confidence            999999875

>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=99.80  E-value=1.6e-19  Score=131.64  Aligned_cols=83  Identities=24%  Similarity=0.482  Sum_probs=76.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .++++|||+|||+.+|+++|+++|++||.|..|.|+.   ++.++|||||+|.+.++|.+|++.||+..|.|+.|.|.++
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   99 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC   99 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEe
Confidence            4678999999999999999999999999999999954   5677999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 023765           81 HGGRRH   86 (277)
Q Consensus        81 ~~~~~~   86 (277)
                      ......
T Consensus       100 ~~~~~~  105 (126)
T 3ex7_B          100 FVRGPP  105 (126)
T ss_dssp             EESSSC
T ss_pred             cCCCCC
Confidence            865543

>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=99.80  E-value=1e-19  Score=128.35  Aligned_cols=80  Identities=25%  Similarity=0.283  Sum_probs=72.1

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcC--CcccCCceEEEEE
Q 023765            3 SRSSRTLYVGNLPGD-TRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRD--GYNFDGYRLRVEL   79 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~-~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~--~~~~~g~~i~v~~   79 (277)
                      ..++++|||+|||++ +|+++|+++|++||+|..|.|+.   .+|||||+|.+.++|..|+..|+  +..|.|+.|.|.+
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~---~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~   98 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR---MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDL   98 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET---TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec---CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            467899999999998 99999999999999999999973   48999999999999999999885  4669999999999


Q ss_pred             ccCCCC
Q 023765           80 AHGGRR   85 (277)
Q Consensus        80 a~~~~~   85 (277)
                      +.....
T Consensus        99 a~~~~~  104 (112)
T 1x4f_A           99 SEKYKK  104 (112)
T ss_dssp             ECSCSS
T ss_pred             Cccccc
Confidence            986543

>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=99.80  E-value=1.3e-19  Score=128.32  Aligned_cols=81  Identities=27%  Similarity=0.479  Sum_probs=74.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      ..++++|||+|||+.+|+++|+++|++||+|..|.++.   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.+
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  102 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGH  102 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            35788999999999999999999999999999999964   467789999999999999999999999999999999999


Q ss_pred             ccCC
Q 023765           80 AHGG   83 (277)
Q Consensus        80 a~~~   83 (277)
                      +.+.
T Consensus       103 a~~k  106 (108)
T 2jrs_A          103 VTER  106 (108)
T ss_dssp             SCSS
T ss_pred             cccC
Confidence            8754

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

Probab=99.80  E-value=1.8e-19  Score=127.79  Aligned_cols=80  Identities=25%  Similarity=0.468  Sum_probs=74.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecC-CCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP-PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~-~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      .+.++|||+|||+++|+++|+++|++||+|..|.|..+ +.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++..
T Consensus        27 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  106 (109)
T 2err_A           27 SQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA  106 (109)
T ss_dssp             TCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            57899999999999999999999999999999999653 45789999999999999999999999999999999999875


Q ss_pred             C
Q 023765           83 G   83 (277)
Q Consensus        83 ~   83 (277)
                      .
T Consensus       107 ~  107 (109)
T 2err_A          107 R  107 (109)
T ss_dssp             S
T ss_pred             C
Confidence            4

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

Probab=99.80  E-value=2.3e-19  Score=126.44  Aligned_cols=80  Identities=28%  Similarity=0.422  Sum_probs=73.7

Q ss_pred             CCCCeEEEcCCCCCC------CHHHHHHHhhccCCeeEEEeec-CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCc-eE
Q 023765            4 RSSRTLYVGNLPGDT------RMREVEDLFYKYGPIVDIDLKI-PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGY-RL   75 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~------t~~~l~~~F~~~G~v~~v~~~~-~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~-~i   75 (277)
                      ..+++|||+|||+.+      |+++|+++|++||+|..|.|+. ++.++|||||+|.+.++|..|+..|||..|.|+ .|
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l   92 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   92 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEE
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceE
Confidence            357899999999999      7899999999999999999963 678899999999999999999999999999999 99


Q ss_pred             EEEEccCC
Q 023765           76 RVELAHGG   83 (277)
Q Consensus        76 ~v~~a~~~   83 (277)
                      .|.++...
T Consensus        93 ~V~~a~~~  100 (105)
T 2nlw_A           93 RVNLFTDF  100 (105)
T ss_dssp             EEECSCCC
T ss_pred             EEEEcchH
Confidence            99998754

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

Probab=99.80  E-value=1.8e-19  Score=129.83  Aligned_cols=78  Identities=21%  Similarity=0.454  Sum_probs=72.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|..|++.|||..|.|+.|.|.++
T Consensus        38 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a  117 (118)
T 2khc_A           38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK  117 (118)
T ss_dssp             CCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            5678999999999999999999999999999999964   4678999999999999999999999999999999999987


Q ss_pred             c
Q 023765           81 H   81 (277)
Q Consensus        81 ~   81 (277)
                      +
T Consensus       118 k  118 (118)
T 2khc_A          118 K  118 (118)
T ss_dssp             -
T ss_pred             C
Confidence            4

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

Probab=99.80  E-value=1.6e-19  Score=125.85  Aligned_cols=78  Identities=29%  Similarity=0.435  Sum_probs=72.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeE--------EEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVD--------IDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDG   72 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~--------v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g   72 (277)
                      .+.++|||+|||+++|+++|+++|++||.|..        +.+..   ++.++|||||+|.+.++|..|++.|||..|.|
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g   90 (99)
T 2la6_A           11 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   90 (99)
T ss_dssp             CCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            57899999999999999999999999999999        88854   46778999999999999999999999999999


Q ss_pred             ceEEEEEcc
Q 023765           73 YRLRVELAH   81 (277)
Q Consensus        73 ~~i~v~~a~   81 (277)
                      +.|.|.+|+
T Consensus        91 ~~l~V~~A~   99 (99)
T 2la6_A           91 NPIKVSFAT   99 (99)
T ss_dssp             SBCEEEECC
T ss_pred             cEEEEEecC
Confidence            999999974

>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=99.80  E-value=5e-19  Score=125.63  Aligned_cols=79  Identities=20%  Similarity=0.379  Sum_probs=73.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      .+.++|||+|||+.+|+++|+++|++||.|..|.|+.+   +|||||+|.+.++|..|+..||+..|.|+.|.|.++...
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~---~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   99 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE---KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   99 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC---CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCC
Confidence            46789999999999999999999999999999999865   899999999999999999999999999999999999875


Q ss_pred             CC
Q 023765           84 RR   85 (277)
Q Consensus        84 ~~   85 (277)
                      ..
T Consensus       100 ~~  101 (109)
T 1x4g_A          100 PD  101 (109)
T ss_dssp             CS
T ss_pred             CC
Confidence            53

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

Probab=99.80  E-value=3.6e-19  Score=125.01  Aligned_cols=81  Identities=27%  Similarity=0.520  Sum_probs=73.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      ..+.++|||+|||+++|+++|+++|++|| |..|.|+.   ++.++|||||+|.+.++|.+|+ .||+..|.|+.|.|.+
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            36788999999999999999999999997 99999965   4677899999999999999999 7999999999999999


Q ss_pred             ccCCCC
Q 023765           80 AHGGRR   85 (277)
Q Consensus        80 a~~~~~   85 (277)
                      +.....
T Consensus        90 a~~~~~   95 (103)
T 2dng_A           90 AEGRKQ   95 (103)
T ss_dssp             CCCCCC
T ss_pred             ecCCCC
Confidence            987543

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

Probab=99.80  E-value=3e-19  Score=127.62  Aligned_cols=82  Identities=27%  Similarity=0.468  Sum_probs=75.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCee--------EEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIV--------DIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDG   72 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~--------~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g   72 (277)
                      .+.++|||+|||+++|+++|+++|++||.|.        .|.|+.   ++.++|||||+|.+.++|.+|++.||+..|.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   92 (113)
T 2cpe_A           13 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   92 (113)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccCC
Confidence            5789999999999999999999999999999        588854   46789999999999999999999999999999


Q ss_pred             ceEEEEEccCCCC
Q 023765           73 YRLRVELAHGGRR   85 (277)
Q Consensus        73 ~~i~v~~a~~~~~   85 (277)
                      +.|.|.++.....
T Consensus        93 ~~l~V~~a~~~~~  105 (113)
T 2cpe_A           93 SKLKVSLARKKPP  105 (113)
T ss_dssp             EECEEECSSCCCC
T ss_pred             CEEEEEECCCCCC
Confidence            9999999987554

>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=99.80  E-value=2.8e-19  Score=124.70  Aligned_cols=79  Identities=32%  Similarity=0.457  Sum_probs=73.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      .+.++|||+|||+.+|+++|+++|++||+|..|.++.+   +|||||+|.+.++|.+|++.||+..|.|+.|.|.++...
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~---kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   89 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD---KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS   89 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT---TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC---CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCC
Confidence            46789999999999999999999999999999999843   799999999999999999999999999999999999875


Q ss_pred             CC
Q 023765           84 RR   85 (277)
Q Consensus        84 ~~   85 (277)
                      ..
T Consensus        90 ~~   91 (99)
T 2cpj_A           90 AS   91 (99)
T ss_dssp             SC
T ss_pred             CC
Confidence            43

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

Probab=99.80  E-value=2.9e-19  Score=125.77  Aligned_cols=83  Identities=22%  Similarity=0.331  Sum_probs=76.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhc-cCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcc-cCCceEEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYK-YGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYN-FDGYRLRVE   78 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~-~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~-~~g~~i~v~   78 (277)
                      ..++++|||+|||+++|+++|+++|++ ||.|..|.|+.  ++.++|||||+|.+.++|.+|+..||+.. |.|+.|.|.
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~   85 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            357899999999999999999999999 99999999965  56778999999999999999999999999 999999999


Q ss_pred             EccCCCC
Q 023765           79 LAHGGRR   85 (277)
Q Consensus        79 ~a~~~~~   85 (277)
                      ++.....
T Consensus        86 ~a~~~~~   92 (104)
T 2dhg_A           86 VAIPKAS   92 (104)
T ss_dssp             BCCCCCS
T ss_pred             EccCCCc
Confidence            9976543

>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=99.80  E-value=7.3e-19  Score=124.78  Aligned_cols=83  Identities=23%  Similarity=0.316  Sum_probs=75.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCC-eeEEEee-c---CCCCCcEEEEEEcChHHHHHHHHhcC--CcccCCceE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGP-IVDIDLK-I---PPRPPGYAFLEFEDYRDAEDAIRGRD--GYNFDGYRL   75 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~-v~~v~~~-~---~~~~~g~afV~f~~~~~a~~a~~~l~--~~~~~g~~i   75 (277)
                      +.+.++|||+|||+++|+++|+++|++||. |..|.++ .   ++.++|||||+|.+.++|..|+..||  +..|.|+.|
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            467899999999999999999999999998 9999996 3   34789999999999999999999996  589999999


Q ss_pred             EEEEccCCCC
Q 023765           76 RVELAHGGRR   85 (277)
Q Consensus        76 ~v~~a~~~~~   85 (277)
                      .|.++.+...
T Consensus        85 ~V~~a~~~~~   94 (109)
T 2dis_A           85 AVDWAEPEID   94 (109)
T ss_dssp             EEEESCSSCS
T ss_pred             EEEEcCCCCC
Confidence            9999987554

>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=4.1e-19  Score=120.79  Aligned_cols=77  Identities=27%  Similarity=0.551  Sum_probs=70.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      ..+.++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|.+|++ +++..|.|+.|.|.+
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEe
Confidence            36789999999999999999999999999999999964   46778999999999999999997 688899999999987


Q ss_pred             c
Q 023765           80 A   80 (277)
Q Consensus        80 a   80 (277)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.80  E-value=1.1e-19  Score=121.82  Aligned_cols=72  Identities=29%  Similarity=0.494  Sum_probs=66.8

Q ss_pred             CCeEEEcCCCCCC------CHHHHHHHhhccCCeeEEEeec-CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCc-eEEE
Q 023765            6 SRTLYVGNLPGDT------RMREVEDLFYKYGPIVDIDLKI-PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGY-RLRV   77 (277)
Q Consensus         6 ~~~l~V~nL~~~~------t~~~l~~~F~~~G~v~~v~~~~-~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~-~i~v   77 (277)
                      +++|||+|||+.+      |+++|+++|++||+|..|.|+. ++.++|||||+|.+.++|.+|+..|||..|.|+ .|.|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            4799999999999      7799999999999999999863 678899999999999999999999999999999 8875

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

Probab=99.80  E-value=2.6e-19  Score=126.65  Aligned_cols=77  Identities=29%  Similarity=0.510  Sum_probs=72.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      ..++++|||+|||+++|+++|+++|++||.|..|.+.     +|||||+|.+.++|.+|+..|||..|.|+.|.|.++..
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-----kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  102 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-----NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKL  102 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-----TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-----CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecC
Confidence            3578999999999999999999999999999999998     79999999999999999999999999999999999886


Q ss_pred             CC
Q 023765           83 GR   84 (277)
Q Consensus        83 ~~   84 (277)
                      ..
T Consensus       103 ~~  104 (108)
T 2jvo_A          103 PA  104 (108)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.80  E-value=4.4e-19  Score=123.02  Aligned_cols=75  Identities=25%  Similarity=0.503  Sum_probs=71.2

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            4 RSSRTLYVGNLPG-DTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         4 ~~~~~l~V~nL~~-~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      .++++|||+|||+ ++++++|+++|++||.|..|.+.     +|||||+|.+.++|.+|+..|||..|.|+.|.|.++..
T Consensus        20 ~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~-----~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   94 (97)
T 2xnq_A           20 HMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-----NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSS   94 (97)
T ss_dssp             CTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC-----SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-----CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCC
Confidence            5789999999998 99999999999999999999995     89999999999999999999999999999999999875


Q ss_pred             C
Q 023765           83 G   83 (277)
Q Consensus        83 ~   83 (277)
                      .
T Consensus        95 ~   95 (97)
T 2xnq_A           95 N   95 (97)
T ss_dssp             C
T ss_pred             C
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=99.80  E-value=3.5e-19  Score=125.64  Aligned_cols=80  Identities=15%  Similarity=0.228  Sum_probs=72.2

Q ss_pred             CCCCCCeEEE--cCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCccc-----CCce
Q 023765            2 SSRSSRTLYV--GNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNF-----DGYR   74 (277)
Q Consensus         2 ~~~~~~~l~V--~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~-----~g~~   74 (277)
                      ...++++|||  +||++++|+++|+++|++||+|..|.|+.   .+|||||+|.+.++|.+|++.|||..|     .|++
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~---~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~   97 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP---NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT   97 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT---TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEE
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC---CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcE
Confidence            4568999999  77999999999999999999999998864   379999999999999999999999988     6889


Q ss_pred             EEEEEccCCC
Q 023765           75 LRVELAHGGR   84 (277)
Q Consensus        75 i~v~~a~~~~   84 (277)
                      |.|.++..-.
T Consensus        98 l~v~~a~~~p  107 (114)
T 2cq2_A           98 LYLNFVEKVQ  107 (114)
T ss_dssp             CEEEEESCCC
T ss_pred             EEEEecccCc
Confidence            9999988543

>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=99.80  E-value=3.6e-19  Score=127.63  Aligned_cols=81  Identities=23%  Similarity=0.414  Sum_probs=73.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCe----eEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPI----VDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v----~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      .++++|||+|||+++|+++|+++|++||.|    ..+.+. ++.++|||||+|.+.++|..|+..||+..|.|+.|.|.+
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~-~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM-TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE-CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC-CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            467999999999999999999999999998    555555 778899999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 023765           80 AHGGRR   85 (277)
Q Consensus        80 a~~~~~   85 (277)
                      +.....
T Consensus       102 a~~~~~  107 (115)
T 2cpx_A          102 GKNKKQ  107 (115)
T ss_dssp             CCCCSC
T ss_pred             ccCCCC
Confidence            987654

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=2.8e-19  Score=125.11  Aligned_cols=81  Identities=26%  Similarity=0.393  Sum_probs=71.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      .++++|||+|||+++|+++|+++|++||.|.-+ ...++.++|||||+|.+.++|.+|+..||+..|.|+.|.|.++...
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~-~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   91 (101)
T 2fc9_A           13 GESKTLVLSNLSYSATEETLQEVFEKATFIKVP-QNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPR   91 (101)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHCSSCSEEECC-BCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCEEEEE-ECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCC
Confidence            578999999999999999999999999988322 2246778999999999999999999999999999999999999875


Q ss_pred             CC
Q 023765           84 RR   85 (277)
Q Consensus        84 ~~   85 (277)
                      ..
T Consensus        92 ~~   93 (101)
T 2fc9_A           92 GS   93 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

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

Probab=99.79  E-value=6.9e-19  Score=127.88  Aligned_cols=83  Identities=23%  Similarity=0.350  Sum_probs=76.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      .++++|||+|||+.+++++|+++|++||+|..|.|..  ++.++|||||+|.+.++|..|+..||+..|.|+.|.|.++.
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  112 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  112 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeC
Confidence            5678999999999999999999999999999999965  56778999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 023765           82 GGRRH   86 (277)
Q Consensus        82 ~~~~~   86 (277)
                      .....
T Consensus       113 ~~~~~  117 (124)
T 2kt5_A          113 SQIDL  117 (124)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            75543

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

Probab=99.79  E-value=2.4e-19  Score=124.25  Aligned_cols=78  Identities=26%  Similarity=0.490  Sum_probs=72.1

Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            3 SRSSRTLYVGNLPG-DTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         3 ~~~~~~l~V~nL~~-~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      ..++++|||+|||+ .+|+++|+++|++||+|..|.+.     +|||||+|.+.++|..|+..||+..|.|+.|.|.++.
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   81 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-----NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSS   81 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-----TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-----CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcC
Confidence            36789999999998 99999999999999999999996     7999999999999999999999999999999999998


Q ss_pred             CCCC
Q 023765           82 GGRR   85 (277)
Q Consensus        82 ~~~~   85 (277)
                      ....
T Consensus        82 ~~~~   85 (96)
T 2kvi_A           82 SNAR   85 (96)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            6543

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

Probab=99.79  E-value=9.4e-19  Score=121.96  Aligned_cols=77  Identities=30%  Similarity=0.439  Sum_probs=72.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhcc--CCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKY--GPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~--G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      .++++|||+|||+++|+++|+++|++|  |.|..|.+.     ++||||+|.+.++|.+|+..||+..|.|+.|.|.++.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   87 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-----RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   87 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-----SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe-----CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            468899999999999999999999999  999999876     7899999999999999999999999999999999998


Q ss_pred             CCCC
Q 023765           82 GGRR   85 (277)
Q Consensus        82 ~~~~   85 (277)
                      +...
T Consensus        88 ~~~~   91 (99)
T 2cpd_A           88 PVDK   91 (99)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7543

>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=99.79  E-value=1.7e-19  Score=129.12  Aligned_cols=79  Identities=54%  Similarity=1.006  Sum_probs=66.9

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeeccccee-eEEEEee
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR-SYVRVRE  185 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~-~~i~~~~  185 (277)
                      ...++|||+|||..+++++|+++|.+||+|..|.|+.+   +||||+|.+.++|++||+.|||..++|+.+. ..|.+..
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~   90 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   90 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT---SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC---CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEecc
Confidence            45789999999999999999999999999999999877   7999999999999999999999999996532 2456666


Q ss_pred             cCC
Q 023765          186 YDS  188 (277)
Q Consensus       186 ~~~  188 (277)
                      ..+
T Consensus        91 ~~~   93 (115)
T 3beg_B           91 DGP   93 (115)
T ss_dssp             CC-
T ss_pred             CCC
Confidence            543

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

Probab=99.79  E-value=7.8e-19  Score=130.20  Aligned_cols=83  Identities=31%  Similarity=0.587  Sum_probs=76.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+++|+++|+++|+.||+|..|.|+.   ++.++|||||+|.+.++|.+|+..||+..|.|+.|.|.++
T Consensus        40 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  119 (139)
T 1u6f_A           40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            5678999999999999999999999999999999964   4567899999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 023765           81 HGGRRH   86 (277)
Q Consensus        81 ~~~~~~   86 (277)
                      ......
T Consensus       120 ~~~~~~  125 (139)
T 1u6f_A          120 ASGHQR  125 (139)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            876543

>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=99.79  E-value=4.4e-19  Score=120.09  Aligned_cols=75  Identities=28%  Similarity=0.464  Sum_probs=70.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhc-CCcccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGR-DGYNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l-~~~~~~g~~i~v~~a~   81 (277)
                      .+.++|||+|||+++|+++|+++|++||+|..|.++.   .+|||||+|.+.++|..|+..| ++..|.|+.|.|.+++
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~---~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ---RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG---GGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC---CCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            5678999999999999999999999999999999985   3799999999999999999988 9999999999999974

>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=8.4e-19  Score=124.32  Aligned_cols=80  Identities=18%  Similarity=0.356  Sum_probs=71.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+++|+++|+++|+.||+|..|.|+.   ++.++|||||+|.+.++|.+|+..+ +..|.|+.|.|.++
T Consensus        23 ~~~~~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           23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKVA  101 (109)
T ss_dssp             ---CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEEc
Confidence            5788999999999999999999999999999999965   4778999999999999999999966 59999999999999


Q ss_pred             cCCC
Q 023765           81 HGGR   84 (277)
Q Consensus        81 ~~~~   84 (277)
                      ....
T Consensus       102 ~~~~  105 (109)
T 2rs2_A          102 FPRR  105 (109)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8654

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

Probab=99.79  E-value=3.4e-19  Score=134.25  Aligned_cols=78  Identities=17%  Similarity=0.244  Sum_probs=72.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccC--CeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYG--PIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G--~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      ..++|||+|||+++|+++|+++|+.||  .|..|.|+.   ++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.+
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  999999954   577899999999999999999999999999999999999


Q ss_pred             ccC
Q 023765           80 AHG   82 (277)
Q Consensus        80 a~~   82 (277)
                      +..
T Consensus       134 a~~  136 (156)
T 3n9u_C          134 ATR  136 (156)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            874

>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=99.79  E-value=3.1e-19  Score=126.96  Aligned_cols=78  Identities=27%  Similarity=0.303  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      ++.++|||+|||+++|+++|+++|++||.|..|.|+.   .++||||+|.+.++|..|+..|||..|.|+.|.|.|+...
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~---~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   84 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE---GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS---SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC---CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            3567999999999999999999999999999999874   5789999999999999999999999999999999999864


Q ss_pred             C
Q 023765           84 R   84 (277)
Q Consensus        84 ~   84 (277)
                      .
T Consensus        85 ~   85 (111)
T 1whx_A           85 V   85 (111)
T ss_dssp             T
T ss_pred             c
Confidence            3

>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=99.79  E-value=6.1e-19  Score=133.39  Aligned_cols=82  Identities=33%  Similarity=0.474  Sum_probs=75.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .++++|||+|||+.+|+++|+++|++||+|..|.|+.   ++.+++||||+|.+.++|.+|+..||+..|.|+.|.|.++
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            4679999999999999999999999999999999965   4567899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 023765           81 HGGRR   85 (277)
Q Consensus        81 ~~~~~   85 (277)
                      .+...
T Consensus       117 ~~~~~  121 (156)
T 1h2v_Z          117 AGFKE  121 (156)
T ss_dssp             SCCCT
T ss_pred             CCCCC
Confidence            87543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=3.7e-19  Score=123.54  Aligned_cols=79  Identities=30%  Similarity=0.487  Sum_probs=71.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      ..+++|||+|||+++|+++|+++|++||.|. +.++ ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+.
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   94 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLT-WQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ   94 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEE-EETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEE-cCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCC
Confidence            3478999999999999999999999999996 5554 3467899999999999999999999999999999999999865


Q ss_pred             C
Q 023765           84 R   84 (277)
Q Consensus        84 ~   84 (277)
                      .
T Consensus        95 ~   95 (97)
T 2e5j_A           95 R   95 (97)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.79  E-value=2.6e-19  Score=118.23  Aligned_cols=72  Identities=22%  Similarity=0.376  Sum_probs=67.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            8 TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         8 ~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      +|||+|||+++|+++|+++|++||+|..+.++.   ++.++|||||+|.++++|.+|++ ||+..|.|+.|.|.+|
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            599999999999999999999999999999964   56788999999999999999998 9999999999999875

>2dh8_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=2.7e-19  Score=126.18  Aligned_cols=82  Identities=20%  Similarity=0.338  Sum_probs=75.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      ..+.++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|.+|+.. ++..|.|+.|.|.+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKP   91 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEE
Confidence            36789999999999999999999999999999999965   457789999999999999999997 99999999999999


Q ss_pred             ccCCCC
Q 023765           80 AHGGRR   85 (277)
Q Consensus        80 a~~~~~   85 (277)
                      +.+...
T Consensus        92 a~~~~~   97 (105)
T 2dh8_A           92 CTPRGM   97 (105)
T ss_dssp             SCCSSC
T ss_pred             ccCCCC
Confidence            986554

>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=99.79  E-value=3.3e-19  Score=125.46  Aligned_cols=80  Identities=35%  Similarity=0.673  Sum_probs=74.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      +.++|||+|||+.+++++|+++|++||.|..|.++.   ++.++|||||+|.+.++|..|++.|||..|.|+.|.|.++.
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            568999999999999999999999999999999964   56678999999999999999999999999999999999988


Q ss_pred             CCC
Q 023765           82 GGR   84 (277)
Q Consensus        82 ~~~   84 (277)
                      ...
T Consensus        87 ~~~   89 (104)
T 1p1t_A           87 SEK   89 (104)
T ss_dssp             CTT
T ss_pred             Ccc
Confidence            644

>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=99.79  E-value=1.7e-19  Score=125.49  Aligned_cols=80  Identities=23%  Similarity=0.325  Sum_probs=71.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEee---cCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLK---IPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~---~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      ...++|||+|||+++|+++|+++|++||.|..+.++   .++.++|||||+|.+.++|.+|+..||+..|.|+.|.|.++
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            456889999999999999999999999999865553   35677899999999999999999999999999999999998


Q ss_pred             cCC
Q 023765           81 HGG   83 (277)
Q Consensus        81 ~~~   83 (277)
                      ..+
T Consensus        93 ~~~   95 (98)
T 2cqp_A           93 SGP   95 (98)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            753

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

Probab=99.78  E-value=3.3e-19  Score=124.80  Aligned_cols=76  Identities=24%  Similarity=0.428  Sum_probs=71.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      ...++|||+|||+++++++|+++|++||.|..|.+.   .++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~---~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY---PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe---cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            347899999999999999999999999999999997   4589999999999999999999999999999999999874

>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=99.78  E-value=5.8e-19  Score=121.59  Aligned_cols=79  Identities=25%  Similarity=0.379  Sum_probs=71.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCC-eeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCC-cccCCceEEEEEc
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGP-IVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDG-YNFDGYRLRVELA   80 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~-v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~-~~~~g~~i~v~~a   80 (277)
                      ..+.++|||+|||+++|+++|+++|++||. |..+.+.    ++|||||+|.+.++|.+|++.||+ ..|.|+.|.|.++
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a   80 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL----KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYS   80 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE----ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc----CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEc
Confidence            467899999999999999999999999999 7766664    379999999999999999999999 9999999999999


Q ss_pred             cCCCC
Q 023765           81 HGGRR   85 (277)
Q Consensus        81 ~~~~~   85 (277)
                      .+...
T Consensus        81 ~~~~~   85 (93)
T 2cqh_A           81 VSKKL   85 (93)
T ss_dssp             CCCCC
T ss_pred             cCccc
Confidence            86543

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

Probab=99.78  E-value=9.5e-20  Score=123.38  Aligned_cols=79  Identities=22%  Similarity=0.333  Sum_probs=72.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      ..++++|||+|||+++++++|+++|++||+|..+.|+.   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.+
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~   81 (85)
T 1x4e_A            2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSG   81 (85)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecC
Confidence            35789999999999999999999999999999999965   467899999999999999999999999999999988766


Q ss_pred             cc
Q 023765           80 AH   81 (277)
Q Consensus        80 a~   81 (277)
                      +.
T Consensus        82 ~~   83 (85)
T 1x4e_A           82 PS   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

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

Probab=99.78  E-value=3.4e-19  Score=131.20  Aligned_cols=83  Identities=37%  Similarity=0.556  Sum_probs=76.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .++++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|.+|+..||+..|.|+.|.|.++
T Consensus        45 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a  124 (135)
T 2lea_A           45 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  124 (135)
T ss_dssp             GGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4578999999999999999999999999999999964   5678999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 023765           81 HGGRRH   86 (277)
Q Consensus        81 ~~~~~~   86 (277)
                      ......
T Consensus       125 ~~~~~~  130 (135)
T 2lea_A          125 RYGRPP  130 (135)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876543

>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=99.78  E-value=5.6e-19  Score=126.41  Aligned_cols=78  Identities=27%  Similarity=0.458  Sum_probs=72.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      +.++|||+|||+++|+++|+++|++||.|..|.|+.   ++.++|||||+|.+.++|.+|+ .||+..|.|+.|.|.++.
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            457999999999999999999999999999999964   4678999999999999999999 899999999999999987


Q ss_pred             CC
Q 023765           82 GG   83 (277)
Q Consensus        82 ~~   83 (277)
                      ..
T Consensus       103 ~~  104 (114)
T 2cq4_A          103 AE  104 (114)
T ss_dssp             HH
T ss_pred             CC
Confidence            53

>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=99.78  E-value=1.3e-18  Score=131.85  Aligned_cols=83  Identities=37%  Similarity=0.556  Sum_probs=76.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  147 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  147 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            3478999999999999999999999999999999965   5788999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 023765           81 HGGRRH   86 (277)
Q Consensus        81 ~~~~~~   86 (277)
                      .+....
T Consensus       148 ~~~~~~  153 (158)
T 2kn4_A          148 RYGRPP  153 (158)
T ss_dssp             CCSSCC
T ss_pred             CCCCCC
Confidence            976543

>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=99.78  E-value=8.1e-19  Score=124.72  Aligned_cols=76  Identities=28%  Similarity=0.576  Sum_probs=70.7

Q ss_pred             CCCeEEEcCCCCC-CCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            5 SSRTLYVGNLPGD-TRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         5 ~~~~l~V~nL~~~-~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      .+++|||+|||++ +|+++|+++|++||+|..|.|     +++||||+|.+.++|..|+..||+..|.|+.|.|.++...
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-----~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~  100 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-----HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEP  100 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-----ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-----eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            3489999999999 999999999999999999999     3899999999999999999999999999999999999864


Q ss_pred             CC
Q 023765           84 RR   85 (277)
Q Consensus        84 ~~   85 (277)
                      ..
T Consensus       101 ~~  102 (110)
T 1wf1_A          101 KP  102 (110)
T ss_dssp             CS
T ss_pred             CC
Confidence            43

>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=99.78  E-value=2.9e-19  Score=124.78  Aligned_cols=78  Identities=27%  Similarity=0.491  Sum_probs=70.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec----CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI----PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~----~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      ...++|||+|||+++++++|+++|++|| |..|.|+.    ++.++|||||+|.+.++|.+|+ .|||..|.|+.|.|.+
T Consensus        17 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~~   94 (100)
T 2j76_E           17 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDV   94 (100)
T ss_dssp             ---CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEEe
Confidence            4679999999999999999999999999 99999964    5678999999999999999999 7999999999999999


Q ss_pred             ccCC
Q 023765           80 AHGG   83 (277)
Q Consensus        80 a~~~   83 (277)
                      +...
T Consensus        95 a~~~   98 (100)
T 2j76_E           95 ADQA   98 (100)
T ss_dssp             CCCS
T ss_pred             ccCC
Confidence            8754

>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=99.78  E-value=7.5e-18  Score=119.26  Aligned_cols=82  Identities=55%  Similarity=0.987  Sum_probs=71.9

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccc-eeeEEE
Q 023765          104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAF-SRSYVR  182 (277)
Q Consensus       104 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~-~~~~i~  182 (277)
                      ++....++|||+|||..+++++|+++|.+||.|..|.|+.+   +||||+|.+.++|++||+.|||..+.|+. ....|.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~---g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~   86 (108)
T 1x4c_A           10 PSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   86 (108)
T ss_dssp             CCCSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT---TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC---CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEE
Confidence            34456889999999999999999999999999999999887   79999999999999999999999999832 235777


Q ss_pred             EeecCC
Q 023765          183 VREYDS  188 (277)
Q Consensus       183 ~~~~~~  188 (277)
                      |..+.+
T Consensus        87 V~~a~~   92 (108)
T 1x4c_A           87 VKVDGP   92 (108)
T ss_dssp             EEESSC
T ss_pred             EEeCCC
Confidence            877765

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

Probab=99.78  E-value=5.7e-19  Score=129.49  Aligned_cols=82  Identities=20%  Similarity=0.380  Sum_probs=74.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeE--EEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCc----ccCCc
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVD--IDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGY----NFDGY   73 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~--v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~----~~~g~   73 (277)
                      ..++++|||+|||+++|+++|+++|++||.|..  |.|+.   ++.++|||||+|.+. +|.+|+..||+.    .|.|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            457899999999999999999999999999966  88854   578899999999999 999999999999    99999


Q ss_pred             eEEEEEccCCCC
Q 023765           74 RLRVELAHGGRR   85 (277)
Q Consensus        74 ~i~v~~a~~~~~   85 (277)
                      .|.|.++.+...
T Consensus        99 ~l~V~~a~~~~~  110 (131)
T 2m2b_A           99 TINVEFAKGSKR  110 (131)
T ss_dssp             CCCCEECCCSCC
T ss_pred             EEEEEECCCCCC
Confidence            999999987543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.78  E-value=2.5e-19  Score=124.16  Aligned_cols=79  Identities=24%  Similarity=0.348  Sum_probs=73.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      .+.++|||+|||+.+|+++|+++|++||.|..+  ..++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++.+.
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~--~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   91 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK   91 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE--EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe--CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            467899999999999999999999999999887  567778999999999999999999999999999999999998764


Q ss_pred             C
Q 023765           84 R   84 (277)
Q Consensus        84 ~   84 (277)
                      .
T Consensus        92 ~   92 (96)
T 1fjc_A           92 G   92 (96)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.78  E-value=1.5e-19  Score=125.12  Aligned_cols=79  Identities=20%  Similarity=0.288  Sum_probs=70.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+++|+++|+++|++||.|..+.++.   ++.++|||||+|.++++|.+|++.||+..|.|+.|.|.++
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            3568999999999999999999999999998766643   5677899999999999999999999999999999999987


Q ss_pred             cC
Q 023765           81 HG   82 (277)
Q Consensus        81 ~~   82 (277)
                      ..
T Consensus        93 ~s   94 (95)
T 2ek1_A           93 SS   94 (95)
T ss_dssp             C-
T ss_pred             cC
Confidence            63

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=1.3e-18  Score=119.34  Aligned_cols=78  Identities=17%  Similarity=0.290  Sum_probs=72.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      .+.++|||+|||+++|+++|+++|+.| .|..|.|+.  ++.++|||||+|.+.++|.+|+. ||+..|.|+.|.|.++.
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a~   85 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREK   85 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEES
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEECC
Confidence            567899999999999999999999999 999999965  46678999999999999999999 99999999999999988


Q ss_pred             CC
Q 023765           82 GG   83 (277)
Q Consensus        82 ~~   83 (277)
                      ..
T Consensus        86 ~~   87 (91)
T 2dgw_A           86 SG   87 (91)
T ss_dssp             SC
T ss_pred             cC
Confidence            65

>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=99.78  E-value=5.6e-19  Score=120.33  Aligned_cols=77  Identities=31%  Similarity=0.413  Sum_probs=72.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      +...++|||+|||+++++++|+++|++| .|..+.+.   .++|||||+|.+.++|.+|+..|||..|.|+.|.|.++..
T Consensus         2 s~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~---~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   77 (88)
T 1wg1_A            2 SSGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD---RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE---GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe---CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCC
Confidence            5678999999999999999999999999 99999885   5689999999999999999999999999999999999875


Q ss_pred             C
Q 023765           83 G   83 (277)
Q Consensus        83 ~   83 (277)
                      .
T Consensus        78 ~   78 (88)
T 1wg1_A           78 D   78 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.78  E-value=4e-19  Score=117.95  Aligned_cols=73  Identities=16%  Similarity=0.373  Sum_probs=68.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      ++|||+|||+++++++|+++|++||+|..+.++.   ++.++|||||+|.+.++|.+|+..++ ..|.|+.|.|.+|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            5899999999999999999999999999999965   46789999999999999999999999 9999999999986

>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=99.77  E-value=4.1e-19  Score=132.37  Aligned_cols=83  Identities=24%  Similarity=0.410  Sum_probs=75.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeE--------EEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCce
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVD--------IDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYR   74 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~--------v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~   74 (277)
                      ..++++|||+|||+++|+++|+++|++||.|..        +.+..++.++|||||+|.+.++|..|+..|||..|.|+.
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            357899999999999999999999999998876        555667888999999999999999999999999999999


Q ss_pred             EEEEEccCCCC
Q 023765           75 LRVELAHGGRR   85 (277)
Q Consensus        75 i~v~~a~~~~~   85 (277)
                      |.|.++.....
T Consensus       122 l~V~~a~~~~~  132 (143)
T 3egn_A          122 MVVQFARSARP  132 (143)
T ss_dssp             CEEEECCCSCC
T ss_pred             EEEEECCCCCC
Confidence            99999986543

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

Probab=99.77  E-value=1.4e-18  Score=126.26  Aligned_cols=80  Identities=26%  Similarity=0.477  Sum_probs=73.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      +.++|||+|||+++|+++|+++|++||.|..|.|+.   ++.++|||||+|.+.++|..|+ .|||..|.|+.|.|.++.
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            357999999999999999999999999999999954   6788999999999999999999 699999999999999998


Q ss_pred             CCCC
Q 023765           82 GGRR   85 (277)
Q Consensus        82 ~~~~   85 (277)
                      ....
T Consensus       114 ~~~~  117 (124)
T 2jwn_A          114 TNMP  117 (124)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            6543

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

Probab=99.77  E-value=5.9e-19  Score=123.73  Aligned_cols=82  Identities=21%  Similarity=0.314  Sum_probs=72.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      .++++|||+|||+++|+++|+++|+.|+.|..+....++.++|||||+|.+.++|.+|++.||+..|.|+.|.|.++.+.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~   92 (102)
T 2fc8_A           13 QPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPK   92 (102)
T ss_dssp             CCCSSEEEECCCTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CCCCEEEEeCCCCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCC
Confidence            57899999999999999999999999875555444456778899999999999999999999999999999999999875


Q ss_pred             CC
Q 023765           84 RR   85 (277)
Q Consensus        84 ~~   85 (277)
                      ..
T Consensus        93 ~~   94 (102)
T 2fc8_A           93 GE   94 (102)
T ss_dssp             CS
T ss_pred             CC
Confidence            43

>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=99.77  E-value=1.9e-19  Score=123.25  Aligned_cols=78  Identities=29%  Similarity=0.583  Sum_probs=69.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      ++|||+|||+++++++|+++|++||+|..|.++.   ++.++|||||+|.+.+ |..|+..|||..|.|+.|.|.+|...
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            5899999999999999999999999999999965   4678999999999999 99999999999999999999999875


Q ss_pred             CC
Q 023765           84 RR   85 (277)
Q Consensus        84 ~~   85 (277)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            43

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

Probab=99.77  E-value=1.6e-18  Score=128.73  Aligned_cols=77  Identities=34%  Similarity=0.572  Sum_probs=71.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+.+|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|.+|++.||+..|.|+.|.|.+|
T Consensus        61 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A           61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             CCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            5789999999999999999999999999999999965   4678999999999999999999999999999999999875

>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=99.77  E-value=1.6e-18  Score=121.90  Aligned_cols=79  Identities=16%  Similarity=0.230  Sum_probs=71.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeE-EEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVD-IDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~-v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+++|+++|+++|++||.|.. |.|+.  ++.++|||||+|.++++|.+|+.. |+..|.|+.|.|.++
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 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEEC
Confidence            46789999999999999999999999999987 77754  567899999999999999999996 999999999999998


Q ss_pred             cCC
Q 023765           81 HGG   83 (277)
Q Consensus        81 ~~~   83 (277)
                      ...
T Consensus        92 ~~~   94 (104)
T 1wg5_A           92 SRA   94 (104)
T ss_dssp             CTT
T ss_pred             CHH
Confidence            754

>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=99.77  E-value=2.6e-18  Score=120.58  Aligned_cols=81  Identities=19%  Similarity=0.400  Sum_probs=73.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      ..+.++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|.+|+.  ++..|.|+.|.|.+
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~   89 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEEC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEe
Confidence            35789999999999999999999999999999999965   46778999999999999999999  47799999999999


Q ss_pred             ccCCCC
Q 023765           80 AHGGRR   85 (277)
Q Consensus        80 a~~~~~   85 (277)
                      +.....
T Consensus        90 a~~~~~   95 (103)
T 2cqg_A           90 PNSKQS   95 (103)
T ss_dssp             CCTTCC
T ss_pred             cCCCCc
Confidence            987554

>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=99.77  E-value=8e-19  Score=133.93  Aligned_cols=82  Identities=23%  Similarity=0.409  Sum_probs=74.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .++++|||+|||+.+|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|..||..|||..|.|+.|.|.++
T Consensus        70 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  149 (165)
T 1rk8_A           70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC  149 (165)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            4567899999999999999999999999999999964   5677899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 023765           81 HGGRR   85 (277)
Q Consensus        81 ~~~~~   85 (277)
                      .....
T Consensus       150 ~~~~~  154 (165)
T 1rk8_A          150 FVKGP  154 (165)
T ss_dssp             EECC-
T ss_pred             cCCCC
Confidence            86543

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

Probab=99.77  E-value=1.9e-18  Score=124.01  Aligned_cols=80  Identities=19%  Similarity=0.382  Sum_probs=73.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      +.++|||+|||+++|+++|+++|++||.|..|.|+.   ++.++|||||+|.+.++|.+|+.. ++..|.|+.|.|.++.
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECC
Confidence            358999999999999999999999999999999965   467899999999999999999996 9999999999999998


Q ss_pred             CCCC
Q 023765           82 GGRR   85 (277)
Q Consensus        82 ~~~~   85 (277)
                      ....
T Consensus       105 ~~~~  108 (116)
T 1x4b_A          105 AREE  108 (116)
T ss_dssp             SCCC
T ss_pred             CCcc
Confidence            7654

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=2.8e-18  Score=118.38  Aligned_cols=78  Identities=19%  Similarity=0.414  Sum_probs=68.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      +..++|||+|||+++|+++|+++|++||+|..|.+ .....+ ||||+|.+.++|.+|+. ||+..|.|+.|.|.++...
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~-~~~~g~-~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~   82 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVM-DKDKGV-FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQK   82 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEE-CSSSCC-EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEE-cCCCCc-EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcC
Confidence            56789999999999999999999999999999833 222223 99999999999999999 9999999999999988754


Q ss_pred             C
Q 023765           84 R   84 (277)
Q Consensus        84 ~   84 (277)
                      .
T Consensus        83 ~   83 (94)
T 2e5g_A           83 E   83 (94)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.77  E-value=3.1e-18  Score=114.66  Aligned_cols=75  Identities=27%  Similarity=0.355  Sum_probs=67.8

Q ss_pred             CCCCe-EEEcCCCCCCCHHH----HHHHhhcc-CCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEE
Q 023765            4 RSSRT-LYVGNLPGDTRMRE----VEDLFYKY-GPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV   77 (277)
Q Consensus         4 ~~~~~-l~V~nL~~~~t~~~----l~~~F~~~-G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v   77 (277)
                      .++.| |||+|||..+++++    |+++|++| |+|.+|    +   .|+|||+|.++++|.+|++.|||..|.|++|.|
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V----t---gG~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v   78 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI----T---GCSAILRFINQDSAERAQKRMENEDVFGNRIIV   78 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC----C---TTCEEEEESSHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE----e---cCEEEEEECCHHHHHHHHHHhcCCccCCceEEE
Confidence            46777 99999999999998    55899999 599998    3   299999999999999999999999999999999


Q ss_pred             EEccCCCC
Q 023765           78 ELAHGGRR   85 (277)
Q Consensus        78 ~~a~~~~~   85 (277)
                      .+|+....
T Consensus        79 ~~A~~~sd   86 (96)
T 2diu_A           79 SFTPKNRE   86 (96)
T ss_dssp             ESSCCSCC
T ss_pred             EecCCCcc
Confidence            99997654

>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=99.77  E-value=8.1e-19  Score=125.50  Aligned_cols=79  Identities=14%  Similarity=0.122  Sum_probs=72.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCe-eEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPI-VDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v-~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+++|+++|+++|+.||.| ..|.|+.  ++.++|||||+|.+.++|.+|+.. |+..|.|+.|.|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~a   91 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVV   91 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEEC
Confidence            567899999999999999999999999999 7788854  567899999999999999999996 999999999999998


Q ss_pred             cCC
Q 023765           81 HGG   83 (277)
Q Consensus        81 ~~~   83 (277)
                      ...
T Consensus        92 ~~~   94 (114)
T 2cpy_A           92 TLE   94 (114)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            754

>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=99.77  E-value=1.1e-18  Score=124.90  Aligned_cols=76  Identities=24%  Similarity=0.337  Sum_probs=66.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCce-----EEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYR-----LRVE   78 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~-----i~v~   78 (277)
                      ...++|||+|||+++|+++|+++|++||+|..|.|+.+    |||||+|.+.++|.+||+.||+..|.|+.     |.|.
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~----g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~   89 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   89 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT----SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC----CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEec
Confidence            45689999999999999999999999999999999754    99999999999999999999999999998     7777


Q ss_pred             EccCC
Q 023765           79 LAHGG   83 (277)
Q Consensus        79 ~a~~~   83 (277)
                      .+.+.
T Consensus        90 ~~~~~   94 (115)
T 3beg_B           90 VDGPR   94 (115)
T ss_dssp             ECC--
T ss_pred             cCCCC
Confidence            76653

>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=99.76  E-value=1.5e-18  Score=124.15  Aligned_cols=79  Identities=19%  Similarity=0.325  Sum_probs=72.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCccc--------CCc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNF--------DGY   73 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~--------~g~   73 (277)
                      .+.++|||+|||+++|+++|+++|++||.|..|.|+.  ++.++|||||+|.+.++|..|+..|||..|        .++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~  102 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE  102 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCC
Confidence            4678999999999999999999999999999999965  466789999999999999999999999999        578


Q ss_pred             eEEEEEccC
Q 023765           74 RLRVELAHG   82 (277)
Q Consensus        74 ~i~v~~a~~   82 (277)
                      +|.|.|+.+
T Consensus       103 ~l~v~~a~p  111 (114)
T 1x5o_A          103 PLLCKFSGP  111 (114)
T ss_dssp             CBEEEECCC
T ss_pred             ceeEEccCC
Confidence            899999884

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=6.3e-18  Score=117.29  Aligned_cols=77  Identities=26%  Similarity=0.468  Sum_probs=71.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      .++++|||+||  ++|+++|+++|++||+|..|.|.   ..+|||||+|.+.++|.+|+..||+..|.|+.|.|.++...
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~---~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~   87 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD---PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   87 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE---TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSC
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec---CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCC
Confidence            46789999996  99999999999999999999995   46899999999999999999999999999999999999875


Q ss_pred             CC
Q 023765           84 RR   85 (277)
Q Consensus        84 ~~   85 (277)
                      ..
T Consensus        88 ~~   89 (97)
T 1x5p_A           88 PM   89 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.5e-18  Score=121.34  Aligned_cols=79  Identities=20%  Similarity=0.304  Sum_probs=70.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      .+.++|||+|||+++|+++|+++|++||.| .|.|+.  ++.++|||||+|.++++|.+|++ +|+..|.|+.|.|.++.
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~~   90 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECC
Confidence            567899999999999999999999999955 888854  56778999999999999999996 89999999999999987


Q ss_pred             CCC
Q 023765           82 GGR   84 (277)
Q Consensus        82 ~~~   84 (277)
                      ...
T Consensus        91 ~~~   93 (102)
T 1wez_A           91 TAG   93 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            544

>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=99.76  E-value=1.7e-18  Score=130.07  Aligned_cols=78  Identities=45%  Similarity=0.735  Sum_probs=73.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      .+.++|||+|||+++|+++|+++|++||.|..|.++.+  ++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+.
T Consensus        71 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN--PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             TTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS--SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC--CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            46789999999999999999999999999999999765  5899999999999999999999999999999999998864

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.76  E-value=1e-18  Score=125.71  Aligned_cols=78  Identities=18%  Similarity=0.283  Sum_probs=71.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCC---eeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGP---IVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVE   78 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~---v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~   78 (277)
                      .+.++|||+|||+++|+++|+++|+.||.   |..|.|+.  .+.++|||||+|.+.++|.+|++ ||+..|.|+.|.|.
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~   93 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVF   93 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEE
Confidence            46789999999999999999999999998   88998864  46778999999999999999999 99999999999999


Q ss_pred             EccC
Q 023765           79 LAHG   82 (277)
Q Consensus        79 ~a~~   82 (277)
                      ++..
T Consensus        94 ~a~~   97 (118)
T 2db1_A           94 KSHR   97 (118)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            9864

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

Probab=99.76  E-value=3.6e-18  Score=118.29  Aligned_cols=79  Identities=15%  Similarity=0.372  Sum_probs=70.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEE-eecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDID-LKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~-~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      ..+++|||+|||+++|+++|+++|++||.|..|. |+.+. ..+.|||+|.+.++|..|+..|||..|.|+.|.|.++.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~-~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   91 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS-ETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPD   91 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSS-SSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCC
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCC-CCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCc
Confidence            3578999999999999999999999999999994 65433 245599999999999999999999999999999999987


Q ss_pred             C
Q 023765           83 G   83 (277)
Q Consensus        83 ~   83 (277)
                      .
T Consensus        92 ~   92 (96)
T 2e44_A           92 E   92 (96)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.76  E-value=9.7e-19  Score=115.43  Aligned_cols=72  Identities=19%  Similarity=0.461  Sum_probs=66.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            8 TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         8 ~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      +|||+|||+++|+++|+++|++||+|..+.++.   ++.++|||||+|.+.++|.+|+. +++..|.|+.|.|.+|
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            699999999999999999999999999999964   46789999999999999999999 5899999999999875

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.76  E-value=3.7e-19  Score=124.53  Aligned_cols=80  Identities=19%  Similarity=0.331  Sum_probs=71.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEe--ecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL--KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~--~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      .+.++|||+|||+++|+++|+++|++||.|..+.+  ..++.++|||||+|.+.++|.+|++ ||+..|.|+.|.|.++.
T Consensus        15 ~~~~~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           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   93 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcC
Confidence            46789999999999999999999999998887222  2356789999999999999999999 99999999999999998


Q ss_pred             CCC
Q 023765           82 GGR   84 (277)
Q Consensus        82 ~~~   84 (277)
                      ...
T Consensus        94 ~~~   96 (101)
T 1fj7_A           94 GRD   96 (101)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

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

Probab=99.75  E-value=3.2e-18  Score=131.75  Aligned_cols=81  Identities=23%  Similarity=0.368  Sum_probs=75.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      .++++|||+|||+.+++++|+++|++||+|..|.|+.  ++.++|||||+|.+.++|.+|++.||+..|.|+.|.|.++.
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~  165 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  165 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            4578999999999999999999999999999999965  46788999999999999999999999999999999999998


Q ss_pred             CCC
Q 023765           82 GGR   84 (277)
Q Consensus        82 ~~~   84 (277)
                      ...
T Consensus       166 ~~~  168 (177)
T 2f3j_A          166 SQI  168 (177)
T ss_dssp             SGG
T ss_pred             CCC
Confidence            644

>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=99.75  E-value=2.1e-18  Score=138.29  Aligned_cols=78  Identities=17%  Similarity=0.210  Sum_probs=71.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccC--CeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYG--PIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G--~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      ..++|||+||++++|+++|+++|++||  .|..|.|+.   ++.++|||||+|.+.++|.+||+.||+..|.|+.|.|.+
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            567899999999999999999999999  999999964   567899999999999999999999999999999999999


Q ss_pred             ccC
Q 023765           80 AHG   82 (277)
Q Consensus        80 a~~   82 (277)
                      +..
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            874

>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=99.75  E-value=2e-18  Score=125.42  Aligned_cols=78  Identities=22%  Similarity=0.304  Sum_probs=70.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeE-EEe--ecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVD-IDL--KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~-v~~--~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+++|+++|+++|+.||.|.. +.+  ..++.++|||||+|.+.++|.+|+. ||+..|.|+.|.|.++
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            45689999999999999999999999999876 333  3467789999999999999999999 9999999999999998


Q ss_pred             cC
Q 023765           81 HG   82 (277)
Q Consensus        81 ~~   82 (277)
                      ..
T Consensus       102 ~~  103 (124)
T 1wel_A          102 TK  103 (124)
T ss_dssp             CH
T ss_pred             CH
Confidence            74

>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=1.6e-18  Score=127.18  Aligned_cols=78  Identities=17%  Similarity=0.242  Sum_probs=71.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCC---eeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGP---IVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVE   78 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~---v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~   78 (277)
                      .+.++|||+|||+++|+++|+++|++||.   |..|.|+.  .+.++|||||+|.+.++|.+|++ ||+..|.|+.|.|.
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~  120 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVF  120 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEE
Confidence            46789999999999999999999999999   88888864  36778999999999999999999 99999999999999


Q ss_pred             EccC
Q 023765           79 LAHG   82 (277)
Q Consensus        79 ~a~~   82 (277)
                      ++..
T Consensus       121 ~a~~  124 (136)
T 2hgl_A          121 KSHR  124 (136)
T ss_dssp             ECCH
T ss_pred             ECCh
Confidence            9764

>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=99.75  E-value=6.6e-18  Score=126.38  Aligned_cols=77  Identities=22%  Similarity=0.261  Sum_probs=69.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCC--ceEEEEEccCCC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDG--YRLRVELAHGGR   84 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g--~~i~v~~a~~~~   84 (277)
                      .+|||+||++.+|+++|+++|++||+|..|.|.. +..++||||+|.+.++|..|++.|||..|.|  +.|.|.|++...
T Consensus        47 l~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~-k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~~  125 (164)
T 1sjr_A           47 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFT-KNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS  125 (164)
T ss_dssp             EEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEE-SSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSSS
T ss_pred             EEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEe-CCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCCc
Confidence            4588999999999999999999999999999853 3357899999999999999999999999965  999999999764

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.75  E-value=6.3e-18  Score=121.91  Aligned_cols=76  Identities=22%  Similarity=0.308  Sum_probs=68.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcE-EEEEEcChHHHHHHHHhcCCcccCC--ceEEEEEccCC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGY-AFLEFEDYRDAEDAIRGRDGYNFDG--YRLRVELAHGG   83 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~-afV~f~~~~~a~~a~~~l~~~~~~g--~~i~v~~a~~~   83 (277)
                      ..|||+||++.+|+++|+++|++||+|..|.+...  .+|| |||+|.+.++|..|++.|||..|.|  +.|.|+|++..
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~--~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~  106 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK--NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT  106 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE--TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCS
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC--CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCC
Confidence            34679999999999999999999999999988642  3688 9999999999999999999999988  89999999875


Q ss_pred             C
Q 023765           84 R   84 (277)
Q Consensus        84 ~   84 (277)
                      .
T Consensus       107 ~  107 (130)
T 3zzy_A          107 S  107 (130)
T ss_dssp             S
T ss_pred             c
Confidence            4

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

Probab=99.75  E-value=7.4e-18  Score=118.88  Aligned_cols=75  Identities=19%  Similarity=0.210  Sum_probs=68.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      ..+|||+|||+++|+++|+++|++| .|..|.|+.  ++.++|||||+|.+.++|.+|+. ||+..|.|+.|.|..+..
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-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALK-RNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHHH-TTTEEETTEEEEEEECCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEEECCc
Confidence            4689999999999999999999999 899999965  46789999999999999999995 999999999999988764

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.74  E-value=1.1e-17  Score=120.26  Aligned_cols=77  Identities=21%  Similarity=0.218  Sum_probs=68.4

Q ss_pred             CCCe--EEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcE-EEEEEcChHHHHHHHHhcCCcccCC--ceEEEEE
Q 023765            5 SSRT--LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGY-AFLEFEDYRDAEDAIRGRDGYNFDG--YRLRVEL   79 (277)
Q Consensus         5 ~~~~--l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~-afV~f~~~~~a~~a~~~l~~~~~~g--~~i~v~~   79 (277)
                      ++++  |||+||++.+|+++|+++|++||+|..|.|...   .|| |||+|.+.++|..|++.|||..|.|  +.|.|.+
T Consensus        22 ps~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           22 GNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR---NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEY   98 (124)
T ss_dssp             CCSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES---SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEEC
T ss_pred             CCcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC---CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEE
Confidence            3455  579999999999999999999999999999642   386 9999999999999999999999987  6899999


Q ss_pred             ccCCC
Q 023765           80 AHGGR   84 (277)
Q Consensus        80 a~~~~   84 (277)
                      |++..
T Consensus        99 Ak~~~  103 (124)
T 2e5i_A           99 ARPTR  103 (124)
T ss_dssp             CSCSC
T ss_pred             ecCCc
Confidence            98654

>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=99.74  E-value=6.9e-18  Score=114.62  Aligned_cols=74  Identities=31%  Similarity=0.587  Sum_probs=68.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhcc----C-------CeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCccc
Q 023765            2 SSRSSRTLYVGNLPGDTRMREVEDLFYKY----G-------PIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNF   70 (277)
Q Consensus         2 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~----G-------~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~   70 (277)
                      ..++.++|||+|||+++|+++|+++|++|    |       +|..+.+..+   +|||||+|.+.++|.+|+ .||+..|
T Consensus         2 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~---kg~afV~f~~~~~a~~A~-~l~g~~~   77 (87)
T 2hzc_A            2 PLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD---KNFAFLEFRSVDETTQAM-AFDGIIF   77 (87)
T ss_dssp             CSGGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS---SSEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC---CcEEEEEcCCHHHHHHHH-hcCCCEE
Confidence            35678999999999999999999999999    8       9999998744   899999999999999999 8999999


Q ss_pred             CCceEEEEE
Q 023765           71 DGYRLRVEL   79 (277)
Q Consensus        71 ~g~~i~v~~   79 (277)
                      .|+.|.|..
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

>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=99.74  E-value=1.4e-17  Score=127.01  Aligned_cols=135  Identities=15%  Similarity=0.111  Sum_probs=70.8

Q ss_pred             EEEcChHHHHHHHHhcCCcccC--CceEEEEEccCCCCCCCCCCCCC-CCCCCCCCCCCCCCCceEEEeCCCCCCCHHHH
Q 023765           50 LEFEDYRDAEDAIRGRDGYNFD--GYRLRVELAHGGRRHSSSMDRYS-SYSSGGSRGVSRRSDYRVLVTGLPSSASWQDL  126 (277)
Q Consensus        50 V~f~~~~~a~~a~~~l~~~~~~--g~~i~v~~a~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l  126 (277)
                      .+|.+.++|..|+..|++....  |+.+.+.++.......-. .... ........+....+.++|||+|||..+++++|
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~-~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L   89 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYE-RVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEI   89 (165)
T ss_dssp             --------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCcc-ccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHH
Confidence            7899999999999999987665  666665553321100000 0000 00001112233455789999999999999999


Q ss_pred             HHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeecCCC
Q 023765          127 KDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDSR  189 (277)
Q Consensus       127 ~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~~~  189 (277)
                      .++|.+||.|..|.|+.+..+    +||||+|.+.++|..||..|||..|.|    ..|.|......
T Consensus        90 ~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g----~~l~V~~a~~~  152 (165)
T 1rk8_A           90 QEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG----QTIQVDWCFVK  152 (165)
T ss_dssp             HHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETT----EECEEEESEEC
T ss_pred             HHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECC----EEEEEEEecCC
Confidence            999999999999999987543    599999999999999999999999999    56666665443

>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=99.74  E-value=2.5e-18  Score=121.54  Aligned_cols=79  Identities=16%  Similarity=0.198  Sum_probs=72.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCC---eeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGP---IVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV   77 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~---v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v   77 (277)
                      ..+.++|||+|||+++|+++|+++|+.||.   |..|.|+.  .+.++|||||+|.+.++|.+|+. ||+..|.|+.|.|
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V   86 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEV   86 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEE
Confidence            357789999999999999999999999998   89999865  36789999999999999999999 9999999999999


Q ss_pred             EEccC
Q 023765           78 ELAHG   82 (277)
Q Consensus        78 ~~a~~   82 (277)
                      .++..
T Consensus        87 ~~a~~   91 (107)
T 2lmi_A           87 YEINN   91 (107)
T ss_dssp             EECCH
T ss_pred             EECCH
Confidence            99874

>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=99.73  E-value=2.6e-18  Score=126.35  Aligned_cols=79  Identities=19%  Similarity=0.262  Sum_probs=70.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      .+.++|||+|||+++|+++|+++|++|| |..|.|+.  ++.++|||||+|.++++|.+|+ .+|+..|.|+.|.|.++.
T Consensus        44 ~~~~~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           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNS  121 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECC
Confidence            4567999999999999999999999999 67888865  4678999999999999999999 699999999999999987


Q ss_pred             CCC
Q 023765           82 GGR   84 (277)
Q Consensus        82 ~~~   84 (277)
                      ...
T Consensus       122 ~~~  124 (139)
T 2hgn_A          122 TTG  124 (139)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            644

>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=99.73  E-value=1.7e-17  Score=113.00  Aligned_cols=75  Identities=24%  Similarity=0.469  Sum_probs=62.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcc--cCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYN--FDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~--~~g~~i~v~~a~   81 (277)
                      .+.++|||+|||+++|+++|+++|++||+|.+|.|+.+  ++|||||+|.+.++|.+    |++..  +.|+.|.|.++.
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--FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAE   82 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS--CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC--CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcC
Confidence            57899999999999999999999999999999999763  78999999999999984    34444  569999999988


Q ss_pred             CCC
Q 023765           82 GGR   84 (277)
Q Consensus        82 ~~~   84 (277)
                      +..
T Consensus        83 ~k~   85 (89)
T 3d2w_A           83 PKH   85 (89)
T ss_dssp             ---
T ss_pred             CCC
Confidence            643

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=3.7e-18  Score=122.98  Aligned_cols=78  Identities=22%  Similarity=0.216  Sum_probs=69.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCe----eEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPI----VDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV   77 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v----~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v   77 (277)
                      .+..+|||+|||+++|+++|+++|++||+|    ..|.|+.  ++.++|||||+|.+.++|.+|++. |+..|.|+.|.|
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 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIEL   99 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEE
Confidence            467899999999999999999999999975    5777754  677889999999999999999995 999999999999


Q ss_pred             EEccC
Q 023765           78 ELAHG   82 (277)
Q Consensus        78 ~~a~~   82 (277)
                      ..+..
T Consensus       100 ~~a~~  104 (123)
T 2dha_A          100 FRSTA  104 (123)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            88763

>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=99.73  E-value=8e-18  Score=114.59  Aligned_cols=79  Identities=24%  Similarity=0.442  Sum_probs=67.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      +.++++|||+|||+++|+++|+++|++||+|..|.|+.+  ++|||||+|.+.++|++|+.  ....+.|..|.|.++.+
T Consensus         2 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~--~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a~~   77 (88)
T 1wf0_A            2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP--FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEP   77 (88)
T ss_dssp             CSCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS--CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC--CCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEecCC
Confidence            467899999999999999999999999999999999754  68999999999999986543  23556899999999886


Q ss_pred             CCC
Q 023765           83 GRR   85 (277)
Q Consensus        83 ~~~   85 (277)
                      ...
T Consensus        78 ~~~   80 (88)
T 1wf0_A           78 KHN   80 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.72  E-value=1.3e-17  Score=120.32  Aligned_cols=77  Identities=21%  Similarity=0.248  Sum_probs=68.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCee--EEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIV--DIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~--~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      .+.++|||+|||+++|+++|+++|++| .|.  .|.|+.  .+.++|||||+|.++++|.+|++ +++..|.|+.|.|..
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-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFK  117 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEEEE
Confidence            457899999999999999999999999 576  888864  46789999999999999999999 578999999999988


Q ss_pred             ccC
Q 023765           80 AHG   82 (277)
Q Consensus        80 a~~   82 (277)
                      +..
T Consensus       118 a~~  120 (126)
T 2hgm_A          118 SSQ  120 (126)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            753

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.56  E-value=4.3e-19  Score=127.40  Aligned_cols=82  Identities=28%  Similarity=0.402  Sum_probs=74.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeE--------EEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVD--------IDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDG   72 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~--------v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g   72 (277)
                      .++++|||+|||+++++++|+++|++||.|..        |.|+.   ++.++|||||+|.+.++|.+|+..||+..|.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            57899999999999999999999999999998        77754   46789999999999999999999999999999


Q ss_pred             ceEEEEEccCCCC
Q 023765           73 YRLRVELAHGGRR   85 (277)
Q Consensus        73 ~~i~v~~a~~~~~   85 (277)
                      +.|.|.++.....
T Consensus        85 ~~l~V~~a~~~~~   97 (116)
T 2lcw_A           85 NPIKVSFATRRAD   97 (116)
Confidence            9999999986543

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

Probab=99.71  E-value=6.1e-17  Score=115.66  Aligned_cols=76  Identities=32%  Similarity=0.496  Sum_probs=63.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---C---CCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---P---PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLR   76 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~---~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~   76 (277)
                      ..++++|||+|||+++|+++|+++|++||+|. +.++.   +   +.++|||||+|.+.++|.+|++.|+  .++|+.|.
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~   81 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYL   81 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEE
Confidence            46789999999999999999999999999999 66644   2   5789999999999999999999883  35666666


Q ss_pred             EEEcc
Q 023765           77 VELAH   81 (277)
Q Consensus        77 v~~a~   81 (277)
                      +..+.
T Consensus        82 ~~~~~   86 (114)
T 2dnl_A           82 CVSSP   86 (114)
T ss_dssp             EECCS
T ss_pred             eccCC
Confidence            65433

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.71  E-value=8.2e-18  Score=117.84  Aligned_cols=79  Identities=22%  Similarity=0.447  Sum_probs=72.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      .++++|||+|||+++|+++|+++|++||.|..|.|+.  ++.++|||||+|.+.++|.+|+.  ++..|.|+.|.|.++.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~   84 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAI   84 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECC
Confidence            3568999999999999999999999999999999965  55678999999999999999999  9999999999999988


Q ss_pred             CCC
Q 023765           82 GGR   84 (277)
Q Consensus        82 ~~~   84 (277)
                      ...
T Consensus        85 ~~~   87 (102)
T 2xs2_A           85 RKQ   87 (102)
T ss_dssp             ECC
T ss_pred             cCc
Confidence            644

>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=1.7e-17  Score=122.04  Aligned_cols=119  Identities=15%  Similarity=0.065  Sum_probs=71.5

Q ss_pred             cEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHH
Q 023765           46 GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQD  125 (277)
Q Consensus        46 g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~  125 (277)
                      -++|++|.++..+..|+..+++....|..- +.+                    ...++......+|||+|||..+++++
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~g~~~-~~~--------------------~~~~~~~~~~~~l~V~nLp~~~te~~   63 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQMGRGS-MSY--------------------GRPPPDVEGMTSLKVDNLTYRTSPDT   63 (135)
T ss_dssp             -------------------------------CCS--------------------CCSCSSGGGCCCEEEECCCSSCHHHH
T ss_pred             ccccccccCCCchhhhhhhccCCCCCCCCC-CCc--------------------CCCCCCCCCCCEEEEeCCCCCCCHHH
Confidence            467888888888889998888765554431 000                    11123344578999999999999999


Q ss_pred             HHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeecCCC
Q 023765          126 LKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDSR  189 (277)
Q Consensus       126 l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~~~  189 (277)
                      |+++|.+||.|..|.+..+..    .+||||+|.+.++|++|+..|||..+.|    ..|.|......
T Consensus        64 L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g----~~l~V~~a~~~  127 (135)
T 2lea_A           64 LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG----RELRVQMARYG  127 (135)
T ss_dssp             HHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSS----SCCEEEECCCC
T ss_pred             HHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECC----EEEEEEECCCC
Confidence            999999999999999987643    4599999999999999999999999999    46666666544

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

Probab=99.70  E-value=1.3e-16  Score=110.80  Aligned_cols=75  Identities=21%  Similarity=0.358  Sum_probs=68.1

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      +++|||+|||..+++++|+++|.+||.|..|.+..+..+    |||||+|.+.++|++|++.|||..+.|    ..|.|.
T Consensus        19 gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g----r~l~V~   94 (99)
T 4fxv_A           19 GTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQS----KTIKVS   94 (99)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETT----EECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECC----EEEEEE
Confidence            578999999999999999999999999999999987654    499999999999999999999999999    567776


Q ss_pred             ecC
Q 023765          185 EYD  187 (277)
Q Consensus       185 ~~~  187 (277)
                      .++
T Consensus        95 ~Ak   97 (99)
T 4fxv_A           95 YAR   97 (99)
T ss_dssp             ECC
T ss_pred             Eee
Confidence            654

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

Probab=99.70  E-value=7.3e-17  Score=113.02  Aligned_cols=80  Identities=20%  Similarity=0.229  Sum_probs=71.3

Q ss_pred             CCCCCeEEEcCCCC-----CCCHHHHHHHhhccCCeeEEEeecC----CCCCcEEEEEEcChHHHHHHHHhcCCcccCCc
Q 023765            3 SRSSRTLYVGNLPG-----DTRMREVEDLFYKYGPIVDIDLKIP----PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGY   73 (277)
Q Consensus         3 ~~~~~~l~V~nL~~-----~~t~~~l~~~F~~~G~v~~v~~~~~----~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~   73 (277)
                      ..++++|+|.||..     +.++++|+++|++||+|..|.|+.+    +.++|||||+|.+.++|.+|+..|||..|.|+
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr   84 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR   84 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            46899999999963     2378999999999999999999653    46799999999999999999999999999999


Q ss_pred             eEEEEEccC
Q 023765           74 RLRVELAHG   82 (277)
Q Consensus        74 ~i~v~~a~~   82 (277)
                      .|.|.++..
T Consensus        85 ~i~v~~a~~   93 (105)
T 2pe8_A           85 VVKACFYNL   93 (105)
T ss_dssp             ECEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999999874

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.70  E-value=5.9e-17  Score=114.46  Aligned_cols=79  Identities=33%  Similarity=0.519  Sum_probs=70.4

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcC-CeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAG-DVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g-~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      ...++|||+|||+.+++++|+++|.+|| +|..+.+......|||||+|.+.++|++|++.|||..+.|    ..|.|..
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~G----r~i~V~~  101 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRG----SVITVER  101 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETT----EEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECC----eEEEEEE
Confidence            3478999999999999999999999999 9999999766677899999999999999999999999999    6777877


Q ss_pred             cCCC
Q 023765          186 YDSR  189 (277)
Q Consensus       186 ~~~~  189 (277)
                      +...
T Consensus       102 a~~~  105 (111)
T 2jvr_A          102 DDNP  105 (111)
T ss_dssp             SCC-
T ss_pred             CCCC
Confidence            6543

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.70  E-value=3.7e-17  Score=115.77  Aligned_cols=77  Identities=19%  Similarity=0.293  Sum_probs=67.9

Q ss_pred             CeEEEcCC----CCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcC----hHH----HHHHHH--hcCCcc
Q 023765            7 RTLYVGNL----PGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFED----YRD----AEDAIR--GRDGYN   69 (277)
Q Consensus         7 ~~l~V~nL----~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~----~~~----a~~a~~--~l~~~~   69 (277)
                      +.|||+||    |+.+++++|+++|+.||+|..+.+..   |+.++|||||+|.+    +++    |..|+.  .|||..
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            78999999    99999999999999999999999954   67889999999996    433    788888  789999


Q ss_pred             cCCceEEEEEccCC
Q 023765           70 FDGYRLRVELAHGG   83 (277)
Q Consensus        70 ~~g~~i~v~~a~~~   83 (277)
                      |.|+.|.|.+-...
T Consensus        83 I~Gr~irV~ln~~g   96 (136)
T 2j8a_A           83 IMGFKFEVILNKHS   96 (136)
T ss_dssp             ETTEEEEEEECCTT
T ss_pred             ecCcEEEEEECccc
Confidence            99999999996643

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

Probab=99.70  E-value=4.8e-17  Score=129.31  Aligned_cols=79  Identities=22%  Similarity=0.361  Sum_probs=72.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec-CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI-PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~-~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      ..++|||+|||+.+|+++|+++|+.||.|..|.|+. .+.++|||||+|.+.++|.+|++.|||..|.|+.|.|.++...
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~  181 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR  181 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCH
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            467899999999999999999999999999999965 3456899999999999999999999999999999999998753

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

Probab=99.69  E-value=1e-16  Score=127.48  Aligned_cols=82  Identities=24%  Similarity=0.442  Sum_probs=75.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+++|+++|+++|+.||.|..|.+..   ++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++
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            3568999999999999999999999999999999965   4577899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 023765           81 HGGRR   85 (277)
Q Consensus        81 ~~~~~   85 (277)
                      .....
T Consensus       203 ~~~~~  207 (216)
T 2qfj_A          203 VTPPM  207 (216)
T ss_dssp             SSCSS
T ss_pred             cCCCC
Confidence            87643

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

Probab=99.69  E-value=1e-16  Score=122.03  Aligned_cols=78  Identities=22%  Similarity=0.424  Sum_probs=73.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .++++|||+|||+.+|+++|+++|++||.|..+.+..   ++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.+|
T Consensus        85 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  164 (166)
T 3md3_A           85 DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA  164 (166)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEec
Confidence            4678999999999999999999999999999999964   5677899999999999999999999999999999999998


Q ss_pred             c
Q 023765           81 H   81 (277)
Q Consensus        81 ~   81 (277)
                      .
T Consensus       165 ~  165 (166)
T 3md3_A          165 A  165 (166)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.67  E-value=2.9e-16  Score=111.71  Aligned_cols=80  Identities=24%  Similarity=0.348  Sum_probs=70.5

Q ss_pred             CCCCeEEEcCCCCCCC-----------HHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCC
Q 023765            4 RSSRTLYVGNLPGDTR-----------MREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDG   72 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t-----------~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g   72 (277)
                      .++++|+|.||....+           +++|+++|++||+|..|.| .+..++|||||+|.+.++|.+|+..|||..|.|
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~g   91 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDRHPDGVASVSFRDPEEADYCIQTLDGRWFGG   91 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETTCTTCEEEEECSCHHHHHHHHHHSTTCEETT
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecCCCCEEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            5789999999944432           5899999999999999977 445689999999999999999999999999999


Q ss_pred             ceEEEEEccCCC
Q 023765           73 YRLRVELAHGGR   84 (277)
Q Consensus        73 ~~i~v~~a~~~~   84 (277)
                      +.|.|.++.+..
T Consensus        92 r~l~v~~a~~~~  103 (112)
T 2dit_A           92 RQITAQAWDGTT  103 (112)
T ss_dssp             EECEEEECCSCC
T ss_pred             cEEEEEEeCCCC
Confidence            999999988644

>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=99.67  E-value=8.2e-16  Score=110.03  Aligned_cols=79  Identities=14%  Similarity=0.251  Sum_probs=69.4

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC---CCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR---GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~---~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ....+|||+|||..+++++|+++|.+||.|..|.+..+.   ..+||||+|.+.++|++|+..|||..+.|    ..|.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g----~~l~V   80 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHG----KAIKV   80 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSS----SBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECC----EEEEE
Confidence            346799999999999999999999999999999999876   23699999999999999999999999999    46666


Q ss_pred             eecCCC
Q 023765          184 REYDSR  189 (277)
Q Consensus       184 ~~~~~~  189 (277)
                      ......
T Consensus        81 ~~a~~~   86 (116)
T 2fy1_A           81 EQAKKP   86 (116)
T ss_dssp             EECCCS
T ss_pred             EECCCC
Confidence            666544

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.67  E-value=8.5e-17  Score=128.34  Aligned_cols=78  Identities=24%  Similarity=0.347  Sum_probs=70.9

Q ss_pred             CCCCeEEEcCCCCCC---------CHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCccc----
Q 023765            4 RSSRTLYVGNLPGDT---------RMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNF----   70 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~---------t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~----   70 (277)
                      .++++|||+||+..+         ++++|+++|++||+|..|.|+.   .+|||||+|.+.++|..|++.|+|..|    
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~---~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~  208 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE---SKNCGFVKFKYQANAEFAKEAMSNQTLLLPS  208 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG---GGTEEEEEESSHHHHHHHHHHHTTCCCCCTT
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC---CCCEEEEEeCCHHHHHHHHHHhCCCEEeccc
Confidence            568999999999998         7999999999999999999974   489999999999999999999999999    


Q ss_pred             --------CCceEEEEEccCCC
Q 023765           71 --------DGYRLRVELAHGGR   84 (277)
Q Consensus        71 --------~g~~i~v~~a~~~~   84 (277)
                              .|+.|.|.||....
T Consensus       209 ~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          209 DKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             STTGGGGGGSCCCEEEECC---
T ss_pred             cccccccCCCCEEEEEEccCCC
Confidence                    89999999998643

>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=99.67  E-value=1.2e-16  Score=123.07  Aligned_cols=77  Identities=23%  Similarity=0.341  Sum_probs=72.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      +.++|||+|||+.+|+++|+++|++||.|..+  ..++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++.++
T Consensus        98 ~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~--~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B           98 AARTLLAKNLSFNITEDELKEVFEDALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE--CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe--cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            56899999999999999999999999999888  667788999999999999999999999999999999999998753

>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=99.67  E-value=4.9e-16  Score=111.07  Aligned_cols=78  Identities=22%  Similarity=0.325  Sum_probs=69.0

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC--cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG--MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~--~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      ...+|||+|||..+++++|+++|.+||.|..|.|+.+..+  +||||+|.+.++|+.||..|||..+.|    ..|.|..
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g----~~i~V~~   79 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLND----RKVFVGR   79 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETT----EECEEEE
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECC----EEEEEEE
Confidence            3568999999999999999999999999999999987653  599999999999999999999999999    5677776


Q ss_pred             cCCC
Q 023765          186 YDSR  189 (277)
Q Consensus       186 ~~~~  189 (277)
                      ...+
T Consensus        80 a~~~   83 (115)
T 4f25_A           80 FKSR   83 (115)
T ss_dssp             SSCC
T ss_pred             CCCc
Confidence            6543

>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=99.67  E-value=1.5e-16  Score=122.02  Aligned_cols=77  Identities=29%  Similarity=0.533  Sum_probs=71.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      +.++|||+|||+.+|+++|+++|++||+|..+.+..   ++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.+|.
T Consensus        93 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A           93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             TTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            468999999999999999999999999999999954   55678999999999999999999999999999999999873

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

Probab=99.67  E-value=2.3e-16  Score=123.76  Aligned_cols=81  Identities=30%  Similarity=0.524  Sum_probs=75.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+.+|+++|+++|++||.|..|.+..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
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            4679999999999999999999999999999999964   5667899999999999999999999999999999999999


Q ss_pred             cCCC
Q 023765           81 HGGR   84 (277)
Q Consensus        81 ~~~~   84 (277)
                      .+..
T Consensus       192 ~~~~  195 (198)
T 2yh0_A          192 SVGA  195 (198)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8654

>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=99.67  E-value=1.5e-16  Score=121.32  Aligned_cols=78  Identities=19%  Similarity=0.492  Sum_probs=72.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      ++++|||+|||+++|+++|+++|++||.|..+.+..   ++.++|||||+|.+.++|.+|++ +++..|.|+.|.|.++.
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecC
Confidence            467899999999999999999999999999999964   56789999999999999999999 99999999999999987


Q ss_pred             CC
Q 023765           82 GG   83 (277)
Q Consensus        82 ~~   83 (277)
                      +.
T Consensus       165 pk  166 (167)
T 2cjk_A          165 PR  166 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

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

Probab=99.66  E-value=6.3e-16  Score=102.58  Aligned_cols=72  Identities=13%  Similarity=0.146  Sum_probs=66.0

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      ...|+|+||++.+++++|+++|.+||+|..+++..  ..|||||+|.+.++|.+|++.||+..+.|    ..|.|..+
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~--~kGfaFVey~~~~eA~~Ai~~Ln~~~l~g----r~I~V~~A   78 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL--NQGIALCKYTTREEANKAQMALNNCVLAN----TTIFAESP   78 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET--TTTEEEEEESSHHHHHHHHHHHTTEEETT----EEEEEECC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC--CCcEEEEEECCHHHHHHHHHHhcCCEECC----cEEEEEEC
Confidence            67899999999999999999999999999999866  56799999999999999999999999999    67777654

>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=99.66  E-value=3.5e-16  Score=113.79  Aligned_cols=80  Identities=20%  Similarity=0.302  Sum_probs=69.0

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      .....+|||+|||..+++++|+++|.+||.|..|.|+.+..    .+||||+|.+.++|++|++.|||..+.|+    .|
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~----~l   94 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ----PI   94 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSS----BC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCe----EE
Confidence            34578999999999999999999999999999999987753    35999999999999999999999999994    55


Q ss_pred             EEeecCCC
Q 023765          182 RVREYDSR  189 (277)
Q Consensus       182 ~~~~~~~~  189 (277)
                      .|..+...
T Consensus        95 ~v~~a~~~  102 (126)
T 3ex7_B           95 SVDWCFVR  102 (126)
T ss_dssp             EEEESEES
T ss_pred             EEEEecCC
Confidence            56555433

>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=99.66  E-value=2e-15  Score=106.85  Aligned_cols=83  Identities=22%  Similarity=0.275  Sum_probs=72.3

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC-CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG-GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       104 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~-~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      .......+|||+|||..+++++|+++|.+||.|..|.+..+.. .+||||+|.+.++|++|++.||+..+.|    ..|.
T Consensus        17 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g----~~l~   92 (109)
T 1x4a_A           17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDG----YRLR   92 (109)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETT----EECE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECC----eEEE
Confidence            3445678999999999999999999999999999999976543 5699999999999999999999999999    6777


Q ss_pred             EeecCCCC
Q 023765          183 VREYDSRR  190 (277)
Q Consensus       183 ~~~~~~~r  190 (277)
                      |......+
T Consensus        93 V~~a~~~~  100 (109)
T 1x4a_A           93 VEFPRSGR  100 (109)
T ss_dssp             EECCCCCC
T ss_pred             EEEcccCC
Confidence            87776543

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

Probab=99.66  E-value=1.1e-15  Score=108.07  Aligned_cols=77  Identities=17%  Similarity=0.089  Sum_probs=69.4

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      +..+|||+||+..+++++|+++|.+||.|..|.|+.+..+    |||||+|.+.++|++|++.|||..+.|    ..|.|
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~g----r~i~V   80 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMG----NIIHA   80 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT----EECEE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECC----eEEEE
Confidence            4679999999999999999999999999999999988663    599999999999999999999999999    56677


Q ss_pred             eecCC
Q 023765          184 REYDS  188 (277)
Q Consensus       184 ~~~~~  188 (277)
                      ..+..
T Consensus        81 ~~a~~   85 (110)
T 3s8s_A           81 QLDIK   85 (110)
T ss_dssp             EECST
T ss_pred             EECCC
Confidence            66643

>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=99.66  E-value=4.1e-15  Score=104.12  Aligned_cols=82  Identities=10%  Similarity=0.080  Sum_probs=72.5

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC--cEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG--MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~--~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      ......+|||+|||..+++++|+++|.+||.|..|.+..+..+  +||||+|.+.++|++|+..||+..+.|    ..|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----~~l~   86 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILG----KEVK   86 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETT----EEEE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCC----CeEE
Confidence            3455789999999999999999999999999999999886543  699999999999999999999999999    6788


Q ss_pred             EeecCCCC
Q 023765          183 VREYDSRR  190 (277)
Q Consensus       183 ~~~~~~~r  190 (277)
                      |.......
T Consensus        87 V~~a~~~~   94 (103)
T 2cqi_A           87 VNWATTPS   94 (103)
T ss_dssp             EEECCCTT
T ss_pred             EEECCCCc
Confidence            88776543

>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=99.65  E-value=3.7e-16  Score=109.47  Aligned_cols=81  Identities=23%  Similarity=0.397  Sum_probs=70.7

Q ss_pred             CCCCCCeEEEcCC--CCCCC--------HHHHHHHhhccCCeeEEEeecC-----CCCCcEEEEEEcChHHHHHHHHhcC
Q 023765            2 SSRSSRTLYVGNL--PGDTR--------MREVEDLFYKYGPIVDIDLKIP-----PRPPGYAFLEFEDYRDAEDAIRGRD   66 (277)
Q Consensus         2 ~~~~~~~l~V~nL--~~~~t--------~~~l~~~F~~~G~v~~v~~~~~-----~~~~g~afV~f~~~~~a~~a~~~l~   66 (277)
                      ++.|+++|.|.|+  |..+.        +++|+++|++||+|..|.|+.+     +.++|+|||+|.++++|.+|++.||
T Consensus         1 ~g~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~ln   80 (105)
T 3v4m_A            1 GGHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLT   80 (105)
T ss_dssp             CCSCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHT
T ss_pred             CCCCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhC
Confidence            4679999999999  43443        4689999999999999999653     2568999999999999999999999


Q ss_pred             CcccCCceEEEEEccC
Q 023765           67 GYNFDGYRLRVELAHG   82 (277)
Q Consensus        67 ~~~~~g~~i~v~~a~~   82 (277)
                      |..|.|+.|.|.++..
T Consensus        81 G~~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           81 GRKFANRVVVTKYCDP   96 (105)
T ss_dssp             TCEETTEECEEEEECH
T ss_pred             CCEeCCCEEEEEEeCH
Confidence            9999999999999763

>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=99.65  E-value=4.4e-16  Score=121.46  Aligned_cols=78  Identities=15%  Similarity=0.371  Sum_probs=69.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      .++|||+|||+++|+++|.++|++||+|..|.|+.  ++.++|||||+|.+.++|..|+..+ +..|.|+.|.|.++...
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDDY  187 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTTC
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHHH
Confidence            47899999999999999999999999999999965  4667899999999999999999855 45999999999998764


Q ss_pred             C
Q 023765           84 R   84 (277)
Q Consensus        84 ~   84 (277)
                      .
T Consensus       188 ~  188 (193)
T 2voo_A          188 F  188 (193)
T ss_dssp             -
T ss_pred             H
Confidence            3

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=6.5e-16  Score=107.32  Aligned_cols=77  Identities=6%  Similarity=0.080  Sum_probs=67.3

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCC--CeecccceeeEEEEe
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDR--SEFRNAFSRSYVRVR  184 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g--~~~~g~~~~~~i~~~  184 (277)
                      .+..+|||+|||+.+++++|+++|.+||.|..|.++.+  .+||||+|.+.++|..|++.|++  ..+.|    ..|.|.
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~--kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~G----r~l~V~   87 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG--KNQAFIEMNTEEAANTMVNYYTSVTPVLRG----QPIYIQ   87 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT--TTEEEEEESSHHHHHHHHHHHTTSCCEETT----EECCBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCEEEEEECCHHHHHHHHHHhccCCceECC----EEEEEE
Confidence            44789999999999999999999999999999999876  47999999999999999998864  78888    567776


Q ss_pred             ecCCC
Q 023765          185 EYDSR  189 (277)
Q Consensus       185 ~~~~~  189 (277)
                      ....+
T Consensus        88 ~A~~~   92 (105)
T 1sjq_A           88 FSNHK   92 (105)
T ss_dssp             CCSSS
T ss_pred             EcCCC
Confidence            66543

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

Probab=99.65  E-value=1.5e-15  Score=106.38  Aligned_cols=82  Identities=17%  Similarity=0.109  Sum_probs=71.6

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceee
Q 023765          104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRS  179 (277)
Q Consensus       104 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  179 (277)
                      +...+..+|||+|||..+++++|+++|.+||.|..|.+..+..    .+||||+|.+.++|++|+..|||..+.|    .
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g----~   83 (103)
T 2dnm_A            8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDG----R   83 (103)
T ss_dssp             SCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTT----B
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECC----c
Confidence            3445678999999999999999999999999999999987654    3699999999999999999999999999    5


Q ss_pred             EEEEeecCCC
Q 023765          180 YVRVREYDSR  189 (277)
Q Consensus       180 ~i~~~~~~~~  189 (277)
                      .|.|......
T Consensus        84 ~l~V~~a~~~   93 (103)
T 2dnm_A           84 ELRVQVARYG   93 (103)
T ss_dssp             CCEEEECSSC
T ss_pred             EEEEEECCcC
Confidence            6677766544

>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=99.65  E-value=3.2e-16  Score=120.37  Aligned_cols=77  Identities=19%  Similarity=0.317  Sum_probs=70.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccC---CceEEEEE
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFD---GYRLRVEL   79 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~---g~~i~v~~   79 (277)
                      +.++|||+|||+.+|+++|+++|++||.|..+.++.  ++.++|||||+|.+.++|.+|+..|||..+.   |++|.|.|
T Consensus        94 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~  173 (175)
T 3nmr_A           94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKF  173 (175)
T ss_dssp             GGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEE
T ss_pred             CCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEe
Confidence            568999999999999999999999999999999965  4567899999999999999999999998776   48999999


Q ss_pred             cc
Q 023765           80 AH   81 (277)
Q Consensus        80 a~   81 (277)
                      |.
T Consensus       174 ad  175 (175)
T 3nmr_A          174 AD  175 (175)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>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=99.65  E-value=4.9e-16  Score=121.69  Aligned_cols=81  Identities=22%  Similarity=0.425  Sum_probs=70.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      +.++|||+|||+++|+++|+++|+.||.|..|.++.   ++.++|||||+|.+.++|.+|+.. ++..|.|+.|.|.++.
T Consensus       103 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~  181 (196)
T 1l3k_A          103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKAL  181 (196)
T ss_dssp             CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecC
Confidence            468999999999999999999999999999999965   467789999999999999999985 8999999999999998


Q ss_pred             CCCCC
Q 023765           82 GGRRH   86 (277)
Q Consensus        82 ~~~~~   86 (277)
                      +....
T Consensus       182 ~k~~~  186 (196)
T 1l3k_A          182 SKQEM  186 (196)
T ss_dssp             -----
T ss_pred             ChhHh
Confidence            76543

>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=99.65  E-value=5e-16  Score=118.52  Aligned_cols=77  Identities=32%  Similarity=0.526  Sum_probs=71.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCC--ceEEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDG--YRLRVE   78 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g--~~i~v~   78 (277)
                      .+.++|||+|||+.+++++|+++|++||.|..+.+..   ++.++|||||+|.+.++|.+|+..|||..|.|  ++|.|.
T Consensus        87 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~  166 (168)
T 1b7f_A           87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR  166 (168)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEE
Confidence            4678999999999999999999999999999999965   45668999999999999999999999999988  999998


Q ss_pred             Ec
Q 023765           79 LA   80 (277)
Q Consensus        79 ~a   80 (277)
                      +|
T Consensus       167 ~A  168 (168)
T 1b7f_A          167 LA  168 (168)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>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=99.65  E-value=5.2e-15  Score=103.63  Aligned_cols=83  Identities=18%  Similarity=0.221  Sum_probs=72.7

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC--CcEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG--GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       104 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~--~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      .......+|||+|||..+++++|+++|.+||.|..|.++.+..  .+||||+|.+.++|++|+..|||..+.|    ..|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----~~l   85 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEG----RKI   85 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETT----EEC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECC----EEE
Confidence            3345578999999999999999999999999999999987754  4699999999999999999999999999    677


Q ss_pred             EEeecCCCC
Q 023765          182 RVREYDSRR  190 (277)
Q Consensus       182 ~~~~~~~~r  190 (277)
                      .|.....+.
T Consensus        86 ~v~~a~~~~   94 (103)
T 2cq3_A           86 EVNNATARV   94 (103)
T ss_dssp             EEEECCSSC
T ss_pred             EEEEcccCC
Confidence            777776543

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

Probab=99.65  E-value=2.8e-15  Score=104.22  Aligned_cols=80  Identities=16%  Similarity=0.143  Sum_probs=71.1

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC----CCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR----GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      .+..+|||+|||..+++++|+++|.+||.|..|.+..+.    ..+||||+|.+.++|..|+..|||..+.|    ..|.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----~~l~   81 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQG----RMLH   81 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSS----CEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECC----cEEE
Confidence            347899999999999999999999999999999998775    33699999999999999999999999999    6777


Q ss_pred             EeecCCCC
Q 023765          183 VREYDSRR  190 (277)
Q Consensus       183 ~~~~~~~r  190 (277)
                      |.......
T Consensus        82 V~~a~~~~   89 (99)
T 1whw_A           82 VLPSTIKK   89 (99)
T ss_dssp             EEECCCCS
T ss_pred             EEEcCCCc
Confidence            87776654

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

Probab=99.64  E-value=1.9e-15  Score=105.85  Aligned_cols=82  Identities=15%  Similarity=0.193  Sum_probs=71.0

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEec--CCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD--RGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~--~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      ......+|||+|||..+++++|+++|.+||.|..|.+..+  ...+||||+|.+.++|.+|+..|||..+.|    ..|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g----~~l~   86 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVAT----KPLY   86 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSS----SBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCC----cEEE
Confidence            3446789999999999999999999999999999999987  223599999999999999999999999999    5666


Q ss_pred             EeecCCCC
Q 023765          183 VREYDSRR  190 (277)
Q Consensus       183 ~~~~~~~r  190 (277)
                      |.......
T Consensus        87 V~~a~~~~   94 (103)
T 2d9p_A           87 VALAQRKE   94 (103)
T ss_dssp             EEECSSCC
T ss_pred             EEEecccc
Confidence            77665543

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

Probab=99.64  E-value=3.4e-15  Score=104.59  Aligned_cols=81  Identities=15%  Similarity=0.188  Sum_probs=72.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      .....+|||+|||..+++++|+++|.+||.|..|.+..+..+    +||||+|.+.++|++|+..|||..+.|    ..|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g----~~l   87 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDH----LIL   87 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETT----EEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCC----cEE
Confidence            455789999999999999999999999999999999987543    599999999999999999999999999    677


Q ss_pred             EEeecCCCC
Q 023765          182 RVREYDSRR  190 (277)
Q Consensus       182 ~~~~~~~~r  190 (277)
                      .|.......
T Consensus        88 ~v~~a~~~~   96 (103)
T 2cq0_A           88 NVEWAKPST   96 (103)
T ss_dssp             EEEESSCCC
T ss_pred             EEEECCCCC
Confidence            777776553

>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=99.64  E-value=7e-15  Score=105.10  Aligned_cols=81  Identities=21%  Similarity=0.259  Sum_probs=71.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      .....+|||+|||..+++++|+++|.+||.|..|.+..+..+    +||||+|.+.++|++|++.||+..+.|    ..|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----~~l   97 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGM----KRL   97 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETT----EEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECC----EEE
Confidence            345689999999999999999999999999999999987643    499999999999999999999999999    677


Q ss_pred             EEeecCCCC
Q 023765          182 RVREYDSRR  190 (277)
Q Consensus       182 ~~~~~~~~r  190 (277)
                      .|.....+.
T Consensus        98 ~V~~a~~~~  106 (115)
T 2cpz_A           98 KVQLKRSKN  106 (115)
T ss_dssp             EEECCCCSC
T ss_pred             EEEEcCCCC
Confidence            787776543

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

Probab=99.63  E-value=3.8e-15  Score=101.62  Aligned_cols=77  Identities=17%  Similarity=0.280  Sum_probs=68.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      ..+..+|||+|||..+++++|+++|.+||.|..+.+.    .+||||+|.+.++|++|+..||+..+.|    ..|.|..
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----KNYGFVHIEDKTAAEDAIRNLHHYKLHG----VNINVEA   76 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE----TTEEEEEESSHHHHHHHHHHHTTCBCSS----CBCEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE----CCEEEEEECCHHHHHHHHHHhcCCccCC----cEEEEEE
Confidence            3457899999999999999999999999999999998    3599999999999999999999999999    5677777


Q ss_pred             cCCCC
Q 023765          186 YDSRR  190 (277)
Q Consensus       186 ~~~~r  190 (277)
                      .....
T Consensus        77 a~~~~   81 (90)
T 2dnq_A           77 SKNKS   81 (90)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            65543

>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=99.63  E-value=1.1e-15  Score=106.06  Aligned_cols=77  Identities=10%  Similarity=0.078  Sum_probs=67.2

Q ss_pred             CCCceEEEeCCCC-CCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCC--eecccceeeEEEE
Q 023765          107 RSDYRVLVTGLPS-SASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRS--EFRNAFSRSYVRV  183 (277)
Q Consensus       107 ~~~~~l~v~~l~~-~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~--~~~g~~~~~~i~~  183 (277)
                      .+..+|||+|||+ .+++++|+++|.+||.|..|.++.++  +||||+|++.++|..|++.||+.  .+.|    ..|.|
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~k--g~aFVef~~~~~A~~Ai~~l~~~~~~~~G----r~l~V   86 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI--NEAFIEMATTEDAQAAVDYYTTTPALVFG----KPVRV   86 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS--SCEEEEESSHHHHHHHHHHHHHSCCEETT----EECEE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCC--CEEEEEECCHHHHHHHHHHHcCCCceECC----cEEEE
Confidence            3578999999999 99999999999999999999998764  59999999999999999999864  4888    67777


Q ss_pred             eecCCC
Q 023765          184 REYDSR  189 (277)
Q Consensus       184 ~~~~~~  189 (277)
                      ......
T Consensus        87 ~~a~~~   92 (102)
T 1x4d_A           87 HLSQKY   92 (102)
T ss_dssp             EEECCC
T ss_pred             EECCCC
Confidence            776543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=2.9e-15  Score=103.73  Aligned_cols=80  Identities=20%  Similarity=0.205  Sum_probs=69.8

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      ......+|||+|||..+++++|+++|.+||.|. +.+..+...+||||+|.+.++|+.|+..|||..+.|    ..|.|.
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-LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGT----DTLRVA   89 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSS----SCCEEE
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECC----cEEEEE
Confidence            345578999999999999999999999999997 777777778899999999999999999999999999    456666


Q ss_pred             ecCCC
Q 023765          185 EYDSR  189 (277)
Q Consensus       185 ~~~~~  189 (277)
                      ...++
T Consensus        90 ~a~~~   94 (97)
T 2e5j_A           90 LARQQ   94 (97)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            65443

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

Probab=99.63  E-value=1.5e-14  Score=103.33  Aligned_cols=82  Identities=17%  Similarity=0.240  Sum_probs=72.3

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeE
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSY  180 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  180 (277)
                      ......+|||+|||..+++++|+++|.+||.|..|.++.+..+    +||||+|.+.++|++|+..|||..+.|    ..
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----~~   86 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGG----RQ   86 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETT----EE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC----EE
Confidence            3455789999999999999999999999999999999987543    599999999999999999999999999    67


Q ss_pred             EEEeecCCCC
Q 023765          181 VRVREYDSRR  190 (277)
Q Consensus       181 i~~~~~~~~r  190 (277)
                      |.|.......
T Consensus        87 l~V~~a~~~~   96 (115)
T 2dgo_A           87 IRTNWATRKP   96 (115)
T ss_dssp             CEEEESSCCC
T ss_pred             EEEEEccCCC
Confidence            7777776543

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

Probab=99.63  E-value=3.9e-15  Score=103.45  Aligned_cols=80  Identities=15%  Similarity=0.299  Sum_probs=69.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      ..+..+|||+|||..+++++|+++|.+||.|..|.++.+..    .+||||+|.+.++|++|++ ||+..+.|    ..|
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g----~~l   81 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMG----KKV   81 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSS----CBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECC----eEE
Confidence            34578999999999999999999999999999999987653    4699999999999999998 99999999    566


Q ss_pred             EEeecCCCC
Q 023765          182 RVREYDSRR  190 (277)
Q Consensus       182 ~~~~~~~~r  190 (277)
                      .|....++.
T Consensus        82 ~V~~a~~~~   90 (99)
T 2dgs_A           82 EVKRAEPRD   90 (99)
T ss_dssp             EEEECCCCC
T ss_pred             EEEECCCCc
Confidence            777665543

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

Probab=99.63  E-value=5.5e-15  Score=101.25  Aligned_cols=77  Identities=23%  Similarity=0.348  Sum_probs=69.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      .....+|||+|||..+++++|+++|.+||.|..+.+..+    ||||+|.+.++|++|+..|||..+.|    ..|.|..
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~----~afV~f~~~~~a~~A~~~l~g~~~~g----~~l~V~~   78 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD----YAFVHMERAEDAVEAIRGLDNTEFQG----KRMHVQL   78 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS----EEEEEESCHHHHHHHHHHHTTEEETT----EEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC----EEEEEECCHHHHHHHHHHhCCCeeCC----cEEEEEE
Confidence            345789999999999999999999999999999999866    99999999999999999999999999    6788887


Q ss_pred             cCCCC
Q 023765          186 YDSRR  190 (277)
Q Consensus       186 ~~~~r  190 (277)
                      ...+.
T Consensus        79 a~~~~   83 (92)
T 2dgt_A           79 STSRL   83 (92)
T ss_dssp             SSCCC
T ss_pred             ccCCC
Confidence            76543

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

Probab=99.63  E-value=6.3e-15  Score=101.58  Aligned_cols=80  Identities=19%  Similarity=0.225  Sum_probs=70.5

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceee
Q 023765          104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRS  179 (277)
Q Consensus       104 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  179 (277)
                      ....+..+|||+|||..+++++|+++|.+||.|..+.+..+..+    +||||+|.+.++|++|+..|||..+.|    .
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g----~   85 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDG----R   85 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETT----E
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECC----E
Confidence            34456789999999999999999999999999999999987553    599999999999999999999999999    5


Q ss_pred             EEEEeecC
Q 023765          180 YVRVREYD  187 (277)
Q Consensus       180 ~i~~~~~~  187 (277)
                      .|.|...+
T Consensus        86 ~l~v~~a~   93 (95)
T 2cqc_A           86 RIRVSGPS   93 (95)
T ss_dssp             EEEEECCS
T ss_pred             EEEEEecC
Confidence            67776553

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

Probab=99.63  E-value=4.1e-15  Score=102.52  Aligned_cols=79  Identities=15%  Similarity=0.187  Sum_probs=70.1

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      +..+|||+|||..+++++|+++|.+||.|..+.+..+..    .+||||+|.+.++|++|+..|||..+.|    ..|.|
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----~~l~V   79 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAG----RPMRV   79 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSS----SCCEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCC----cEEEE
Confidence            468999999999999999999999999999999988754    3699999999999999999999999999    56677


Q ss_pred             eecCCCC
Q 023765          184 REYDSRR  190 (277)
Q Consensus       184 ~~~~~~r  190 (277)
                      .....+.
T Consensus        80 ~~a~~~~   86 (95)
T 2dnz_A           80 GHVTERL   86 (95)
T ss_dssp             EESSCCC
T ss_pred             EEccccc
Confidence            7665543

>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=99.63  E-value=9.9e-16  Score=116.67  Aligned_cols=76  Identities=32%  Similarity=0.588  Sum_probs=69.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCce--EEEEE
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYR--LRVEL   79 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~--i~v~~   79 (277)
                      +.++|||+|||+.+++++|+++|++||.|..+.+..   ++.++|||||+|.+.++|.+|+..|||..|.|+.  |.|.|
T Consensus        87 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~  166 (167)
T 1fxl_A           87 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF  166 (167)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEe
Confidence            568899999999999999999999999999999954   4567899999999999999999999999999965  88887


Q ss_pred             c
Q 023765           80 A   80 (277)
Q Consensus        80 a   80 (277)
                      |
T Consensus       167 A  167 (167)
T 1fxl_A          167 A  167 (167)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.63  E-value=2.5e-15  Score=102.01  Aligned_cols=76  Identities=11%  Similarity=0.186  Sum_probs=68.0

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC-----CCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR-----GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~-----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ..+|||+|||..+++++|.++|.+||.|..+.+..+.     ..+||||+|.+.++|++|+..|||..+.|    ..|.|
T Consensus         4 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----~~l~v   79 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDG----QEITA   79 (88)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETT----EECEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECC----eEEEE
Confidence            5799999999999999999999999999999998775     45699999999999999999999999999    56666


Q ss_pred             eecCC
Q 023765          184 REYDS  188 (277)
Q Consensus       184 ~~~~~  188 (277)
                      ....+
T Consensus        80 ~~a~~   84 (88)
T 4a8x_A           80 TAVLA   84 (88)
T ss_dssp             EEECC
T ss_pred             EECCC
Confidence            66543

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

Probab=99.63  E-value=2.8e-15  Score=104.80  Aligned_cols=80  Identities=21%  Similarity=0.201  Sum_probs=71.3

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      .+..+|||+|||..+++++|+++|.+||.|..|.++.+..    .+||||+|.+.++|++|++.|||..+.|    ..|.
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g----~~l~   85 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG----RTIR   85 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETT----EEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC----cEEE
Confidence            4578999999999999999999999999999999987643    4699999999999999999999999999    6788


Q ss_pred             EeecCCCC
Q 023765          183 VREYDSRR  190 (277)
Q Consensus       183 ~~~~~~~r  190 (277)
                      |.......
T Consensus        86 V~~a~~~~   93 (102)
T 2cqb_A           86 VNLAKPMR   93 (102)
T ss_dssp             EEECCCCC
T ss_pred             EEeCCCCC
Confidence            88776554

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

Probab=99.63  E-value=4.3e-15  Score=104.24  Aligned_cols=81  Identities=17%  Similarity=0.346  Sum_probs=70.6

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC-----CcEEEEEEechhHHHHHHHhcCCCeeccccee
Q 023765          104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG-----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       104 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~-----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  178 (277)
                      .+..+..+|||+|||..+++++|+++|.+|| |..|.++.+..     .+||||+|.+.++|++|| .||+..+.|    
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g----   83 (104)
T 1wi8_A           10 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGN----   83 (104)
T ss_dssp             CCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETT----
T ss_pred             CCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCC----
Confidence            3445678999999999999999999999999 99999987754     359999999999999999 999999999    


Q ss_pred             eEEEEeecCCCC
Q 023765          179 SYVRVREYDSRR  190 (277)
Q Consensus       179 ~~i~~~~~~~~r  190 (277)
                      ..|.|.....+.
T Consensus        84 ~~l~V~~a~~~~   95 (104)
T 1wi8_A           84 KRIRVDVADQAQ   95 (104)
T ss_dssp             EECEEEECCCCC
T ss_pred             cEEEEEEccCCC
Confidence            677777776554

>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=99.63  E-value=8.6e-15  Score=102.48  Aligned_cols=77  Identities=9%  Similarity=0.160  Sum_probs=68.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      ..+..+|||+|||..+++++|+++|.+||.|..|.+..+    ||||+|.+.++|++|+..||+..+.|    ..|.|..
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 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD----YAFIHFDERDGAVKAMEEMNGKDLEG----ENIEIVF   79 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECSS----CEEEEESSHHHHHHHHHHHTTEEETT----EEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC----EEEEEeCCHHHHHHHHHHHCCCccCC----CEEEEEE
Confidence            345789999999999999999999999999999998855    99999999999999999999999999    6777877


Q ss_pred             cCCCC
Q 023765          186 YDSRR  190 (277)
Q Consensus       186 ~~~~r  190 (277)
                      .....
T Consensus        80 a~~~~   84 (103)
T 2dgu_A           80 AKPPD   84 (103)
T ss_dssp             CCCCC
T ss_pred             cCCCc
Confidence            76543

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

Probab=99.63  E-value=2.7e-15  Score=104.84  Aligned_cols=80  Identities=21%  Similarity=0.316  Sum_probs=69.2

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      .....+|||+|||..+++++|+++|.+||.|..|.+..+..    .+||||+|.+.++|+.|++.||+..+.|+    .|
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~----~l   84 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGR----QI   84 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSC----CC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCe----EE
Confidence            34578999999999999999999999999999999987653    35999999999999999999999999994    55


Q ss_pred             EEeecCCC
Q 023765          182 RVREYDSR  189 (277)
Q Consensus       182 ~~~~~~~~  189 (277)
                      .|......
T Consensus        85 ~v~~a~~~   92 (102)
T 1x5s_A           85 RVDQAGKS   92 (102)
T ss_dssp             EEEEEECC
T ss_pred             EEEECCCC
Confidence            56555443

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

Probab=99.63  E-value=3.6e-15  Score=102.50  Aligned_cols=76  Identities=14%  Similarity=0.149  Sum_probs=66.6

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCe--ecccceeeEEEEe
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSE--FRNAFSRSYVRVR  184 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~--~~g~~~~~~i~~~  184 (277)
                      .+..+|||+|||..+++++|.++|.+||.|..+.++..  .+||||+|++.++|.+|++.|++..  +.|    ..|.|.
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~--kg~AFVef~~~~~A~~Av~~ln~~~~~i~G----r~i~V~   92 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK--KRQALVEFEDVLGACNAVNYAADNQIYIAG----HPAFVN   92 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT--TTEEEEEESSHHHHHHHHHHHHHSCEEETT----EEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC--CCEEEEEECCHHHHHHHHHHhcCCCceeCC----cEEEEE
Confidence            45789999999999999999999999999999988754  4699999999999999999999876  668    677777


Q ss_pred             ecCC
Q 023765          185 EYDS  188 (277)
Q Consensus       185 ~~~~  188 (277)
                      ....
T Consensus        93 ~S~~   96 (100)
T 3r27_A           93 YSTS   96 (100)
T ss_dssp             ECSC
T ss_pred             eccc
Confidence            6643

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

Probab=99.63  E-value=3.8e-15  Score=103.32  Aligned_cols=79  Identities=15%  Similarity=0.244  Sum_probs=70.0

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC-------CcEEEEEEechhHHHHHHHhcCCCeecccceeeE
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG-------GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSY  180 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~-------~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  180 (277)
                      +..+|||+|||..+++++|+++|.+||.|..|.+..+..       .+||||+|.+.++|++|+..|||..+.|    ..
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----~~   79 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDG----HK   79 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETT----EE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCC----eE
Confidence            367999999999999999999999999999999987654       3599999999999999999999999999    67


Q ss_pred             EEEeecCCCC
Q 023765          181 VRVREYDSRR  190 (277)
Q Consensus       181 i~~~~~~~~r  190 (277)
                      |.|.......
T Consensus        80 l~V~~a~~~~   89 (98)
T 2cpf_A           80 LEVRISERAT   89 (98)
T ss_dssp             CEEECSSCSS
T ss_pred             EEEEEccCCC
Confidence            7777776543

>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=99.62  E-value=1.4e-15  Score=126.00  Aligned_cols=75  Identities=21%  Similarity=0.384  Sum_probs=70.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccC-CceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFD-GYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~-g~~i~v~~a~   81 (277)
                      ++++|||+|||..+|+++|+++|+.||.|..|.|....  +|||||+|.+.++|.+|+..|||..|. |+.|.|.|++
T Consensus       206 ~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          206 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR--HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC--CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            67899999999999999999999999999999998543  589999999999999999999999999 9999999985

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

Probab=99.62  E-value=4.6e-15  Score=101.22  Aligned_cols=75  Identities=21%  Similarity=0.337  Sum_probs=68.2

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      ....+|||+|||..+++++|+++|.+||.|..+.+..+    ||||+|.+.++|+.|+..|||..+.|    ..|.|...
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 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD----YAFVHMEKEADAKAAIAQLNGKEVKG----KRINVELS   78 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS----CEEEEESCHHHHHHHHHHHTTCEETT----EECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC----EEEEEECCHHHHHHHHHHhCCCEECC----cEEEEEEC
Confidence            44789999999999999999999999999999999865    99999999999999999999999999    67777777


Q ss_pred             CCC
Q 023765          187 DSR  189 (277)
Q Consensus       187 ~~~  189 (277)
                      ...
T Consensus        79 ~~~   81 (90)
T 2dnp_A           79 TKG   81 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            554

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

Probab=99.62  E-value=1.2e-14  Score=101.25  Aligned_cols=81  Identities=20%  Similarity=0.335  Sum_probs=71.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC---cEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG---MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      .....+|||+|||..+++++|.++|.+||.|..|.+..+..+   +||||+|.+.++|++|+..|||..+.|    ..|.
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----~~l~   89 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKE----NIIK   89 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSS----CEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECC----EEEE
Confidence            345789999999999999999999999999999999987632   599999999999999999999999999    6777


Q ss_pred             EeecCCCC
Q 023765          183 VREYDSRR  190 (277)
Q Consensus       183 ~~~~~~~r  190 (277)
                      |....++.
T Consensus        90 v~~a~~~~   97 (100)
T 2do4_A           90 VAISNSGP   97 (100)
T ss_dssp             EEECCCCS
T ss_pred             EEECCCCC
Confidence            77776543

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

Probab=99.62  E-value=5.2e-15  Score=102.83  Aligned_cols=83  Identities=8%  Similarity=0.090  Sum_probs=73.0

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCee-EEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVC-FSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~-~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      .+..+|||+|||..+++++|+++|.+||.|. .+.++.+..+    +||||+|.+.++|++|+..|||..+.|+.....|
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l   86 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRF   86 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEEC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeE
Confidence            3478999999999999999999999999999 9999988643    5999999999999999999999999997655557


Q ss_pred             EEeecCCC
Q 023765          182 RVREYDSR  189 (277)
Q Consensus       182 ~~~~~~~~  189 (277)
                      .|......
T Consensus        87 ~v~~a~~~   94 (99)
T 2div_A           87 KLNYATYS   94 (99)
T ss_dssp             CEEETTCC
T ss_pred             EEeecCCC
Confidence            77776544

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

Probab=99.62  E-value=5e-15  Score=102.27  Aligned_cols=79  Identities=16%  Similarity=0.195  Sum_probs=70.6

Q ss_pred             CCCceEEEeCCCCCCCHHHHH----HHHHhcCCeeEEEEEecCC-CcEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          107 RSDYRVLVTGLPSSASWQDLK----DHMRRAGDVCFSQVFRDRG-GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~----~~f~~~g~v~~~~~~~~~~-~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      ....+|||+|||..+++++|+    ++|.+||.|..|.++.+.. .+||||+|.+.++|++|++.|||..+.|    ..|
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g----r~l   82 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGS----KKI   82 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETT----EEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECC----eEE
Confidence            346799999999999999999    9999999999999986644 4699999999999999999999999999    678


Q ss_pred             EEeecCCC
Q 023765          182 RVREYDSR  189 (277)
Q Consensus       182 ~~~~~~~~  189 (277)
                      .|..+.+.
T Consensus        83 ~V~~a~~~   90 (96)
T 2dgx_A           83 LVSLATGA   90 (96)
T ss_dssp             EEEECCCS
T ss_pred             EEEEcCCC
Confidence            88877554

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

Probab=99.62  E-value=1.1e-14  Score=102.03  Aligned_cols=81  Identities=19%  Similarity=0.299  Sum_probs=70.6

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceee
Q 023765          104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRS  179 (277)
Q Consensus       104 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  179 (277)
                      .+..+..+|||+|||..+++++|+++|.+|| |..|.++.+..+    +||||+|.+.++|++|+ .|||..+.|    .
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g----~   83 (103)
T 2dng_A           10 LPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGD----R   83 (103)
T ss_dssp             CCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETT----E
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECC----e
Confidence            3445678999999999999999999999997 999999988653    59999999999999999 899999999    6


Q ss_pred             EEEEeecCCCC
Q 023765          180 YVRVREYDSRR  190 (277)
Q Consensus       180 ~i~~~~~~~~r  190 (277)
                      .|.|.......
T Consensus        84 ~l~V~~a~~~~   94 (103)
T 2dng_A           84 SLRVDIAEGRK   94 (103)
T ss_dssp             ECEEEECCCCC
T ss_pred             EEEEEEecCCC
Confidence            77777776543

>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=99.62  E-value=4.4e-15  Score=100.62  Aligned_cols=77  Identities=17%  Similarity=0.205  Sum_probs=67.3

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      .+..+|||+|||..+++++|+++|.+||.|..+.+..+..+    +||||+|.+.++|+.|+..|||..+.|    ..|.
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g----~~l~   79 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGG----RQIR   79 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT----EECE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECC----eEEE
Confidence            34679999999999999999999999999999999987533    599999999999999999999999999    5666


Q ss_pred             EeecC
Q 023765          183 VREYD  187 (277)
Q Consensus       183 ~~~~~  187 (277)
                      |....
T Consensus        80 v~~a~   84 (87)
T 3bs9_A           80 TNWAT   84 (87)
T ss_dssp             EEEEC
T ss_pred             EEecC
Confidence            66554

>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=99.62  E-value=5.7e-15  Score=102.23  Aligned_cols=77  Identities=21%  Similarity=0.234  Sum_probs=68.4

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeec--ccceeeEEEEe
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFR--NAFSRSYVRVR  184 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~--g~~~~~~i~~~  184 (277)
                      .+..+|||+|||..+++++|+++|.+||.|..|.+..+  .+||||+|.+.++|++|++.|||..+.  |    ..|.|.
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--DSFAYIQYESLDAAQAACAKMRGFPLGGPD----RRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS--SCCEEEEESSHHHHHHHHHHHTTCBCSSSS----CBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC--CCEEEEEECCHHHHHHHHHHHCCCEeCCCC----cEEEEE
Confidence            45689999999999999999999999999999998876  569999999999999999999999999  7    566676


Q ss_pred             ecCCC
Q 023765          185 EYDSR  189 (277)
Q Consensus       185 ~~~~~  189 (277)
                      ...++
T Consensus        89 ~a~~~   93 (97)
T 1why_A           89 FAKSG   93 (97)
T ss_dssp             ECCCC
T ss_pred             ECCCC
Confidence            66544

>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=99.62  E-value=4.5e-15  Score=100.11  Aligned_cols=75  Identities=21%  Similarity=0.206  Sum_probs=66.3

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      .+..+|||+|||..+++++|+++|.+||.|..+.+..+..    .+||||+|.+.++|..|+..|||..+.|    ..|.
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----~~l~   80 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG----RTIR   80 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETT----EECE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECC----cEEE
Confidence            3478999999999999999999999999999999987643    3599999999999999999999999999    4555


Q ss_pred             Eee
Q 023765          183 VRE  185 (277)
Q Consensus       183 ~~~  185 (277)
                      |..
T Consensus        81 v~~   83 (85)
T 3mdf_A           81 VNL   83 (85)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            554

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

Probab=99.62  E-value=9.5e-15  Score=103.71  Aligned_cols=82  Identities=10%  Similarity=0.155  Sum_probs=71.9

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcC------CCeecc
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLD------RSEFRN  174 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~------g~~~~g  174 (277)
                      ...+..+|||+|||..+++++|+++|.+||.|..|.++.+..    .+||||+|.+.++|.+|+..||      +..+.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            345578999999999999999999999999999999987744    4699999999999999999999      999999


Q ss_pred             cceeeEEEEeecCCCC
Q 023765          175 AFSRSYVRVREYDSRR  190 (277)
Q Consensus       175 ~~~~~~i~~~~~~~~r  190 (277)
                          ..|.|.....+.
T Consensus        91 ----~~l~v~~a~~~~  102 (111)
T 1x4h_A           91 ----RQLKVDLAVTRD  102 (111)
T ss_dssp             ----CEEEEECCCCCC
T ss_pred             ----EEEEEEECCCCc
Confidence                677777776543

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

Probab=99.62  E-value=2.5e-14  Score=102.06  Aligned_cols=79  Identities=22%  Similarity=0.320  Sum_probs=70.0

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC---cEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG---MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      ..+..+|||+|||..+++++|+++|.+||.|..|.+..+..+   +||||+|.+.++|++|+..||+..+.|    ..|.
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----~~l~   87 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFD----RPMH   87 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETT----EECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCC----CEEE
Confidence            345789999999999999999999999999999999987653   599999999999999999999999999    5667


Q ss_pred             EeecCC
Q 023765          183 VREYDS  188 (277)
Q Consensus       183 ~~~~~~  188 (277)
                      |.....
T Consensus        88 v~~a~~   93 (114)
T 2do0_A           88 VKMDER   93 (114)
T ss_dssp             EEECSC
T ss_pred             EEEccc
Confidence            766544

>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=99.62  E-value=9.3e-15  Score=102.68  Aligned_cols=81  Identities=28%  Similarity=0.354  Sum_probs=71.1

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeE
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSY  180 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  180 (277)
                      ......+|||+|||..+++++|+++|.+||.|..|.+..+..    .+||||+|.+.++|++|+..||+..+.|    ..
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----~~   86 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYG----KP   86 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSS----CB
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECC----eE
Confidence            345578999999999999999999999999999999988753    3599999999999999999999999999    56


Q ss_pred             EEEeecCCC
Q 023765          181 VRVREYDSR  189 (277)
Q Consensus       181 i~~~~~~~~  189 (277)
                      |.|......
T Consensus        87 l~v~~a~~~   95 (105)
T 1x5u_A           87 IRVNKASAH   95 (105)
T ss_dssp             CEEEETTTT
T ss_pred             EEEEECCCC
Confidence            677766554

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

Probab=99.61  E-value=6.6e-15  Score=101.27  Aligned_cols=79  Identities=16%  Similarity=0.216  Sum_probs=69.1

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceee
Q 023765          104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRS  179 (277)
Q Consensus       104 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  179 (277)
                      ....+..+|||+|||..+++++|+++|.+||.|..+.+..+..    .+||||+|.+.++|++|++.|||..+.|    .
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g----~   86 (94)
T 2e5h_A           11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFG----R   86 (94)
T ss_dssp             SCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETT----E
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCC----c
Confidence            3445678999999999999999999999999999999987654    3699999999999999999999999999    5


Q ss_pred             EEEEeec
Q 023765          180 YVRVREY  186 (277)
Q Consensus       180 ~i~~~~~  186 (277)
                      .|.|..+
T Consensus        87 ~l~v~~a   93 (94)
T 2e5h_A           87 VIKASIA   93 (94)
T ss_dssp             EEEEEEC
T ss_pred             EEEEEec
Confidence            6666543

>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=99.61  E-value=6.2e-15  Score=103.79  Aligned_cols=81  Identities=19%  Similarity=0.250  Sum_probs=70.0

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCee---ccccee
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEF---RNAFSR  178 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~---~g~~~~  178 (277)
                      .....+|||+|||..+++++|+++|.+||.|..|.++.+..    .+||||+|.+.++|.+|++.||+..+   .|    
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g----   85 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMN----   85 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCS----
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCC----
Confidence            44578999999999999999999999999999999988654    46999999999999999999999987   66    


Q ss_pred             eEEEEeecCCCC
Q 023765          179 SYVRVREYDSRR  190 (277)
Q Consensus       179 ~~i~~~~~~~~r  190 (277)
                      ..|.|.......
T Consensus        86 ~~l~v~~a~~~~   97 (106)
T 2dgp_A           86 RPIQVKPADSES   97 (106)
T ss_dssp             SCCEEEECCCCS
T ss_pred             ceEEEEECCccc
Confidence            566676665543

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

Probab=99.61  E-value=9e-15  Score=103.10  Aligned_cols=83  Identities=17%  Similarity=0.266  Sum_probs=71.3

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC-----CCcEEEEEEechhHHHHHHHhc-CCCeecccce
Q 023765          104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR-----GGMTGIVDYTSYDDMKYAIRKL-DRSEFRNAFS  177 (277)
Q Consensus       104 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~-----~~~~~fv~f~~~~~a~~a~~~l-~g~~~~g~~~  177 (277)
                      .......+|||+|||..+++++|+++|.+||.|..|.++.+.     ..+||||+|.+.++|++|+..| |+..+.|   
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g---   86 (107)
T 2cph_A           10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYG---   86 (107)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSS---
T ss_pred             ccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECC---
Confidence            344567899999999999999999999999999999998772     2369999999999999999999 9999999   


Q ss_pred             eeEEEEeecCCCC
Q 023765          178 RSYVRVREYDSRR  190 (277)
Q Consensus       178 ~~~i~~~~~~~~r  190 (277)
                       ..|.|.......
T Consensus        87 -~~l~v~~a~~~~   98 (107)
T 2cph_A           87 -RRLVLEWADSEV   98 (107)
T ss_dssp             -CBCEEEECCCCC
T ss_pred             -CEEEEEeCCCCC
Confidence             566676665543

>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=99.61  E-value=1.1e-14  Score=101.00  Aligned_cols=78  Identities=8%  Similarity=0.086  Sum_probs=67.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhc--CCCeecccceeeEEEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKL--DRSEFRNAFSRSYVRV  183 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l--~g~~~~g~~~~~~i~~  183 (277)
                      ..+..+|||+|||..+++++|+++|.+||.|..|.++.+  .+||||+|.+.++|..|++.|  ++..+.|    ..|.|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~--kg~aFVef~~~~~A~~Ai~~l~~~~~~~~G----r~l~V   85 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG--KNQAFLELATEEAAITMVNYYSAVTPHLRN----QPIYI   85 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT--TTEEEEEESSHHHHHHHHHHHHHSCCEETT----EECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC--CCEEEEEECCHHHHHHHHHHhccCCceECC----cEEEE
Confidence            345789999999999999999999999999999988865  579999999999999999977  4677888    67777


Q ss_pred             eecCCC
Q 023765          184 REYDSR  189 (277)
Q Consensus       184 ~~~~~~  189 (277)
                      .....+
T Consensus        86 ~~a~~~   91 (101)
T 2cq1_A           86 QYSNHK   91 (101)
T ss_dssp             EECSCS
T ss_pred             EEcCcc
Confidence            776543

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

Probab=99.61  E-value=4.6e-15  Score=102.47  Aligned_cols=79  Identities=15%  Similarity=0.205  Sum_probs=69.8

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEE-EEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFS-QVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~-~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      +.++|||+|||..+++++|.++|.+||.|..+ .++.+..    .+||||+|.+.++|++|+..|||..+.|    ..|.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g----~~l~   79 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCN----RPIT   79 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETT----EECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECC----EEEE
Confidence            46899999999999999999999999999999 8887643    3599999999999999999999999999    6777


Q ss_pred             EeecCCCC
Q 023765          183 VREYDSRR  190 (277)
Q Consensus       183 ~~~~~~~r  190 (277)
                      |.......
T Consensus        80 v~~a~~~~   87 (96)
T 1x5t_A           80 VSYAFKKD   87 (96)
T ss_dssp             EEESCCCC
T ss_pred             EEEecccC
Confidence            77765543

>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=99.61  E-value=9.3e-15  Score=103.39  Aligned_cols=78  Identities=14%  Similarity=0.173  Sum_probs=70.2

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      ...++|||+|||..+++++|+++|.+||.|..|.+..+  .+||||+|.+.++|+.|+..|||..+.|    ..|.|...
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~afV~f~~~~~a~~A~~~l~g~~~~g----~~l~v~~a   96 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE--KGYSFVRFSTHESAAHAIVSVNGTTIEG----HVVKCYWG   96 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT--TTEEEEEESSHHHHHHHHHHHTTCEETT----EECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC--CCEEEEEECCHHHHHHHHHHcCCCEECC----cEEEEEec
Confidence            45789999999999999999999999999999999877  5699999999999999999999999999    67777776


Q ss_pred             CCCC
Q 023765          187 DSRR  190 (277)
Q Consensus       187 ~~~r  190 (277)
                      ....
T Consensus        97 ~~~~  100 (109)
T 1x4g_A           97 KESP  100 (109)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

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

Probab=99.61  E-value=1.6e-15  Score=119.12  Aligned_cols=78  Identities=18%  Similarity=0.266  Sum_probs=71.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccC-CeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccC-CceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYG-PIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFD-GYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G-~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~-g~~i~v~~a~   81 (277)
                      .++++|||+|||+.+|+++|+++|+.|| .|..|.+..+  .+|||||+|.+.++|.+|+..|||..|. |+.|.|.|+.
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~  195 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK--DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK  195 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST--TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEEC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeec
Confidence            3588999999999999999999999999 9999999653  3799999999999999999999999999 9999999987


Q ss_pred             CC
Q 023765           82 GG   83 (277)
Q Consensus        82 ~~   83 (277)
                      +.
T Consensus       196 ~~  197 (198)
T 1qm9_A          196 ST  197 (198)
T ss_dssp             CC
T ss_pred             cc
Confidence            53

>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=99.61  E-value=6.1e-15  Score=101.88  Aligned_cols=77  Identities=12%  Similarity=0.212  Sum_probs=69.1

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      ..+|||+|||..+++++|.++|.+||.|..+.+..+..    .+||||+|.+.++|++|++.|||..+.|    ..|.|.
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g----~~l~V~   77 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGS----RFLKCG   77 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETT----EECEEE
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECC----eEEEEE
Confidence            57999999999999999999999999999999987754    4699999999999999999999999999    677777


Q ss_pred             ecCCC
Q 023765          185 EYDSR  189 (277)
Q Consensus       185 ~~~~~  189 (277)
                      .....
T Consensus        78 ~a~~~   82 (96)
T 2x1f_A           78 YSSNS   82 (96)
T ss_dssp             ECSCS
T ss_pred             EcCCC
Confidence            66544

>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=99.61  E-value=1.4e-14  Score=101.82  Aligned_cols=82  Identities=22%  Similarity=0.219  Sum_probs=69.4

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC---cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG---MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ....+|||+|||..+++++|.++|.+||.|..|.+..+..+   +||||+|.+.++|++|+..|||..+.|. ....|.|
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 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPG-ASSSLVV   91 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTT-CSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCC-CCccEEE
Confidence            45789999999999999999999999999999999987643   5999999999999999999999998871 1134566


Q ss_pred             eecCCC
Q 023765          184 REYDSR  189 (277)
Q Consensus       184 ~~~~~~  189 (277)
                      ......
T Consensus        92 ~~a~~~   97 (105)
T 2dnh_A           92 KFADTD   97 (105)
T ss_dssp             EESCSS
T ss_pred             EECccC
Confidence            666544

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

Probab=99.60  E-value=2e-14  Score=99.79  Aligned_cols=76  Identities=18%  Similarity=0.144  Sum_probs=67.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRA--GDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~--g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ..+..+|||+|||..+++++|+++|.+|  |.|..+.+..    +||||+|.+.++|++|+..|||..+.|    ..|.|
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 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR----DYAFVHFSNREDAVEAMKALNGKVLDG----SPIEV   83 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEECS----SEEEEEESSHHHHHHHHHHHSSEEETT----EEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEeC----CeEEEEeCCHHHHHHHHHHhCCCEeCC----cEEEE
Confidence            3457899999999999999999999999  8999888764    399999999999999999999999998    67888


Q ss_pred             eecCCC
Q 023765          184 REYDSR  189 (277)
Q Consensus       184 ~~~~~~  189 (277)
                      ......
T Consensus        84 ~~a~~~   89 (99)
T 2cpd_A           84 TLAKPV   89 (99)
T ss_dssp             ECCCCC
T ss_pred             EECCCC
Confidence            877654

>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=99.60  E-value=9e-15  Score=98.14  Aligned_cols=75  Identities=17%  Similarity=0.254  Sum_probs=67.2

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      .+|||+|||..+++++|.++|.+||.|..+.+..+..+    +||||+|.+.++|+.|+..|||..+.|    ..|.|..
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g----~~l~v~~   77 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNG----RPLRINW   77 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETT----EECEEEE
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCC----cEEEEEe
Confidence            58999999999999999999999999999999887543    599999999999999999999999999    5667766


Q ss_pred             cCC
Q 023765          186 YDS  188 (277)
Q Consensus       186 ~~~  188 (277)
                      ..+
T Consensus        78 a~~   80 (83)
T 3md1_A           78 AAK   80 (83)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            544

>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=99.60  E-value=5.5e-15  Score=103.26  Aligned_cols=78  Identities=17%  Similarity=0.191  Sum_probs=66.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCC--eecccceeeEEEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRS--EFRNAFSRSYVRV  183 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~--~~~g~~~~~~i~~  183 (277)
                      ..+..+|||+|||..+++++|+++|.+||.|..|.++.+  .+||||+|.+.++|.+|++.|++.  .+.|    ..|.|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~--kg~aFVef~~~~~A~~Ai~~l~~~~~~i~G----r~l~V   85 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF--KRQALVEFENIDSAKECVTFAADVPVYIAG----QQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT--TTEEEEEESSHHHHHHHHHHHHHSCCBSSS----SBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC--CCEEEEEECCHHHHHHHHHHhccCCceECC----EEEEE
Confidence            345789999999999999999999999999999988764  569999999999999999988764  4788    56667


Q ss_pred             eecCCC
Q 023765          184 REYDSR  189 (277)
Q Consensus       184 ~~~~~~  189 (277)
                      .....+
T Consensus        86 ~~a~~~   91 (104)
T 1wex_A           86 NYSTSK   91 (104)
T ss_dssp             EECSSS
T ss_pred             EEccCc
Confidence            666543

>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=99.60  E-value=3.4e-15  Score=119.93  Aligned_cols=77  Identities=18%  Similarity=0.273  Sum_probs=71.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccC-CeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccC-CceEEEEEccC
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYG-PIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFD-GYRLRVELAHG   82 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G-~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~-g~~i~v~~a~~   82 (277)
                      ++++|||+|||+.+|+++|+++|++|| .|..|.+...  .+|||||+|.+.++|.+|+..|||..|. |+.|.|.|+.+
T Consensus       150 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~--~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~  227 (229)
T 2adc_A          150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK--DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  227 (229)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS--STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC--CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecC
Confidence            478999999999999999999999999 9999999543  3799999999999999999999999999 99999999875


Q ss_pred             C
Q 023765           83 G   83 (277)
Q Consensus        83 ~   83 (277)
                      .
T Consensus       228 ~  228 (229)
T 2adc_A          228 T  228 (229)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

Probab=99.60  E-value=3.5e-15  Score=104.09  Aligned_cols=75  Identities=23%  Similarity=0.208  Sum_probs=67.8

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeecCCC
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDSR  189 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~~~  189 (277)
                      ++|||+|||..+++++|+++|.+||.|..+.+..+ ..+||||+|.+.++|++|++.|||..+.|    ..|.|......
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-PPGFAFVEFEDPRDAEDAVRGLDGKVICG----SRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-SSSEEEEECSSHHHHHHHHHHHHHSCSSS----CCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-CCCEEEEEECCHHHHHHHHHHHCCCeECC----cEEEEEEccCC
Confidence            47999999999999999999999999999999888 66799999999999999999999999999    45677766554

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

Probab=99.60  E-value=4.8e-15  Score=104.59  Aligned_cols=77  Identities=16%  Similarity=0.200  Sum_probs=68.8

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      ......+|||+|||..+++++|+++|.+||.|..+.+.    .+||||+|.+.++|++|+..|||..+.|    ..|.|.
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----NGFAFVEFEEAESAAKAIEEVHGKSFAN----QPLEVV   98 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE----TTEEEEECSSHHHHHHHHHHHTTCEETT----EECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE----CCEEEEEECCHHHHHHHHHHcCCCEECC----eEEEEE
Confidence            34557899999999999999999999999999999998    5699999999999999999999999998    677777


Q ss_pred             ecCCC
Q 023765          185 EYDSR  189 (277)
Q Consensus       185 ~~~~~  189 (277)
                      .....
T Consensus        99 ~a~~~  103 (108)
T 2jvo_A           99 YSKLP  103 (108)
T ss_dssp             SCSCC
T ss_pred             EecCC
Confidence            76554

>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=99.60  E-value=1.3e-15  Score=119.98  Aligned_cols=76  Identities=14%  Similarity=0.173  Sum_probs=67.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCe--eEEEeecC-CCCCcEEEEEEcChHHHHHHHHhcCCcccCCc----eEEE
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPI--VDIDLKIP-PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGY----RLRV   77 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v--~~v~~~~~-~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~----~i~v   77 (277)
                      ++++|||+|||+.+|+++|+++|++||.|  ..+.+..+ +..+|||||+|.+.++|..|+..|||..|.|.    ++.|
T Consensus       122 p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~v  201 (205)
T 3tyt_A          122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTL  201 (205)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEEC
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEE
Confidence            56789999999999999999999999999  88888654 34569999999999999999999999999887    5777


Q ss_pred             EEc
Q 023765           78 ELA   80 (277)
Q Consensus        78 ~~a   80 (277)
                      ++|
T Consensus       202 k~~  204 (205)
T 3tyt_A          202 KLC  204 (205)
T ss_dssp             EEE
T ss_pred             Eec
Confidence            765

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=4.4e-15  Score=105.71  Aligned_cols=78  Identities=6%  Similarity=0.075  Sum_probs=67.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCC--CeecccceeeEEEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDR--SEFRNAFSRSYVRV  183 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g--~~~~g~~~~~~i~~  183 (277)
                      ..+..+|||+|||+.+++++|+++|.+||.|..|.++.+  .+||||+|++.++|.+|++.|++  ..+.|    ..|.|
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~--kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~G----r~l~V  101 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG--KNQAFIEMNTEEAANTMVNYYTSVTPVLRG----QPIYI  101 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG--GTEEEEECSCHHHHHHHHHHHHHHCCCBTT----BCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC--CCEEEEEECCHHHHHHHHHHhccCCceECC----eEEEE
Confidence            345789999999999999999999999999999999876  46999999999999999998874  67888    56677


Q ss_pred             eecCCC
Q 023765          184 REYDSR  189 (277)
Q Consensus       184 ~~~~~~  189 (277)
                      .....+
T Consensus       102 ~~a~~k  107 (119)
T 2ad9_A          102 QFSNHK  107 (119)
T ss_dssp             EECSSS
T ss_pred             EEccCC
Confidence            766543

>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=99.60  E-value=1.1e-14  Score=103.23  Aligned_cols=74  Identities=14%  Similarity=0.157  Sum_probs=66.1

Q ss_pred             CCCceEEEeCCCCC-CCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          107 RSDYRVLVTGLPSS-ASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       107 ~~~~~l~v~~l~~~-~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      ....+|||+|||.. +++++|+++|.+||.|..|.+    ..+||||+|.+.++|++|+..|||..+.|    ..|.|..
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i----~~g~afV~f~~~~~A~~A~~~l~g~~~~g----~~l~V~~   96 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV----HKGYAFVQYSNERHARAAVLGENGRVLAG----QTLDINM   96 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE----ETTEEEEECSSSHHHHHHHHHHTTCEETT----EECCEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE----eCCEEEEEECCHHHHHHHHHHcCCCEECC----eEEEEEE
Confidence            34689999999999 999999999999999999998    34599999999999999999999999999    5677776


Q ss_pred             cCC
Q 023765          186 YDS  188 (277)
Q Consensus       186 ~~~  188 (277)
                      ...
T Consensus        97 a~~   99 (110)
T 1wf1_A           97 AGE   99 (110)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            654

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

Probab=99.60  E-value=9e-15  Score=101.61  Aligned_cols=75  Identities=20%  Similarity=0.268  Sum_probs=66.5

Q ss_pred             CCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeE--------EEEEecCCC----cEEEEEEechhHHHHHHHhcCCC
Q 023765          103 GVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCF--------SQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRS  170 (277)
Q Consensus       103 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~--------~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~  170 (277)
                      ..+..+.++|||+|||..+++++|+++|.+||.|..        +.+..+..+    |||||+|.+.++|+.|++.|||.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~   86 (99)
T 2la6_A            7 HHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK   86 (99)
T ss_dssp             CCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            344556889999999999999999999999999999        999887543    59999999999999999999999


Q ss_pred             eecccce
Q 023765          171 EFRNAFS  177 (277)
Q Consensus       171 ~~~g~~~  177 (277)
                      .+.|+.+
T Consensus        87 ~~~g~~l   93 (99)
T 2la6_A           87 EFSGNPI   93 (99)
T ss_dssp             BSSSSBC
T ss_pred             EeCCcEE
Confidence            9999533

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

Probab=99.59  E-value=9.8e-15  Score=99.99  Aligned_cols=80  Identities=21%  Similarity=0.390  Sum_probs=68.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC--CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG--GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~--~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ..+..+|||+|||..+++++|+++|.+||.|..+.+..+..  .+||||+|.+.++|++|+..|||..+.|+    .|.|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~----~l~v   80 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGR----EIDV   80 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTB----CCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCc----EEEE
Confidence            34578999999999999999999999999999999987532  36999999999999999999999999994    5555


Q ss_pred             eecCCC
Q 023765          184 REYDSR  189 (277)
Q Consensus       184 ~~~~~~  189 (277)
                      ......
T Consensus        81 ~~a~~~   86 (92)
T 2dgv_A           81 RIDRNA   86 (92)
T ss_dssp             EECSCC
T ss_pred             EEcCCC
Confidence            555443

>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=99.59  E-value=1.2e-14  Score=98.00  Aligned_cols=75  Identities=15%  Similarity=0.240  Sum_probs=65.8

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhc-CCCeecccceeeEEEE
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKL-DRSEFRNAFSRSYVRV  183 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l-~g~~~~g~~~~~~i~~  183 (277)
                      ......+|||+|||..+++++|+++|.+||.|..+.+..+  .+||||+|.+.++|..|+..| +|..+.|    ..|.|
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~--kg~afV~f~~~~~A~~a~~~l~~~~~~~g----~~l~v   81 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR--QQCAFIQFATRQAAEVAAEKSFNKLIVNG----RRLNV   81 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG--GTEEEEEESSHHHHHHHHHTTTTTCEETT----EECCE
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC--CCEEEEEECCHHHHHHHHHHhcCCeeECC----CEEEE
Confidence            3455789999999999999999999999999999999875  469999999999999999999 9999999    44554


Q ss_pred             ee
Q 023765          184 RE  185 (277)
Q Consensus       184 ~~  185 (277)
                      ..
T Consensus        82 ~~   83 (85)
T 2ytc_A           82 KW   83 (85)
T ss_dssp             EE
T ss_pred             Ee
Confidence            43

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.59  E-value=2.2e-15  Score=102.90  Aligned_cols=76  Identities=14%  Similarity=0.247  Sum_probs=65.8

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcC-CeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcC-CCeecccceeeEEEE
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRAG-DVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLD-RSEFRNAFSRSYVRV  183 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~g-~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~-g~~~~g~~~~~~i~~  183 (277)
                      ++|||+|||+.+++++|+++|.+|| .|..|.++.++.    .|||||+|.+.++|++|++.++ +..+.|    ..|.|
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~g----r~i~V   77 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILG----QKVSM   77 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETT----EEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECC----EEEEE
Confidence            5899999999999999999999999 899999887643    4699999999999999999874 567888    67888


Q ss_pred             eecCCC
Q 023765          184 REYDSR  189 (277)
Q Consensus       184 ~~~~~~  189 (277)
                      ....++
T Consensus        78 ~~a~~~   83 (91)
T 2lxi_A           78 HYSDPK   83 (91)
T ss_dssp             ECCCSC
T ss_pred             EEcCCC
Confidence            776544

>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=99.59  E-value=1.3e-14  Score=99.97  Aligned_cols=78  Identities=22%  Similarity=0.284  Sum_probs=69.0

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC---cEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG---MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      ......+|||+|||..+++++|+++|.+||.|..|.+..+..+   +||||+|.+.++|.+|+..|||..+.|    ..|
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----~~l   87 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYG----RPI   87 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETT----EEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECC----CEE
Confidence            3455789999999999999999999999999999999987653   599999999999999999999999999    566


Q ss_pred             EEeec
Q 023765          182 RVREY  186 (277)
Q Consensus       182 ~~~~~  186 (277)
                      .|...
T Consensus        88 ~V~~a   92 (95)
T 2ywk_A           88 NVSGP   92 (95)
T ss_dssp             EEECC
T ss_pred             EEEEc
Confidence            66544

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

Probab=99.59  E-value=4.7e-14  Score=104.29  Aligned_cols=82  Identities=20%  Similarity=0.198  Sum_probs=72.6

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceee
Q 023765          104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRS  179 (277)
Q Consensus       104 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  179 (277)
                      +......+|||+|||..+++++|.++|..||.|..|.+..+..+    +||||+|.+.++|.+|++.|||..+.|    .
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----~  112 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN----K  112 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSS----C
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC----e
Confidence            34456789999999999999999999999999999999987653    599999999999999999999999999    6


Q ss_pred             EEEEeecCCC
Q 023765          180 YVRVREYDSR  189 (277)
Q Consensus       180 ~i~~~~~~~~  189 (277)
                      .|.|..+...
T Consensus       113 ~l~v~~a~~~  122 (139)
T 1u6f_A          113 RLKVALAASG  122 (139)
T ss_dssp             EEEEEESSCC
T ss_pred             EEEEEECCCC
Confidence            7778777654

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=6.9e-15  Score=102.59  Aligned_cols=81  Identities=16%  Similarity=0.261  Sum_probs=66.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      ..+..+|||+|||..+++++|+++|.+||.|..+........+||||+|.+.++|++|+..||+..+.|    ..|.|..
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 SGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEG----RAIRLEL   87 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEEECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETT----EEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCC----eEEEEEE
Confidence            345789999999999999999999999998832222222344699999999999999999999999999    6788887


Q ss_pred             cCCCC
Q 023765          186 YDSRR  190 (277)
Q Consensus       186 ~~~~r  190 (277)
                      ...+.
T Consensus        88 a~~~~   92 (101)
T 2fc9_A           88 QGPRG   92 (101)
T ss_dssp             CSSCC
T ss_pred             cCCCC
Confidence            76553

>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=99.59  E-value=7.8e-15  Score=104.12  Aligned_cols=80  Identities=13%  Similarity=0.145  Sum_probs=71.2

Q ss_pred             CCCceEEEeCCCCCCCHHHHH---HHHHhcCCeeEEEEEecCC-------CcEEEEEEechhHHHHHHHhcCCCeecccc
Q 023765          107 RSDYRVLVTGLPSSASWQDLK---DHMRRAGDVCFSQVFRDRG-------GMTGIVDYTSYDDMKYAIRKLDRSEFRNAF  176 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~---~~f~~~g~v~~~~~~~~~~-------~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  176 (277)
                      ...++|||+|||+.+++++|.   ++|.+||.|..|.+..+..       .+||||+|.+.++|++|++.|||..++|  
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~g--   90 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDG--   90 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETT--
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECC--
Confidence            447899999999999999999   9999999999999987754       2699999999999999999999999999  


Q ss_pred             eeeEEEEeecCCCC
Q 023765          177 SRSYVRVREYDSRR  190 (277)
Q Consensus       177 ~~~~i~~~~~~~~r  190 (277)
                        ..|.|.....+.
T Consensus        91 --r~l~V~~a~~k~  102 (111)
T 2cpi_A           91 --RTLKASLGTTKY  102 (111)
T ss_dssp             --EEEEEESCCCCS
T ss_pred             --EEEEEEeccccc
Confidence              678888776553

>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=99.59  E-value=1.5e-14  Score=101.92  Aligned_cols=79  Identities=19%  Similarity=0.245  Sum_probs=68.5

Q ss_pred             CCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC---cEEEEEEechhHHHHHHHhcCCCeecccceee
Q 023765          103 GVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG---MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRS  179 (277)
Q Consensus       103 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  179 (277)
                      ++...+..+|||+|||..+++++|+++|.+||.|..|.+..+..+   +||||+|.+.++|++|+..|||..+.|    .
T Consensus        23 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----~   98 (107)
T 3ulh_A           23 GAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDG----R   98 (107)
T ss_dssp             -CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETT----E
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCC----c
Confidence            344556889999999999999999999999999999999987633   499999999999999999999999999    4


Q ss_pred             EEEEee
Q 023765          180 YVRVRE  185 (277)
Q Consensus       180 ~i~~~~  185 (277)
                      .|.|..
T Consensus        99 ~l~V~~  104 (107)
T 3ulh_A           99 PMNIQL  104 (107)
T ss_dssp             ECEEEE
T ss_pred             EEEEEE
Confidence            555544

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

Probab=99.59  E-value=1.4e-14  Score=103.14  Aligned_cols=81  Identities=22%  Similarity=0.354  Sum_probs=70.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCee--------EEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeec
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVC--------FSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFR  173 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~--------~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~  173 (277)
                      ....++|||+|||..+++++|+++|.+||.|.        .|.++.+..    .+||||+|.+.++|++|+..|||..+.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   91 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   91 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccC
Confidence            44578999999999999999999999999998        688887743    359999999999999999999999999


Q ss_pred             ccceeeEEEEeecCCCC
Q 023765          174 NAFSRSYVRVREYDSRR  190 (277)
Q Consensus       174 g~~~~~~i~~~~~~~~r  190 (277)
                      |    ..|.|.......
T Consensus        92 g----~~l~V~~a~~~~  104 (113)
T 2cpe_A           92 G----SKLKVSLARKKP  104 (113)
T ss_dssp             T----EECEEECSSCCC
T ss_pred             C----CEEEEEECCCCC
Confidence            9    677787776543

>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=99.59  E-value=7.3e-15  Score=107.01  Aligned_cols=81  Identities=19%  Similarity=0.207  Sum_probs=70.8

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeE
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSY  180 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  180 (277)
                      ...+..+|||+|||..+++++|+++|.+||.|..|.+..+..    .+||||+|.+.++|++|+..|||..+.|    ..
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g----~~  117 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDG----RR  117 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSS----SC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECC----EE
Confidence            345678999999999999999999999999999999987643    4699999999999999999999999999    56


Q ss_pred             EEEeecCCC
Q 023765          181 VRVREYDSR  189 (277)
Q Consensus       181 i~~~~~~~~  189 (277)
                      |.|......
T Consensus       118 l~V~~a~~~  126 (129)
T 2kxn_B          118 IRVDFSITK  126 (129)
T ss_dssp             CEESCCSSS
T ss_pred             EEEEEecCC
Confidence            677666544

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

Probab=99.59  E-value=1.2e-14  Score=102.32  Aligned_cols=77  Identities=19%  Similarity=0.299  Sum_probs=67.9

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      ...++|||+|||..+++++|.++|.+||.|..|.+..+..+    +||||+|.+.++|+.|+..|||..+.|+    .|.
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~----~l~   96 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ----PIS   96 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSS----BCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCc----EEE
Confidence            45789999999999999999999999999999999987653    5999999999999999999999999994    455


Q ss_pred             EeecC
Q 023765          183 VREYD  187 (277)
Q Consensus       183 ~~~~~  187 (277)
                      |....
T Consensus        97 V~~a~  101 (106)
T 1p27_B           97 VDWCF  101 (106)
T ss_dssp             EEESE
T ss_pred             EEeec
Confidence            55443

>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=99.59  E-value=4.3e-15  Score=124.75  Aligned_cols=77  Identities=17%  Similarity=0.250  Sum_probs=67.9

Q ss_pred             CCCCCCeEEEcC--CCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccC---Cc--e
Q 023765            2 SSRSSRTLYVGN--LPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFD---GY--R   74 (277)
Q Consensus         2 ~~~~~~~l~V~n--L~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~---g~--~   74 (277)
                      ++.++++|||+|  |+..+|+++|+++|++||+|..|.|..   ++|||||+|.+.++|.+|++.|||..+.   |+  .
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~---~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~   90 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP---NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT   90 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT---TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEE
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC---CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceE
Confidence            467999999999  578999999999999999999998864   5899999999999999999999998883   44  5


Q ss_pred             EEEEEcc
Q 023765           75 LRVELAH   81 (277)
Q Consensus        75 i~v~~a~   81 (277)
                      |.|.++.
T Consensus        91 ly~~~~~   97 (345)
T 3tht_A           91 LYLNFVE   97 (345)
T ss_dssp             CEEEECS
T ss_pred             EEEEEee
Confidence            7777764

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

Probab=99.58  E-value=1.1e-14  Score=100.60  Aligned_cols=79  Identities=23%  Similarity=0.291  Sum_probs=69.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEE-EEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFS-QVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~-~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      .....+|||+|||..+++++|+++|.+||.|..+ .++.+..++.|||+|.+.++|..|+..|||..+.|    ..|.|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g----~~l~V~   87 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLEN----FTLKVA   87 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSS----CBCEEE
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECC----cEEEEE
Confidence            3457899999999999999999999999999999 58888777789999999999999999999999999    455666


Q ss_pred             ecCC
Q 023765          185 EYDS  188 (277)
Q Consensus       185 ~~~~  188 (277)
                      ...+
T Consensus        88 ~a~~   91 (96)
T 2e44_A           88 YIPD   91 (96)
T ss_dssp             ECCC
T ss_pred             EcCc
Confidence            5543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.58  E-value=4.4e-15  Score=101.96  Aligned_cols=78  Identities=9%  Similarity=0.082  Sum_probs=66.3

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCC--eeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCe----eccc
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGD--VCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSE----FRNA  175 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~--v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~----~~g~  175 (277)
                      .....+|||+|||+.+|+++|.++|.+||.  +..|.++.++.    .|||||+|.+.++|++|++.|||..    ++| 
T Consensus         6 ~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~G-   84 (95)
T 2lkz_A            6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDG-   84 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETT-
T ss_pred             CCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECC-
Confidence            344789999999999999999999999995  66788887654    3699999999999999999999974    788 


Q ss_pred             ceeeEEEEeecC
Q 023765          176 FSRSYVRVREYD  187 (277)
Q Consensus       176 ~~~~~i~~~~~~  187 (277)
                         ..|.|..++
T Consensus        85 ---r~i~V~~Ak   93 (95)
T 2lkz_A           85 ---KTIGVDFAK   93 (95)
T ss_dssp             ---EEEEEEECC
T ss_pred             ---EEEEEEEcc
Confidence               677776653

>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=1.2e-14  Score=108.78  Aligned_cols=81  Identities=17%  Similarity=0.177  Sum_probs=69.9

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      .....|||+||++.+++++|.++|.+||+|..|.+......+||||+|.+.++|++|++.|||..|.|.  ...|+|...
T Consensus        44 s~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           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNA--CCTLRIDFS  121 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSS--CSCEEEEEC
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCC--CcEEEEEEe
Confidence            335679999999999999999999999999999998776677999999999999999999999999652  146777776


Q ss_pred             CCC
Q 023765          187 DSR  189 (277)
Q Consensus       187 ~~~  189 (277)
                      +.+
T Consensus       122 k~~  124 (164)
T 1sjr_A          122 KLT  124 (164)
T ss_dssp             SSS
T ss_pred             cCC
Confidence            544

>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=99.58  E-value=1.2e-14  Score=102.92  Aligned_cols=80  Identities=15%  Similarity=0.185  Sum_probs=70.0

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      .....+|||+|||..+++++|.++|.+||.|..|.+..+..    .+||||+|.+.++|..|+..|||..+.|    ..|
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g----~~l   98 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG----QTI   98 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETT----EEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECC----cEE
Confidence            34578999999999999999999999999999999987753    3699999999999999999999999999    566


Q ss_pred             EEeecCCC
Q 023765          182 RVREYDSR  189 (277)
Q Consensus       182 ~~~~~~~~  189 (277)
                      .|.....+
T Consensus        99 ~V~~a~~~  106 (110)
T 1oo0_B           99 QVDWCFVK  106 (110)
T ss_dssp             EEEESEES
T ss_pred             EEEEcccC
Confidence            67665443

>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=99.58  E-value=1.6e-14  Score=100.40  Aligned_cols=78  Identities=18%  Similarity=0.215  Sum_probs=68.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      ..+..+|||+|||..+++++|+++|.+||.|..|.+..+  .+||||+|.+.++|++|++.|||..+.|    ..|.|..
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--KGFGFIRLETRTLAEIAKVELDNMPLRG----KQLRVRF   85 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT--TTEEEEECSSSHHHHHHHHHHTTCCBTT----BCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC--CCEEEEEECCHHHHHHHHHHhCCCEeCC----ceEEEEE
Confidence            345789999999999999999999999999999998865  4699999999999999999999999999    5666766


Q ss_pred             cCCC
Q 023765          186 YDSR  189 (277)
Q Consensus       186 ~~~~  189 (277)
                      ....
T Consensus        86 a~~~   89 (99)
T 2cpj_A           86 ACHS   89 (99)
T ss_dssp             SSCC
T ss_pred             cCCC
Confidence            6544

>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=99.58  E-value=2e-14  Score=102.71  Aligned_cols=80  Identities=8%  Similarity=0.086  Sum_probs=69.8

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCe----eEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDV----CFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v----~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      .+..+|||+|||..+++++|.++|.+||.|    ..+.+......+||||+|.+.++|+.|+..|||..+.|    ..|.
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g----~~l~   98 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYG----KILV   98 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSS----CBCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCC----cEEE
Confidence            457899999999999999999999999998    66777766667899999999999999999999999998    5667


Q ss_pred             EeecCCCC
Q 023765          183 VREYDSRR  190 (277)
Q Consensus       183 ~~~~~~~r  190 (277)
                      |.......
T Consensus        99 v~~a~~~~  106 (115)
T 2cpx_A           99 IEFGKNKK  106 (115)
T ss_dssp             EEECCCCS
T ss_pred             EEEccCCC
Confidence            77766543

>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=99.58  E-value=1e-14  Score=101.08  Aligned_cols=79  Identities=14%  Similarity=0.124  Sum_probs=67.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      .....+|||+|||..+++++|+++|.+||.|..+.++.+..+    +||||+|.+.++|++|+..|||..+.|    ..|
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g----~~l   87 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGS----RKV   87 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETT----EEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCC----eEE
Confidence            445789999999999999999999999999987766655433    599999999999999999999999999    566


Q ss_pred             EEeecCC
Q 023765          182 RVREYDS  188 (277)
Q Consensus       182 ~~~~~~~  188 (277)
                      .|.....
T Consensus        88 ~V~~a~~   94 (98)
T 2cqp_A           88 KLVLGSG   94 (98)
T ss_dssp             EEEESSC
T ss_pred             EEEEcCC
Confidence            6666543

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=2.4e-14  Score=100.58  Aligned_cols=82  Identities=13%  Similarity=0.201  Sum_probs=71.4

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceee
Q 023765          104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRS  179 (277)
Q Consensus       104 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  179 (277)
                      .......+|||+|||..+++++|+++|.+||.|..|.++.+..+    +||||+|.+.++|++||.. ++..+.|    .
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g----~   85 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDG----R   85 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETT----E
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECC----E
Confidence            34456789999999999999999999999999999999987543    5999999999999999998 9999999    6


Q ss_pred             EEEEeecCCCC
Q 023765          180 YVRVREYDSRR  190 (277)
Q Consensus       180 ~i~~~~~~~~r  190 (277)
                      .|.|....++.
T Consensus        86 ~l~V~~a~~~~   96 (105)
T 2dh8_A           86 NIDPKPCTPRG   96 (105)
T ss_dssp             EEBCCCSCCSS
T ss_pred             EEEEEEccCCC
Confidence            77777665543

>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=99.58  E-value=7.6e-15  Score=100.77  Aligned_cols=77  Identities=16%  Similarity=0.155  Sum_probs=66.0

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCC-eeEEEEEecCCCcEEEEEEechhHHHHHHHhcCC-CeecccceeeEEEEe
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGD-VCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDR-SEFRNAFSRSYVRVR  184 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~-v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g-~~~~g~~~~~~i~~~  184 (277)
                      .+..+|||+|||..+++++|+++|.+||. |..+.+.   ..+||||+|.+.++|++|+..||| ..+.|    ..|.|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~---~~g~afV~f~~~~~A~~A~~~l~g~~~~~g----~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL---KSGYAFVDYPDQNWAIRAIETLSGKVELHG----KIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE---ETTEEEECCSCHHHHHHHHHHHTTTCEETT----EECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc---CCCEEEEEECCHHHHHHHHHHccCCeeECC----EEEEEE
Confidence            34679999999999999999999999999 6656554   246999999999999999999999 99999    677777


Q ss_pred             ecCCCC
Q 023765          185 EYDSRR  190 (277)
Q Consensus       185 ~~~~~r  190 (277)
                      ....+.
T Consensus        79 ~a~~~~   84 (93)
T 2cqh_A           79 YSVSKK   84 (93)
T ss_dssp             ECCCCC
T ss_pred             EccCcc
Confidence            776543

>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=99.58  E-value=2.2e-14  Score=101.20  Aligned_cols=80  Identities=16%  Similarity=0.185  Sum_probs=69.8

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeE
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSY  180 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  180 (277)
                      ...+..+|||+|||..+++++|+++|.+||.|..+.+..+..+    +||||+|.+.++|+.|+..|||..+.|    ..
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g----~~   97 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAG----RP   97 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSS----SC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECC----EE
Confidence            3455789999999999999999999999999999999987543    599999999999999999999999999    45


Q ss_pred             EEEeecCC
Q 023765          181 VRVREYDS  188 (277)
Q Consensus       181 i~~~~~~~  188 (277)
                      |.|....+
T Consensus        98 l~V~~a~~  105 (108)
T 2jrs_A           98 MKVGHVTE  105 (108)
T ss_dssp             CEEECSCS
T ss_pred             EEEEEccc
Confidence            66665543

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

Probab=99.58  E-value=1.1e-14  Score=103.00  Aligned_cols=80  Identities=16%  Similarity=0.215  Sum_probs=70.0

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC--CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG--GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~--~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      ......+|||+|||..+++++|+++|.+||.|..|.+..+..  .+||||+|.+.++|++|+..|||..+.|    ..|.
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g----~~l~  100 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEG----RKIE  100 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETT----EECE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECC----EEEE
Confidence            344578999999999999999999999999999999987643  4699999999999999999999999999    5666


Q ss_pred             EeecCC
Q 023765          183 VREYDS  188 (277)
Q Consensus       183 ~~~~~~  188 (277)
                      |.....
T Consensus       101 V~~a~~  106 (109)
T 2err_A          101 VNNATA  106 (109)
T ss_dssp             EEECCC
T ss_pred             EEECCC
Confidence            666543

>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=99.57  E-value=3.3e-14  Score=107.21  Aligned_cols=79  Identities=15%  Similarity=0.164  Sum_probs=70.8

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      .+..+|||+|||..+++++|+++|.+||.|..|.|+.+..+    +||||+|.+.++|++||..||+..|.|    ..|.
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g----~~l~  112 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDD----RIIR  112 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETT----EECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECC----eEEE
Confidence            45789999999999999999999999999999999988653    599999999999999999999999999    6777


Q ss_pred             EeecCCC
Q 023765          183 VREYDSR  189 (277)
Q Consensus       183 ~~~~~~~  189 (277)
                      |..+...
T Consensus       113 V~~a~~~  119 (156)
T 1h2v_Z          113 TDWDAGF  119 (156)
T ss_dssp             EEEESCC
T ss_pred             EEECCCC
Confidence            7777654

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

Probab=99.57  E-value=2.9e-14  Score=98.56  Aligned_cols=76  Identities=24%  Similarity=0.360  Sum_probs=65.2

Q ss_pred             CCCeEEEcCCC-------CCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEE
Q 023765            5 SSRTLYVGNLP-------GDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV   77 (277)
Q Consensus         5 ~~~~l~V~nL~-------~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v   77 (277)
                      ..+.|.|.-..       ..+|+++|+++|++||+|..|.|+  +.++|||||+|.+.++|..|++.+++  +.|++|.|
T Consensus         9 ~~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~--~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V   84 (100)
T 2d9o_A            9 GTPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS--SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKI   84 (100)
T ss_dssp             SSCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE--SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEE
T ss_pred             ccceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc--cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEE
Confidence            45677777654       458999999999999999999997  46799999999999999999997654  67999999


Q ss_pred             EEccCCC
Q 023765           78 ELAHGGR   84 (277)
Q Consensus        78 ~~a~~~~   84 (277)
                      .|+....
T Consensus        85 ~~a~~~~   91 (100)
T 2d9o_A           85 SWLEGQP   91 (100)
T ss_dssp             ECSSCCC
T ss_pred             EEccCCC
Confidence            9988654

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

Probab=99.57  E-value=4.7e-14  Score=100.89  Aligned_cols=80  Identities=18%  Similarity=0.150  Sum_probs=69.7

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceee
Q 023765          104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRS  179 (277)
Q Consensus       104 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  179 (277)
                      .......+|||+|||..+++++|+++|.+||.|..|.|+.+..    .+||||+|.+.++|++|+..|++ .+.|    .
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g----~   86 (116)
T 2cqd_A           12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDG----R   86 (116)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETT----E
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCC----E
Confidence            3345678999999999999999999999999999999987753    36999999999999999999998 8988    6


Q ss_pred             EEEEeecCC
Q 023765          180 YVRVREYDS  188 (277)
Q Consensus       180 ~i~~~~~~~  188 (277)
                      .|.|.....
T Consensus        87 ~l~V~~a~~   95 (116)
T 2cqd_A           87 KANVNLAYL   95 (116)
T ss_dssp             ECEEEESTT
T ss_pred             EEEEEEccc
Confidence            777777654

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

Probab=99.57  E-value=2.7e-14  Score=100.09  Aligned_cols=80  Identities=18%  Similarity=0.172  Sum_probs=68.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHh-cCCeeEEEEEecCCC---cEEEEEEechhHHHHHHHhcCCCe-ecccceeeE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRR-AGDVCFSQVFRDRGG---MTGIVDYTSYDDMKYAIRKLDRSE-FRNAFSRSY  180 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~-~g~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~-~~g~~~~~~  180 (277)
                      ..+..+|||+|||..+++++|+++|.+ ||.|..|.++.+..+   +||||+|.+.++|.+|+..|||.. +.|+    .
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~----~   81 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSK----P   81 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSS----C
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCE----e
Confidence            345789999999999999999999999 999999999987632   499999999999999999999999 9994    5


Q ss_pred             EEEeecCCC
Q 023765          181 VRVREYDSR  189 (277)
Q Consensus       181 i~~~~~~~~  189 (277)
                      |.|......
T Consensus        82 l~v~~a~~~   90 (104)
T 2dhg_A           82 VRLSVAIPK   90 (104)
T ss_dssp             CCCCBCCCC
T ss_pred             EEEEEccCC
Confidence            556555433

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

Probab=99.57  E-value=3e-14  Score=102.29  Aligned_cols=71  Identities=20%  Similarity=0.301  Sum_probs=64.5

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                      .....++|||+|||..+++++|+++|.+||.|..|.+..+..    .+||||+|.+.++|+.|++.|||..+.|+
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  110 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTK  110 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            345678999999999999999999999999999999987643    46999999999999999999999999994

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

Probab=99.57  E-value=1.5e-14  Score=100.92  Aligned_cols=74  Identities=14%  Similarity=0.096  Sum_probs=65.7

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      ...++|||+|||..+++++|+++|.+||.|..+.+.  ...+||||+|.+.++|..|+..|||..+.|    ..|.|...
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~--~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g----~~l~V~~a   98 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY--PEKGCCFIKYDTHEQAAVCIVALANFPFQG----RNLRTGWG   98 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE--TTTTEEEEECSSHHHHHHHHHHHTTCEETT----EECCCCBC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe--cCCCEEEEEECCHHHHHHHHHHhCCCeECC----eEEEEEec
Confidence            346899999999999999999999999999999988  445799999999999999999999999999    45555544

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

Probab=99.56  E-value=2e-14  Score=100.33  Aligned_cols=72  Identities=18%  Similarity=0.249  Sum_probs=64.3

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC---CcEEEEEEechhHHHHHHHhcCCCeecccceeeE
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG---GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSY  180 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  180 (277)
                      ...+|||+|||..+++++|.++|.+||.|..|.++.+..   .|||||+|.+.++|..|+. +++..+.|+.+.+.
T Consensus        10 ~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~   84 (103)
T 1s79_A           10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLIL   84 (103)
T ss_dssp             GGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            467999999999999999999999999999999998654   4699999999999999999 99999999655443

>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=99.56  E-value=2.8e-14  Score=98.60  Aligned_cols=75  Identities=13%  Similarity=0.158  Sum_probs=66.3

Q ss_pred             CCCCCceEEEeCCCC-CCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          105 SRRSDYRVLVTGLPS-SASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~-~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ...+..+|||+|||. .+++++|+++|.+||.|..+.+.    .+||||+|.+.++|.+|+..|||..+.|    ..|.|
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----NAFGFIQFDNPQSVRDAIEXESQEMNFG----KKLIL   89 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC----SSEEEEEESSHHHHHHHHHHHTTSEETT----EECEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe----CCEEEEEECCHHHHHHHHHHcCCCEECC----EEEEE
Confidence            345678999999998 99999999999999999999985    4699999999999999999999999998    56666


Q ss_pred             eecC
Q 023765          184 REYD  187 (277)
Q Consensus       184 ~~~~  187 (277)
                      ....
T Consensus        90 ~~a~   93 (97)
T 2xnq_A           90 EVSS   93 (97)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            6654

>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=99.56  E-value=5.4e-15  Score=100.85  Aligned_cols=75  Identities=17%  Similarity=0.189  Sum_probs=63.2

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcC--CeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRAG--DVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~g--~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      .+|||+|||..+++++|+++|.+||  .|..+.++.+..+    |||||+|.+.++|++|++.|||..+.|    ..|.|
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~g----r~i~V   77 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHG----QNPVV   77 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSS----CCCEE
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCC----EEEEE
Confidence            4799999999999999999999999  9999999987543    599999999999999999999999999    45666


Q ss_pred             eecCC
Q 023765          184 REYDS  188 (277)
Q Consensus       184 ~~~~~  188 (277)
                      ....+
T Consensus        78 ~~~~~   82 (90)
T 3p5t_L           78 TPSNK   82 (90)
T ss_dssp             CCC--
T ss_pred             EECCC
Confidence            65543

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

Probab=99.56  E-value=5e-14  Score=101.99  Aligned_cols=81  Identities=17%  Similarity=0.143  Sum_probs=70.6

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC---CCcEEEEEEechhHHHHHHHhcCCCeecccceeeE
Q 023765          104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR---GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSY  180 (277)
Q Consensus       104 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~---~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  180 (277)
                      ......++|||+|||..+++++|+++|.+||.|..|.+..+.   ..+||||+|.+.++|.+|+..|||..+.|    ..
T Consensus        30 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g----~~  105 (124)
T 2kt5_A           30 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDG----RP  105 (124)
T ss_dssp             CCCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSS----CE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECC----cE
Confidence            345667899999999999999999999999999999998875   33699999999999999999999999999    56


Q ss_pred             EEEeecCC
Q 023765          181 VRVREYDS  188 (277)
Q Consensus       181 i~~~~~~~  188 (277)
                      |.|.....
T Consensus       106 l~V~~a~~  113 (124)
T 2kt5_A          106 MDIQLVAS  113 (124)
T ss_dssp             EEEEEECC
T ss_pred             EEEEEeCC
Confidence            66665543

>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=99.55  E-value=5.4e-14  Score=95.60  Aligned_cols=75  Identities=17%  Similarity=0.299  Sum_probs=67.1

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      ..+|||+|||..+++++|+++|.+||.|..+.+..+..    .+||||+|.+.++|++|+ .|||..+.|    ..|.|.
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g----~~l~V~   80 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRG----RQIKVI   80 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETT----EECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECC----cEEEEE
Confidence            56899999999999999999999999999999987753    359999999999999999 999999999    677777


Q ss_pred             ecCC
Q 023765          185 EYDS  188 (277)
Q Consensus       185 ~~~~  188 (277)
                      ....
T Consensus        81 ~a~~   84 (89)
T 3ucg_A           81 PKRT   84 (89)
T ss_dssp             ETTT
T ss_pred             EccC
Confidence            6644

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

Probab=99.55  E-value=2.8e-14  Score=103.26  Aligned_cols=78  Identities=10%  Similarity=0.123  Sum_probs=66.3

Q ss_pred             CCCceEEEeCCCCCCCHHHHH----HHHHhcCCeeEEEEEec-CCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          107 RSDYRVLVTGLPSSASWQDLK----DHMRRAGDVCFSQVFRD-RGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~----~~f~~~g~v~~~~~~~~-~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      .+..+|||+|||+.+++++|+    ++|.+||.|..|.+... ...|||||+|.+.++|..|+..|||..+.|+    .|
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr----~l  102 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGN----PL  102 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTS----CC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCC----EE
Confidence            447899999999999998876    69999999999888653 4457999999999999999999999999994    56


Q ss_pred             EEeecCC
Q 023765          182 RVREYDS  188 (277)
Q Consensus       182 ~~~~~~~  188 (277)
                      .|.....
T Consensus       103 ~V~~a~~  109 (127)
T 2a3j_A          103 VITFSET  109 (127)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            6665543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=8.6e-14  Score=95.02  Aligned_cols=78  Identities=15%  Similarity=0.219  Sum_probs=68.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC---CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG---GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      .....+|||+|||..+++++|+++|.+| .|..|.++.+..   .+||||+|.+.++|.+|+. |||..+.|    ..|.
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~g----r~i~   80 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGG----RYIE   80 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETT----EEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCC----cEEE
Confidence            3457899999999999999999999999 999999998743   3599999999999999999 99999999    5777


Q ss_pred             EeecCCC
Q 023765          183 VREYDSR  189 (277)
Q Consensus       183 ~~~~~~~  189 (277)
                      |.....+
T Consensus        81 v~~a~~~   87 (91)
T 2dgw_A           81 VFREKSG   87 (91)
T ss_dssp             EEEESSC
T ss_pred             EEECCcC
Confidence            7766543

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=1.6e-13  Score=94.84  Aligned_cols=76  Identities=13%  Similarity=0.146  Sum_probs=66.9

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      .+.++|||+||  .+++++|+++|.+||.|..|.+.  ...+||||+|.+.++|++|+..|||..+.|    ..|.|...
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--PPRNCAFVTYEKMESADQAVAELNGTQVES----VQLKVNIA   84 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE--TTTTEEEEEESSHHHHHHHHHHTTTEEETT----EEEEEECC
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec--CCCCEEEEEECCHHHHHHHHHHhCCCeECC----eEEEEEEC
Confidence            45789999996  89999999999999999999885  455799999999999999999999999998    67888877


Q ss_pred             CCCC
Q 023765          187 DSRR  190 (277)
Q Consensus       187 ~~~r  190 (277)
                      ....
T Consensus        85 ~~~~   88 (97)
T 1x5p_A           85 RKQP   88 (97)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            6543

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

Probab=99.55  E-value=3.4e-14  Score=101.51  Aligned_cols=79  Identities=20%  Similarity=0.226  Sum_probs=68.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC-CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG-GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~-~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      ..+..+|||+|||..+++++|.++|.+||.|..|.+..+.. .+||||+|.+.++|..|+..|||..+.|    ..|.|.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g----~~l~v~   80 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSN----RYLVVL   80 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSS----CBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECC----eEEEEE
Confidence            34478999999999999999999999999999999987644 4699999999999999999999999999    455665


Q ss_pred             ecCC
Q 023765          185 EYDS  188 (277)
Q Consensus       185 ~~~~  188 (277)
                      ....
T Consensus        81 ~a~~   84 (115)
T 3lqv_A           81 YYNA   84 (115)
T ss_dssp             ECCH
T ss_pred             EecC
Confidence            5543

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

Probab=99.55  E-value=5.4e-15  Score=99.73  Aligned_cols=68  Identities=21%  Similarity=0.275  Sum_probs=62.8

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                      +..+|||+|||..+++++|+++|.+||.|..+.+..+..    .+||||+|.+.++|..|+..|||..+.|+
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   75 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQ   75 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeE
Confidence            478999999999999999999999999999999987754    46999999999999999999999999984

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.55  E-value=7.8e-14  Score=100.08  Aligned_cols=77  Identities=10%  Similarity=0.053  Sum_probs=65.9

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcE-EEEEEechhHHHHHHHhcCCCeecccceeeEEEEeecC
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMT-GIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYD  187 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~-~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~  187 (277)
                      ...|||+||++.+++++|.++|.+||.|..|.+...  .|| |||+|.+.++|..|+..|||..|.|..  ..|+|..++
T Consensus        25 vl~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           25 VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR--NGIQAMVEFESVLCAQKAKAALNGADIYAGC--CTLKIEYAR  100 (124)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES--SSEEEEEEESSHHHHHHHHHHHTTCCCBTTB--SEEEEECCS
T ss_pred             EEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC--CCCEEEEEECCHHHHHHHHHHhCCCEecCCC--eEEEEEEec
Confidence            345789999999999999999999999999998764  375 999999999999999999999998731  367777765


Q ss_pred             CC
Q 023765          188 SR  189 (277)
Q Consensus       188 ~~  189 (277)
                      ..
T Consensus       101 ~~  102 (124)
T 2e5i_A          101 PT  102 (124)
T ss_dssp             CS
T ss_pred             CC
Confidence            44

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

Probab=99.55  E-value=1.4e-14  Score=100.78  Aligned_cols=70  Identities=20%  Similarity=0.171  Sum_probs=64.0

Q ss_pred             CceEEEeCCCC------CCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecc-cce
Q 023765          109 DYRVLVTGLPS------SASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRN-AFS  177 (277)
Q Consensus       109 ~~~l~v~~l~~------~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g-~~~  177 (277)
                      .++|||+|||.      .+++++|.++|.+||.|..|.++.+..+    |||||+|.+.++|++|+..|||..+.| +.+
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            67999999999      9999999999999999999999987753    699999999999999999999999998 544


Q ss_pred             e
Q 023765          178 R  178 (277)
Q Consensus       178 ~  178 (277)
                      .
T Consensus        86 ~   86 (100)
T 3ns6_A           86 F   86 (100)
T ss_dssp             E
T ss_pred             E
Confidence            3

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

Probab=99.54  E-value=3.4e-14  Score=98.06  Aligned_cols=69  Identities=14%  Similarity=0.130  Sum_probs=62.1

Q ss_pred             CCCceEEEeCCCC-CCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceee
Q 023765          107 RSDYRVLVTGLPS-SASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRS  179 (277)
Q Consensus       107 ~~~~~l~v~~l~~-~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  179 (277)
                      .+..+|||+|||. .+++++|.++|.+||.|..+.+.    .+||||+|.+.++|..|+..|||..+.|+.+.+
T Consensus         8 ~~~~~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            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK----NAFGFIQFDNPQSVRDAIECESQEMNFGKKLIL   77 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE----TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe----CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            4578999999998 99999999999999999999996    459999999999999999999999999954443

>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=99.54  E-value=2.2e-14  Score=100.95  Aligned_cols=77  Identities=13%  Similarity=0.115  Sum_probs=65.4

Q ss_pred             CCCCceEEEeCCCCC-CCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCC--CeecccceeeEEE
Q 023765          106 RRSDYRVLVTGLPSS-ASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDR--SEFRNAFSRSYVR  182 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~-~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g--~~~~g~~~~~~i~  182 (277)
                      ..+..+|||+|||+. +++++|+++|.+||.|..|.+...  .+||||+|.+.++|..|++.|++  ..+.|    ..|.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~--kg~aFVef~~~~~A~~Ai~~l~~~~~~l~G----r~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM--KSQAFIEMETREDAMAMVDHCLKKALWFQG----RCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT--TTEEEEECSSHHHHHHHHHHHHHSCCCSSS----SCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC--CCEEEEEECCHHHHHHHHHHhccCCceECC----EEEE
Confidence            456889999999998 999999999999999999999754  56999999999999999998864  56888    4566


Q ss_pred             EeecCC
Q 023765          183 VREYDS  188 (277)
Q Consensus       183 ~~~~~~  188 (277)
                      |.....
T Consensus        96 V~~a~~  101 (112)
T 1x4f_A           96 VDLSEK  101 (112)
T ss_dssp             EEEECS
T ss_pred             EEECcc
Confidence            665543

>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=99.54  E-value=8.4e-14  Score=94.23  Aligned_cols=74  Identities=16%  Similarity=0.238  Sum_probs=64.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      .....+|||+|||..+++++|+++|.+||.|..+.++.+..    .+||||+|.+.++|++|++ +++..++|    ..|
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g----~~i   82 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDG----RVI   82 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETT----EEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECC----EEE
Confidence            34578999999999999999999999999999999998765    3599999999999999996 58888998    455


Q ss_pred             EEe
Q 023765          182 RVR  184 (277)
Q Consensus       182 ~~~  184 (277)
                      .|.
T Consensus        83 ~v~   85 (87)
T 3s7r_A           83 DPK   85 (87)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            554

>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=99.54  E-value=2e-14  Score=101.30  Aligned_cols=79  Identities=15%  Similarity=0.125  Sum_probs=65.1

Q ss_pred             CCCceEEE--eCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCee-cccceeeEEEE
Q 023765          107 RSDYRVLV--TGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEF-RNAFSRSYVRV  183 (277)
Q Consensus       107 ~~~~~l~v--~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~-~g~~~~~~i~~  183 (277)
                      .+..+|||  +||+..+++++|+++|.+||.|..|.+..+  .+||||+|.+.++|++|++.|||.++ ..-..+..+.+
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~--rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v  100 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN--KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYL  100 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT--CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC--CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEE
Confidence            34678999  779999999999999999999999888653  56999999999999999999999988 21111356666


Q ss_pred             eecC
Q 023765          184 REYD  187 (277)
Q Consensus       184 ~~~~  187 (277)
                      ....
T Consensus       101 ~~a~  104 (114)
T 2cq2_A          101 NFVE  104 (114)
T ss_dssp             EEES
T ss_pred             Eecc
Confidence            6654

>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=99.54  E-value=1.9e-15  Score=105.65  Aligned_cols=69  Identities=22%  Similarity=0.375  Sum_probs=58.6

Q ss_pred             cCCCCCCCHHHHHHHh------------hccCCeeEEEeecC--CCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEE
Q 023765           12 GNLPGDTRMREVEDLF------------YKYGPIVDIDLKIP--PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV   77 (277)
Q Consensus        12 ~nL~~~~t~~~l~~~F------------~~~G~v~~v~~~~~--~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v   77 (277)
                      .||++.+++++|+++|            ++||+|..|.|+.+  +.++|||||+|.++++|.+|+..|||..|.|+.|.|
T Consensus        21 ~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~v  100 (104)
T 1jmt_A           21 DGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHA  100 (104)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCE
T ss_pred             CCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEEE
Confidence            3444555666666665            99999999999653  467899999999999999999999999999999999


Q ss_pred             EEc
Q 023765           78 ELA   80 (277)
Q Consensus        78 ~~a   80 (277)
                      .++
T Consensus       101 ~~s  103 (104)
T 1jmt_A          101 ELS  103 (104)
T ss_dssp             EEC
T ss_pred             EEc
Confidence            986

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.54  E-value=1.6e-14  Score=96.42  Aligned_cols=66  Identities=11%  Similarity=0.123  Sum_probs=59.6

Q ss_pred             ceEEEeCCCCCC------CHHHHHHHHHhcCCeeEEEEEec--CCCcEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          110 YRVLVTGLPSSA------SWQDLKDHMRRAGDVCFSQVFRD--RGGMTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       110 ~~l~v~~l~~~~------~~~~l~~~f~~~g~v~~~~~~~~--~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                      ++|||+|||..+      ++++|+++|.+||.|..+.+...  ...|||||+|.+.++|.+|+..|||..+.|+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~   75 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   75 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSS
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCc
Confidence            589999999999      77999999999999999998743  2346999999999999999999999999995

>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=99.54  E-value=1.8e-14  Score=102.17  Aligned_cols=73  Identities=22%  Similarity=0.325  Sum_probs=64.4

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      ..++|||+|||..+++++|+++|.+||.|..|.+..  ..+||||+|.+.++|..|+..|||..+.|+    .|.|...
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~--~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~----~l~V~~a   81 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE--GGITAIVEFLEPLEARKAFRHLAYSKFHHV----PLYLEWA   81 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS--SSSCEEEEESCHHHHHHHHHHHTTCBSSSS----BCEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC--CCCEEEEEeCCHHHHHHHHHHhCCCEECCe----EEEEEEC
Confidence            467999999999999999999999999999998874  446999999999999999999999999995    4555444

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

Probab=99.54  E-value=5.4e-14  Score=105.71  Aligned_cols=76  Identities=20%  Similarity=0.119  Sum_probs=67.2

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcC--CeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAG--DVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g--~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      ...+|||+|||..+++++|+++|.+||  .|..|.++.+..+    |||||+|.+.++|++||..|||..+.|    ..|
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~G----r~l  129 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNG----EKV  129 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETT----EEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECC----eEe
Confidence            457999999999999999999999999  9999999988544    599999999999999999999999999    566


Q ss_pred             EEeecC
Q 023765          182 RVREYD  187 (277)
Q Consensus       182 ~~~~~~  187 (277)
                      .|..+.
T Consensus       130 ~V~~a~  135 (156)
T 3n9u_C          130 DVRPAT  135 (156)
T ss_dssp             EEEECC
T ss_pred             EEEEcC
Confidence            666554

>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=99.54  E-value=5.4e-14  Score=100.25  Aligned_cols=77  Identities=19%  Similarity=0.256  Sum_probs=68.3

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      ....+|||+|||..+++++|+++|.+||.|..|.++.+..    .+||||+|.+.++|++|| .|||..+.|    ..|.
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g----~~l~   97 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLG----VPII   97 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETT----EEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCC----eEEE
Confidence            3467999999999999999999999999999999987654    369999999999999999 999999999    6777


Q ss_pred             EeecCC
Q 023765          183 VREYDS  188 (277)
Q Consensus       183 ~~~~~~  188 (277)
                      |.....
T Consensus        98 V~~a~~  103 (114)
T 2cq4_A           98 VQASQA  103 (114)
T ss_dssp             EEEHHH
T ss_pred             EEecCC
Confidence            776544

>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=99.54  E-value=1.3e-14  Score=99.97  Aligned_cols=76  Identities=14%  Similarity=0.135  Sum_probs=65.0

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      ++..+|||+|||..+++++|+++|.+||.|..+.++.+..+    +||||+|.+.++|++|+..||+..+.|    ..|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g----r~l~   88 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGS----RKVK   88 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETT----EECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECC----cEEE
Confidence            34689999999999999999999999999988777765443    599999999999999999999999999    5666


Q ss_pred             Eeec
Q 023765          183 VREY  186 (277)
Q Consensus       183 ~~~~  186 (277)
                      |...
T Consensus        89 v~~a   92 (95)
T 2ek1_A           89 LSGP   92 (95)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            6543

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

Probab=99.54  E-value=6.8e-14  Score=101.31  Aligned_cols=77  Identities=17%  Similarity=0.289  Sum_probs=68.0

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ...+|||+|||..+++++|+++|.+||.|..|.+..+..    .+||||+|.+.++|..|+ .|||..+.|    ..|.|
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g----~~l~V  109 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRG----RTIKV  109 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETT----EECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECC----eEEEE
Confidence            367999999999999999999999999999999987743    359999999999999999 899999999    67777


Q ss_pred             eecCCC
Q 023765          184 REYDSR  189 (277)
Q Consensus       184 ~~~~~~  189 (277)
                      ......
T Consensus       110 ~~a~~~  115 (124)
T 2jwn_A          110 LPKRTN  115 (124)
T ss_dssp             EESSCC
T ss_pred             EECCCC
Confidence            766543

>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=99.53  E-value=2e-14  Score=102.57  Aligned_cols=79  Identities=20%  Similarity=0.249  Sum_probs=68.3

Q ss_pred             CCCCeEEEcCCCC--CC---CHHHHHHHhhccCCeeEEEeecC-------CCCCcEEEEEEcChHHHHHHHHhcCCcccC
Q 023765            4 RSSRTLYVGNLPG--DT---RMREVEDLFYKYGPIVDIDLKIP-------PRPPGYAFLEFEDYRDAEDAIRGRDGYNFD   71 (277)
Q Consensus         4 ~~~~~l~V~nL~~--~~---t~~~l~~~F~~~G~v~~v~~~~~-------~~~~g~afV~f~~~~~a~~a~~~l~~~~~~   71 (277)
                      .++++|+|.||-.  ++   -+++|+++|++||+|..|.|+.+       +.++|+|||+|.+.++|.+|++.|||..|.
T Consensus        18 ~ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~   97 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA   97 (118)
T ss_dssp             HSCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEEC
Confidence            4789999999932  22   37899999999999999999643       235699999999999999999999999999


Q ss_pred             CceEEEEEccC
Q 023765           72 GYRLRVELAHG   82 (277)
Q Consensus        72 g~~i~v~~a~~   82 (277)
                      |+.|.|.++..
T Consensus        98 GR~i~v~~~~~  108 (118)
T 3ue2_A           98 GRKVVAEVYDQ  108 (118)
T ss_dssp             TEECEEEEECH
T ss_pred             CcEEEEEEcCh
Confidence            99999999764

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=8.8e-14  Score=95.58  Aligned_cols=73  Identities=18%  Similarity=0.224  Sum_probs=61.9

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCc-EEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGM-TGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~-~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      ...+|||+|||..+++++|+++|.+||.|..|  +.+..++ ||||+|.+.++|.+|+. |||..+.|    ..|.|...
T Consensus         7 ~~~~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            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGVFAIVEMGDVGAREAVLS-QSQHSLGG----HRLRVRPR   79 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCCEEEEEESSHHHHHHHHT-CSCCEETT----EECCCBCS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCcEEEEEECCHHHHHHHHh-cCCeEECC----EEEEEEEC
Confidence            35799999999999999999999999999987  3333222 99999999999999999 99999999    56666544


Q ss_pred             C
Q 023765          187 D  187 (277)
Q Consensus       187 ~  187 (277)
                      .
T Consensus        80 ~   80 (94)
T 2e5g_A           80 E   80 (94)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.53  E-value=7.6e-14  Score=100.56  Aligned_cols=80  Identities=18%  Similarity=0.163  Sum_probs=68.2

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcE-EEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMT-GIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~-~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      .....|||+||++.+++++|.++|.+||.|..|.+..... +| |||+|.+.++|..|++.|||..+.|.  ...|+++.
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~-gfqAFVef~~~~~A~~Ai~~LnG~~i~g~--~~~LrI~~  102 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN-QFQALLQYADPVSAQHAKLSLDGQNIYNA--CCTLRIDF  102 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETT-EEEEEEEESCHHHHHHHHHHHTTCEEETT--EEEEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCC-CcEEEEEECCHHHHHHHHHHcCCCeecCC--CcEEEEEe
Confidence            3456788999999999999999999999999998887653 55 99999999999999999999999873  24677777


Q ss_pred             cCCC
Q 023765          186 YDSR  189 (277)
Q Consensus       186 ~~~~  189 (277)
                      .+..
T Consensus       103 ak~~  106 (130)
T 3zzy_A          103 SKLT  106 (130)
T ss_dssp             CSCS
T ss_pred             cCCC
Confidence            6543

>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=99.53  E-value=3.5e-13  Score=94.18  Aligned_cols=79  Identities=24%  Similarity=0.349  Sum_probs=67.9

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeE
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSY  180 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  180 (277)
                      ......+|||+|||..+++++|+++|.+||.|..|.++.+..+    +||||+|.+.++|++|+.  ++..++|    ..
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g----~~   84 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDG----RW   84 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETT----EE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCC----eE
Confidence            3445789999999999999999999999999999999987653    599999999999999998  4678888    67


Q ss_pred             EEEeecCCC
Q 023765          181 VRVREYDSR  189 (277)
Q Consensus       181 i~~~~~~~~  189 (277)
                      |.|.....+
T Consensus        85 l~v~~a~~~   93 (103)
T 2cqg_A           85 CDCKLPNSK   93 (103)
T ss_dssp             EEEECCCTT
T ss_pred             EEEEecCCC
Confidence            777776554

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

Probab=99.53  E-value=2.1e-14  Score=100.65  Aligned_cols=78  Identities=28%  Similarity=0.358  Sum_probs=68.9

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ...+|||+|||..+++++|+++|.+||.|..+.+..+..+    +||||+|.+.++|+.|++.|||..+.|    ..|.|
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----~~l~v   82 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSG----RALRV   82 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSS----SCBEE
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCC----cEEEE
Confidence            4679999999999999999999999999999999987543    599999999999999999999999999    46666


Q ss_pred             eecCCC
Q 023765          184 REYDSR  189 (277)
Q Consensus       184 ~~~~~~  189 (277)
                      ......
T Consensus        83 ~~a~~~   88 (104)
T 1p1t_A           83 DNAASE   88 (104)
T ss_dssp             EETTCT
T ss_pred             EeCCCc
Confidence            666543

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

Probab=99.53  E-value=4.6e-14  Score=99.05  Aligned_cols=77  Identities=13%  Similarity=0.156  Sum_probs=65.6

Q ss_pred             CCceEEEeCCCCCC------CHHHHHHHHHhcCCeeEEEEEec--CCCcEEEEEEechhHHHHHHHhcCCCeecccceee
Q 023765          108 SDYRVLVTGLPSSA------SWQDLKDHMRRAGDVCFSQVFRD--RGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRS  179 (277)
Q Consensus       108 ~~~~l~v~~l~~~~------~~~~l~~~f~~~g~v~~~~~~~~--~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  179 (277)
                      ..++|||+|||..+      ++++|.++|.+||.|..|.+...  ...|||||+|.+.++|..|+..|||..+.|+   .
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~---~   90 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ---H   90 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTT---C
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCC---c
Confidence            36799999999999      78999999999999999998833  2346999999999999999999999999993   1


Q ss_pred             EEEEeecC
Q 023765          180 YVRVREYD  187 (277)
Q Consensus       180 ~i~~~~~~  187 (277)
                      .|.|....
T Consensus        91 ~l~V~~a~   98 (105)
T 2nlw_A           91 TFRVNLFT   98 (105)
T ss_dssp             EEEEECSC
T ss_pred             eEEEEEcc
Confidence            56666543

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

Probab=99.53  E-value=8.6e-14  Score=99.54  Aligned_cols=79  Identities=16%  Similarity=0.240  Sum_probs=70.0

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      ....+|||+|||..+++++|+++|.+||.|..|.++.+..    .+||||+|.+.++|+.||.. ++..+.|    ..|.
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g----~~l~   99 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDG----RVVE   99 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETT----EEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECC----EEEE
Confidence            3468999999999999999999999999999999998754    36999999999999999997 9999999    6788


Q ss_pred             EeecCCCC
Q 023765          183 VREYDSRR  190 (277)
Q Consensus       183 ~~~~~~~r  190 (277)
                      |.....+.
T Consensus       100 V~~a~~~~  107 (116)
T 1x4b_A          100 PKRAVARE  107 (116)
T ss_dssp             EECCSSCC
T ss_pred             EEECCCCc
Confidence            88776553

>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=99.53  E-value=2.8e-14  Score=98.68  Aligned_cols=80  Identities=16%  Similarity=0.213  Sum_probs=68.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHH----HHHHhcCCeeEEEEEec-CCCcEEEEEEechhHHHHHHHhcCCCeecccceeeE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLK----DHMRRAGDVCFSQVFRD-RGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSY  180 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~----~~f~~~g~v~~~~~~~~-~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  180 (277)
                      ..+..+|||+|||..+++++|+    ++|.+||.|..|.+... ...+||||+|.+.++|..|+..|||..+.|    ..
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g----~~   80 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYD----KP   80 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETT----EE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECC----cE
Confidence            3457899999999999999999    99999999999988742 234699999999999999999999999998    66


Q ss_pred             EEEeecCCC
Q 023765          181 VRVREYDSR  189 (277)
Q Consensus       181 i~~~~~~~~  189 (277)
                      |.|......
T Consensus        81 l~v~~a~~~   89 (97)
T 1nu4_A           81 MRIQYAKTD   89 (97)
T ss_dssp             CEEEECSSC
T ss_pred             EEEEEccCC
Confidence            777766543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.53  E-value=2.8e-14  Score=98.51  Aligned_cols=79  Identities=13%  Similarity=0.158  Sum_probs=67.3

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      ..+..+|||+|||..+++++|+++|.+||.|..+ .......+||||+|.+.++|.+|+..|||..+.|    ..|.|..
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----~~l~v~~   87 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG----RSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETT----EEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC----eEEEEEE
Confidence            3457899999999999999999999999998877 3333345699999999999999999999999999    6778877


Q ss_pred             cCCC
Q 023765          186 YDSR  189 (277)
Q Consensus       186 ~~~~  189 (277)
                      ...+
T Consensus        88 a~~~   91 (96)
T 1fjc_A           88 TGEK   91 (96)
T ss_dssp             CSSS
T ss_pred             cCCC
Confidence            6544

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

Probab=99.53  E-value=1.1e-13  Score=102.40  Aligned_cols=77  Identities=22%  Similarity=0.206  Sum_probs=67.9

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceee
Q 023765          104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRS  179 (277)
Q Consensus       104 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  179 (277)
                      .......+|||+|||..+++++|+++|.+||.|..+.+..++.    .+||||+|.+.++|++|++.|||..+.|    .
T Consensus        58 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----~  133 (140)
T 2ku7_A           58 GSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG----R  133 (140)
T ss_dssp             SSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETT----E
T ss_pred             CCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECC----E
Confidence            3445688999999999999999999999999999999987643    4699999999999999999999999999    4


Q ss_pred             EEEEe
Q 023765          180 YVRVR  184 (277)
Q Consensus       180 ~i~~~  184 (277)
                      .|.|.
T Consensus       134 ~l~v~  138 (140)
T 2ku7_A          134 TIRVN  138 (140)
T ss_dssp             EEEEE
T ss_pred             EEEEE
Confidence            55554

>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=99.52  E-value=6.4e-14  Score=98.16  Aligned_cols=73  Identities=16%  Similarity=0.148  Sum_probs=62.9

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeE-EEEEecC---CCcEEEEEEechhHHHHHHHhcCCCeecccce
Q 023765          104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCF-SQVFRDR---GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFS  177 (277)
Q Consensus       104 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~-~~~~~~~---~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  177 (277)
                      +......+|||+|||+.+++++|+++|.+||.|.. |.|..+.   ..|||||+|.+.++|++||.. |+..+.|+.+
T Consensus        10 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i   86 (104)
T 1wg5_A           10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYI   86 (104)
T ss_dssp             SSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEE
Confidence            34456789999999999999999999999999987 7777653   246999999999999999997 9999999533

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

Probab=99.52  E-value=5.5e-14  Score=98.94  Aligned_cols=75  Identities=28%  Similarity=0.331  Sum_probs=65.1

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC---CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG---GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ....+|||+|||+.+++++|+++|..| .|..|.|+.+..   .|||||+|.+.++|++|| .+|+..+.|    ..|.|
T Consensus        14 ~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~g----r~i~V   87 (109)
T 2dnn_A           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQ----RYVEV   87 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETT----EEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECC----eEEEE
Confidence            346799999999999999999999999 899999987654   469999999999999999 699999999    56666


Q ss_pred             eecC
Q 023765          184 REYD  187 (277)
Q Consensus       184 ~~~~  187 (277)
                      ....
T Consensus        88 ~~a~   91 (109)
T 2dnn_A           88 SPAT   91 (109)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            5543

>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=99.52  E-value=5.8e-14  Score=99.44  Aligned_cols=77  Identities=14%  Similarity=0.191  Sum_probs=66.8

Q ss_pred             CCCCeEEEcCCCCCC----------CHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCc
Q 023765            4 RSSRTLYVGNLPGDT----------RMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGY   73 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~----------t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~   73 (277)
                      .++++|.|.||=...          -+++|+++|++||.|..|.|..+ .++|+|||+|.+.++|.+|++.|||..|.|+
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~-~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR   83 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKN-SAQGNVYVKCPSIAAAIAAVNALHGRWFAGK   83 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTT-CTTCCEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecC-CCcEEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            478999999993322          24578999999999999999654 3589999999999999999999999999999


Q ss_pred             eEEEEEcc
Q 023765           74 RLRVELAH   81 (277)
Q Consensus        74 ~i~v~~a~   81 (277)
                      .|.|.++.
T Consensus        84 ~i~v~~~~   91 (114)
T 3s6e_A           84 MITAAYVP   91 (114)
T ss_dssp             ECEEEEEC
T ss_pred             EEEEEEEc
Confidence            99999986

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

Probab=99.52  E-value=5.7e-14  Score=102.67  Aligned_cols=79  Identities=6%  Similarity=0.130  Sum_probs=67.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeE--EEEEecCC----CcEEEEEEechhHHHHHHHhcCCC----eeccc
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCF--SQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRS----EFRNA  175 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~--~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~----~~~g~  175 (277)
                      ..+..+|||+|||+.+++++|+++|.+||.|..  |.|+.+..    .|||||+|.+. +|.+|+..|||.    .++| 
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g-   97 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG-   97 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG-
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC-
Confidence            345789999999999999999999999999976  88887763    36999999999 999999999999    9999 


Q ss_pred             ceeeEEEEeecCCC
Q 023765          176 FSRSYVRVREYDSR  189 (277)
Q Consensus       176 ~~~~~i~~~~~~~~  189 (277)
                         ..|.|....+.
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               45556655443

>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=99.51  E-value=2.5e-13  Score=96.80  Aligned_cols=82  Identities=16%  Similarity=0.254  Sum_probs=70.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC---cEEEEEEechhHHHHHHHhcCCCeecccc----ee
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG---MTGIVDYTSYDDMKYAIRKLDRSEFRNAF----SR  178 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~----~~  178 (277)
                      ....++|||+|||..+++++|+++|.+||.|..+.++.+..+   +||||+|.+.++|++|+..|||..+.+..    ..
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~  101 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT  101 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCC
Confidence            345689999999999999999999999999999999987632   59999999999999999999999997654    23


Q ss_pred             eEEEEeecC
Q 023765          179 SYVRVREYD  187 (277)
Q Consensus       179 ~~i~~~~~~  187 (277)
                      ..|.|...+
T Consensus       102 ~~l~v~~a~  110 (114)
T 1x5o_A          102 EPLLCKFSG  110 (114)
T ss_dssp             SCBEEEECC
T ss_pred             CceeEEccC
Confidence            556666654

>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=99.51  E-value=3.7e-14  Score=116.10  Aligned_cols=81  Identities=21%  Similarity=0.208  Sum_probs=71.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCC-cccC---CceEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDG-YNFD---GYRLRV   77 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~-~~~~---g~~i~v   77 (277)
                      .+.++|||+|||+.+|+++|+++|+.||.|..|.|+.  ++.++|||||+|.+.++|..|+..||+ ..+.   +++|.|
T Consensus        94 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v  173 (261)
T 3sde_A           94 THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIV  173 (261)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEE
T ss_pred             ccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEE
Confidence            4678999999999999999999999999999999964  566789999999999999999999955 4444   999999


Q ss_pred             EEccCCC
Q 023765           78 ELAHGGR   84 (277)
Q Consensus        78 ~~a~~~~   84 (277)
                      .++....
T Consensus       174 ~~~~~~~  180 (261)
T 3sde_A          174 EPMEQFD  180 (261)
T ss_dssp             EECCCEE
T ss_pred             eeccccC
Confidence            9988653

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.51  E-value=7.4e-14  Score=100.10  Aligned_cols=78  Identities=27%  Similarity=0.384  Sum_probs=67.5

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCC---eeEEEEEecCCC---cEEEEEEechhHHHHHHHhcCCCeeccccee
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGD---VCFSQVFRDRGG---MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~---v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  178 (277)
                      ......+|||+|||+.+++++|+++|..||.   |..|.++.+..+   +||||+|.+.++|++||. ||+..+.|    
T Consensus        13 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~g----   87 (118)
T 2db1_A           13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGH----   87 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETT----
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECC----
Confidence            3455789999999999999999999999998   889999877553   599999999999999999 99999999    


Q ss_pred             eEEEEeecC
Q 023765          179 SYVRVREYD  187 (277)
Q Consensus       179 ~~i~~~~~~  187 (277)
                      ..|.|....
T Consensus        88 r~i~V~~a~   96 (118)
T 2db1_A           88 RYIEVFKSH   96 (118)
T ss_dssp             EEEEEEEEC
T ss_pred             eEEEEEECC
Confidence            566665543

>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=99.51  E-value=1.1e-14  Score=101.26  Aligned_cols=78  Identities=18%  Similarity=0.331  Sum_probs=63.6

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC-----CCcEEEEEEechhHHHHHHHhcCCCeeccccee
Q 023765          104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR-----GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       104 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~-----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  178 (277)
                      ......++|||+|||..+++++|+++|.+|| |..|.+..+.     ..|||||+|.+.++|.+|+ .|||..+.|+   
T Consensus        14 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~---   88 (100)
T 2j76_E           14 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNR---   88 (100)
T ss_dssp             ------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTB---
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCe---
Confidence            3445678999999999999999999999999 9999998765     2469999999999999999 8999999994   


Q ss_pred             eEEEEeecC
Q 023765          179 SYVRVREYD  187 (277)
Q Consensus       179 ~~i~~~~~~  187 (277)
                       .|.|....
T Consensus        89 -~l~V~~a~   96 (100)
T 2j76_E           89 -RIRVDVAD   96 (100)
T ss_dssp             -CCCCEECC
T ss_pred             -EEEEEecc
Confidence             45555443

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

Probab=99.50  E-value=1.4e-13  Score=97.25  Aligned_cols=79  Identities=19%  Similarity=0.265  Sum_probs=66.8

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      ...++|||+|||..+++++|+++|.+||.|..|.+..+..    .|||||+|.+.++|.+|+..+ +..+.|    ..|.
T Consensus        23 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g----~~l~   97 (109)
T 2rs2_A           23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDS----KTID   97 (109)
T ss_dssp             ---CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETT----EEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCC----EEEE
Confidence            4578999999999999999999999999999999988754    369999999999999999976 588888    6777


Q ss_pred             EeecCCCC
Q 023765          183 VREYDSRR  190 (277)
Q Consensus       183 ~~~~~~~r  190 (277)
                      |.....+.
T Consensus        98 V~~a~~~~  105 (109)
T 2rs2_A           98 PKVAFPRR  105 (109)
T ss_dssp             EEECCCCC
T ss_pred             EEEccCCC
Confidence            77765543

>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=99.50  E-value=1.3e-14  Score=106.66  Aligned_cols=111  Identities=12%  Similarity=0.099  Sum_probs=60.6

Q ss_pred             cEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHH
Q 023765           46 GYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQD  125 (277)
Q Consensus        46 g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~  125 (277)
                      ++||.+|..++.+..++..+..+ +.|...--..                  .............+|||+|||+.+++++
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~-~gg~~~g~~~------------------g~~~~~~~~~~~~~lfV~nLp~~~te~d   62 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASM-TGGQQMGRGS------------------GDSEFTVQSTTGHCVHMRGLPYKATEND   62 (139)
T ss_dssp             --------------------------------------------------------------CCCCEECCSCCTTCCHHH
T ss_pred             CcccccccCccccchhcccchhc-cCCCCCCCCC------------------CCcccCCCCCCCCEEEEeCCCCCCCHHH
Confidence            67888888888777776654432 2222110000                  0001112234467999999999999999


Q ss_pred             HHHHHHhcCCeeEEEEEecCC---CcEEEEEEechhHHHHHHHhcCCCeecccce
Q 023765          126 LKDHMRRAGDVCFSQVFRDRG---GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFS  177 (277)
Q Consensus       126 l~~~f~~~g~v~~~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  177 (277)
                      |+++|.+|| |..|.|+.+..   .+||||+|.+.++|++|| .+|+..+.|+.+
T Consensus        63 L~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i  115 (139)
T 2hgn_A           63 IYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYI  115 (139)
T ss_dssp             HHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCC
T ss_pred             HHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEE
Confidence            999999999 67898887654   469999999999999999 799999999533

>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=99.50  E-value=1.3e-13  Score=96.10  Aligned_cols=71  Identities=15%  Similarity=0.240  Sum_probs=61.3

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC---cEEEEEEechhHHHHHHHhcCCCeecccce
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG---MTGIVDYTSYDDMKYAIRKLDRSEFRNAFS  177 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  177 (277)
                      ......+|||+|||+.+++++|+++|.+||.+ .|.|+.+..+   +||||+|.+.++|++|| .+|+..+.|+.+
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i   84 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYV   84 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHH-TTSSCCSSSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHH-HhCCCeECCcEE
Confidence            34457899999999999999999999999954 8999887643   49999999999999999 479999999533

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

Probab=99.50  E-value=1.2e-13  Score=92.40  Aligned_cols=71  Identities=15%  Similarity=0.233  Sum_probs=60.9

Q ss_pred             CceEEEeCCCCCCCHHH----HHHHHHhcC-CeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          109 DYRVLVTGLPSSASWQD----LKDHMRRAG-DVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~----l~~~f~~~g-~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      .+.|||.|||..+++++    |.++|.+|| +|..|.      +|+|||.|.+.++|..|++.|||..+.|    ..|++
T Consensus         9 ~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~Vt------gG~AfV~F~~~esA~~A~~~l~G~~l~g----r~i~v   78 (96)
T 2diu_A            9 HTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSIT------GCSAILRFINQDSAERAQKRMENEDVFG----NRIIV   78 (96)
T ss_dssp             SEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEECC------TTCEEEEESSHHHHHHHHHHHTTCCSSS----SCCEE
T ss_pred             ceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEEe------cCEEEEEECCHHHHHHHHHHhcCCccCC----ceEEE
Confidence            33499999999999887    568999995 998882      3799999999999999999999999999    57777


Q ss_pred             eecCCC
Q 023765          184 REYDSR  189 (277)
Q Consensus       184 ~~~~~~  189 (277)
                      ..+...
T Consensus        79 ~~A~~~   84 (96)
T 2diu_A           79 SFTPKN   84 (96)
T ss_dssp             ESSCCS
T ss_pred             EecCCC
Confidence            776554

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

Probab=99.50  E-value=3.3e-13  Score=94.13  Aligned_cols=79  Identities=20%  Similarity=0.292  Sum_probs=65.7

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeE
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSY  180 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  180 (277)
                      ...+..+|||+|||..+++++|+++|..|+   .+.++.+..    .+||||+|.+.++|++||..|||..+.|    ..
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g----~~   83 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDG----NK   83 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETT----EE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECC----eE
Confidence            345678999999999999999999999875   455555543    3599999999999999999999999999    67


Q ss_pred             EEEeecCCCC
Q 023765          181 VRVREYDSRR  190 (277)
Q Consensus       181 i~~~~~~~~r  190 (277)
                      |.|....++.
T Consensus        84 l~V~~a~~~~   93 (102)
T 2fc8_A           84 VTLDWAKPKG   93 (102)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEEecCCC
Confidence            7787776554

>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=99.49  E-value=8e-14  Score=99.34  Aligned_cols=78  Identities=17%  Similarity=0.149  Sum_probs=67.2

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCe-eEEEEEecC---CCcEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDV-CFSQVFRDR---GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v-~~~~~~~~~---~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      .....+|||+|||..+++++|+++|.+||.| ..|.|+.+.   ..+||||+|.+.++|++||.. |+..+.|    ..|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~g----r~i   86 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNG----REA   86 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETT----EEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCC----eEE
Confidence            3457899999999999999999999999999 888888765   346999999999999999987 9999999    566


Q ss_pred             EEeecCC
Q 023765          182 RVREYDS  188 (277)
Q Consensus       182 ~~~~~~~  188 (277)
                      .|.....
T Consensus        87 ~v~~a~~   93 (114)
T 2cpy_A           87 FVHVVTL   93 (114)
T ss_dssp             EEEEECH
T ss_pred             EEEECCH
Confidence            6665543

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.49  E-value=5.7e-14  Score=102.82  Aligned_cols=78  Identities=24%  Similarity=0.341  Sum_probs=67.5

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHHHhcCC---eeEEEEEecCCC---cEEEEEEechhHHHHHHHhcCCCeecccce
Q 023765          104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGD---VCFSQVFRDRGG---MTGIVDYTSYDDMKYAIRKLDRSEFRNAFS  177 (277)
Q Consensus       104 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~---v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  177 (277)
                      ++.....+|||+|||+.+++++|+++|.+||.   |..|.|+.+..+   |||||+|.+.++|++||. ||+..+.|   
T Consensus        39 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~g---  114 (136)
T 2hgl_A           39 PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGH---  114 (136)
T ss_dssp             SSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSS---
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECC---
Confidence            34455789999999999999999999999999   888999877653   599999999999999999 99999999   


Q ss_pred             eeEEEEeec
Q 023765          178 RSYVRVREY  186 (277)
Q Consensus       178 ~~~i~~~~~  186 (277)
                       ..|.|...
T Consensus       115 -r~i~V~~a  122 (136)
T 2hgl_A          115 -RYIEVFKS  122 (136)
T ss_dssp             -SEEEEEEC
T ss_pred             -EEEEEEEC
Confidence             46666544

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

Probab=99.49  E-value=4.3e-14  Score=92.86  Aligned_cols=66  Identities=21%  Similarity=0.301  Sum_probs=59.8

Q ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccce
Q 023765          111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFS  177 (277)
Q Consensus       111 ~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  177 (277)
                      +|||+|||..+++++|+++|.+||.|..+.+..++.    .+||||+|.+.++|++|++ ||+..++|+.+
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l   70 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMV   70 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEE
Confidence            489999999999999999999999999999987653    3699999999999999997 99999999543

>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=99.49  E-value=8.9e-14  Score=100.66  Aligned_cols=74  Identities=20%  Similarity=0.245  Sum_probs=61.5

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEec-CC---CcEEEEEEechhHHHHHHHhcCCCeeccccee
Q 023765          104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD-RG---GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       104 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~-~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  178 (277)
                      .+.....+|||+|||+.+++++|+++|..||.|..+.++.+ ..   .+||||+|.+.++|.+||. |||..|.|+.+.
T Consensus        20 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   97 (124)
T 1wel_A           20 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQ   97 (124)
T ss_dssp             SCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEE
Confidence            34456789999999999999999999999999987444333 22   3599999999999999999 999999995443

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

Probab=99.49  E-value=2.1e-13  Score=104.73  Aligned_cols=76  Identities=17%  Similarity=0.116  Sum_probs=67.0

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC---CCcEEEEEEechhHHHHHHHhcCCCeecccceeeE
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR---GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSY  180 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~---~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  180 (277)
                      ...+.++|||+|||..+++++|+++|.+||.|..|.|..+.   ..+||||+|.+.++|++|++.|||..+.|+.+.+.
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 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  162 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999998765   33699999999999999999999999999544433

>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=99.49  E-value=1.6e-13  Score=92.82  Aligned_cols=65  Identities=22%  Similarity=0.318  Sum_probs=60.1

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhc----C-------CeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRA----G-------DVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~----g-------~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                      ...+|||+|||..+++++|+++|.+|    |       .|..+.+..+  .+||||+|.+.++|.+|+ .|||..+.|+
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~--kg~afV~f~~~~~a~~A~-~l~g~~~~g~   80 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD--KNFAFLEFRSVDETTQAM-AFDGIIFQGQ   80 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS--SSEEEEEESSHHHHHHHG-GGTTCEETTE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC--CcEEEEEcCCHHHHHHHH-hcCCCEECCe
Confidence            46899999999999999999999999    8       8988888765  579999999999999999 9999999994

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.48  E-value=9e-14  Score=94.29  Aligned_cols=73  Identities=22%  Similarity=0.315  Sum_probs=65.3

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeecCC
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDS  188 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~~  188 (277)
                      ..+|||+|||..+++++|+++|.+| .|..+.+.  ...+||||+|.+.++|++|++.|||..+.|    ..|.|.....
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--RNKRTAFVTLLNGEQAQNAIQMFHQYSFRG----KDLIVQLQPT   77 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE--GGGTEEEECCSCHHHHHHHHHHHTTEEETT----EEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe--CCCcEEEEEECCHHHHHHHHHHhCCCeECC----cEEEEEEcCC
Confidence            6789999999999999999999999 99999885  556799999999999999999999999999    5677766543

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

Probab=99.48  E-value=2.6e-13  Score=95.86  Aligned_cols=78  Identities=18%  Similarity=0.279  Sum_probs=67.2

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCC-eeEEEEE-ecC----CCcEEEEEEechhHHHHHHHhcC--CCeecccceee
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGD-VCFSQVF-RDR----GGMTGIVDYTSYDDMKYAIRKLD--RSEFRNAFSRS  179 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~-v~~~~~~-~~~----~~~~~fv~f~~~~~a~~a~~~l~--g~~~~g~~~~~  179 (277)
                      +.++|||+|||..+++++|.++|.+||. |..+.++ .+.    ..+||||+|.+.++|..|+..||  +..+.|    .
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g----~   82 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWG----H   82 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTT----B
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecC----C
Confidence            4689999999999999999999999998 9999887 443    34699999999999999999996  589998    5


Q ss_pred             EEEEeecCCC
Q 023765          180 YVRVREYDSR  189 (277)
Q Consensus       180 ~i~~~~~~~~  189 (277)
                      .|.|....+.
T Consensus        83 ~l~V~~a~~~   92 (109)
T 2dis_A           83 QIAVDWAEPE   92 (109)
T ss_dssp             CCEEEESCSS
T ss_pred             eEEEEEcCCC
Confidence            6677766554

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

Probab=99.47  E-value=9.4e-14  Score=91.67  Aligned_cols=68  Identities=16%  Similarity=0.235  Sum_probs=61.1

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeeccccee
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  178 (277)
                      ++|||+|||..+++++|+++|.+||.|..+.+..++.    .+||||+|.+.++|++|+..++ ..+.|+.+.
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~   72 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTID   72 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEE
Confidence            3799999999999999999999999999999987754    4699999999999999999999 999985443

>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=99.47  E-value=2e-13  Score=109.29  Aligned_cols=76  Identities=17%  Similarity=0.187  Sum_probs=66.3

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcC--CeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAG--DVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g--~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      ..++|||+||+..+++++|+++|.+||  .|..|.|+.+..+    +||||+|.+.++|++||+.||+..|.|+    .|
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr----~l  142 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQ----NP  142 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTB----CC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCE----Ee
Confidence            467899999999999999999999999  9999999988644    4999999999999999999999999994    55


Q ss_pred             EEeecC
Q 023765          182 RVREYD  187 (277)
Q Consensus       182 ~~~~~~  187 (277)
                      .|..+.
T Consensus       143 ~V~~a~  148 (229)
T 3q2s_C          143 VVTPVN  148 (229)
T ss_dssp             EEEECC
T ss_pred             EEEECC
Confidence            565443

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

Probab=99.46  E-value=3.4e-13  Score=91.55  Aligned_cols=77  Identities=10%  Similarity=0.097  Sum_probs=59.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      ..+.++|||+|||.++++++|+++|.+||.|..|.++.+ ..|||||+|.+.++|.+    +++..+.+.  +..|.+..
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-srGfaFV~F~~~~~A~~----~~~~~~~~~--g~~v~v~~   80 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-FRAFAFVTFADDKVAQS----LCGEDLIIK--GISVHISN   80 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-CCSEEEEEESCHHHHHH----HTTCEEEET--TEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-CCCEEEEEECCHHHHHH----HcCCCcccC--CEEEEEEE
Confidence            345789999999999999999999999999999999876 56799999999999883    566665421  15666666


Q ss_pred             cCCC
Q 023765          186 YDSR  189 (277)
Q Consensus       186 ~~~~  189 (277)
                      +.++
T Consensus        81 a~~k   84 (89)
T 3d2w_A           81 AEPK   84 (89)
T ss_dssp             CC--
T ss_pred             cCCC
Confidence            5443

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.46  E-value=2.8e-13  Score=94.31  Aligned_cols=78  Identities=17%  Similarity=0.205  Sum_probs=64.4

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEE---EEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFS---QVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~---~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ....+|||+|||..+++++|+++|.+||.|..+   ........+||||+|.+.++|++|++ |||..+.|    ..|.|
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g----~~l~V   89 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFG----NEIKL   89 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTT----BCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECC----cEEEE
Confidence            357899999999999999999999999987661   12234456799999999999999998 99999999    56677


Q ss_pred             eecCCC
Q 023765          184 REYDSR  189 (277)
Q Consensus       184 ~~~~~~  189 (277)
                      .....+
T Consensus        90 ~~a~~~   95 (101)
T 1fj7_A           90 EKPKGR   95 (101)
T ss_dssp             ECCSCC
T ss_pred             EEcCCC
Confidence            766543

>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=99.46  E-value=9.4e-14  Score=94.62  Aligned_cols=68  Identities=26%  Similarity=0.319  Sum_probs=61.7

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeeccccee
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  178 (277)
                      .+|||+|||..+++++|+++|.+||.|..+.+..+..    .+||||+|.+.+ |..|+..|||..+.|+.+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~   73 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIR   73 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCS
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEE
Confidence            4799999999999999999999999999999987654    469999999999 9999999999999995443

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

Probab=99.45  E-value=1.1e-13  Score=97.36  Aligned_cols=71  Identities=14%  Similarity=0.187  Sum_probs=62.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCC---eeEEEEEecCC---CcEEEEEEechhHHHHHHHhcCCCeecccce
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGD---VCFSQVFRDRG---GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFS  177 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~---v~~~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  177 (277)
                      .....+|||+|||+.+++++|+++|..||.   |..|.+..+..   .|||||+|.+.++|.+||. +|+..+.|+.+
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i   84 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYV   84 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEE
Confidence            345789999999999999999999999988   88999887654   4699999999999999999 99999999543

>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=99.45  E-value=4e-13  Score=99.73  Aligned_cols=79  Identities=15%  Similarity=0.112  Sum_probs=66.6

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeE--------EEEE-ecCCCcEEEEEEechhHHHHHHHhcCCCeecccce
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCF--------SQVF-RDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFS  177 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~--------~~~~-~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  177 (277)
                      .+..+|||+|||..+++++|.++|.+||.|..        +.+. .+...+||||+|.+.++|..|+..|||..+.|   
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g---  119 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFG---  119 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETT---
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCC---
Confidence            34689999999999999999999999998865        3333 34556799999999999999999999999999   


Q ss_pred             eeEEEEeecCCC
Q 023765          178 RSYVRVREYDSR  189 (277)
Q Consensus       178 ~~~i~~~~~~~~  189 (277)
                       ..|.|..+...
T Consensus       120 -~~l~V~~a~~~  130 (143)
T 3egn_A          120 -KPMVVQFARSA  130 (143)
T ss_dssp             -EECEEEECCCS
T ss_pred             -cEEEEEECCCC
Confidence             67777776544

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.43  E-value=3.1e-13  Score=97.14  Aligned_cols=68  Identities=15%  Similarity=0.152  Sum_probs=59.7

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCe----eEEEEEecCCC---cEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDV----CFSQVFRDRGG---MTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v----~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                      ....+|||+|||+.+++++|+++|.+||.|    ..|.|+.+..+   |||||+|.+.++|++||.. |+..+.|+
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR   95 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKR   95 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCe
Confidence            446899999999999999999999999975    57888876433   5999999999999999986 99999885

>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=99.42  E-value=2.2e-13  Score=89.44  Aligned_cols=67  Identities=10%  Similarity=0.140  Sum_probs=59.5

Q ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeeccccee
Q 023765          111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       111 ~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  178 (277)
                      +|||+|||..+++++|+++|.+||.|..+.+..+..    .+||||+|.+.++|..|+. +++..+.|+.+.
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~   71 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCE   71 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEE
Confidence            589999999999999999999999999999987643    4699999999999999998 588999995443

>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=99.42  E-value=5.5e-13  Score=96.04  Aligned_cols=73  Identities=12%  Similarity=0.148  Sum_probs=61.4

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCee--EEEEEecCC---CcEEEEEEechhHHHHHHHhcCCCeecccceee
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVC--FSQVFRDRG---GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRS  179 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~--~~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  179 (277)
                      ......+|||+|||+.+++++|+++|.+| .|.  .|.|+.+..   .|||||+|.+.++|++||. +++..+.|+.+.+
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V  115 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEV  115 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEE
Confidence            34457899999999999999999999999 666  788887654   4699999999999999998 5779999964433

>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=99.41  E-value=3.3e-13  Score=91.46  Aligned_cols=74  Identities=11%  Similarity=0.126  Sum_probs=60.5

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCee--cccceeeEEEEee
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEF--RNAFSRSYVRVRE  185 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~--~g~~~~~~i~~~~  185 (277)
                      ...+|||+|||..+++++|+++|.+||.|..|.+..+ ..+||||+|.+.++|++|    ++..+  .|    ..|.+..
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-~~g~afV~f~~~~~a~~~----~~~~~~~~g----~~l~v~~   74 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-FRAFAFVTFADDQIAQSL----CGEDLIIKG----ISVHISN   74 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-CCSCCEEECSCHHHHHHT----TTCEEEETT----EEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-CCCEEEEEECCHHHHHHH----hcCCceeCC----EEEEEEe
Confidence            3689999999999999999999999999999999876 557999999999999753    44444  44    5677776


Q ss_pred             cCCCC
Q 023765          186 YDSRR  190 (277)
Q Consensus       186 ~~~~r  190 (277)
                      ..++.
T Consensus        75 a~~~~   79 (88)
T 1wf0_A           75 AEPKH   79 (88)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            65543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.40  E-value=8.8e-13  Score=91.96  Aligned_cols=68  Identities=19%  Similarity=0.286  Sum_probs=60.7

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC---cEEEEEEechhHHHHHHHhcCCCeecccc
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG---MTGIVDYTSYDDMKYAIRKLDRSEFRNAF  176 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  176 (277)
                      ...++|||+|||..+++++|.++|.+||.|..|.++.+..+   +||||+|.+.++|++|+.  ++..++|+.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~   77 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKK   77 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEE
Confidence            34689999999999999999999999999999999987632   599999999999999998  888888843

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.39  E-value=2.1e-12  Score=91.48  Aligned_cols=74  Identities=15%  Similarity=0.196  Sum_probs=64.2

Q ss_pred             ceEEEeCC----CCCCCHHHHHHHHHhcCCeeEEEEEecCCCc----EEEEEEec----hhH----HHHHHH--hcCCCe
Q 023765          110 YRVLVTGL----PSSASWQDLKDHMRRAGDVCFSQVFRDRGGM----TGIVDYTS----YDD----MKYAIR--KLDRSE  171 (277)
Q Consensus       110 ~~l~v~~l----~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~----~~fv~f~~----~~~----a~~a~~--~l~g~~  171 (277)
                      ..|+|+||    |+.+++++|+++|..||+|..+.++.++.++    ||||+|.+    +++    |.+|+.  .|+|..
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    9999999999999999999999999998874    99999996    433    788988  789999


Q ss_pred             ecccceeeEEEEeecC
Q 023765          172 FRNAFSRSYVRVREYD  187 (277)
Q Consensus       172 ~~g~~~~~~i~~~~~~  187 (277)
                      |+|    ..|+|..++
T Consensus        83 I~G----r~irV~ln~   94 (136)
T 2j8a_A           83 IMG----FKFEVILNK   94 (136)
T ss_dssp             ETT----EEEEEEECC
T ss_pred             ecC----cEEEEEECc
Confidence            999    667776554

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.09  E-value=3.2e-14  Score=101.81  Aligned_cols=78  Identities=21%  Similarity=0.308  Sum_probs=67.8

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeE--------EEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCF--------SQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~--------~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                      +..+|||+|||..+++++|+++|.+||.|..        |.++.+..    .+||||+|.+.++|.+|+..|||..+.| 
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g-   84 (116)
T 2lcw_A            6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG-   84 (116)
Confidence            4679999999999999999999999999988        77876643    4699999999999999999999999999 


Q ss_pred             ceeeEEEEeecCCC
Q 023765          176 FSRSYVRVREYDSR  189 (277)
Q Consensus       176 ~~~~~i~~~~~~~~  189 (277)
                         ..|.|.....+
T Consensus        85 ---~~l~V~~a~~~   95 (116)
T 2lcw_A           85 ---NPIKVSFATRR   95 (116)
Confidence               56667666544

>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=99.37  E-value=1.5e-11  Score=95.67  Aligned_cols=117  Identities=13%  Similarity=0.170  Sum_probs=80.9

Q ss_pred             ChHHHHHHHHhc--CCcccCCceEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHH
Q 023765           54 DYRDAEDAIRGR--DGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMR  131 (277)
Q Consensus        54 ~~~~a~~a~~~l--~~~~~~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~  131 (277)
                      +.+.+..|+...  ....+.+....|....... .+...          ..........+|||+|||..+++++|+++|.
T Consensus        63 d~~~I~~Al~~S~~~~lev~ed~~~vrR~~~~p-~p~~~----------~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~  131 (193)
T 2voo_A           63 DFNVIVEALSKSKAELMEISEDKTKIRRSPSKP-LPEVT----------DEYKNDVKNRSVYIKGFPTDATLDDIKEWLE  131 (193)
T ss_dssp             CHHHHHHHHHTCSSCCEEECTTSSEEEECTTSC-CCCCC----------HHHHHHHHHTEEEEECCCTTCCHHHHHHHHT
T ss_pred             CHHHHHHHHhhcccceEEEecccceEEecccCC-Ccccc----------hhhhhccccCEEEecCCCCcCCHHHHHHHHh
Confidence            566777777766  5555555555555442111 00000          0000112357999999999999999999999


Q ss_pred             hcCCeeEEEEEecCC---CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          132 RAGDVCFSQVFRDRG---GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       132 ~~g~v~~~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      +||.|..|.+..+..   .|||||+|.+.++|.+|+..++ ..+.|+    .|.|...
T Consensus       132 ~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr----~l~V~~~  184 (193)
T 2voo_A          132 DKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG-QKYKET----DLLILFK  184 (193)
T ss_dssp             TSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTT-CEETTE----ECEEEET
T ss_pred             cCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCC-CeECCE----EEEEEEh
Confidence            999999999987654   3699999999999999998665 589984    5555443

>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=99.37  E-value=9.6e-12  Score=88.16  Aligned_cols=80  Identities=16%  Similarity=0.290  Sum_probs=66.1

Q ss_pred             CCCCceEEEeCCCCCCC-----------HHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecc
Q 023765          106 RRSDYRVLVTGLPSSAS-----------WQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRN  174 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~-----------~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g  174 (277)
                      +.+..+|+|.||.....           +++|+++|.+||.|..|.|......|||||+|.+.++|++|+..|||..++|
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~g   91 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGG   91 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETT
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            34578999999944432           5799999999999999977544456899999999999999999999999999


Q ss_pred             cceeeEEEEeecCCC
Q 023765          175 AFSRSYVRVREYDSR  189 (277)
Q Consensus       175 ~~~~~~i~~~~~~~~  189 (277)
                          ..|.|....+.
T Consensus        92 ----r~l~v~~a~~~  102 (112)
T 2dit_A           92 ----RQITAQAWDGT  102 (112)
T ss_dssp             ----EECEEEECCSC
T ss_pred             ----cEEEEEEeCCC
Confidence                57777776554

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

Probab=99.37  E-value=8.4e-13  Score=94.00  Aligned_cols=59  Identities=15%  Similarity=0.208  Sum_probs=52.8

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEec-------CCCcEEEEEEechhHHHHHHHhc
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD-------RGGMTGIVDYTSYDDMKYAIRKL  167 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~-------~~~~~~fv~f~~~~~a~~a~~~l  167 (277)
                      ...+|||+|||..+++++|+++|.+||.|. +.++.+       ...+||||+|.+.++|++|++.|
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~   72 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDAC   72 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHS
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhh
Confidence            467999999999999999999999999999 766654       33569999999999999999998

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

Probab=99.36  E-value=5.8e-12  Score=87.98  Aligned_cols=77  Identities=14%  Similarity=0.174  Sum_probs=64.1

Q ss_pred             CCCceEEEeCCCC-----CCCHHHHHHHHHhcCCeeEEEEEecC-----CCcEEEEEEechhHHHHHHHhcCCCeecccc
Q 023765          107 RSDYRVLVTGLPS-----SASWQDLKDHMRRAGDVCFSQVFRDR-----GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAF  176 (277)
Q Consensus       107 ~~~~~l~v~~l~~-----~~~~~~l~~~f~~~g~v~~~~~~~~~-----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  176 (277)
                      .+..+|+|.||..     +.++++|+++|.+||.|..|.|+.++     ..|||||+|.+.++|.+|+..|||..++|  
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~G--   83 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGG--   83 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETT--
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECC--
Confidence            3467999999963     23689999999999999999998764     34799999999999999999999999999  


Q ss_pred             eeeEEEEeecC
Q 023765          177 SRSYVRVREYD  187 (277)
Q Consensus       177 ~~~~i~~~~~~  187 (277)
                        ..|.+....
T Consensus        84 --r~i~v~~a~   92 (105)
T 2pe8_A           84 --RVVKACFYN   92 (105)
T ss_dssp             --EECEEEECC
T ss_pred             --cEEEEEEcC
Confidence              556665543

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.33  E-value=9.4e-12  Score=88.12  Aligned_cols=76  Identities=17%  Similarity=0.185  Sum_probs=67.1

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcC-hHHHHHHHHhcC--CcccCCceEEEEE
Q 023765            4 RSSRTLYVGNLPGD-TRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFED-YRDAEDAIRGRD--GYNFDGYRLRVEL   79 (277)
Q Consensus         4 ~~~~~l~V~nL~~~-~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~-~~~a~~a~~~l~--~~~~~g~~i~v~~   79 (277)
                      .+.+.|+|+||++. ++.++|+++|++||+|..|.+....   ..|||.|.+ +++|..|+..||  +..|.|..+.++.
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~---~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~ev   92 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA---KEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   92 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC---SEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCC---CEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEE
Confidence            46789999999999 9999999999999999999997643   379999999 899999999994  7889999899887


Q ss_pred             ccC
Q 023765           80 AHG   82 (277)
Q Consensus        80 a~~   82 (277)
                      ...
T Consensus        93 L~G   95 (121)
T 1owx_A           93 LEG   95 (121)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            653

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.27  E-value=1.1e-11  Score=98.88  Aligned_cols=65  Identities=14%  Similarity=0.251  Sum_probs=59.8

Q ss_pred             CCCCceEEEeCCCCCC---------CHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCee
Q 023765          106 RRSDYRVLVTGLPSSA---------SWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEF  172 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~---------~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~  172 (277)
                      .....+|||+||+..+         ++++|.++|.+||+|..|.|+..  .+||||+|.+.++|+.|++.|+|..+
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~--kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES--KNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG--GTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC--CCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            3457899999999998         79999999999999999999864  46999999999999999999999999

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.25  E-value=3.1e-11  Score=80.08  Aligned_cols=74  Identities=15%  Similarity=0.177  Sum_probs=62.0

Q ss_pred             CCCeEEEcCCC----CCCCH----HHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEE
Q 023765            5 SSRTLYVGNLP----GDTRM----REVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLR   76 (277)
Q Consensus         5 ~~~~l~V~nL~----~~~t~----~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~   76 (277)
                      +--||+|.-++    .++-+    .+|.+.|.+||+|..+++..+     .+||+|.+.++|.+|+. |||..+.|+.|+
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d-----~~fVtF~d~~sAlaAi~-mnG~~v~Gr~Lk   79 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED-----KMWVTFLEGSSALNVLS-LNGKELLNRTIT   79 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS-----SEEEEESSHHHHHHGGG-GTTCEETTEEEE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC-----CEEEEECChHHHHHHHh-cCCeEeCCeEEE
Confidence            45577777766    23434    678999999999999999853     49999999999999999 999999999999


Q ss_pred             EEEccCCC
Q 023765           77 VELAHGGR   84 (277)
Q Consensus        77 v~~a~~~~   84 (277)
                      |.++.+.-
T Consensus        80 V~lkt~dW   87 (91)
T 2dnr_A           80 IALKSPSG   87 (91)
T ss_dssp             EEECCCSS
T ss_pred             EEeCCCCc
Confidence            99988643

>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=99.24  E-value=2.9e-11  Score=84.41  Aligned_cols=75  Identities=21%  Similarity=0.223  Sum_probs=61.5

Q ss_pred             CCceEEEeCC--CCCCC--------HHHHHHHHHhcCCeeEEEEEecC------CCcEEEEEEechhHHHHHHHhcCCCe
Q 023765          108 SDYRVLVTGL--PSSAS--------WQDLKDHMRRAGDVCFSQVFRDR------GGMTGIVDYTSYDDMKYAIRKLDRSE  171 (277)
Q Consensus       108 ~~~~l~v~~l--~~~~~--------~~~l~~~f~~~g~v~~~~~~~~~------~~~~~fv~f~~~~~a~~a~~~l~g~~  171 (277)
                      +..+|.|.|+  |..+.        +++|+++|.+||.|..|.|+.+.      ..|+|||+|.+.++|.+|+..|||..
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            3678999998  33332        47899999999999999998764      34799999999999999999999999


Q ss_pred             ecccceeeEEEEeec
Q 023765          172 FRNAFSRSYVRVREY  186 (277)
Q Consensus       172 ~~g~~~~~~i~~~~~  186 (277)
                      ++|    ..|.+...
T Consensus        84 f~G----R~i~v~~~   94 (105)
T 3v4m_A           84 FAN----RVVVTKYC   94 (105)
T ss_dssp             ETT----EECEEEEE
T ss_pred             eCC----CEEEEEEe
Confidence            999    45555543

>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=99.23  E-value=1.6e-11  Score=103.04  Aligned_cols=66  Identities=17%  Similarity=0.134  Sum_probs=59.0

Q ss_pred             CCCCceEEEeC--CCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeec
Q 023765          106 RRSDYRVLVTG--LPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFR  173 (277)
Q Consensus       106 ~~~~~~l~v~~--l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~  173 (277)
                      ..+..+|||+|  |+..+++++|+++|.+||+|..|.+..  ..+||||+|.+.++|++|++.|||.++.
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~--~kgfaFV~f~~~~~A~~Ai~~lnG~~~~   82 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP--NKPYSFARYRTTEESKRAYVTLNGKEVV   82 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT--TCSEEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC--CCCEEEEEECCHHHHHHHHHHhCCCccc
Confidence            34578999999  578999999999999999999887754  4579999999999999999999999994

>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=99.22  E-value=6.2e-11  Score=83.79  Aligned_cols=76  Identities=12%  Similarity=0.068  Sum_probs=62.5

Q ss_pred             CCCceEEEeCCCCCCC----------HHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccc
Q 023765          107 RSDYRVLVTGLPSSAS----------WQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAF  176 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~----------~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  176 (277)
                      .+..+|.+.|+-....          +++|+++|.+||.|..|.|..+...|++||+|.+.++|.+|+..|||.+++|+ 
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR-   83 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGK-   83 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTE-
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCE-
Confidence            3467888998733221          46899999999999999998877778999999999999999999999999994 


Q ss_pred             eeeEEEEeec
Q 023765          177 SRSYVRVREY  186 (277)
Q Consensus       177 ~~~~i~~~~~  186 (277)
                         .|.+...
T Consensus        84 ---~i~v~~~   90 (114)
T 3s6e_A           84 ---MITAAYV   90 (114)
T ss_dssp             ---ECEEEEE
T ss_pred             ---EEEEEEE
Confidence               5555443

>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=99.21  E-value=5.5e-11  Score=84.63  Aligned_cols=75  Identities=13%  Similarity=0.236  Sum_probs=61.8

Q ss_pred             CCceEEEeCCCC--CC---CHHHHHHHHHhcCCeeEEEEEecCCC--------cEEEEEEechhHHHHHHHhcCCCeecc
Q 023765          108 SDYRVLVTGLPS--SA---SWQDLKDHMRRAGDVCFSQVFRDRGG--------MTGIVDYTSYDDMKYAIRKLDRSEFRN  174 (277)
Q Consensus       108 ~~~~l~v~~l~~--~~---~~~~l~~~f~~~g~v~~~~~~~~~~~--------~~~fv~f~~~~~a~~a~~~l~g~~~~g  174 (277)
                      +..+|+|.|+-.  ++   -+++|+++|.+||.|..|.|+.+..+        |++||+|.+.++|.+|+..|||.+++|
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            467899999842  22   37899999999999999999877532        699999999999999999999999999


Q ss_pred             cceeeEEEEeec
Q 023765          175 AFSRSYVRVREY  186 (277)
Q Consensus       175 ~~~~~~i~~~~~  186 (277)
                      +    .|.+...
T Consensus        99 R----~i~v~~~  106 (118)
T 3ue2_A           99 R----KVVAEVY  106 (118)
T ss_dssp             E----ECEEEEE
T ss_pred             c----EEEEEEc
Confidence            4    4555443

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.15  E-value=1.9e-10  Score=81.36  Aligned_cols=73  Identities=12%  Similarity=0.191  Sum_probs=63.5

Q ss_pred             CCCCCCceEEEeCCCCC-CCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEec-hhHHHHHHHhcC--CCeeccccee
Q 023765          104 VSRRSDYRVLVTGLPSS-ASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTS-YDDMKYAIRKLD--RSEFRNAFSR  178 (277)
Q Consensus       104 ~~~~~~~~l~v~~l~~~-~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~-~~~a~~a~~~l~--g~~~~g~~~~  178 (277)
                      ...+.+..|+|+||+.. ++.++|+++|.+||+|.+|.+..+..  .|||.|.+ .++|..|+..|+  +..|.|....
T Consensus        13 ~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~--tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~   89 (121)
T 1owx_A           13 LEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK--EGIILFKEKAKEALGKAKDANNGNLQLRNKEVT   89 (121)
T ss_dssp             CSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS--EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEE
T ss_pred             ccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC--EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEE
Confidence            34566899999999999 99999999999999999999988876  69999999 899999999994  6777774333

>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=99.11  E-value=2.7e-11  Score=84.49  Aligned_cols=64  Identities=22%  Similarity=0.252  Sum_probs=52.9

Q ss_pred             EeCCCCCCCHHHHHHHH------------HhcCCeeEEEEEecCC---CcEEEEEEechhHHHHHHHhcCCCeecccce
Q 023765          114 VTGLPSSASWQDLKDHM------------RRAGDVCFSQVFRDRG---GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFS  177 (277)
Q Consensus       114 v~~l~~~~~~~~l~~~f------------~~~g~v~~~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  177 (277)
                      +.||+..+++++|+++|            .+||.|..|.|+.+..   .|||||+|.+.++|.+|+..|||..++|+.+
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 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            45666677777666555            9999999999987653   4699999999999999999999999999533

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

Probab=99.11  E-value=1.7e-09  Score=74.51  Aligned_cols=64  Identities=11%  Similarity=0.148  Sum_probs=52.4

Q ss_pred             CCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeecCCC
Q 023765          119 SSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDSR  189 (277)
Q Consensus       119 ~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~~~  189 (277)
                      ..+++++|+++|.+||.|..|.|+ ....|||||+|.+.++|+.|+..+++  +.|    ..|.|......
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g----~~l~V~~a~~~   90 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-SKKPGTAVVEFATVKAAELAVQNEVG--LVD----NPLKISWLEGQ   90 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-SSSSSEEEEEESCHHHHHHHHHTCCB--CSS----SBCEEECSSCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-cCCCCEEEEEECCHHHHHHHHHhcCC--CCC----CeEEEEEccCC
Confidence            468999999999999999999988 35567999999999999999998655  445    45666665443

>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=99.08  E-value=2.7e-10  Score=75.87  Aligned_cols=71  Identities=18%  Similarity=0.228  Sum_probs=60.2

Q ss_pred             CCCeEEEcCCCCC-----CCH----HHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceE
Q 023765            5 SSRTLYVGNLPGD-----TRM----REVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRL   75 (277)
Q Consensus         5 ~~~~l~V~nL~~~-----~t~----~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i   75 (277)
                      +--||+|.-++..     +-+    .+|.+.|.+||+|..+++..+     -+||+|.+.++|.+|+. |||..+.|+.|
T Consensus        14 pD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d-----~~fVtF~d~~sAl~AI~-ldG~~v~Gr~L   87 (95)
T 1ufw_A           14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG-----QMLVTFADSHSALSVLD-VDGMKVKGRAV   87 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT-----EEEEECSCSHHHHHHHH-GGGSEETTEEE
T ss_pred             CCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecC-----cEEEEEcChHHHHHHHh-cCCeeeCCeEE
Confidence            5568888888643     323    568899999999999999854     39999999999999999 99999999999


Q ss_pred             EEEEcc
Q 023765           76 RVELAH   81 (277)
Q Consensus        76 ~v~~a~   81 (277)
                      .|.+..
T Consensus        88 ~V~~k~   93 (95)
T 1ufw_A           88 KISGPS   93 (95)
T ss_dssp             EEECCC
T ss_pred             EEeccC
Confidence            998743

>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=98.99  E-value=1.6e-09  Score=86.24  Aligned_cols=78  Identities=21%  Similarity=0.247  Sum_probs=64.3

Q ss_pred             CCCeEEEcCCC-----CCCCHHHHHHHhhccCCeeEEEeec-------CCCCCcEEEEEEcChHHHHHHHHhcCCcccCC
Q 023765            5 SSRTLYVGNLP-----GDTRMREVEDLFYKYGPIVDIDLKI-------PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDG   72 (277)
Q Consensus         5 ~~~~l~V~nL~-----~~~t~~~l~~~F~~~G~v~~v~~~~-------~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g   72 (277)
                      .+..+.+.|+-     ..-.+++|.+.|++||+|..+.+..       ++.++|++||+|.+.++|.+|+..|||..|.|
T Consensus       123 ~s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~g  202 (222)
T 3dxb_A          123 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG  202 (222)
T ss_dssp             BCSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSS
T ss_pred             ccccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECC
Confidence            34555555552     2345788999999999999999952       23678999999999999999999999999999


Q ss_pred             ceEEEEEccC
Q 023765           73 YRLRVELAHG   82 (277)
Q Consensus        73 ~~i~v~~a~~   82 (277)
                      +.|.|.++..
T Consensus       203 r~i~~~~~~~  212 (222)
T 3dxb_A          203 RKVVAEVYDQ  212 (222)
T ss_dssp             SBCEEEECCH
T ss_pred             eEEEEEEcCH
Confidence            9999999763

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.93  E-value=3.6e-09  Score=70.15  Aligned_cols=70  Identities=17%  Similarity=0.182  Sum_probs=56.4

Q ss_pred             CceEEEeCCCC----CC-C---HHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeE
Q 023765          109 DYRVLVTGLPS----SA-S---WQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSY  180 (277)
Q Consensus       109 ~~~l~v~~l~~----~~-~---~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  180 (277)
                      ..+|+|.-.+.    +. .   ..+|.+.|.+||+|..+.+..+.    +||+|.+.++|.+|+. |||..++|    ..
T Consensus         7 d~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~----~fVtF~d~~sAlaAi~-mnG~~v~G----r~   77 (91)
T 2dnr_A            7 GGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK----MWVTFLEGSSALNVLS-LNGKELLN----RT   77 (91)
T ss_dssp             SCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS----EEEEESSHHHHHHGGG-GTTCEETT----EE
T ss_pred             CCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC----EEEEECChHHHHHHHh-cCCeEeCC----eE
Confidence            55666666552    22 2   36799999999999999999884    9999999999999998 99999999    56


Q ss_pred             EEEeecC
Q 023765          181 VRVREYD  187 (277)
Q Consensus       181 i~~~~~~  187 (277)
                      |+|..+.
T Consensus        78 LkV~lkt   84 (91)
T 2dnr_A           78 ITIALKS   84 (91)
T ss_dssp             EEEEECC
T ss_pred             EEEEeCC
Confidence            6666554

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.86  E-value=1.4e-08  Score=68.89  Aligned_cols=72  Identities=17%  Similarity=0.094  Sum_probs=66.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcc-----CCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKY-----GPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~-----G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      ..++|-|-|||-.+++..|+.|++++     |.|..|.+..+   -+-|+|+|.+...|.+|.-.|+|..|.|+.|.|.-
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD---H~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gT   96 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD---FNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGT   96 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT---TTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC---CCceEEEEccchhhHHHHhhcCCeeecCeEEEecC
Confidence            47899999999999999999999999     99999999754   46799999999999999988999999999999865

>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=98.79  E-value=1.2e-08  Score=67.88  Aligned_cols=70  Identities=11%  Similarity=0.202  Sum_probs=57.8

Q ss_pred             CCceEEEeCCCCC-----C-C---HHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeeccccee
Q 023765          108 SDYRVLVTGLPSS-----A-S---WQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       108 ~~~~l~v~~l~~~-----~-~---~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  178 (277)
                      +..+|+|.-++..     + .   ..+|.+.|.+||+|..+.+..+.    +||+|.+.++|.+||. |||.+++|    
T Consensus        14 pD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~----~fVtF~d~~sAl~AI~-ldG~~v~G----   84 (95)
T 1ufw_A           14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ----MLVTFADSHSALSVLD-VDGMKVKG----   84 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE----EEEECSCSHHHHHHHH-GGGSEETT----
T ss_pred             CCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc----EEEEEcChHHHHHHHh-cCCeeeCC----
Confidence            3678888877632     2 2   25699999999999999999884    9999999999999998 99999999    


Q ss_pred             eEEEEeec
Q 023765          179 SYVRVREY  186 (277)
Q Consensus       179 ~~i~~~~~  186 (277)
                      ..|+|...
T Consensus        85 r~L~V~~k   92 (95)
T 1ufw_A           85 RAVKISGP   92 (95)
T ss_dssp             EEEEEECC
T ss_pred             eEEEEecc
Confidence            56666554

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.75  E-value=2e-07  Score=62.80  Aligned_cols=90  Identities=23%  Similarity=0.277  Sum_probs=73.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhc----c-CCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYK----Y-GPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV   77 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~----~-G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v   77 (277)
                      +....+|.|.|||+.+.++.|.-+|++    . |+|..|....     +-|+|+|.+.+.|+..++ -....|.+..|.|
T Consensus         5 ~~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-----~~AvItF~d~~va~rVL~-k~~H~L~~~~LsV   78 (104)
T 2dhx_A            5 SSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-----CGGVLTFREPADAERVLA-QADHELHGAQLSL   78 (104)
T ss_dssp             CCCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-----TEEEEEESSHHHHHHHHT-CSCCBSSSSBCEE
T ss_pred             ccCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-----CcEEEEEcChHHHHHHhc-CCcceecCeEEEE
Confidence            346789999999999999999999987    2 5999998862     789999999999999998 3367888999999


Q ss_pred             EEccCCCCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCC
Q 023765           78 ELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSAS  122 (277)
Q Consensus        78 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~  122 (277)
                      .......                        ..+|.+.+|++.++
T Consensus        79 ~P~~~~~------------------------~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           79 RPAPPRA------------------------PARLLLQGLPPGTS   99 (104)
T ss_dssp             EECCCCC------------------------CCCCCCCSCCCCCC
T ss_pred             EcCCCCC------------------------cceEeeecCCCCCC
Confidence            7754322                        45677778877664

>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=98.44  E-value=4.4e-07  Score=72.01  Aligned_cols=57  Identities=14%  Similarity=0.221  Sum_probs=49.6

Q ss_pred             CHHHHHHHHHhcCCeeEEEEEecCCC--------cEEEEEEechhHHHHHHHhcCCCeeccccee
Q 023765          122 SWQDLKDHMRRAGDVCFSQVFRDRGG--------MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       122 ~~~~l~~~f~~~g~v~~~~~~~~~~~--------~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  178 (277)
                      .+++|.+.|.+||.|..+.|..+..+        |++||+|.+.++|.+|+..|||.+++|+.+.
T Consensus       142 ~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~  206 (222)
T 3dxb_A          142 LEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVV  206 (222)
T ss_dssp             HHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             HHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEE
Confidence            46889999999999999999855332        6999999999999999999999999995443

>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=98.43  E-value=9.4e-07  Score=59.88  Aligned_cols=78  Identities=19%  Similarity=0.126  Sum_probs=65.6

Q ss_pred             CCCCCeEEEcCCCCCC-C----HHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEE
Q 023765            3 SRSSRTLYVGNLPGDT-R----MREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV   77 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~-t----~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v   77 (277)
                      +.-.++|+|+||+..+ +    .+.++++|..|+++....+...   -.=..|.|.++++|.+|-..|++..|.|..|.|
T Consensus         2 s~~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS---FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            2 SSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS---FKRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CSCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT---TTEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CCCCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc---ceEEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            3456899999998865 3    2577899999999888888643   346799999999999999999999999999999


Q ss_pred             EEccCC
Q 023765           78 ELAHGG   83 (277)
Q Consensus        78 ~~a~~~   83 (277)
                      .++++.
T Consensus        79 YFgq~~   84 (104)
T 1wey_A           79 YFAQTL   84 (104)
T ss_dssp             ECCCCS
T ss_pred             EecCCC
Confidence            999843

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.22  E-value=9.2e-06  Score=55.23  Aligned_cols=69  Identities=13%  Similarity=0.121  Sum_probs=61.8

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhc-----CCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRA-----GDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~-----g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ..+|-+-|||..++...|+.++.++     |.+..+.+..+..  -|+|+|.+...|-+|.-.|+|.+|.|    ..|++
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~--GAivef~d~~~AgKasLaL~G~ef~g----r~Lr~   94 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFN--GAIIIFRDSKFAAKMLMILNGSQFQG----KVIRS   94 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTT--EEEEECSCHHHHHHHHHHHSSEEETT----EEEEE
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCC--ceEEEEccchhhHHHHhhcCCeeecC----eEEEe
Confidence            5689999999999999999999999     9999988887765  49999999999999999999999998    45554

>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=98.18  E-value=1.6e-05  Score=52.91  Aligned_cols=75  Identities=17%  Similarity=0.179  Sum_probs=59.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecC-----CCCCcEEEEEEcChHHHHHHHHhcCCcccCCc-----eEE
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP-----PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGY-----RLR   76 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~-----~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~-----~i~   76 (277)
                      ++|.|.+||+.+|++++.+.+..+..+....+...     ...-.-|||.|.+.+++....+.++|..|.+.     ...
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a~   81 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeeeE
Confidence            58999999999999999999999988877766331     12235799999999999999999999888543     234


Q ss_pred             EEEcc
Q 023765           77 VELAH   81 (277)
Q Consensus        77 v~~a~   81 (277)
                      |++|.
T Consensus        82 VE~AP   86 (91)
T 1uw4_A           82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            55554

>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=98.09  E-value=9.8e-06  Score=53.92  Aligned_cols=55  Identities=18%  Similarity=0.278  Sum_probs=45.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcC
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRD   66 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~   66 (277)
                      .+.++| ++|+.+...||.++|+.||.|.--.+.     -..|||.|.+++.|..|+..+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv~I~Wid-----DTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQISWID-----DTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSCCCEEEE-----TTEEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCEEEEEEc-----CCeEEEEecCHHHHHHHHHhcc
Confidence            456777 999999999999999999954444443     3589999999999999998663

>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=97.96  E-value=5.3e-05  Score=52.81  Aligned_cols=72  Identities=17%  Similarity=0.245  Sum_probs=60.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCC-ceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDG-YRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g-~~i~v~~a~   81 (277)
                      +.+.|.|-+.|+. ..+.|...|++||+|.+....   ...++..|.|.+..+|.+|+. .||..|.| ..|-|....
T Consensus        23 ~~~wVtVFGFp~~-~~~~VL~~F~~~G~Iv~~~~~---~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~~   95 (119)
T 1wwh_A           23 DDTWVTVFGFPQA-SASYILLQFAQYGNILKHVMS---NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   95 (119)
T ss_dssp             GGGEEEEECCCGG-GHHHHHHHHHTTSCEEEEEEC---SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             CCCEEEEECCCHH-HHHHHHHHHHhhCcEEEeccC---CCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEECC
Confidence            3567999999988 478888999999999998873   336899999999999999999 89999985 667777754

>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=97.94  E-value=1.3e-05  Score=53.53  Aligned_cols=54  Identities=20%  Similarity=0.325  Sum_probs=44.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRD   66 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~   66 (277)
                      +.++| ++|+.+...||.++|+.||.| .|.+..    -..|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv-~I~Wid----DTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWID----DTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEE----TTEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCE-EEEEEc----CCeEEEEecCHHHHHHHHHhcc
Confidence            45667 999999999999999999933 333433    3589999999999999999764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.67  E-value=0.00015  Score=48.50  Aligned_cols=77  Identities=18%  Similarity=0.148  Sum_probs=56.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CC--CCCcEEEEEEcChHHHHHHHHhcCCcccCCc-----e
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PP--RPPGYAFLEFEDYRDAEDAIRGRDGYNFDGY-----R   74 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~--~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~-----~   74 (277)
                      .+-+|.|..|||.+|++++.+.+..+=++....+..   +.  ..-.-|||.|.+.+++....+.++|..|.+.     +
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~   87 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYP   87 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEE
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEee
Confidence            466899999999999999988887765544333321   11  1224589999999999999999999888543     2


Q ss_pred             EEEEEcc
Q 023765           75 LRVELAH   81 (277)
Q Consensus        75 i~v~~a~   81 (277)
                      ..|++|.
T Consensus        88 a~VE~AP   94 (97)
T 2l08_A           88 AVVEFAP   94 (97)
T ss_dssp             EEEEECC
T ss_pred             eEEEecC
Confidence            4455554

>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=97.58  E-value=0.00092  Score=44.42  Aligned_cols=67  Identities=13%  Similarity=0.325  Sum_probs=57.1

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC------cEEEEEEechhHHHHHHHhcCCCeecccc
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG------MTGIVDYTSYDDMKYAIRKLDRSEFRNAF  176 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~------~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  176 (277)
                      .+|.|.+||+.+|++++.+.+....++....+..+...      .-|+|.|.+.+++..-.+.++|..+-+..
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~k   74 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNK   74 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTT
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCC
Confidence            47899999999999999999999988877777655432      27999999999999999999999886644

>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=97.49  E-value=0.00077  Score=44.87  Aligned_cols=55  Identities=16%  Similarity=0.221  Sum_probs=45.0

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcC
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLD  168 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~  168 (277)
                      ...++| ++|+.+...||.++|..||.|. |.++.+.   .|||.|.+.+.|..|+..+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv~-I~WidDT---sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT---SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSCC-CEEEETT---EEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCEE-EEEEcCC---eEEEEecCHHHHHHHHHhcc
Confidence            556777 9999999999999999999543 4444443   69999999999999998653

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=97.38  E-value=0.00042  Score=48.95  Aligned_cols=76  Identities=20%  Similarity=0.270  Sum_probs=57.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEE-eec---------------CC-CCCcEEEEEEcChHHHHHHHHhcC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDID-LKI---------------PP-RPPGYAFLEFEDYRDAEDAIRGRD   66 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~-~~~---------------~~-~~~g~afV~f~~~~~a~~a~~~l~   66 (277)
                      ....-|.|-+.|+. ....|...|++||.|.+-. +..               .. ...++..|+|.+..+|.+|+. .|
T Consensus         5 ~~e~~VtVFGFp~~-~~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~N   82 (132)
T 3p3d_A            5 NGELAILVFGYPET-MANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-EN   82 (132)
T ss_dssp             ---CEEEEECCCGG-GHHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TT
T ss_pred             cCceEEEEEecCHH-HHHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hC
Confidence            45677889999655 5667788999999987722 110               00 135678999999999999999 99


Q ss_pred             CcccCCceEEEEEcc
Q 023765           67 GYNFDGYRLRVELAH   81 (277)
Q Consensus        67 ~~~~~g~~i~v~~a~   81 (277)
                      |..|.|..|-|.+..
T Consensus        83 G~ii~G~mIGV~Py~   97 (132)
T 3p3d_A           83 GAVFNGVLLGVIPYT   97 (132)
T ss_dssp             TCEETTEECEEEECC
T ss_pred             CeEeCcEEEEEEECC
Confidence            999999988888765

>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=97.37  E-value=0.00081  Score=45.52  Aligned_cols=73  Identities=11%  Similarity=0.067  Sum_probs=58.2

Q ss_pred             CceEEEeCCCCCC-C----HHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          109 DYRVLVTGLPSSA-S----WQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       109 ~~~l~v~~l~~~~-~----~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      .++|+|.||+..+ .    .+.++++|..|+++........-.  -..|.|.+.++|.+|-..||+..+.|.    .+++
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR--Rirv~F~~~~~A~~AR~~Lh~~~f~g~----~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK--RVRINFSNPLSAADARLRLHKTEFLGK----EMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT--EEEEECSSTTHHHHHHHTSTTSEETTE----ECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce--EEEEEeCChHHHHHHHHHhccceecCc----eeEE
Confidence            5689999998755 2    367899999999988766655432  478999999999999999999999994    5566


Q ss_pred             eecC
Q 023765          184 REYD  187 (277)
Q Consensus       184 ~~~~  187 (277)
                      ....
T Consensus        79 YFgq   82 (104)
T 1wey_A           79 YFAQ   82 (104)
T ss_dssp             ECCC
T ss_pred             EecC
Confidence            5544

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.34  E-value=0.0013  Score=44.37  Aligned_cols=70  Identities=19%  Similarity=0.227  Sum_probs=53.2

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHh-----cCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRR-----AGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~-----~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ..+|.|.|||+.+.++.|+-+|+.     -|+|..+....    .-|+|+|.+.+.|+..|+. ....+.+    ..+.|
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~----~~AvItF~d~~va~rVL~k-~~H~L~~----~~LsV   78 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG----CGGVLTFREPADAERVLAQ-ADHELHG----AQLSL   78 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET----TEEEEEESSHHHHHHHHTC-SCCBSSS----SBCEE
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC----CcEEEEEcChHHHHHHhcC-CcceecC----eEEEE
Confidence            579999999999999999999997     24787777655    3699999999999999974 2334444    34445


Q ss_pred             eecC
Q 023765          184 REYD  187 (277)
Q Consensus       184 ~~~~  187 (277)
                      ..+.
T Consensus        79 ~P~~   82 (104)
T 2dhx_A           79 RPAP   82 (104)
T ss_dssp             EECC
T ss_pred             EcCC
Confidence            4443

>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=97.29  E-value=0.0007  Score=45.20  Aligned_cols=55  Identities=18%  Similarity=0.178  Sum_probs=44.7

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcC
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLD  168 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~  168 (277)
                      ...++| ++|+.+...||.++|..|| -..|.++.+.   .|||.|.+.+.|..|+..+.
T Consensus         6 ~HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT---sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            6 DHVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT---SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT---EEEEEEEEECHHHHHHHHHT
T ss_pred             CeEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC---eEEEEecCHHHHHHHHHhcc
Confidence            345666 9999999999999999999 3345555443   69999999999999998764

>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=97.25  E-value=0.0015  Score=45.52  Aligned_cols=65  Identities=18%  Similarity=0.179  Sum_probs=53.5

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                      .....|.|-++|+.. ...|..+|.+||+|.....  ......-.|.|.+..+|++||. .||..++|.
T Consensus        22 ~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~--~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~   86 (119)
T 1wwh_A           22 LDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVM--SNTGNWMHIRYQSKLQARKALS-KDGRIFGES   86 (119)
T ss_dssp             GGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEE--CSSSSEEEEEESSHHHHHHHHT-TTTCEETTT
T ss_pred             CCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEecc--CCCCCeEEEEeCCHHHHHHHHH-hCCeEecCC
Confidence            346789999998885 6678899999999988776  3334589999999999999997 799999863

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=97.11  E-value=0.00028  Score=61.37  Aligned_cols=56  Identities=18%  Similarity=0.215  Sum_probs=43.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHH
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIR   63 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~   63 (277)
                      +.++|+|. .|..+++.+|.++|++||+|..+.+..+.  .-||.|||.+.+++..++.
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~--g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF--GLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS--SEEEEEECC---CCHHHHS
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC--CeEEEEEeCCHHHHHHHHh
Confidence            45789997 79999999999999999999999997543  4799999999999998876

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.59  E-value=0.0045  Score=41.37  Aligned_cols=70  Identities=14%  Similarity=0.224  Sum_probs=52.8

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC------cEEEEEEechhHHHHHHHhcCCCeeccccee
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG------MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~------~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  178 (277)
                      .-+|.|..||+.+|++++.+.+...-++....+..+...      .-|+|.|.+.+++..-.+.++|..+-+....
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~   84 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGL   84 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCC
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCC
Confidence            568999999999999998888876655433333222211      1689999999999999999999998665433

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.47  E-value=0.0097  Score=51.75  Aligned_cols=55  Identities=13%  Similarity=0.231  Sum_probs=42.0

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHH
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIR  165 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~  165 (277)
                      ...|+|. .|..+++.+|.++|++||.|..+.+..+.. .||.|||.+.+++..++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g-~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFG-LYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSS-EEEEEECC---CCHHHHS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCC-eEEEEEeCCHHHHHHHHh
Confidence            4689997 688999999999999999999998887543 599999999999987764

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=94.93  E-value=0.045  Score=38.64  Aligned_cols=66  Identities=17%  Similarity=0.229  Sum_probs=47.8

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeE-EEEEe--------------cC---CCcEEEEEEechhHHHHHHHhcCCC
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCF-SQVFR--------------DR---GGMTGIVDYTSYDDMKYAIRKLDRS  170 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~-~~~~~--------------~~---~~~~~fv~f~~~~~a~~a~~~l~g~  170 (277)
                      ...|.|-+.|+..+. .+.+.|.+||.|.. +.+..              -+   ......|.|++..+|.+||. .||.
T Consensus         7 e~~VtVFGFp~~~~~-~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMAN-QVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGGGHH-HHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHHHHH-HHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            457888888766554 46788999999866 21111              01   12377899999999999996 8999


Q ss_pred             eecccc
Q 023765          171 EFRNAF  176 (277)
Q Consensus       171 ~~~g~~  176 (277)
                      .++|..
T Consensus        85 ii~G~m   90 (132)
T 3p3d_A           85 VFNGVL   90 (132)
T ss_dssp             EETTEE
T ss_pred             EeCcEE
Confidence            999943

>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=94.18  E-value=0.1  Score=46.15  Aligned_cols=56  Identities=20%  Similarity=0.272  Sum_probs=44.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCC
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDG   67 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~   67 (277)
                      .+.++|+ +|+.+...+|.++|+.||.|. |.+..    ...|||.|.+.+.|..++..++.
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v~-V~wid----dt~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNIQ-ISWID----DTSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCCE-EEECS----SSEEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCEE-EEEEc----CCeEEEEECCHHHHHHHHHHHHh
Confidence            3466776 899999999999999999653 33332    45799999999999999987753

>4eyt_A Telomerase associated protein P65; RNA, LA protein, LARP7, RRM, XRRM, RNA binding protein; 2.50A {Tetrahymena thermophila} PDB: 4erd_A

Probab=88.80  E-value=3.4  Score=26.70  Aligned_cols=69  Identities=20%  Similarity=0.225  Sum_probs=53.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      +.++-|.|-|||..+-..++.-.....|---.+...     .|.|+|.|.+.++-..|+..|-+.  ....|.++.
T Consensus        10 kqnclikiinipqgtlkaevvlavrhlgyefycdyi-----dgqamirfqnsdeqrlaiqkllnh--nnnklqiei   78 (129)
T 4eyt_A           10 KQNCLIKIINIPQGTLKAEVVLAVRHLGYEFYCDYI-----DGQAMIRFQNSDEQRLAIQKLLNH--NNNKLQIEI   78 (129)
T ss_dssp             CCSCEEEEECCCTTCCHHHHHHHHHTTCCCEEEEEC-----SSCEEEEESSHHHHHHHHHHHEET--TTTEEEEEE
T ss_pred             hhCcEEEEEecCCCceeeeeEEeehhcCeeEeeeee-----cCeeEEEecCChHHHHHHHHHHhc--CCCEEEEEE
Confidence            567889999999999999988888888866666665     578999999999999888765321  234555555

>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=86.94  E-value=1.5  Score=38.67  Aligned_cols=55  Identities=18%  Similarity=0.242  Sum_probs=44.1

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcC
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLD  168 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~  168 (277)
                      ...++|+ +|..+...+|.+.|..||.+ .|.++.+.   .|||.|.+.+.|..++..++
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widdt---~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDDT---SAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSSS---EEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcCC---eEEEEECCHHHHHHHHHHHH
Confidence            4567776 89999999999999999954 34443332   69999999999999998875

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=80.82  E-value=5.4  Score=24.81  Aligned_cols=68  Identities=16%  Similarity=0.198  Sum_probs=43.0

Q ss_pred             eEEEcCC-CCCCCHHHHHHHhhccC-----CeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            8 TLYVGNL-PGDTRMREVEDLFYKYG-----PIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         8 ~l~V~nL-~~~~t~~~l~~~F~~~G-----~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      +|+|..= ...+...+|..++..-+     .|-.|.+.     ..|.||+... +.|..++..|++..+.|+.+.|+.+.
T Consensus         2 ~~~i~~Grk~~~~p~~ivg~i~~~~gi~~~~IG~I~i~-----d~~s~v~v~~-~~~~~~~~~l~~~~i~g~~~~v~~~~   75 (76)
T 2g0c_A            2 KLYFNGGKKKKIRAVDFVGTIAKIDGVSADDIGIITIM-----DNASYVEILN-GKGPHVLKVMKNTTVKGKQLKVNKAN   75 (76)
T ss_dssp             EEEESCCCC----CHHHHHHHHTSTTCCGGGEEEEEEC-----SSCEEEEECT-TCHHHHHHHHTTCCC---CCCEEECC
T ss_pred             EEEEeCCCccCCCHHHHHHHHHHccCCChhhccEEEEe-----CCcEEEEECH-HHHHHHHHHhccccCcCceEEEEECC
Confidence            4555311 33577888888887543     45566665     4688998864 55778888899999999999988754

---

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	277
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-20
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	7e-06
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	5e-18
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-06
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-17
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-07
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	7e-17
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	5e-06
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-16
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	4e-05
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-16
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	5e-05
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-16
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	5e-06
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	7e-16
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-06
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-16
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.003
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	3e-15
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-07
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-15
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	6e-05
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	4e-15
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-06
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	5e-15
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	6e-04
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	7e-15
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-14
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	8e-04
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-14
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-14
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	5e-05
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-14
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-04
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-14
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	0.002
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-14
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	1e-04
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	4e-14
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-05
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-14
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-04
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	5e-14
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	0.001
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	6e-14
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	0.002
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	6e-14
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-04
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	7e-14
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-08
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-13
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-04
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-13
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	8e-05
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-13
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-04
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-12
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	6e-06
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	1e-12
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-12
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	8e-04
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-12
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-05
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	4e-12
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	6e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	5e-12
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	7e-12
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	0.001
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	8e-12
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	9e-12
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-11
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	0.003
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-11
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	3e-04
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-11
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-11
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-04
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	6e-11
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	6e-11
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	8e-05
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	7e-11
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	7e-11
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	8e-11
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-10
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-10
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-10
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	0.001
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-10
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	3e-10
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	4e-04
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	4e-10
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	5e-10
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	5e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	6e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	5e-07
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-09
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	1e-09
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	0.001
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-09
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	3e-05
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	2e-09
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	0.003
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-09
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-09
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-09
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	0.004
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	3e-09
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	5e-09
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	0.002
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	6e-09
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	7e-09
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	8e-09
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.001
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	8e-09
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	9e-09
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	1e-08
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-08
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	2e-08
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	3e-08
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-05
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	1e-07
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-07
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	5e-07
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	7e-07
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	1e-06
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	4e-04
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	1e-04
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	0.004
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	2e-04
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-04
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-04

>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 = 81.6 bits (201), Expect = 3e-20
 Identities = 28/87 (32%), Positives = 41/87 (47%)

Query: 1  MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
          +    +R LY+ NLP      E+ D+F KYGPI  I +   P   G A++ +ED  DA++
Sbjct: 2  LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKN 61

Query: 61 AIRGRDGYNFDGYRLRVELAHGGRRHS 87
          A     G+N     L V   +  R   
Sbjct: 62 ACDHLSGFNVCNRYLVVLYYNANRAFQ 88

>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 = 41.9 bits (98), Expect = 7e-06
 Identities = 18/90 (20%), Positives = 34/90 (37%), Gaps = 9/90 (10%)

Query: 112 VLVTGLPSSASWQDLKDHMRRAGDV---CFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLD 168
           + +  LP   + +++ D   + G +           RG  T  V Y    D K A   L 
Sbjct: 10  LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRG--TAYVVYEDIFDAKNACDHLS 67

Query: 169 RSEFRNAFSRSYVRVREYDSRRSYSRSPSR 198
                N     Y+ V  Y++ R++ +  ++
Sbjct: 68  GFNVCN----RYLVVLYYNANRAFQKMDTK 93

>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 = 75.0 bits (184), Expect = 5e-18
 Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 5/84 (5%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDI----DLKIPPRPPGYAFLEFEDYRDA 58
           +++  + V N+P     RE+ +LF  +G +  +     +       G+ F++F   +DA
Sbjct: 5  KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 59 EDAIRG-RDGYNFDGYRLRVELAH 81
          + A        +  G RL +E A 
Sbjct: 65 KKAFNALCHSTHLYGRRLVLEWAD 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 = 43.0 bits (101), Expect = 2e-06
 Identities = 13/70 (18%), Positives = 32/70 (45%), Gaps = 5/70 (7%)

Query: 106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG-----GMTGIVDYTSYDDM 160
           +++  ++LV  +P  A+ +++++     G++   ++ +           G VD+ +  D 
Sbjct: 5   KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 161 KYAIRKLDRS 170
           K A   L  S
Sbjct: 65  KKAFNALCHS 74

>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 = 73.1 bits (179), Expect = 2e-17
 Identities = 25/83 (30%), Positives = 38/83 (45%), Gaps = 5/83 (6%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAE 59
          S     LYV NLP      +++ +F KYG IV  ++        P G AF+ +    +A+
Sbjct: 3  SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ 62

Query: 60 DAIRGRDGYNFDGY--RLRVELA 80
          +AI   +    +G    L V LA
Sbjct: 63 EAISALNNVIPEGGSQPLSVRLA 85

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 45.3 bits (107), Expect = 3e-07
 Identities = 16/79 (20%), Positives = 27/79 (34%), Gaps = 4/79 (5%)

Query: 108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMT----GIVDYTSYDDMKYA 163
            D  + VT LP + +   L     + G +    + RD+          V Y   ++ + A
Sbjct: 5   KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 64

Query: 164 IRKLDRSEFRNAFSRSYVR 182
           I  L+            VR
Sbjct: 65  ISALNNVIPEGGSQPLSVR 83

>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 = 71.9 bits (176), Expect = 7e-17
 Identities = 28/85 (32%), Positives = 43/85 (50%), Gaps = 3/85 (3%)

Query: 4  RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAED 60
          + S TLYVGNL   T   ++ +LF K G I  I +   K+     G+ F+E+    DAE+
Sbjct: 5  KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 64

Query: 61 AIRGRDGYNFDGYRLRVELAHGGRR 85
          A+R  +G   D   +R +   G + 
Sbjct: 65 AMRYINGTRLDDRIIRTDWDAGFKE 89

>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 = 41.9 bits (98), Expect = 5e-06
 Identities = 14/85 (16%), Positives = 34/85 (40%), Gaps = 9/85 (10%)

Query: 111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGI----VDYTSYDDMKYAIRK 166
            + V  L    + + + +   ++GD+    +  D+   T      V+Y S  D + A+R 
Sbjct: 9   TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 68

Query: 167 LDRSEFRN-----AFSRSYVRVREY 186
           ++ +   +      +   +   R+Y
Sbjct: 69  INGTRLDDRIIRTDWDAGFKEGRQY 93

>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 = 70.7 bits (173), Expect = 2e-16
 Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 3/77 (3%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAEDAIRG 64
          +LYVG+L  D     + + F   GPI+ I +          GYA++ F+   DAE A+  
Sbjct: 2  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 65 RDGYNFDGYRLRVELAH 81
           +     G  +R+  + 
Sbjct: 62 MNFDVIKGKPVRIMWSQ 78

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.1 bits (91), Expect = 4e-05
 Identities = 11/65 (16%), Positives = 23/65 (35%), Gaps = 4/65 (6%)

Query: 114 VTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGI----VDYTSYDDMKYAIRKLDR 169
           V  L    +   L +    AG +   +V RD      +    V++    D + A+  ++ 
Sbjct: 5   VGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNF 64

Query: 170 SEFRN 174
              + 
Sbjct: 65  DVIKG 69

>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 = 70.8 bits (173), Expect = 2e-16
 Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 3/79 (3%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
          SS  + T+Y G +      + +   F  +G I++I +       GY+F+ F  +  A  A
Sbjct: 14 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRV---FPEKGYSFVRFSTHESAAHA 70

Query: 62 IRGRDGYNFDGYRLRVELA 80
          I   +G   +G+ ++    
Sbjct: 71 IVSVNGTTIEGHVVKCYWG 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 = 39.2 bits (91), Expect = 5e-05
 Identities = 11/70 (15%), Positives = 29/70 (41%), Gaps = 2/70 (2%)

Query: 105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAI 164
           S   +  V   G+ S  + Q ++      G +   +VF ++      V +++++   +AI
Sbjct: 14  SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK--GYSFVRFSTHESAAHAI 71

Query: 165 RKLDRSEFRN 174
             ++ +    
Sbjct: 72  VSVNGTTIEG 81

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 70.0 bits (171), Expect = 3e-16
 Identities = 27/82 (32%), Positives = 38/82 (46%), Gaps = 3/82 (3%)

Query: 5  SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAEDA 61
          S+  L V  LP D   RE+  LF   GPI    +    +     GYAF++F    D++ A
Sbjct: 1  SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 60

Query: 62 IRGRDGYNFDGYRLRVELAHGG 83
          I+  +G      RL+V  A  G
Sbjct: 61 IKVLNGITVRNKRLKVSYARPG 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 = 41.5 bits (97), Expect = 5e-06
 Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 4/71 (5%)

Query: 108 SDYRVLVTGLPSSASWQDLKDHMRRAGDV----CFSQVFRDRGGMTGIVDYTSYDDMKYA 163
           S+  ++V  LP   + ++L    R  G +                   VD+TS  D + A
Sbjct: 1   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 60

Query: 164 IRKLDRSEFRN 174
           I+ L+    RN
Sbjct: 61  IKVLNGITVRN 71

>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 = 68.8 bits (168), Expect = 7e-16
 Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 2/74 (2%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDAEDAIRGRD 66
          L V NL       ++++LF ++G +    +      R  G A + FE   DA  A++  +
Sbjct: 3  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 67 GYNFDGYRLRVELA 80
          G   DG  + ++L 
Sbjct: 63 GVPLDGRPMNIQLV 76

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.0 bits (101), Expect = 2e-06
 Identities = 11/67 (16%), Positives = 22/67 (32%), Gaps = 3/67 (4%)

Query: 111 RVLVTGLPSSASWQDLKDHMRRAG---DVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKL 167
           ++LV+ L    S  D+++     G             R   T  V +    D   A+++ 
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 61

Query: 168 DRSEFRN 174
           +      
Sbjct: 62  NGVPLDG 68

>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 = 69.1 bits (169), Expect = 8e-16
 Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 6/84 (7%)

Query: 6  SRTLYVGNLPGD-TRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRG 64
          +  +++GNL     +  +VE +F KYG IV   +       G+AF+++ + R+A  A+ G
Sbjct: 15 NSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-----HKGFAFVQYVNERNARAAVAG 69

Query: 65 RDGYNFDGYRLRVELAHGGRRHSS 88
           DG    G  L + LA   + + S
Sbjct: 70 EDGRMIAGQVLDINLAAEPKVNRS 93

>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 = 34.1 bits (78), Expect = 0.003
 Identities = 16/104 (15%), Positives = 32/104 (30%), Gaps = 14/104 (13%)

Query: 100 GSRGVSRRSD-----YRVLVTGL-PSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVD 153
           GS G S ++D      RV +  L        D++    + G +    V +    +     
Sbjct: 1   GSSGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQ---- 56

Query: 154 YTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDSRRSYSRSPS 197
           Y +  + + A+   D            + +      +     PS
Sbjct: 57  YVNERNARAAVAGEDGRMIAG----QVLDINLAAEPKVNRSGPS 96

>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 = 67.8 bits (165), Expect = 3e-15
 Identities = 49/83 (59%), Positives = 61/83 (73%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
          +  +   +YVGNLP D R +++ED+FYKYG I DIDLK     P +AF+EFED RDAEDA
Sbjct: 10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDA 69

Query: 62 IRGRDGYNFDGYRLRVELAHGGR 84
          + GRDGY++DGYRLRVE    GR
Sbjct: 70 VYGRDGYDYDGYRLRVEFPRSGR 92

>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 = 46.2 bits (109), Expect = 2e-07
 Identities = 23/97 (23%), Positives = 39/97 (40%), Gaps = 6/97 (6%)

Query: 97  SSGGS-RGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR-GGMTGIVDY 154
           S GG  RG +  +D R+ V  LP     +D++D   + G +    +   R G     V++
Sbjct: 1   SGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEF 60

Query: 155 TSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDSRRS 191
               D + A+   D  ++        +RV    S R 
Sbjct: 61  EDPRDAEDAVYGRDGYDYDG----YRLRVEFPRSGRG 93

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 67.0 bits (163), Expect = 3e-15
 Identities = 18/85 (21%), Positives = 38/85 (44%), Gaps = 6/85 (7%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPG------YAFLEFEDYRDAEDAI 62
          L++ NL   T    ++ +F K G I    +       G      + F+E++    A+ A+
Sbjct: 1  LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 63 RGRDGYNFDGYRLRVELAHGGRRHS 87
          +   G+  DG++L V ++    + +
Sbjct: 61 KQLQGHTVDGHKLEVRISERATKPA 85

>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 = 38.9 bits (90), Expect = 6e-05
 Identities = 10/68 (14%), Positives = 24/68 (35%), Gaps = 7/68 (10%)

Query: 114 VTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMT-------GIVDYTSYDDMKYAIRK 166
           +  L  S + + LK    + G +    + + +           G V+Y   +  + A+++
Sbjct: 3   IKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQ 62

Query: 167 LDRSEFRN 174
           L       
Sbjct: 63  LQGHTVDG 70

>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 = 66.9 bits (163), Expect = 4e-15
 Identities = 28/85 (32%), Positives = 38/85 (44%), Gaps = 7/85 (8%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGR 65
             L+VGNLP D    E+  LF KYG   ++      +  G+ F+  E    AE A    
Sbjct: 8  RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF---IHKDKGFGFIRLETRTLAEIAKVEL 64

Query: 66 DGYNFDGYRLRVELAHGGRRHSSSM 90
          D     G +LRV  A     HS+S+
Sbjct: 65 DNMPLRGKQLRVRFA----CHSASL 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 = 43.4 bits (102), Expect = 1e-06
 Identities = 15/75 (20%), Positives = 31/75 (41%), Gaps = 4/75 (5%)

Query: 100 GSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDD 159
           G +  ++RS  R+ V  LP   + ++++    + G     +VF  +    G +   +   
Sbjct: 1   GEKTFTQRS--RLFVGNLPPDITEEEMRKLFEKYG--KAGEVFIHKDKGFGFIRLETRTL 56

Query: 160 MKYAIRKLDRSEFRN 174
            + A  +LD    R 
Sbjct: 57  AEIAKVELDNMPLRG 71

>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 = 67.0 bits (163), Expect = 5e-15
 Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 4/84 (4%)

Query: 4  RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIR 63
          R++RTL   NL  +    E++++F     I  +      +  G A++EF+   DAE  + 
Sbjct: 14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVS--QDGKSKGIAYIEFKSEADAEKNLE 71

Query: 64 GRDGYNFDGYRLRVELAH--GGRR 85
           + G   DG  + +      GG R
Sbjct: 72 EKQGAEIDGRSVSLYYTGEKGGTR 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 = 36.2 bits (83), Expect = 6e-04
 Identities = 11/85 (12%), Positives = 29/85 (34%), Gaps = 5/85 (5%)

Query: 107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRK 166
           R+   +L   L  + +  +LK+    A ++          G+   +++ S  D +  + +
Sbjct: 14  RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGI-AYIEFKSEADAEKNLEE 72

Query: 167 LDRSEFRNAFSRSYVRVREYDSRRS 191
              +E         V +     +  
Sbjct: 73  KQGAEIDG----RSVSLYYTGEKGG 93

>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 = 66.2 bits (161), Expect = 7e-15
 Identities = 22/82 (26%), Positives = 43/82 (52%), Gaps = 4/82 (4%)

Query: 4  RSSRTLYVGNLPGDTRMREVE----DLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAE 59
          R + T+Y+ NL    +  E++     +F ++G I+DI +    +  G AF+ F++   A 
Sbjct: 1  RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 60

Query: 60 DAIRGRDGYNFDGYRLRVELAH 81
          +A+R   G+ F    +R++ A 
Sbjct: 61 NALRSMQGFPFYDKPMRIQYAK 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 = 65.5 bits (159), Expect = 1e-14
 Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 4/76 (5%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDL----KIPPRPPGYAFLEFEDYRDAEDAIRG 64
          +++GNL  +   + + D F  +G I+               GYAF+ F  +  ++ AI  
Sbjct: 1  IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 65 RDGYNFDGYRLRVELA 80
           +G       + V  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 = 35.5 bits (81), Expect = 8e-04
 Identities = 11/85 (12%), Positives = 24/85 (28%), Gaps = 9/85 (10%)

Query: 112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQV-----FRDRGGMTGIVDYTSYDDMKYAIRK 166
           + +  L      + L D     G +  +                 +++ S+D    AI  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 167 LDRSEFRNAFSRSYVRVREYDSRRS 191
           ++     N      + V     + S
Sbjct: 61  MNGQYLCN----RPITVSYAFKKDS 81

>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 = 65.4 bits (159), Expect = 1e-14
 Identities = 25/83 (30%), Positives = 37/83 (44%), Gaps = 3/83 (3%)

Query: 5  SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRG 64
          S + LYV NL   T    +E  F    P     +K   +   YAF+ F +  DA +A++ 
Sbjct: 7  SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK---KIRDYAFVHFSNREDAVEAMKA 63

Query: 65 RDGYNFDGYRLRVELAHGGRRHS 87
           +G   DG  + V LA    + S
Sbjct: 64 LNGKVLDGSPIEVTLAKPVDKDS 86

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.1 bits (158), Expect = 2e-14
 Identities = 27/83 (32%), Positives = 40/83 (48%), Gaps = 4/83 (4%)

Query: 1  MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRD 57
          M++ + R LYVG L  +   + +   F  +G I DI + +        G+AF+EFE   D
Sbjct: 1  MAT-TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 59

Query: 58 AEDAIRGRDGYNFDGYRLRVELA 80
          A  AI   +     G  +RV LA
Sbjct: 60 AAAAIDNMNESELFGRTIRVNLA 82

>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 = 39.3 bits (91), Expect = 5e-05
 Identities = 17/84 (20%), Positives = 27/84 (32%), Gaps = 8/84 (9%)

Query: 111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRK 166
            + V GL      + L       GD+   Q+  D           V++   +D   AI  
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 167 LDRSEFRNAFSRSYVRVREYDSRR 190
           ++ SE         +RV      R
Sbjct: 67  MNESELFG----RTIRVNLAKPMR 86

>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 = 65.1 bits (158), Expect = 2e-14
 Identities = 26/83 (31%), Positives = 36/83 (43%), Gaps = 2/83 (2%)

Query: 1  MSSRS-SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI-PPRPPGYAFLEFEDYRDA 58
          M      RTLYVGNL  D     +  LF + GP     +         Y F+EF ++RDA
Sbjct: 2  MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDA 61

Query: 59 EDAIRGRDGYNFDGYRLRVELAH 81
            A+   +G    G  ++V  A 
Sbjct: 62 AAALAAMNGRKILGKEVKVNWAT 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 = 36.9 bits (85), Expect = 2e-04
 Identities = 8/74 (10%), Positives = 22/74 (29%), Gaps = 3/74 (4%)

Query: 104 VSRRSDYRVL-VTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGI--VDYTSYDDM 160
           +      R L V  L    +   +     + G     ++  +         V++  + D 
Sbjct: 2   MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDA 61

Query: 161 KYAIRKLDRSEFRN 174
             A+  ++  +   
Sbjct: 62  AAALAAMNGRKILG 75

>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 = 64.6 bits (157), Expect = 3e-14
 Identities = 16/82 (19%), Positives = 35/82 (42%), Gaps = 5/82 (6%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDA 58
          + + +  L V  LP  T  +++++ F  +G ++ + +K   +     G+ F+ F +Y   
Sbjct: 4  AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 63

Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
             +  R     DG     +L 
Sbjct: 64 VKVMSQRHM--IDGRWCDCKLP 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 = 34.6 bits (79), Expect = 0.002
 Identities = 23/94 (24%), Positives = 40/94 (42%), Gaps = 12/94 (12%)

Query: 102 RGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMT----GIVDYTSY 157
           R V + S   ++V GLP   + QDLK++    G+V   QV +D         G V +T Y
Sbjct: 3   RAVQKTS--DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEY 60

Query: 158 DDMKYAIRKLDRSEFRNAFSRSYVRVREYDSRRS 191
           +     + +    + R          +  +S++S
Sbjct: 61  ETQVKVMSQRHMIDGRW------CDCKLPNSKQS 88

>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 = 64.7 bits (157), Expect = 3e-14
 Identities = 24/86 (27%), Positives = 36/86 (41%), Gaps = 3/86 (3%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAE 59
               T+YVG L        + +LF + GP+V+  +          GY F+EF    DA+
Sbjct: 6  RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDAD 65

Query: 60 DAIRGRDGYNFDGYRLRVELAHGGRR 85
           AI+  D     G  +RV  A    +
Sbjct: 66 YAIKIMDMIKLYGKPIRVNKASAHNK 91

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

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

 Score = 38.1 bits (88), Expect = 1e-04
 Identities = 20/89 (22%), Positives = 32/89 (35%), Gaps = 8/89 (8%)

Query: 106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGD----VCFSQVFRDRGGMTGIVDYTSYDDMK 161
           R  D  V V GL    S   L +   +AG              +    G V++ S +D  
Sbjct: 6   RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDAD 65

Query: 162 YAIRKLDRSEFRNAFSRSYVRVREYDSRR 190
           YAI+ +D  +         +RV +  +  
Sbjct: 66  YAIKIMDMIKLYG----KPIRVNKASAHN 90

>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 = 64.0 bits (155), Expect = 4e-14
 Identities = 14/77 (18%), Positives = 29/77 (37%), Gaps = 3/77 (3%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIV---DIDLKIPPRPPGYAFLEFEDYRDAEDAIR 63
           TL++ N P     R + DL      +     +          +A+++     DA   + 
Sbjct: 2  CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 64 GRDGYNFDGYRLRVELA 80
            +G   +GY L  +++
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 = 39.8 bits (92), Expect = 2e-05
 Identities = 12/70 (17%), Positives = 30/70 (42%), Gaps = 4/70 (5%)

Query: 109 DYRVLVTGLPSSASWQDLKDHMRRAGDV----CFSQVFRDRGGMTGIVDYTSYDDMKYAI 164
           +  + +T  P S + ++++D ++    V        +  +       +D TS +D +Y +
Sbjct: 1   ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 60

Query: 165 RKLDRSEFRN 174
            KL+  +   
Sbjct: 61  EKLNGLKIEG 70

>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 = 63.9 bits (155), Expect = 5e-14
 Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 3/85 (3%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAI 62
          +  L++G LP      +V++L   +GP+   +L          GYAF E+ D    + AI
Sbjct: 1  AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60

Query: 63 RGRDGYNFDGYRLRVELAHGGRRHS 87
           G +G      +L V+ A  G +++
Sbjct: 61 AGLNGMQLGDKKLLVQRASVGAKNA 85

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.1 bits (88), Expect = 1e-04
 Identities = 10/69 (14%), Positives = 27/69 (39%), Gaps = 4/69 (5%)

Query: 110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIR 165
           +++ + GLP+  +   +K+ +   G +    + +D            +Y   +    AI 
Sbjct: 2   HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61

Query: 166 KLDRSEFRN 174
            L+  +  +
Sbjct: 62  GLNGMQLGD 70

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 63.5 bits (154), Expect = 5e-14
 Identities = 12/75 (16%), Positives = 31/75 (41%), Gaps = 4/75 (5%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAEDAIRGR 65
          +++G L   T    + + F ++G + +  +   P      G+ F+ F D    +  +  +
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 66 DGYNFDGYRLRVELA 80
            +  D   +  ++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 = 34.6 bits (79), Expect = 0.001
 Identities = 12/66 (18%), Positives = 25/66 (37%), Gaps = 5/66 (7%)

Query: 111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGM----TGIVDYTSYDDMKYAIRK 166
           ++ + GL    + + L+++  + G+V    V RD         G V +     +   +  
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-A 60

Query: 167 LDRSEF 172
             R E 
Sbjct: 61  QSRHEL 66

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.9 bits (155), Expect = 6e-14
 Identities = 25/84 (29%), Positives = 40/84 (47%), Gaps = 5/84 (5%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDA 58
          +S     LYV  LP     +E+E LF +YG I+   + +        G  F+ F+   +A
Sbjct: 2  ASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEA 61

Query: 59 EDAIRGRDGYNFDGY--RLRVELA 80
          E+AI+G +G    G    + V+ A
Sbjct: 62 EEAIKGLNGQKPSGATEPITVKFA 85

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.6 bits (79), Expect = 0.002
 Identities = 14/78 (17%), Positives = 34/78 (43%), Gaps = 4/78 (5%)

Query: 109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGI----VDYTSYDDMKYAI 164
           D  + V+GLP + + ++L+    + G +  S++  D+          + +    + + AI
Sbjct: 6   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 65

Query: 165 RKLDRSEFRNAFSRSYVR 182
           + L+  +   A     V+
Sbjct: 66  KGLNGQKPSGATEPITVK 83

>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 = 63.6 bits (154), Expect = 6e-14
 Identities = 23/79 (29%), Positives = 30/79 (37%), Gaps = 3/79 (3%)

Query: 5  SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAEDA 61
          S   L V  LP +    E   LF   G I    L          GY F+ + D +DAE A
Sbjct: 1  SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 62 IRGRDGYNFDGYRLRVELA 80
          I   +G       ++V  A
Sbjct: 61 INTLNGLRLQTKTIKVSYA 79

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.8 bits (87), Expect = 1e-04
 Identities = 14/71 (19%), Positives = 30/71 (42%), Gaps = 4/71 (5%)

Query: 108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR----GGMTGIVDYTSYDDMKYA 163
           S   ++V  LP + + ++ +      G++   ++ RD+        G V+Y    D + A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 164 IRKLDRSEFRN 174
           I  L+    + 
Sbjct: 61  INTLNGLRLQT 71

>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 = 66.2 bits (160), Expect = 7e-14
 Identities = 26/192 (13%), Positives = 60/192 (31%), Gaps = 27/192 (14%)

Query: 6   SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAEDAI 62
            R L++G L  +T    +   F ++G + D  +   P      G+ F+ +    + + A+
Sbjct: 6   LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 65

Query: 63  RGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSAS 122
                                        + +       R  +  +  ++ V G+     
Sbjct: 66  ---------------NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTE 110

Query: 123 WQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR 178
              L+D+  + G +   ++  DRG         V +  +D +   +              
Sbjct: 111 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNG---- 165

Query: 179 SYVRVREYDSRR 190
               VR+  S++
Sbjct: 166 HNCEVRKALSKQ 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 = 50.8 bits (120), Expect = 2e-08
 Identities = 18/83 (21%), Positives = 39/83 (46%), Gaps = 4/83 (4%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRD 57
            +  + + ++VG +  DT    + D F +YG I  I++       +  G+AF+ F+D+  
Sbjct: 92  GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 151

Query: 58  AEDAIRGRDGYNFDGYRLRVELA 80
            +  +  +  +  +G+   V  A
Sbjct: 152 VDKIVI-QKYHTVNGHNCEVRKA 173

>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 = 62.8 bits (152), Expect = 1e-13
 Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 3/79 (3%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDA 58
          +   +  L V  L   T  R++ ++F KYGPI D+ +    +     G+AF+ FE+  DA
Sbjct: 5  NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 64

Query: 59 EDAIRGRDGYNFDGYRLRV 77
          ++A    +G   DG R+RV
Sbjct: 65 KEAKERANGMELDGRRIRV 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.8 bits (87), Expect = 1e-04
 Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 5/79 (6%)

Query: 100 GSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR----GGMTGIVDYT 155
           G+R  +   +  + V GL    + +DL++   + G +    +  D+          V + 
Sbjct: 1   GNRA-NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 59

Query: 156 SYDDMKYAIRKLDRSEFRN 174
           + DD K A  + +  E   
Sbjct: 60  NVDDAKEAKERANGMELDG 78

>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 = 62.8 bits (152), Expect = 2e-13
 Identities = 18/82 (21%), Positives = 35/82 (42%), Gaps = 3/82 (3%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPI---VDIDLKIPPRPPGYAFLEFEDYRDAE 59
          S     L+V ++  + +  E+++ F  YG I        +      GYA +E+E ++ A 
Sbjct: 4  SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 63

Query: 60 DAIRGRDGYNFDGYRLRVELAH 81
           A    +G    G  ++V+   
Sbjct: 64 AAKEALNGAEIMGQTIQVDWCF 85

>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 = 38.2 bits (88), Expect = 8e-05
 Identities = 11/69 (15%), Positives = 27/69 (39%), Gaps = 4/69 (5%)

Query: 110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIR 165
           + + VT +   A   ++++     G++    +  DR         +V+Y ++     A  
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 166 KLDRSEFRN 174
            L+ +E   
Sbjct: 68  ALNGAEIMG 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 = 61.5 bits (149), Expect = 3e-13
 Identities = 14/75 (18%), Positives = 36/75 (48%), Gaps = 4/75 (5%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAEDAIRGR 65
          ++VG L  DT   ++ + F  +G +  I+L +  +     G+ F+ F++    +  +  +
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 66 DGYNFDGYRLRVELA 80
            +N    +  +++A
Sbjct: 62 -YHNVGLSKCEIKVA 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 = 36.9 bits (85), Expect = 2e-04
 Identities = 8/60 (13%), Positives = 23/60 (38%), Gaps = 4/60 (6%)

Query: 111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMT----GIVDYTSYDDMKYAIRK 166
           ++ V GL      + ++++    G+V   ++  D           + +   + +K  + K
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

>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 = 60.5 bits (146), Expect = 1e-12
 Identities = 22/80 (27%), Positives = 42/80 (52%), Gaps = 1/80 (1%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP-GYAFLEFEDYRDAED 60
          S  + + L+V N+P   R  ++  +F ++G I+D+++    R   G+ F+ FE+  DA+ 
Sbjct: 7  SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADR 66

Query: 61 AIRGRDGYNFDGYRLRVELA 80
          A     G   +G ++ V  A
Sbjct: 67 AREKLHGTVVEGRKIEVNNA 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 = 41.6 bits (97), Expect = 6e-06
 Identities = 17/80 (21%), Positives = 31/80 (38%), Gaps = 4/80 (5%)

Query: 97  SSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR--GGMTGIVDY 154
           SSG S   S+ +  R+ V+ +P      DL+    + G +   ++  +       G V +
Sbjct: 1   SSGNSE--SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTF 58

Query: 155 TSYDDMKYAIRKLDRSEFRN 174
            +  D   A  KL  +    
Sbjct: 59  ENSADADRAREKLHGTVVEG 78

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.2 bits (145), Expect = 1e-12
 Identities = 16/76 (21%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          S TL++ N+P      +++ LF   G +V    K   +    A ++     +A  A+   
Sbjct: 10 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF-KFFQKDRKMALIQMGSVEEAVQALIDL 68

Query: 66 DGYNF-DGYRLRVELA 80
            ++  + + LRV  +
Sbjct: 69 HNHDLGENHHLRVSFS 84

>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 = 60.1 bits (145), Expect = 1e-12
 Identities = 28/78 (35%), Positives = 40/78 (51%), Gaps = 3/78 (3%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDID---LKIPPRPPGYAFLEFEDYRDAEDAI 62
          + T+ V NL  DTR  ++++LF  +G I  I     K   +  G+AF+ F    DA  AI
Sbjct: 8  NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 67

Query: 63 RGRDGYNFDGYRLRVELA 80
           G  G+ +D   L VE A
Sbjct: 68 AGVSGFGYDHLILNVEWA 85

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

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

 Score = 35.4 bits (81), Expect = 8e-04
 Identities = 14/76 (18%), Positives = 29/76 (38%), Gaps = 6/76 (7%)

Query: 105 SRRSD--YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYD 158
           +RR+D    + VT L       DL++  R  G +    + +D+          + +   +
Sbjct: 2   NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 61

Query: 159 DMKYAIRKLDRSEFRN 174
           D   AI  +    + +
Sbjct: 62  DAARAIAGVSGFGYDH 77

>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 = 59.7 bits (144), Expect = 2e-12
 Identities = 18/80 (22%), Positives = 33/80 (41%), Gaps = 7/80 (8%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP-----GYAFLEFEDYRDAEDAI 62
           L++G +P   +  E+ +   K    V   +            G+AF+E+E +R A  A 
Sbjct: 3  RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 63 RG--RDGYNFDGYRLRVELA 80
          R          G+++ V+ A
Sbjct: 63 RKLMPGRIQLWGHQIAVDWA 82

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.8 bits (95), Expect = 1e-05
 Identities = 10/69 (14%), Positives = 24/69 (34%), Gaps = 6/69 (8%)

Query: 111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMT------GIVDYTSYDDMKYAI 164
           R+ + G+P     +++ + + +  +     +                V+Y S+     A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 165 RKLDRSEFR 173
           RKL     +
Sbjct: 63  RKLMPGRIQ 71

>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 = 58.9 bits (142), Expect = 4e-12
 Identities = 20/82 (24%), Positives = 33/82 (40%), Gaps = 3/82 (3%)

Query: 2  SSRSS--RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL-KIPPRPPGYAFLEFEDYRDA 58
          S R S    +++ NL      + + D F  +G I+   +        GY F+ FE    A
Sbjct: 2  SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAA 61

Query: 59 EDAIRGRDGYNFDGYRLRVELA 80
          E AI   +G   +  ++ V   
Sbjct: 62 ERAIEKMNGMLLNDRKVFVGRF 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 = 38.9 bits (90), Expect = 6e-05
 Identities = 19/89 (21%), Positives = 35/89 (39%), Gaps = 7/89 (7%)

Query: 105 SRRS-DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG--MTGIVDYTSYDDMK 161
            R+S    + +  L  S   + L D     G++   +V  D  G    G V + + +  +
Sbjct: 3   LRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAE 62

Query: 162 YAIRKLDRSEFRNAFSRSYVRVREYDSRR 190
            AI K++     +      V V  + SR+
Sbjct: 63  RAIEKMNGMLLND----RKVFVGRFKSRK 87

>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 = 58.6 bits (141), Expect = 5e-12
 Identities = 25/86 (29%), Positives = 35/86 (40%), Gaps = 4/86 (4%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAI 62
          S  S  + V NLP D+  +EV DL   Y            R    AF+   +   A++AI
Sbjct: 2  SSGSSGILVKNLPQDSNCQEVHDLLKDYDLKY----CYVDRNKRTAFVTLLNGEQAQNAI 57

Query: 63 RGRDGYNFDGYRLRVELAHGGRRHSS 88
          +    Y+F G  L V+L        S
Sbjct: 58 QMFHQYSFRGKDLIVQLQPTDALLCS 83

>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 = 58.6 bits (141), Expect = 7e-12
 Identities = 23/97 (23%), Positives = 39/97 (40%), Gaps = 11/97 (11%)

Query: 3   SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-----------RPPGYAFLE 51
              +  +YV  L     + ++ D F + G +        P           +P G A + 
Sbjct: 5   DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 64

Query: 52  FEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGRRHSS 88
           +ED   A+ A+   DG +F G +L+V LA      +S
Sbjct: 65  YEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS 101

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.5 bits (81), Expect = 0.001
 Identities = 15/81 (18%), Positives = 26/81 (32%), Gaps = 12/81 (14%)

Query: 106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD------------RGGMTGIVD 153
              +  + V GL  S +  DL D  ++ G V  ++                +      V 
Sbjct: 5   DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 64

Query: 154 YTSYDDMKYAIRKLDRSEFRN 174
           Y      K A+   D  +F+ 
Sbjct: 65  YEDPPTAKAAVEWFDGKDFQG 85

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.7 bits (139), Expect = 8e-12
 Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 5/79 (6%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
          + R   TLYV     D     +   F  +G I+D+       P   AF+ +E    A+ A
Sbjct: 1  APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLS---MDPPRNCAFVTYEKMESADQA 55

Query: 62 IRGRDGYNFDGYRLRVELA 80
          +   +G   +  +L+V +A
Sbjct: 56 VAELNGTQVESVQLKVNIA 74

>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 = 57.7 bits (139), Expect = 9e-12
 Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 4/78 (5%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAI 62
          S  S  ++VG   GD    E+ + F +YG ++D+   IP     +AF+ F D + A+   
Sbjct: 2  SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDV--FIPKPFRAFAFVTFADDQIAQSLC 59

Query: 63 RGRDGYNFDGYRLRVELA 80
             +     G  + +  A
Sbjct: 60 --GEDLIIKGISVHISNA 75

>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 = 58.2 bits (140), Expect = 1e-11
 Identities = 27/86 (31%), Positives = 47/86 (54%), Gaps = 3/86 (3%)

Query: 4  RSSRTLYVGNLPGDTRMREVEDLFYKYGPI---VDIDLKIPPRPPGYAFLEFEDYRDAED 60
          RS R+++VGN+P +    +++D+F + GP+     +  +   +P GY F E++D   A  
Sbjct: 6  RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65

Query: 61 AIRGRDGYNFDGYRLRVELAHGGRRH 86
          A+R  +G  F G  LRV+ A   +  
Sbjct: 66 AMRNLNGREFSGRALRVDNAASEKNK 91

>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 = 34.3 bits (78), Expect = 0.003
 Identities = 24/97 (24%), Positives = 36/97 (37%), Gaps = 8/97 (8%)

Query: 107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGM----TGIVDYTSYDDMKY 162
           RS   V V  +P  A+ + LKD     G V   ++  DR        G  +Y   +    
Sbjct: 6   RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65

Query: 163 AIRKLDRSEFRNAFSRSYVRVREYDSRRSYSRSPSRS 199
           A+R L+  EF        +RV    S ++     S  
Sbjct: 66  AMRNLNGREFSG----RALRVDNAASEKNKEELKSLG 98

>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 = 57.0 bits (137), Expect = 1e-11
 Identities = 15/75 (20%), Positives = 30/75 (40%), Gaps = 4/75 (5%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAEDAIRGR 65
          ++VG L  +T + +V+  F ++G + D  L          G+ F+ FE     E      
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 66 DGYNFDGYRLRVELA 80
            +  +   +  + 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 = 36.6 bits (84), Expect = 3e-04
 Identities = 15/79 (18%), Positives = 33/79 (41%), Gaps = 9/79 (11%)

Query: 111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRK 166
           ++ V GL  + + +D+K +  + G V  + +  D+        G V + S D ++    +
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-E 59

Query: 167 LDRSEFRNAFSRSYVRVRE 185
           +   E  N      V  ++
Sbjct: 60  IHFHEINN----KMVECKK 74

>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 = 56.6 bits (136), Expect = 2e-11
 Identities = 19/81 (23%), Positives = 31/81 (38%), Gaps = 4/81 (4%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDG 67
           LY+GNL       ++  LF      +   +       GYAF+++ D   A  AI    G
Sbjct: 3  KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL---LKSGYAFVDYPDQNWAIRAIETLSG 59

Query: 68 -YNFDGYRLRVELAHGGRRHS 87
               G  + V+ +   +  S
Sbjct: 60 KVELHGKIMEVDYSVSKKLRS 80

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 4e-11
 Identities = 18/75 (24%), Positives = 39/75 (52%), Gaps = 4/75 (5%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAEDAIRGR 65
          +++G L  DT  ++++D F K+G +VD  LK+ P      G+ F+ F++    +  +  +
Sbjct: 2  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-Q 60

Query: 66 DGYNFDGYRLRVELA 80
            +  +G  +  + 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 = 35.0 bits (80), Expect = 9e-04
 Identities = 11/62 (17%), Positives = 26/62 (41%), Gaps = 4/62 (6%)

Query: 111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMT----GIVDYTSYDDMKYAIRK 166
           ++ + GL    + +DLKD+  + G+V    +  D         G V +   + +   + +
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 167 LD 168
            +
Sbjct: 61  KE 62

>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 = 55.7 bits (134), Expect = 6e-11
 Identities = 20/95 (21%), Positives = 35/95 (36%), Gaps = 12/95 (12%)

Query: 3  SRSSRTLYVGNL--PGDTR---------MREVEDLFYKYGPIVDIDLKIPPRPPGYAFLE 51
           R  R + + N+  P D             ++     K+G I  +       P G A + 
Sbjct: 5  MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLL-LFDRHPDGVASVS 63

Query: 52 FEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGRRH 86
          F D  +A+  I+  DG  F G ++  +   G   +
Sbjct: 64 FRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTDY 98

>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 = 55.9 bits (134), Expect = 6e-11
 Identities = 26/90 (28%), Positives = 37/90 (41%), Gaps = 3/90 (3%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYG---PIVDIDLKIPPRPPGYAFLEFEDYRDAE 59
          S  S  L+V NL   +   ++E LF  YG    +      +  +P G+AF+ F     A 
Sbjct: 5  SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAV 64

Query: 60 DAIRGRDGYNFDGYRLRVELAHGGRRHSSS 89
           A    DG  F G  L V  +   +  S S
Sbjct: 65 KAYAEVDGQVFQGRMLHVLPSTIKKEASQS 94

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.5 bits (89), Expect = 8e-05
 Identities = 20/104 (19%), Positives = 35/104 (33%), Gaps = 10/104 (9%)

Query: 100 GSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR----GGMTGIVDYT 155
           GS G S     R+ V  L  ++S +DL+      G +       D           V + 
Sbjct: 1   GSSGSSGSG--RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFM 58

Query: 156 SYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDSRRSYSRSPSRS 199
             +    A  ++D   F+       + V     ++  S+S   S
Sbjct: 59  FPEHAVKAYAEVDGQVFQG----RMLHVLPSTIKKEASQSGPSS 98

>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 = 55.8 bits (134), Expect = 7e-11
 Identities = 15/78 (19%), Positives = 34/78 (43%), Gaps = 4/78 (5%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPP---GYAFLEFEDYRDAEDAI 62
           R L++G L  +T    + + + ++G + D  +   P      G+ F+ F    + + A+
Sbjct: 20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 79

Query: 63 RGRDGYNFDGYRLRVELA 80
               ++ DG  +  + A
Sbjct: 80 AA-RPHSIDGRVVEPKRA 96

>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 = 55.4 bits (133), Expect = 7e-11
 Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 4/77 (5%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAEDAIR 63
          R L++G L  +T    +   F ++G + D  +   P      G+ F+ +    + + A+ 
Sbjct: 7  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66

Query: 64 GRDGYNFDGYRLRVELA 80
              +  DG  +  + A
Sbjct: 67 A-RPHKVDGRVVEPKRA 82

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 8e-11
 Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 4/81 (4%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAE 59
           R +RT++   L    R R++ED F   G + D+ +   +   R  G A++EF + +   
Sbjct: 15 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP 74

Query: 60 DAIRGRDGYNFDGYRLRVELA 80
              G  G    G  + V+ +
Sbjct: 75 -LAIGLTGQRLLGVPIIVQAS 94

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (132), Expect = 1e-10
 Identities = 21/86 (24%), Positives = 32/86 (37%), Gaps = 9/86 (10%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--------RPPGYAFLEFEDYRDA 58
          R LYVGN+P       + D F     +  +              +   +AFLEF    + 
Sbjct: 2  RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 59 EDAIRGRDGYNFDGYRLRVELAHGGR 84
            A+   DG  F G  L++   H  +
Sbjct: 62 TQAMA-FDGIIFQGQSLKIRRPHDYQ 86

>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 = 55.1 bits (132), Expect = 1e-10
 Identities = 25/103 (24%), Positives = 39/103 (37%), Gaps = 11/103 (10%)

Query: 5   SSRTLYVGNLPGDTRMREVEDLF---YKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
           +   ++VG LP  T    +   F         V I  +   +  GY F+   D   AE A
Sbjct: 9   TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 68

Query: 62  IRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGV 104
            +  +    DG +  V LA+ G +  S         +G + GV
Sbjct: 69  CKDPNPI-IDGRKANVNLAYLGAKPRSL-------QTGFAIGV 103

>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 = 55.1 bits (132), Expect = 1e-10
 Identities = 16/78 (20%), Positives = 38/78 (48%), Gaps = 3/78 (3%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP---RPPGYAFLEFEDYRDAEDAI 62
             L++ +LP +   +++  +F  +G +V   + I         + F+ +++   A+ AI
Sbjct: 18 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 77

Query: 63 RGRDGYNFDGYRLRVELA 80
          +  +G+     RL+V+L 
Sbjct: 78 QSMNGFQIGMKRLKVQLK 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 = 35.4 bits (81), Expect = 0.001
 Identities = 16/86 (18%), Positives = 29/86 (33%), Gaps = 6/86 (6%)

Query: 95  SYSSGGSRGVSRRS--DYRVLVTGLPSSASWQDLKDHMRRAGDV----CFSQVFRDRGGM 148
           +  S G+ G  +       + +  LP     QDL       G+V     F     +    
Sbjct: 2   TQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKC 61

Query: 149 TGIVDYTSYDDMKYAIRKLDRSEFRN 174
            G V Y +    + AI+ ++  +   
Sbjct: 62  FGFVSYDNPVSAQAAIQSMNGFQIGM 87

>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 = 55.7 bits (133), Expect = 2e-10
 Identities = 24/95 (25%), Positives = 38/95 (40%), Gaps = 3/95 (3%)

Query: 2   SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGY---AFLEFEDYRDA 58
                R L V  +P      ++  LF +YGPI  + +             F++F+    A
Sbjct: 38  EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSA 97

Query: 59  EDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRY 93
           + AI G +G+N    RL+V LA  G +        
Sbjct: 98  QQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAV 132

>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 = 53.5 bits (128), Expect = 3e-10
 Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 3/79 (3%)

Query: 5  SSRTLYVGNLPGDTRMREVEDLFYKYGP---IVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
              + V N+P    + E+ D FY Y      V +       P G A + FE   +A  A
Sbjct: 8  GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 67

Query: 62 IRGRDGYNFDGYRLRVELA 80
          +   +       ++++ L 
Sbjct: 68 VIDLNDRPIGSRKVKLVLG 86

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.6 bits (84), Expect = 4e-04
 Identities = 16/80 (20%), Positives = 29/80 (36%), Gaps = 6/80 (7%)

Query: 99  GGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR--GGMTGI--VDY 154
           G S G  +     + V  +P + S  ++ D       +  S   +    G  TG   V +
Sbjct: 1   GASSG--KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAF 58

Query: 155 TSYDDMKYAIRKLDRSEFRN 174
            S D+   A+  L+     +
Sbjct: 59  ESRDEATAAVIDLNDRPIGS 78

>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 = 53.6 bits (128), Expect = 4e-10
 Identities = 31/91 (34%), Positives = 49/91 (53%), Gaps = 4/91 (4%)

Query: 1  MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPI---VDIDLKIPPRPPGYAFLEFEDYRD 57
          M+S     L+VG L  DT  + +E +F KYG I   V +  +   R  G+ F+ FE+  D
Sbjct: 1  MASDE-GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDD 59

Query: 58 AEDAIRGRDGYNFDGYRLRVELAHGGRRHSS 88
          A+DA+   +G + DG ++RV+ A     + S
Sbjct: 60 AKDAMMAMNGKSVDGRQIRVDQAGKSSDNRS 90

>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 = 53.2 bits (127), Expect = 5e-10
 Identities = 12/81 (14%), Positives = 33/81 (40%), Gaps = 3/81 (3%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR--PPGYAFLEFEDYRDAE 59
          +   +R++Y+   P D  + ++++     G +++I ++        G  F+ F+    A+
Sbjct: 2  NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 61

Query: 60 DAIRGRDGYNFDGYRLRVELA 80
            +    G  +    L +   
Sbjct: 62 KFVE-TPGQKYKETDLLILFK 81

>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 = 52.8 bits (126), Expect = 5e-10
 Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 4/79 (5%)

Query: 5  SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDA 61
          + + ++VG +  DT    + D F +YG I  I++   +   +  G+AF+ F+D  D+ D 
Sbjct: 1  TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDK 59

Query: 62 IRGRDGYNFDGYRLRVELA 80
          I  +  +  +G+   V  A
Sbjct: 60 IVIQKYHTVNGHNCEVRKA 78

>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 = 53.1 bits (127), Expect = 6e-10
 Identities = 19/83 (22%), Positives = 34/83 (40%), Gaps = 4/83 (4%)

Query: 1  MSSRSS-RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAE 59
          M+ +S    + V NL     +  +  +F K+G ++ I           A L++ D   A+
Sbjct: 1  MAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIIT-FTKNNQFQALLQYADPVSAQ 59

Query: 60 DAIRGRDGYNF--DGYRLRVELA 80
           A    DG N       LR++ +
Sbjct: 60 HAKLSLDGQNIYNACCTLRIDFS 82

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.4 bits (107), Expect = 5e-07
 Identities = 22/109 (20%), Positives = 37/109 (33%), Gaps = 11/109 (10%)

Query: 111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRS 170
           R++V  L    +   L     + G V     F        ++ Y      ++A   LD  
Sbjct: 9   RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQ 68

Query: 171 EFRNAFSRSYVRVREYDSRRSYSRSPSRSPYYSRSRSRSPYYSRSRSPS 219
              NA     +          +S+  S +  Y+  +SR   Y+R   PS
Sbjct: 69  NIYNACCTLRI---------DFSKLTSLNVKYNNDKSRD--YTRPDLPS 106

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 52.1 bits (124), Expect = 1e-09
 Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 6/83 (7%)

Query: 3  SRSSRTLYVGNLPGD-TRMREVEDLFYKYGPI----VDIDLKIPPRPPGYAFLEFEDYRD 57
          +   R + + NL  +      + + F  +G I    +    K        AF+ FE+   
Sbjct: 1  TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDS 60

Query: 58 AEDAIRGRDGYNFDGYRLRVELA 80
          AE A++  +        + V LA
Sbjct: 61 AERALQ-MNRSLLGNREISVSLA 82

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.0 bits (124), Expect = 1e-09
 Identities = 22/85 (25%), Positives = 39/85 (45%), Gaps = 5/85 (5%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAI 62
          +  +  L+VG L  +T +  +   F ++G I  ID     +   +A++++E    A+ A 
Sbjct: 14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTID---HVKGDSFAYIQYESLDAAQAAC 70

Query: 63 RGRDGYNFDGY--RLRVELAHGGRR 85
              G+   G   RLRV+ A  G  
Sbjct: 71 AKMRGFPLGGPDRRLRVDFAKSGPS 95

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.4 bits (81), Expect = 0.001
 Identities = 22/98 (22%), Positives = 31/98 (31%), Gaps = 5/98 (5%)

Query: 95  SYSSGGSRGVSRRSDYRVL-VTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVD 153
           S  S G  G  + +    L V GL  + S   L     R        +   +G     + 
Sbjct: 2   SSGSSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDR--FGSIRTIDHVKGDSFAYIQ 59

Query: 154 YTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDSRRS 191
           Y S D  + A  K+          R  +RV    S  S
Sbjct: 60  YESLDAAQAACAKMRGFPLGGPDRR--LRVDFAKSGPS 95

>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 = 50.9 bits (121), Expect = 2e-09
 Identities = 15/71 (21%), Positives = 26/71 (36%), Gaps = 3/71 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAEDAIRGR 65
          LY+  L   T  +++  L   YG IV     +        GY F++F+    A+ A+   
Sbjct: 1  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 66 DGYNFDGYRLR 76
                    +
Sbjct: 61 KASGVQAQMAK 71

>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 = 39.4 bits (91), Expect = 3e-05
 Identities = 14/66 (21%), Positives = 26/66 (39%), Gaps = 4/66 (6%)

Query: 112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR----GGMTGIVDYTSYDDMKYAIRKL 167
           + + GL    + QDL    +  G +  ++   D+        G VD+ S    + A+  L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 168 DRSEFR 173
             S  +
Sbjct: 61  KASGVQ 66

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 2e-09
 Identities = 14/82 (17%), Positives = 31/82 (37%), Gaps = 6/82 (7%)

Query: 1  MSSRSSRTLYV--GNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDA 58
            S ++++L V  G L       ++  +  K G +  +     P    Y+F  +    ++
Sbjct: 13 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALL---MPPNKPYSFARYRTTEES 69

Query: 59 EDAIRGRDGYN-FDGYRLRVEL 79
          + A    +G    D    ++ L
Sbjct: 70 KRAYVTLNGKEVVDDLGQKITL 91

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.3 bits (78), Expect = 0.003
 Identities = 15/76 (19%), Positives = 26/76 (34%), Gaps = 3/76 (3%)

Query: 100 GSRGVSRRSDYRVLVTG-LPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYD 158
           G   VS  +   V+  G L +  S   L   + + G V    +            Y + +
Sbjct: 10  GIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDA--LLMPPNKPYSFARYRTTE 67

Query: 159 DMKYAIRKLDRSEFRN 174
           + K A   L+  E  +
Sbjct: 68  ESKRAYVTLNGKEVVD 83

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.7 bits (123), Expect = 2e-09
 Identities = 20/106 (18%), Positives = 29/106 (27%), Gaps = 8/106 (7%)

Query: 3   SRSSRTLYVGNLP-----GDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRD 57
           S  S  L                 + E LF  Y            +      + F +   
Sbjct: 2   SSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF---KSFKRVRINFSNPLS 58

Query: 58  AEDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRG 103
           A DA        F G  +++  A      SS +   +   SG S G
Sbjct: 59  AADARLRLHKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDKSGPSSG 104

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.2 bits (122), Expect = 2e-09
 Identities = 16/87 (18%), Positives = 31/87 (35%), Gaps = 6/87 (6%)

Query: 2  SSRSSRTLYVGNLP-GDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
             + R +++ +   G     ++  L   +G I +            AF+E     DA+ 
Sbjct: 4  RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHL---ILNKINEAFIEMATTEDAQA 60

Query: 61 AIRGR--DGYNFDGYRLRVELAHGGRR 85
          A+           G  +RV L+   +R
Sbjct: 61 AVDYYTTTPALVFGKPVRVHLSQKYKR 87

>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 = 51.4 bits (122), Expect = 2e-09
 Identities = 17/84 (20%), Positives = 36/84 (42%), Gaps = 9/84 (10%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAI 62
           +T+++ NL  D+    + ++  ++G +  + +          G AF +F     A+  +
Sbjct: 8  GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 67

Query: 63 RG------RDGYNFDGYRLRVELA 80
                    G   DG +L+V+LA
Sbjct: 68 AAASLEAEGGGLKLDGRQLKVDLA 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 = 33.6 bits (76), Expect = 0.004
 Identities = 6/68 (8%), Positives = 21/68 (30%), Gaps = 4/68 (5%)

Query: 111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR----GGMTGIVDYTSYDDMKYAIRK 166
            V +  L   +  + L + +++ GD+ + +V                + + +  +  +  
Sbjct: 10  TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 69

Query: 167 LDRSEFRN 174
                   
Sbjct: 70  ASLEAEGG 77

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 51.0 bits (121), Expect = 3e-09
 Identities = 15/76 (19%), Positives = 33/76 (43%), Gaps = 3/76 (3%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGR 65
          ++ L++ NLP +T    +  LF ++    ++   + P     AF+EF     +  A    
Sbjct: 8  NQILFLTNLPEETNEMMLSMLFNQFPGFKEVR--LVPNRHDIAFVEFTTELQSNAAKEAL 65

Query: 66 DGYNFD-GYRLRVELA 80
           G+     + +++  A
Sbjct: 66 QGFKITPTHAMKITFA 81

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.6 bits (120), Expect = 5e-09
 Identities = 15/79 (18%), Positives = 25/79 (31%), Gaps = 2/79 (2%)

Query: 4  RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVD--IDLKIPPRPPGYAFLEFEDYRDAEDA 61
          +    LY+ NLP     +E+E++   +G ++   I         G  F   E     E  
Sbjct: 16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAV 75

Query: 62 IRGRDGYNFDGYRLRVELA 80
          I   +G             
Sbjct: 76 IGHFNGKFIKTPPGVSAPT 94

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.8 bits (79), Expect = 0.002
 Identities = 12/84 (14%), Positives = 31/84 (36%), Gaps = 6/84 (7%)

Query: 97  SSGGSRGVSRRSD---YRVLVTGLPSSASWQDLKDHMRRAGDVC---FSQVFRDRGGMTG 150
           +SG    ++++ +     + ++ LP S   Q+L++ ++  G V      +         G
Sbjct: 3   ASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVG 62

Query: 151 IVDYTSYDDMKYAIRKLDRSEFRN 174
                S +  +  I   +    + 
Sbjct: 63  FARMESTEKCEAVIGHFNGKFIKT 86

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.5 bits (120), Expect = 6e-09
 Identities = 22/107 (20%), Positives = 42/107 (39%), Gaps = 6/107 (5%)

Query: 6   SRTLYVGNL-PGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRG 64
           +  L V NL P     + +  LF  YG +  +  KI       A ++  D   A+ A+  
Sbjct: 2   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRV--KILFNKKENALVQMADGNQAQLAMSH 59

Query: 65  RDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSGGSRGVSRRSDYR 111
            +G+   G  +R+ L+   +  +  + R      G ++       +R
Sbjct: 60  LNGHKLHGKPIRITLS---KHQNVQLPREGQEDQGLTKDYGNSPLHR 103

>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 = 50.2 bits (119), Expect = 7e-09
 Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 3/78 (3%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAI 62
          ++ LY+ NL      R++  LF ++       +    +  R  G AF+ F +   A  A+
Sbjct: 18 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 77

Query: 63 RGRDGYNFDGYRLRVELA 80
             +GY   G  L +E  
Sbjct: 78 HLVNGYKLYGKILVIEFG 95

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.3 bits (119), Expect = 8e-09
 Identities = 23/94 (24%), Positives = 39/94 (41%), Gaps = 3/94 (3%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
          S RS   +   NLP  T   E+++ F ++G +  +   + P     A +EF +  +A  A
Sbjct: 6  SGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRV---LLPEGGITAIVEFLEPLEARKA 62

Query: 62 IRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSS 95
           R      F    L +E A  G   ++   + S 
Sbjct: 63 FRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQ 96

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.3 bits (80), Expect = 0.001
 Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 100 GSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDD 159
           GS G S RS   +L   LP+     ++++   R       +V    GG+T IV++    +
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSR--FGSLGRVLLPEGGITAIVEFLEPLE 58

Query: 160 MKYAIRKLDRSEFRN 174
            + A R L  S+F +
Sbjct: 59  ARKAFRHLAYSKFHH 73

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 49.5 bits (117), Expect = 8e-09
 Identities = 19/74 (25%), Positives = 29/74 (39%), Gaps = 2/74 (2%)

Query: 8  TLYVGNLPGDTRMREVEDLFYKYGPIVDIDL-KIPPRPPGYAFLEFEDYRDAEDAIRGRD 66
          T+ V NLP      +V   F   GPI+ +D+     +   +A +EF  Y  A  AI  + 
Sbjct: 2  TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KT 60

Query: 67 GYNFDGYRLRVELA 80
                  + V   
Sbjct: 61 HKVVGQNEIIVSHL 74

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 49.6 bits (117), Expect = 9e-09
 Identities = 15/80 (18%), Positives = 33/80 (41%), Gaps = 3/80 (3%)

Query: 3  SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP--RPPGYAFLEFEDYRDAED 60
          S +   L++GNL  +  + E++    +     D+ +          + +++FE   D E 
Sbjct: 10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEK 69

Query: 61 AIRGRDGYNFDGYRLRVELA 80
          A+    G    G  +++E  
Sbjct: 70 ALE-LTGLKVFGNEIKLEKP 88

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.1 bits (116), Expect = 1e-08
 Identities = 19/72 (26%), Positives = 26/72 (36%), Gaps = 4/72 (5%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          + +  LPGD   +EV DL   Y            +  G AF+   +   AE AI      
Sbjct: 1  ILIRGLPGDVTNQEVHDLLSDYELKY----CFVDKYKGTAFVTLLNGEQAEAAINTFHQS 56

Query: 69 NFDGYRLRVELA 80
                L V+L 
Sbjct: 57 RLRERELSVQLQ 68

>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 = 49.6 bits (118), Expect = 1e-08
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 2/73 (2%)

Query: 9   LYVGNLPGDTRMREVEDLFYKYGPIVDIDL--KIPPRPPGYAFLEFEDYRDAEDAIRGRD 66
           + +     +       ++  KYG + ++++   +     G  +++F    DAE A+   +
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLN 89

Query: 67  GYNFDGYRLRVEL 79
              F+G  +  EL
Sbjct: 90  NRWFNGQPIHAEL 102

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.7 bits (115), Expect = 2e-08
 Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 5/83 (6%)

Query: 1  MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAED 60
          M    SR L++  LPG+    EV  L   +G + +I      +    AFLE      A  
Sbjct: 3  MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNIL---MLKGKNQAFLELATEEAAIT 59

Query: 61 AIRGR--DGYNFDGYRLRVELAH 81
           +        +     + ++ ++
Sbjct: 60 MVNYYSAVTPHLRNQPIYIQYSN 82

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.2 bits (114), Expect = 3e-08
 Identities = 44/91 (48%), Positives = 58/91 (63%), Gaps = 5/91 (5%)

Query: 97  SSGGSRG-VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYT 155
           SSG S G  +RRSD+RVLV+GLP S SWQDLKDHMR   +         +    G+V+Y 
Sbjct: 2   SSGSSGGPPTRRSDFRVLVSGLPPSGSWQDLKDHMR---EAGDVCYADVQKDGMGMVEYL 58

Query: 156 SYDDMKYAIRKLDRSEFRNAFSR-SYVRVRE 185
             +DM+YA+RKLD ++FR+     SY+RV  
Sbjct: 59  RKEDMEYALRKLDDTKFRSHEGETSYIRVYP 89

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.5 bits (94), Expect = 2e-05
 Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 4/79 (5%)

Query: 2  SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDA 61
          + RS   + V  LP     ++++D   + G +         +  G   +E+    D E A
Sbjct: 11 TRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYA----DVQKDGMGMVEYLRKEDMEYA 66

Query: 62 IRGRDGYNFDGYRLRVELA 80
          +R  D   F  +       
Sbjct: 67 LRKLDDTKFRSHEGETSYI 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 = 46.8 bits (110), Expect = 1e-07
 Identities = 13/100 (13%), Positives = 30/100 (30%), Gaps = 4/100 (4%)

Query: 3   SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRDAE 59
           + +    ++ N+P      +V           +    +        G A ++F++  DA 
Sbjct: 5   NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDAR 64

Query: 60  DAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSG 99
            + R       +G    V +           +  +   SG
Sbjct: 65  KSER-LHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSG 103

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.3 bits (109), Expect = 2e-07
 Identities = 17/96 (17%), Positives = 33/96 (34%), Gaps = 8/96 (8%)

Query: 6   SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRG- 64
           S  ++V  L       ++ +   K+G I  + +    R    A +EFE+   A++ +   
Sbjct: 15  SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR---QALVEFENIDSAKECVTFA 71

Query: 65  -RDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSG 99
                   G +     +        +    S  SSG
Sbjct: 72  ADVPVYIAGQQAFFNYS---TSKRITRPGNSGPSSG 104

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.4 bits (104), Expect = 5e-07
 Identities = 15/80 (18%), Positives = 29/80 (36%), Gaps = 9/80 (11%)

Query: 7  RTLYVGNLPGDTR---MREVEDLFYKYGPIVDIDL------KIPPRPPGYAFLEFEDYRD 57
            ++V  L        + +  + F K+G I  + +           P   A++ +    D
Sbjct: 9  NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 58 AEDAIRGRDGYNFDGYRLRV 77
          A  AI+  +    DG  L+ 
Sbjct: 69 ALRAIQCVNNVVVDGRTLKA 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 = 44.7 bits (105), Expect = 7e-07
 Identities = 23/102 (22%), Positives = 40/102 (39%), Gaps = 10/102 (9%)

Query: 1   MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPR---PPGYAFLEFEDYRD 57
           +      T ++GNLP D     +++ F           + P       G+ + EFED   
Sbjct: 10  LPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDS 69

Query: 58  AEDAIRGRDGYNFDGYRLRVELAHGGRRHSSSMDRYSSYSSG 99
              A+   +  +    R+RV++A   +      D+ S  SSG
Sbjct: 70  LLSALS-LNEESLGNKRIRVDVADQAQ------DKDSGPSSG 104

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.7 bits (102), Expect = 1e-06
 Identities = 41/98 (41%), Positives = 54/98 (55%), Gaps = 13/98 (13%)

Query: 111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRS 170
           RV+V+GLP S SWQDLKDHMR                 TG+V++   +DM YA+RKLD +
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMRE---AGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNT 58

Query: 171 EFRNAFSR-SYVRVREYDSRRSYSRSPSRSPYYSRSRS 207
           +FR+     +Y+RV+             RSP Y RSRS
Sbjct: 59  KFRSHEGETAYIRVK---------VDGPRSPSYGRSRS 87

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.4 bits (83), Expect = 4e-04
 Identities = 16/89 (17%), Positives = 26/89 (29%), Gaps = 4/89 (4%)

Query: 9  LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY 68
          + V  LP     ++++D   + G +            G   +EF    D   A+R  D  
Sbjct: 3  VVVSGLPPSGSWQDLKDHMREAGDVCYA----DVYRDGTGVVEFVRKEDMTYAVRKLDNT 58

Query: 69 NFDGYRLRVELAHGGRRHSSSMDRYSSYS 97
           F  +               S     S S
Sbjct: 59 KFRSHEGETAYIRVKVDGPRSPSYGRSRS 87

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.6 bits (89), Expect = 1e-04
 Identities = 14/74 (18%), Positives = 26/74 (35%), Gaps = 4/74 (5%)

Query: 7  RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFED-YRDAEDAIRGR 65
             + G+L   T   ++  LF  +G I  ID     R      + F++  ++A    +  
Sbjct: 12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDF---VRGAKEGIILFKEKAKEALGKAKDA 68

Query: 66 DGYNFDGYRLRVEL 79
          +  N       V  
Sbjct: 69 NNGNLQLRNKEVTW 82

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.4 bits (78), Expect = 0.004
 Identities = 10/84 (11%), Positives = 22/84 (26%), Gaps = 3/84 (3%)

Query: 112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDY-TSYDDMKYAIRKLDRS 170
                L      +DL       G+     +   RG   GI+ +     +     +  +  
Sbjct: 14  KFSGDLDDQTCREDLHILFSNHGE--IKWIDFVRGAKEGIILFKEKAKEALGKAKDANNG 71

Query: 171 EFRNAFSRSYVRVREYDSRRSYSR 194
             +         V E +  +   +
Sbjct: 72  NLQLRNKEVTWEVLEGEVEKEALK 95

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.8 bits (85), Expect = 2e-04
 Identities = 11/67 (16%), Positives = 22/67 (32%), Gaps = 5/67 (7%)

Query: 6  SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGR 65
             + V   P  +    +   F +YG I+            +  + ++    A  A+  +
Sbjct: 4  DTWVTVFGFPQAS-ASYILLQFAQYGNILKHV---MSNTGNWMHIRYQSKLQARKALS-K 58

Query: 66 DGYNFDG 72
          DG  F  
Sbjct: 59 DGRIFGE 65

>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 = 37.0 bits (85), Expect = 3e-04
 Identities = 17/90 (18%), Positives = 31/90 (34%), Gaps = 2/90 (2%)

Query: 1  MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLK-IPPRPPGYAFLEFEDYRDAE 59
            S +   +++  LP      ++ + F    P+          R  G A +EF  + DA 
Sbjct: 10 FQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAV 69

Query: 60 DAIRGRDGYNFDGYRLRVELAHGGRRHSSS 89
           A+  +D  N     + + L        S 
Sbjct: 70 AAMA-KDKANMQHRYVELFLNSTAGTSGSG 98

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.9 bits (85), Expect = 4e-04
 Identities = 19/98 (19%), Positives = 34/98 (34%), Gaps = 15/98 (15%)

Query: 6   SRTLYVGNL--PGDTRMRE-----VEDLFYKYGPIVDI-DLKIP-------PRPPGYAFL 50
           +  L + N+  P +    E     VED+  +      +  ++IP           G  F+
Sbjct: 4   TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFV 63

Query: 51  EFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGRRHSS 88
           EF    D + A++G  G  F    +  +       H  
Sbjct: 64  EFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRR 101

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	277
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.97
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.88
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.88
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.88
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.88
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.87
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.87
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.87
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.87
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.86
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.86
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.86
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.86
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.86
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.86
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.86
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.85
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.85
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.85
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.85
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.85
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.85
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.84
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.84
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.84
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.84
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.84
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.84
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.84
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.84
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.84
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.83
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.83
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.83
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.83
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.83
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.83
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.83
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.83
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.83
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.83
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.83
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.82
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.82
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.82
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.82
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.82
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.82
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.82
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.82
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.82
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.82
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.81
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.81
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.81
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.81
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.81
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.81
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.81
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.81
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.8
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.8
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.79
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.79
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.79
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.77
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.77
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.77
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.77
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.77
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.76
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.76
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.75
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.75
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.73
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.73
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.72
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.7
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.69
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.69
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.69
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.69
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.68
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.68
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.68
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.68
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.68
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.68
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.68
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.67
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.67
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.67
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.67
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.66
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.66
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.66
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.66
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.65
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.65
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.64
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.64
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.64
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.64
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.64
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.64
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.63
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.62
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.62
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.62
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	99.62
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.61
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.61
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.61
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.61
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.61
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.61
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.61
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.6
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.6
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.6
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.6
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.6
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.6
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.6
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.59
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.59
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.59
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.59
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.59
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.59
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.59
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.58
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.58
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.58
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.57
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.57
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.57
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.57
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.57
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.57
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.56
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.56
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.55
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.55
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.55
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.55
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.55
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.55
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.54
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.53
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.53
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.53
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.5
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.49
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.49
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.46
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.44
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.42
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.42
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.42
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.42
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.38
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.36
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.34
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.31
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	99.24
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.23
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.17
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	98.15
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	98.08
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	98.05
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.7
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.5
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.2
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	97.09
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.01
d1vqos1	81	Ribosomal protein L23 {Archaeon Haloarcula marismo	85.53
d1m1ha2	101	N-utilization substance G protein NusG, N-terminal	81.96

>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=99.97  E-value=2.4e-29  Score=194.19  Aligned_cols=161  Identities=17%  Similarity=0.295  Sum_probs=135.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      ++|||+|||+.+|+++|+++|++||+|..+.++.   ++.++|||||+|.+.++|.+|+. +++..+.+..+.+......
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~~   85 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVSR   85 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCCT
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhhc
Confidence            6999999999999999999999999999999864   56778999999999999999999 5667778888887776543


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhH
Q 023765           84 RRHSSSMDRYSSYSSGGSRGVSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDD  159 (277)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~  159 (277)
                      .....              ........+|||+|||..+++++|.++|..||.|..+.+..+..+    +||||+|.+.++
T Consensus        86 ~~~~~--------------~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~  151 (183)
T d1u1qa_          86 EDSQR--------------PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS  151 (183)
T ss_dssp             TGGGS--------------TTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHH
T ss_pred             ccccc--------------cccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHH
Confidence            32111              112334679999999999999999999999999999999987554    499999999999


Q ss_pred             HHHHHHhcCCCeecccceeeEEEEeecC
Q 023765          160 MKYAIRKLDRSEFRNAFSRSYVRVREYD  187 (277)
Q Consensus       160 a~~a~~~l~g~~~~g~~~~~~i~~~~~~  187 (277)
                      |.+|+. +++..+.|    ..|.|..+.
T Consensus       152 A~~Al~-~~~~~~~G----~~i~V~~A~  174 (183)
T d1u1qa_         152 VDKIVI-QKYHTVNG----HNCEVRKAL  174 (183)
T ss_dssp             HHHHHT-SSCEEETT----EEEEEEECC
T ss_pred             HHHHHH-hCCCeECC----EEEEEEecC
Confidence            999996 78889988    567776553

>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=99.88  E-value=5.9e-23  Score=138.51  Aligned_cols=83  Identities=34%  Similarity=0.560  Sum_probs=76.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEE
Q 023765            1 MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV   77 (277)
Q Consensus         1 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v   77 (277)
                      |+. .+++|||+|||+++|+++|+++|++||+|..|.++.   ++.++|||||+|.+.++|..|++.|||..|.|+.|.|
T Consensus         1 ma~-~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v   79 (89)
T d2cqba1           1 MAT-TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV   79 (89)
T ss_dssp             SCC-CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCC-CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            443 678999999999999999999999999999999954   5788999999999999999999999999999999999


Q ss_pred             EEccCCC
Q 023765           78 ELAHGGR   84 (277)
Q Consensus        78 ~~a~~~~   84 (277)
                      .+|.+..
T Consensus        80 ~~a~p~~   86 (89)
T d2cqba1          80 NLAKPMR   86 (89)
T ss_dssp             EECCCCC
T ss_pred             EEeCCCC
Confidence            9998643

>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=99.88  E-value=3.7e-23  Score=146.42  Aligned_cols=81  Identities=33%  Similarity=0.500  Sum_probs=76.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            2 SSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         2 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      ....+++|||+|||..+|+++|.++|++||+|..|.+..++.++|||||+|.+.++|..|++.|||..|.|+.|.|.++.
T Consensus         3 pp~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           3 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            34578899999999999999999999999999999999888889999999999999999999999999999999999987


Q ss_pred             C
Q 023765           82 G   82 (277)
Q Consensus        82 ~   82 (277)
                      .
T Consensus        83 ~   83 (114)
T d2f9da1          83 A   83 (114)
T ss_dssp             H
T ss_pred             C
Confidence            4

>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=99.88  E-value=7.2e-23  Score=136.08  Aligned_cols=77  Identities=32%  Similarity=0.462  Sum_probs=72.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      +++|||+|||+++|+++|+++|++||+|..+.|..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.+|++
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            57899999999999999999999999999999853   567899999999999999999999999999999999999875

>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=99.88  E-value=1.8e-22  Score=137.11  Aligned_cols=81  Identities=33%  Similarity=0.478  Sum_probs=75.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      +.++||||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|..|++.|||..|+|+.|.|.|+
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            5789999999999999999999999999999999954   5677899999999999999999999999999999999998


Q ss_pred             cCCC
Q 023765           81 HGGR   84 (277)
Q Consensus        81 ~~~~   84 (277)
                      .+..
T Consensus        85 ~~~~   88 (93)
T d1h2vz_          85 AGFK   88 (93)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7543

>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=99.87  E-value=6.4e-22  Score=136.15  Aligned_cols=83  Identities=31%  Similarity=0.476  Sum_probs=76.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      +.++++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|..|++.||+..|.|+.|.|.+
T Consensus         5 ~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~   84 (99)
T d1whwa_           5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            45778899999999999999999999999999999964   578899999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 023765           80 AHGGRR   85 (277)
Q Consensus        80 a~~~~~   85 (277)
                      +.....
T Consensus        85 a~~~~~   90 (99)
T d1whwa_          85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             CCCCCc
Confidence            987543

>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=99.87  E-value=2.5e-22  Score=135.88  Aligned_cols=83  Identities=35%  Similarity=0.605  Sum_probs=75.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEE
Q 023765            1 MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV   77 (277)
Q Consensus         1 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v   77 (277)
                      |++ +..+|||+|||+++|+++|+++|++||+|..+.+..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|
T Consensus         1 m~~-~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V   79 (90)
T d1x5sa1           1 MAS-DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRV   79 (90)
T ss_dssp             CCC-CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEE
T ss_pred             CCC-CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            565 677799999999999999999999999999998744   5678999999999999999999999999999999999


Q ss_pred             EEccCCC
Q 023765           78 ELAHGGR   84 (277)
Q Consensus        78 ~~a~~~~   84 (277)
                      .+|....
T Consensus        80 ~~a~~~~   86 (90)
T d1x5sa1          80 DQAGKSS   86 (90)
T ss_dssp             EEEECCC
T ss_pred             EEcCCCC
Confidence            9988654

>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=99.87  E-value=3.9e-22  Score=136.09  Aligned_cols=82  Identities=60%  Similarity=1.067  Sum_probs=76.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      ..++++|||+|||+++|+++|+++|++||.|..+.+..+..+++||||+|.+.++|..|++.||+..|.|+.|.|.++..
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~   90 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   90 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccC
Confidence            36788999999999999999999999999999999988778899999999999999999999999999999999999886


Q ss_pred             CC
Q 023765           83 GR   84 (277)
Q Consensus        83 ~~   84 (277)
                      ..
T Consensus        91 ~r   92 (95)
T d1x4aa1          91 GR   92 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.87  E-value=6e-22  Score=134.76  Aligned_cols=82  Identities=24%  Similarity=0.447  Sum_probs=75.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec----CCCCCcEEEEEEcChHHHHHHHHhc-CCcccCCceEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI----PPRPPGYAFLEFEDYRDAEDAIRGR-DGYNFDGYRLRV   77 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~----~~~~~g~afV~f~~~~~a~~a~~~l-~~~~~~g~~i~v   77 (277)
                      .+++++|||+|||+++++++|+++|++||.|..|.|+.    ++.++|||||+|.+.++|..|+..| |+..|.|+.|.|
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            36789999999999999999999999999999999954    4678999999999999999999988 899999999999


Q ss_pred             EEccCCC
Q 023765           78 ELAHGGR   84 (277)
Q Consensus        78 ~~a~~~~   84 (277)
                      .||....
T Consensus        85 ~~A~~~~   91 (94)
T d2cpha1          85 EWADSEV   91 (94)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCC
Confidence            9998654

>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=99.87  E-value=5.2e-22  Score=134.80  Aligned_cols=81  Identities=30%  Similarity=0.441  Sum_probs=75.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .++++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.+|
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            4578999999999999999999999999999999954   5788999999999999999999999999999999999999


Q ss_pred             cCCC
Q 023765           81 HGGR   84 (277)
Q Consensus        81 ~~~~   84 (277)
                      .+..
T Consensus        87 ~~~~   90 (93)
T d1x5ua1          87 SAHN   90 (93)
T ss_dssp             TTTS
T ss_pred             CCCC
Confidence            8654

>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=99.87  E-value=3.4e-22  Score=132.78  Aligned_cols=77  Identities=29%  Similarity=0.432  Sum_probs=71.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      .++|||+|||+++++++|.++|++||+|..|.++.   ++.++|||||+|.++++|..|+..|||..|.|+.|.|.+|++
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            46799999999999999999999999999999954   467789999999999999999999999999999999999874

>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=99.86  E-value=1.4e-21  Score=131.93  Aligned_cols=82  Identities=30%  Similarity=0.449  Sum_probs=74.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecC-CCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP-PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~-~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      ..+.++|||+|||+++|+++|+++|++||+|..|.|..+ ...++||||+|.+.++|..|+..|||..|.|+.|.|.||.
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            467899999999999999999999999999999998653 3458999999999999999999999999999999999998


Q ss_pred             CCC
Q 023765           82 GGR   84 (277)
Q Consensus        82 ~~~   84 (277)
                      ++.
T Consensus        85 ~~~   87 (90)
T d2cqia1          85 TPS   87 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            543

>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=99.86  E-value=7.7e-22  Score=131.60  Aligned_cols=77  Identities=30%  Similarity=0.541  Sum_probs=72.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      ++|||+|||+.+|+++|+++|++||+|..|.|+.   ++.++|||||+|.++++|..|+..|||..|.|+.|.|.+|...
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            5799999999999999999999999999999954   5788999999999999999999999999999999999999854

>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=99.86  E-value=4.1e-22  Score=134.58  Aligned_cols=80  Identities=35%  Similarity=0.568  Sum_probs=74.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .++++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|..|++.|||..|.|+.|.|.+|
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            5678999999999999999999999999999999964   4678899999999999999999999999999999999999


Q ss_pred             cCC
Q 023765           81 HGG   83 (277)
Q Consensus        81 ~~~   83 (277)
                      .+.
T Consensus        86 kp~   88 (90)
T d2cq0a1          86 KPS   88 (90)
T ss_dssp             SCC
T ss_pred             eCC
Confidence            853

>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=99.86  E-value=6.2e-22  Score=130.65  Aligned_cols=75  Identities=29%  Similarity=0.445  Sum_probs=70.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            8 TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         8 ~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      +|||+|||+.+|+++|.++|++||+|..|.|+.   ++.++|||||+|.++++|..|++.|||..|.|+.|.|.+++.
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~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            699999999999999999999999999999965   467789999999999999999999999999999999999863

>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=99.86  E-value=6.2e-22  Score=133.04  Aligned_cols=79  Identities=24%  Similarity=0.437  Sum_probs=73.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+.++|||+|||+.+|+++|.++|++||+|..|.|+.   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.||
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a   84 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC   84 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            4568999999999999999999999999999999854   5678899999999999999999999999999999999998


Q ss_pred             cC
Q 023765           81 HG   82 (277)
Q Consensus        81 ~~   82 (277)
                      ..
T Consensus        85 ~~   86 (88)
T d1rk8a_          85 FV   86 (88)
T ss_dssp             EE
T ss_pred             cC
Confidence            75

>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=99.86  E-value=2.6e-21  Score=131.35  Aligned_cols=80  Identities=25%  Similarity=0.473  Sum_probs=74.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecC-CCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIP-PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~-~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      ...++|||+|||+++|+++|+++|++||+|..|.+..+ +.++|||||+|.+.++|..|+..||+..|.|+.|.|.+|.+
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~   88 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA   88 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCc
Confidence            56789999999999999999999999999999999653 45689999999999999999999999999999999999986


Q ss_pred             C
Q 023765           83 G   83 (277)
Q Consensus        83 ~   83 (277)
                      .
T Consensus        89 r   89 (93)
T d2cq3a1          89 R   89 (93)
T ss_dssp             S
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=99.86  E-value=1.1e-21  Score=128.63  Aligned_cols=74  Identities=26%  Similarity=0.420  Sum_probs=70.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            8 TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         8 ~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      +|||+|||+++++++|+++|++||+|..+.|..  ++.++|||||+|.+.++|..|++.|||..|.|++|.|.++.
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 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            599999999999999999999999999999964  66789999999999999999999999999999999999975

>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=99.85  E-value=1.6e-21  Score=131.42  Aligned_cols=79  Identities=22%  Similarity=0.361  Sum_probs=72.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec-CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI-PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~-~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      ...+|||+|||+++|+++|+++|++||.|..+.|+. .+.++|||||+|.+.++|..|++.|||..|.|+.|.|.++...
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            356899999999999999999999999999999965 3456899999999999999999999999999999999999854

>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=99.85  E-value=1.2e-21  Score=129.64  Aligned_cols=77  Identities=18%  Similarity=0.307  Sum_probs=68.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      .+||||+|||+++|+++|+++|++||+|..+.+..   ++.++|||||+|.+.++|..|++.|||..|.|+.|.|.++.+
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            37999999999999999999999999998777643   567899999999999999999999999999999999999875

>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=99.85  E-value=1.4e-21  Score=130.36  Aligned_cols=77  Identities=31%  Similarity=0.565  Sum_probs=70.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCC--ceEEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDG--YRLRVE   78 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g--~~i~v~   78 (277)
                      -..++|||+|||+++|+++|+++|++||+|..+.++.   ++.++|||||+|.++++|..|++.|||..+.|  .+|.|.
T Consensus         4 ~k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~   83 (85)
T d1fxla2           4 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK   83 (85)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEE
Confidence            3567899999999999999999999999999999964   46788999999999999999999999999998  459998


Q ss_pred             Ec
Q 023765           79 LA   80 (277)
Q Consensus        79 ~a   80 (277)
                      ||
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>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=99.85  E-value=8.4e-22  Score=133.33  Aligned_cols=80  Identities=28%  Similarity=0.546  Sum_probs=74.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHH----HhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVED----LFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~----~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      +|+++|||+|||+.+|+++|++    +|++||+|..|.+..++.++|||||+|.+.++|..|+..|||..|.|+.|.|.|
T Consensus         1 ~P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~   80 (91)
T d1nu4a_           1 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY   80 (91)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            5899999999999999999864    689999999999987777899999999999999999999999999999999999


Q ss_pred             ccCC
Q 023765           80 AHGG   83 (277)
Q Consensus        80 a~~~   83 (277)
                      |+..
T Consensus        81 ak~~   84 (91)
T d1nu4a_          81 AKTD   84 (91)
T ss_dssp             CSSC
T ss_pred             eCCC
Confidence            9754

>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=99.85  E-value=1.7e-21  Score=134.61  Aligned_cols=80  Identities=20%  Similarity=0.441  Sum_probs=73.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      +.++|||+|||+++|+++|+++|+.||.|..+.++.   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.
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            567899999999999999999999999999998854   56778999999999999999999999999999999999988


Q ss_pred             CCC
Q 023765           82 GGR   84 (277)
Q Consensus        82 ~~~   84 (277)
                      +..
T Consensus        97 ~k~   99 (102)
T d2cpza1          97 SKN   99 (102)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            654

>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=99.85  E-value=1.5e-21  Score=129.79  Aligned_cols=74  Identities=36%  Similarity=0.602  Sum_probs=68.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV   77 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v   77 (277)
                      .++++|||+|||+.+|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|
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            4578999999999999999999999999999999854   4677899999999999999999999999999999987

>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=4.1e-21  Score=129.18  Aligned_cols=80  Identities=20%  Similarity=0.422  Sum_probs=72.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      .+.+++|||+|||+++|+++|+++|+.||+|..|.|+.   ++.++|||||+|.++++|.+|++.+  ..|+|+.|.|.+
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~--~~l~Gr~i~v~~   82 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR--HMIDGRWCDCKL   82 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC--EEETTEEEEEEC
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC--CccCCEEeEEEe
Confidence            45788999999999999999999999999999999965   5788999999999999999999854  479999999999


Q ss_pred             ccCCC
Q 023765           80 AHGGR   84 (277)
Q Consensus        80 a~~~~   84 (277)
                      +.+..
T Consensus        83 a~~k~   87 (90)
T d2cqga1          83 PNSKQ   87 (90)
T ss_dssp             CCTTC
T ss_pred             CCCCC
Confidence            88644

>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=99.84  E-value=3.6e-21  Score=128.52  Aligned_cols=77  Identities=32%  Similarity=0.526  Sum_probs=70.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCC--ceEEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDG--YRLRVE   78 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g--~~i~v~   78 (277)
                      ..+++|||+|||+++++++|+++|++||+|..+.|+.   ++.++|||||+|.+.++|..|++.|||..+.|  ++|.|.
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            3567899999999999999999999999999999964   56788999999999999999999999999977  789999


Q ss_pred             Ec
Q 023765           79 LA   80 (277)
Q Consensus        79 ~a   80 (277)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>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=99.84  E-value=1.2e-20  Score=130.44  Aligned_cols=79  Identities=27%  Similarity=0.414  Sum_probs=71.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      +.++|||+|||+.+|+++|+++|++||+|.+|.|+.   ++.++|||||+|.+.++|..|++.+|+ .|.|+.|.|.++.
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~   87 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAY   87 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEEST
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcC
Confidence            346799999999999999999999999999999965   577899999999999999999998876 7999999999988


Q ss_pred             CCC
Q 023765           82 GGR   84 (277)
Q Consensus        82 ~~~   84 (277)
                      ...
T Consensus        88 ~~~   90 (103)
T d2cqda1          88 LGA   90 (103)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            654

>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=1.6e-21  Score=127.33  Aligned_cols=73  Identities=16%  Similarity=0.385  Sum_probs=68.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      ++|||+|||+++|+++|+++|++||+|..+.|+.   ++.++|||||+|.++++|++|++ +|+..|+|+.|.|..|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            5899999999999999999999999999999954   57889999999999999999998 7999999999999886

>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=99.84  E-value=3.4e-21  Score=128.68  Aligned_cols=75  Identities=24%  Similarity=0.443  Sum_probs=68.4

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CC---CCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PP---RPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         9 l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~---~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      |||+|||+++|+++|+++|++||+|..+.|+.   ++   .++|||||+|.+.++|..|+..|||..|.|+.|.|.++..
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            89999999999999999999999999999954   22   3478999999999999999999999999999999999864


Q ss_pred             C
Q 023765           83 G   83 (277)
Q Consensus        83 ~   83 (277)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.84  E-value=8.2e-21  Score=138.93  Aligned_cols=82  Identities=32%  Similarity=0.591  Sum_probs=74.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      ...++|||+|||+++|+++|+++|++||+|..|.|..   ++.++|||||+|.+.++|..|++.|||..|.|+.|.|.++
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            3457899999999999999999999999999999854   5678899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 023765           81 HGGRR   85 (277)
Q Consensus        81 ~~~~~   85 (277)
                      .....
T Consensus       120 ~~~~~  124 (139)
T d1u6fa1         120 ASGHQ  124 (139)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            86543

>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=99.84  E-value=4.4e-21  Score=131.90  Aligned_cols=77  Identities=26%  Similarity=0.435  Sum_probs=71.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      +.++|||+|||+++|+++|+++|+.||+|.+|.|+.   ++.++|||||+|.+.++|.+|+. |||..|.|+.|.|.++.
T Consensus        17 ~~~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          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            457899999999999999999999999999999965   57899999999999999999996 99999999999999976


Q ss_pred             C
Q 023765           82 G   82 (277)
Q Consensus        82 ~   82 (277)
                      .
T Consensus        96 ~   96 (101)
T d2cq4a1          96 A   96 (101)
T ss_dssp             H
T ss_pred             C
Confidence            4

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.84  E-value=5.1e-21  Score=127.93  Aligned_cols=78  Identities=22%  Similarity=0.309  Sum_probs=69.4

Q ss_pred             CCCeEEEcCCCCCCC-HHHHHHHhhccCCeeEEEeec----CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            5 SSRTLYVGNLPGDTR-MREVEDLFYKYGPIVDIDLKI----PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t-~~~l~~~F~~~G~v~~v~~~~----~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      +.++|||+|||+++| +++|+++|++||+|..|.|..    ++.++|||||+|.+.++|.+|++ ||+..|.|+.|.|.+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            578999999999986 566999999999999999843    56789999999999999999997 999999999999999


Q ss_pred             ccCC
Q 023765           80 AHGG   83 (277)
Q Consensus        80 a~~~   83 (277)
                      +.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8853

>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=99.84  E-value=1e-20  Score=129.00  Aligned_cols=77  Identities=21%  Similarity=0.394  Sum_probs=71.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      .++++|||+|||..+++++|+++|++||+|..|.|..+   +|||||+|.+.++|..|+..|||..|.|+.|.|.|++..
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~---kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~   92 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE---KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   92 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec---ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            34678999999999999999999999999999999854   899999999999999999999999999999999998753

>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=99.84  E-value=6e-21  Score=124.08  Aligned_cols=72  Identities=25%  Similarity=0.564  Sum_probs=66.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            8 TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         8 ~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .|||+|||+++|+++|.++|++||+|..+.|+.   ++.++|||||+|.++++|++|++ +++..|.|+.|.|..|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            589999999999999999999999999999954   57789999999999999999998 8999999999998654

>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=99.83  E-value=3.3e-21  Score=133.78  Aligned_cols=79  Identities=35%  Similarity=0.670  Sum_probs=73.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      +.++|||+|||+++|+++|+++|++||+|..|.|+.   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            457899999999999999999999999999999854   56778999999999999999999999999999999999987


Q ss_pred             CC
Q 023765           82 GG   83 (277)
Q Consensus        82 ~~   83 (277)
                      ..
T Consensus        87 ~~   88 (104)
T d1p1ta_          87 SE   88 (104)
T ss_dssp             CT
T ss_pred             CC
Confidence            53

>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=99.83  E-value=9.4e-21  Score=126.48  Aligned_cols=77  Identities=32%  Similarity=0.471  Sum_probs=71.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCCC
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGR   84 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~~   84 (277)
                      ..++|||+|||+++++++|+++|++||+|..|.|..+   ++||||+|.+.++|..|+..|||..|.|+.|.|.||....
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~---k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD---KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT---TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc---cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            3468999999999999999999999999999999743   7899999999999999999999999999999999998654

>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=99.83  E-value=4.8e-21  Score=134.80  Aligned_cols=78  Identities=27%  Similarity=0.303  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      +.+++|||+|||+.+++++|+++|++||+|..|.|..   .++||||+|.+.++|..|++.|||..|.|+.|.|.|+...
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~---~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~   84 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE---GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS---SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec---cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            5678999999999999999999999999999998863   4799999999999999999999999999999999998764


Q ss_pred             C
Q 023765           84 R   84 (277)
Q Consensus        84 ~   84 (277)
                      .
T Consensus        85 ~   85 (111)
T d1whxa_          85 V   85 (111)
T ss_dssp             T
T ss_pred             c
Confidence            4

>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=99.83  E-value=9.2e-21  Score=125.93  Aligned_cols=75  Identities=20%  Similarity=0.381  Sum_probs=69.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      .++|||+|||+++|+++|+++|++||+|..+.|+.   ++.++|||||+|.++++|.+|++ +++..|.|+.|.|..|.
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 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            46899999999999999999999999999999954   57889999999999999999998 79999999999998875

>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=99.83  E-value=8.1e-21  Score=126.24  Aligned_cols=75  Identities=23%  Similarity=0.451  Sum_probs=68.3

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeeEE-Eeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            9 LYVGNLPGDTRMREVEDLFYKYGPIVDI-DLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         9 l~V~nL~~~~t~~~l~~~F~~~G~v~~v-~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      |||+|||+++|+++|+++|++||.|..+ .++.   ++.++|||||+|.+.++|..|+..|||..|.|++|.|.+|.+.
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            8999999999999999999999998764 4533   5678999999999999999999999999999999999998854

>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=99.83  E-value=1.3e-20  Score=125.15  Aligned_cols=76  Identities=20%  Similarity=0.356  Sum_probs=69.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccC-CceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFD-GYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~-g~~i~v~~a~   81 (277)
                      -|+++|||+|||+++|+++|.++|++||+|..|.+...  .+|||||+|.+.++|..|+..|||..|. |+.|.|.||+
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN--RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT--TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc--cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            57889999999999999999999999999999999653  3689999999999999999999999884 6899999986

>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=99.83  E-value=1.4e-20  Score=125.91  Aligned_cols=77  Identities=31%  Similarity=0.403  Sum_probs=70.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCCC
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGR   84 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~~   84 (277)
                      ..++|||+|||+++|+++|.++|++||.|..+.+.   .++|||||+|.+.++|..|+..|||..|.|+.|.|.|+++..
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~---~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~   83 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK---KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD   83 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE---ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc---cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCC
Confidence            46899999999999999999999999999888775   358999999999999999999999999999999999988543

>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=99.83  E-value=1.3e-20  Score=129.93  Aligned_cols=78  Identities=19%  Similarity=0.384  Sum_probs=71.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      .++|||+|||+++|+++|+++|++||+|..+.|+.   ++.++|||||+|.+.++|.+|++ +++..|.|+.|.|.+|.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            36899999999999999999999999999999954   46789999999999999999997 899999999999999886


Q ss_pred             CC
Q 023765           83 GR   84 (277)
Q Consensus        83 ~~   84 (277)
                      ..
T Consensus        99 ke  100 (103)
T d1x4ba1          99 RE  100 (103)
T ss_dssp             CC
T ss_pred             cC
Confidence            43

>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=6.1e-21  Score=123.67  Aligned_cols=72  Identities=19%  Similarity=0.461  Sum_probs=66.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            8 TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         8 ~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      +|||+|||+++|+++|+++|++||+|.+|.|+.   ++.++|||||+|.+.++|++|++ +++..|.|+.|.|..|
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            599999999999999999999999999999965   57889999999999999999998 6778999999999865

>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=99.83  E-value=1.6e-20  Score=123.57  Aligned_cols=74  Identities=24%  Similarity=0.478  Sum_probs=68.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .++|||+|||+++|+++|+++|++||.|..+.+..   ++.++|||||+|.++++|.+|++ |||..|.|+.|.|..|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            47999999999999999999999999999999954   55778999999999999999997 8999999999999876

>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=99.83  E-value=2.2e-20  Score=130.88  Aligned_cols=77  Identities=21%  Similarity=0.296  Sum_probs=70.8

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCCC
Q 023765            6 SRTLYVGNLPG-DTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGGR   84 (277)
Q Consensus         6 ~~~l~V~nL~~-~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~~   84 (277)
                      +++|||+||++ .+|+++|+++|+.||+|..|.|+.+.  +|||||+|.++++|.+|++.|||..|.|+.|.|.++....
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~~~~   79 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK--KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   79 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT--SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc--cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            68999999966 59999999999999999999997653  7899999999999999999999999999999999987554

>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=99.83  E-value=2.2e-20  Score=125.47  Aligned_cols=77  Identities=19%  Similarity=0.277  Sum_probs=70.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCccc-CCceEEEEEccC
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNF-DGYRLRVELAHG   82 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~-~g~~i~v~~a~~   82 (277)
                      |+++|||+|||+++|+++|+++|+.||.|..+.+.. +..++||||+|.+.++|..|+..|||..| +|+.|.|.|++.
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~-~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~   86 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF-QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS   86 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC-SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee-ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCC
Confidence            688999999999999999999999999998877654 34588999999999999999999999988 589999999875

>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=99.82  E-value=4.5e-21  Score=132.78  Aligned_cols=81  Identities=23%  Similarity=0.385  Sum_probs=75.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .++++|||+|||+++++++|+++|++||.|..+.+..   ++.++|||||+|.+.++|..|++.|||..|.|+.|.|.|+
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            5789999999999999999999999999998887743   6788999999999999999999999999999999999999


Q ss_pred             cCCC
Q 023765           81 HGGR   84 (277)
Q Consensus        81 ~~~~   84 (277)
                      .+..
T Consensus        96 k~k~   99 (102)
T d2cpxa1          96 KNKK   99 (102)
T ss_dssp             CCCS
T ss_pred             CCcc
Confidence            8654

>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=99.82  E-value=3.8e-20  Score=127.13  Aligned_cols=80  Identities=21%  Similarity=0.449  Sum_probs=72.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcC------CcccCCce
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRD------GYNFDGYR   74 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~------~~~~~g~~   74 (277)
                      .+.++|||+|||+++|+++|+++|++||+|..+.+..   ++.++|||||+|.+.++|..|++.||      |..|.|+.
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~   85 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   85 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEE
Confidence            5678999999999999999999999999999999855   45678999999999999999999876      67789999


Q ss_pred             EEEEEccCC
Q 023765           75 LRVELAHGG   83 (277)
Q Consensus        75 i~v~~a~~~   83 (277)
                      |.|.++.++
T Consensus        86 l~v~~a~~k   94 (98)
T d1x4ha1          86 LKVDLAVTR   94 (98)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEECCCC
Confidence            999998864

>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=99.82  E-value=2.2e-20  Score=124.36  Aligned_cols=77  Identities=16%  Similarity=0.412  Sum_probs=70.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      .+++|||+|||+++|+++|.++|+.||+|..|.|..  ++.++|||||+|.++++|.+|++ +++..|.|+.|.|.+...
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~d   83 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKDD   83 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcCC
Confidence            468999999999999999999999999999999954  56778999999999999999997 899999999999998653

>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=99.82  E-value=2.1e-20  Score=121.31  Aligned_cols=73  Identities=26%  Similarity=0.340  Sum_probs=67.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec-CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI-PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~-~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      ++|||+|||+++++++|+++|+.||+|..|.|.. .+...+||||+|.++++|.+|+. ||+..|+|+.|.|..+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            5899999999999999999999999999999955 34557899999999999999996 8999999999999875

>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=99.82  E-value=1.8e-20  Score=128.08  Aligned_cols=76  Identities=32%  Similarity=0.581  Sum_probs=69.5

Q ss_pred             CCCCeEEEcCCC-CCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            4 RSSRTLYVGNLP-GDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         4 ~~~~~l~V~nL~-~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      ..+++|||+||| ..+++++|+++|++||+|..|.|.     +|||||+|.+.++|.+|++.|||..|.|+.|.|.++..
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~-----rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~   87 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-----KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAE   87 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE-----TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTS
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe-----CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            356789999997 568899999999999999999995     79999999999999999999999999999999999975


Q ss_pred             CC
Q 023765           83 GR   84 (277)
Q Consensus        83 ~~   84 (277)
                      ..
T Consensus        88 ~~   89 (98)
T d1wf2a_          88 PK   89 (98)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.82  E-value=2e-20  Score=121.94  Aligned_cols=72  Identities=22%  Similarity=0.376  Sum_probs=67.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            8 TLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         8 ~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .|||+|||+++|+++|+++|++||.|..+.+..   ++.+++||||+|.++++|.+|++ |||..|.|+.|.|.+|
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            499999999999999999999999999998844   56789999999999999999997 9999999999999876

>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=99.82  E-value=5.7e-21  Score=131.68  Aligned_cols=79  Identities=18%  Similarity=0.279  Sum_probs=71.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      ..+.++|||+|||+++|+++|+++|++||+|..+.+..  ++.++|||||+|.+.++|.+|+..|||..|.|+++.|.++
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            35678999999999999999999999999999998854  4567899999999999999999999999999999888765


Q ss_pred             c
Q 023765           81 H   81 (277)
Q Consensus        81 ~   81 (277)
                      +
T Consensus        95 ~   95 (101)
T d1x5oa1          95 E   95 (101)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.82  E-value=4e-20  Score=123.95  Aligned_cols=78  Identities=31%  Similarity=0.409  Sum_probs=67.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      +-.+++|||+|||++++++||+++|++|| +..+.+.   ..++||||+|.+.++|.+|+..||+..|.|+.|.|+++..
T Consensus         2 ~s~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~---~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~   77 (88)
T d1wg1a_           2 SSGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD---RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEE---GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeee---ccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            34688999999999999999999999999 3333332   3479999999999999999999999999999999999875


Q ss_pred             CC
Q 023765           83 GR   84 (277)
Q Consensus        83 ~~   84 (277)
                      ..
T Consensus        78 ~~   79 (88)
T d1wg1a_          78 DA   79 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.82  E-value=1.5e-20  Score=129.95  Aligned_cols=81  Identities=26%  Similarity=0.450  Sum_probs=71.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEE--------eec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDID--------LKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDG   72 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~--------~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g   72 (277)
                      .++++|||+|||+.+|+++|.++|++||+|..+.        +..   ++.++|||||+|.+.++|..|+..|||..|.|
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            4678999999999999999999999999986433        222   46778999999999999999999999999999


Q ss_pred             ceEEEEEccCCC
Q 023765           73 YRLRVELAHGGR   84 (277)
Q Consensus        73 ~~i~v~~a~~~~   84 (277)
                      +.|.|.++....
T Consensus        86 r~i~V~~a~~~~   97 (101)
T d2cpea1          86 SKLKVSLARKKP   97 (101)
T ss_dssp             EECEEECSSCCC
T ss_pred             EEEEEEEcCCCC
Confidence            999999998644

>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=99.82  E-value=6.7e-20  Score=123.06  Aligned_cols=81  Identities=21%  Similarity=0.254  Sum_probs=73.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhc--CCcccCCceEEEE
Q 023765            1 MSSRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGR--DGYNFDGYRLRVE   78 (277)
Q Consensus         1 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l--~~~~~~g~~i~v~   78 (277)
                      |.+.|+++|||+|||+++|+++|+++|++||.|..+.+...   ++||||+|.+.++|..|++.|  ++..+.|++|.|.
T Consensus         3 ~~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~---~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~   79 (88)
T d2cq1a1           3 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG---KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   79 (88)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc---ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEE
Confidence            45679999999999999999999999999999999999743   689999999999999999855  6789999999999


Q ss_pred             EccCCC
Q 023765           79 LAHGGR   84 (277)
Q Consensus        79 ~a~~~~   84 (277)
                      |++...
T Consensus        80 ~sk~~~   85 (88)
T d2cq1a1          80 YSNHKE   85 (88)
T ss_dssp             ECSCSS
T ss_pred             ECCCCC
Confidence            998644

>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=99.81  E-value=2e-20  Score=125.50  Aligned_cols=78  Identities=23%  Similarity=0.411  Sum_probs=70.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765            3 SRSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      +..+++|||+|||+++|+++|+++|++||+|.+|.+..  .+++||||+|.+.++|+.|+.  ++..|.|+.|.|.++.+
T Consensus         2 s~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~--~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~   77 (88)
T d1wf0a_           2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK--PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEP   77 (88)
T ss_dssp             CSCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS--SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee--ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCC
Confidence            56899999999999999999999999999999998753  458999999999999999986  78899999999999976


Q ss_pred             CC
Q 023765           83 GR   84 (277)
Q Consensus        83 ~~   84 (277)
                      +.
T Consensus        78 k~   79 (88)
T d1wf0a_          78 KH   79 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.81  E-value=1e-20  Score=124.59  Aligned_cols=75  Identities=24%  Similarity=0.390  Sum_probs=67.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCc-ccCCceEEEEEccCCC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY-NFDGYRLRVELAHGGR   84 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~-~~~g~~i~v~~a~~~~   84 (277)
                      ++|||+|||+++|+++|+++|++||.|..+.+..   .+|||||+|.+.++|..|++.|||. .|.|+.|.|.++.+..
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~---~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~   77 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL---KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK   77 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE---ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec---ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcC
Confidence            4799999999999999999999999988766653   3799999999999999999999996 6999999999998654

>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=99.81  E-value=3.6e-20  Score=121.68  Aligned_cols=75  Identities=25%  Similarity=0.461  Sum_probs=69.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      +.+++|||+||+  +|+++|+++|++||+|..+.+..   .++||||+|.+.++|..|+..|||..|.|+.|.|.|+.+.
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~---~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDP---PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEET---TTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeecc---CCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            467899999995  99999999999999999999974   3789999999999999999999999999999999999753

>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=99.81  E-value=1e-20  Score=129.16  Aligned_cols=79  Identities=24%  Similarity=0.350  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      +++++|||+|||+++|+++|+++|++||.|..+.  .++.+++||||+|.+.++|..|+..||+..|.|+.|.|.|+.+.
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~--~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k   91 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVS--QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK   91 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE--ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee--ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCC
Confidence            5678999999999999999999999999987764  35667899999999999999999999999999999999999875


Q ss_pred             C
Q 023765           84 R   84 (277)
Q Consensus        84 ~   84 (277)
                      .
T Consensus        92 ~   92 (96)
T d1fjca_          92 G   92 (96)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.81  E-value=9.8e-21  Score=126.81  Aligned_cols=73  Identities=19%  Similarity=0.236  Sum_probs=67.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      ++|||+|||+++|+++|+++|++||+|..+.+..    .|||||+|.+.++|.+|+..|||..|.|+.|.|.++...
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~----~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR----DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT----TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc----cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            5799999999999999999999999999999864    489999999999999999999999999999998887643

>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=99.81  E-value=7.7e-20  Score=126.83  Aligned_cols=80  Identities=26%  Similarity=0.480  Sum_probs=70.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec----CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEE
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI----PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVEL   79 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~----~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~   79 (277)
                      .+.++|||+|||+++|+++|+++|+.|| |..+.++.    ++.++|||||+|.+.++|++|++ ||+..|.|+.|.|.+
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            4678999999999999999999999999 66766643    45678999999999999988876 999999999999999


Q ss_pred             ccCCCC
Q 023765           80 AHGGRR   85 (277)
Q Consensus        80 a~~~~~   85 (277)
                      +.....
T Consensus        91 a~~~~~   96 (104)
T d1wi8a_          91 ADQAQD   96 (104)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            886543

>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=99.81  E-value=3.8e-21  Score=129.77  Aligned_cols=78  Identities=19%  Similarity=0.339  Sum_probs=71.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      ....+|||+|||+++|+++|+++|++||.|..+.|+.  ++.++|||||+|.+.++|.+|++ |||..|.|+.|.|.+++
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak   89 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   89 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecC
Confidence            3456899999999999999999999999998887743  67889999999999999999997 99999999999999987


Q ss_pred             C
Q 023765           82 G   82 (277)
Q Consensus        82 ~   82 (277)
                      .
T Consensus        90 ~   90 (91)
T d1fjeb1          90 G   90 (91)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.81  E-value=8.1e-20  Score=124.85  Aligned_cols=78  Identities=28%  Similarity=0.531  Sum_probs=71.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCC--ceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDG--YRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g--~~i~v~~a~   81 (277)
                      .|+++|||+|||+++|+++|+++|++||+|..+.+..   .++||||+|.+.++|..|++.||+..|.|  ..|.|.|++
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~---~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak   91 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK---GDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAK   91 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECS---SSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeec---cccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCC
Confidence            5789999999999999999999999999999999864   37899999999999999999999999987  479999998


Q ss_pred             CCC
Q 023765           82 GGR   84 (277)
Q Consensus        82 ~~~   84 (277)
                      ..+
T Consensus        92 ~~~   94 (97)
T d1whya_          92 SGP   94 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.80  E-value=1.4e-19  Score=123.45  Aligned_cols=80  Identities=23%  Similarity=0.320  Sum_probs=70.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCC-eeEEEeec----CCCCCcEEEEEEcChHHHHHHHHhcCC--cccCCceEEEE
Q 023765            6 SRTLYVGNLPGDTRMREVEDLFYKYGP-IVDIDLKI----PPRPPGYAFLEFEDYRDAEDAIRGRDG--YNFDGYRLRVE   78 (277)
Q Consensus         6 ~~~l~V~nL~~~~t~~~l~~~F~~~G~-v~~v~~~~----~~~~~g~afV~f~~~~~a~~a~~~l~~--~~~~g~~i~v~   78 (277)
                      ++.|||+|||+.+|+++|+++|+.||+ |..+.|+.    ++.++|||||+|.+.++|..|++.|++  ..+.|+.|.|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            468999999999999999999999996 99999854    357889999999999999999999865  45579999999


Q ss_pred             EccCCCC
Q 023765           79 LAHGGRR   85 (277)
Q Consensus        79 ~a~~~~~   85 (277)
                      ||.+...
T Consensus        81 ~A~p~~~   87 (96)
T d2disa1          81 WAEPEID   87 (96)
T ss_dssp             ESCSSCS
T ss_pred             EcCCCCC
Confidence            9986543

>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=99.80  E-value=1.1e-19  Score=124.07  Aligned_cols=77  Identities=21%  Similarity=0.261  Sum_probs=71.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      ++.++|||+|||+.+++++|+++|++||+|..+.|..    +|||||+|.++++|..||+.|||..|.|+.|.|.++...
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~----~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~   88 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK----DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVY   88 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET----TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc----cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecC
Confidence            5677899999999999999999999999999999873    689999999999999999999999999999999998754


Q ss_pred             C
Q 023765           84 R   84 (277)
Q Consensus        84 ~   84 (277)
                      .
T Consensus        89 ~   89 (98)
T d1wg4a_          89 P   89 (98)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.79  E-value=2.8e-19  Score=115.94  Aligned_cols=71  Identities=27%  Similarity=0.356  Sum_probs=64.4

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccCC
Q 023765            9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHGG   83 (277)
Q Consensus         9 l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~~   83 (277)
                      |||+|||+++++++|+++|++|| +..+.+.   ..+|||||+|.+.++|.+|+..|||..|.|+.|.|+++...
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-LKYCFVD---KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE---TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec---ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 5555553   45899999999999999999999999999999999998753

>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=99.79  E-value=7.7e-19  Score=121.50  Aligned_cols=78  Identities=17%  Similarity=0.162  Sum_probs=71.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhc--CCcccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGR--DGYNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l--~~~~~~g~~i~v~~a~   81 (277)
                      .++++|||+|||+.+|+++|.++|++||.|..+.|..   .+++|||+|.++++|..|+..|  ++..+.|++|.|.|+.
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~---~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~   89 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP---FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYST   89 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET---TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEe---cceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcC
Confidence            5789999999999999999999999999999999974   4789999999999999999877  5677899999999998


Q ss_pred             CCC
Q 023765           82 GGR   84 (277)
Q Consensus        82 ~~~   84 (277)
                      ...
T Consensus        90 ~~~   92 (104)
T d1wexa_          90 SKR   92 (104)
T ss_dssp             SSS
T ss_pred             CCc
Confidence            654

>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=99.79  E-value=7.5e-20  Score=122.83  Aligned_cols=74  Identities=23%  Similarity=0.331  Sum_probs=66.2

Q ss_pred             CCCeEEEcCCCCCCCHHHH---HHHhhccCCeeEEEeecC------CCCCcEEEEEEcChHHHHHHHHhcCCcccCCceE
Q 023765            5 SSRTLYVGNLPGDTRMREV---EDLFYKYGPIVDIDLKIP------PRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRL   75 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l---~~~F~~~G~v~~v~~~~~------~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i   75 (277)
                      ..++|||+|||+++++++|   .++|++||+|..|.++.+      +...|||||+|.+.++|..|++.|||..|+|+.|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            4578999999999999999   678999999999999653      2345899999999999999999999999999999


Q ss_pred             EEE
Q 023765           76 RVE   78 (277)
Q Consensus        76 ~v~   78 (277)
                      .|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            873

>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=99.77  E-value=8.4e-20  Score=117.82  Aligned_cols=67  Identities=22%  Similarity=0.391  Sum_probs=62.8

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceE
Q 023765            9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRL   75 (277)
Q Consensus         9 l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i   75 (277)
                      |||+|||+++|+++|+++|++||.|..+.+..   ++.++|||||+|.+.++|..|++.|||..|.|+.|
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~   70 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA   70 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEC
Confidence            89999999999999999999999999998854   56789999999999999999999999999999876

>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=99.77  E-value=9.5e-19  Score=121.08  Aligned_cols=80  Identities=15%  Similarity=0.166  Sum_probs=70.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEee---cCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLK---IPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~---~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      .+..+|||+|||+++|+++|+++|..||.|..+.++   .++.++|||||+|.++++|.+|++ ||+..|.|+.|.|.++
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEEC
Confidence            355689999999999999999999999988875442   256788999999999999999997 9999999999999998


Q ss_pred             cCCC
Q 023765           81 HGGR   84 (277)
Q Consensus        81 ~~~~   84 (277)
                      ....
T Consensus        92 ~~~~   95 (104)
T d1wg5a_          92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            8654

>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=99.77  E-value=3.5e-19  Score=124.20  Aligned_cols=80  Identities=21%  Similarity=0.249  Sum_probs=71.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCccc--CCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNF--DGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~--~g~~i~v~~a~   81 (277)
                      .+..+|||+|||+.+|+++|+++|++||.|..|.+... ..+|||||+|.++++|..|+..|||..|  .|..|.|.+++
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~-~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~   83 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK   83 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEE-TTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECS
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEee-CCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecC
Confidence            56778999999999999999999999999999998654 3479999999999999999999999988  57889999987


Q ss_pred             CCC
Q 023765           82 GGR   84 (277)
Q Consensus        82 ~~~   84 (277)
                      ...
T Consensus        84 ~~~   86 (108)
T d2adba1          84 LTS   86 (108)
T ss_dssp             SCS
T ss_pred             Ccc
Confidence            654

>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=99.77  E-value=8.6e-19  Score=120.78  Aligned_cols=80  Identities=19%  Similarity=0.114  Sum_probs=71.4

Q ss_pred             CCCCCeEEEcCCCCCC-CH----HHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEE
Q 023765            3 SRSSRTLYVGNLPGDT-RM----REVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRV   77 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~~-t~----~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v   77 (277)
                      +..+++|||+||+.++ ++    ++|.++|++||.|..+.+..   +++||||+|.+.++|..|+..|||..|.|+.|.|
T Consensus         2 ~~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k---~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v   78 (104)
T d1weya_           2 SSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK---SFKRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CSCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET---TTTEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CCCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec---CCCEEEEEECCHHHHHHHHHHhcccccCCCEeEE
Confidence            4578999999999986 33    56999999999999999974   4789999999999999999999999999999999


Q ss_pred             EEccCCCC
Q 023765           78 ELAHGGRR   85 (277)
Q Consensus        78 ~~a~~~~~   85 (277)
                      .|++....
T Consensus        79 ~~a~~~~~   86 (104)
T d1weya_          79 YFAQTLHI   86 (104)
T ss_dssp             ECCCCSSC
T ss_pred             eecccCCC
Confidence            99976543

>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=99.77  E-value=8e-19  Score=117.24  Aligned_cols=76  Identities=24%  Similarity=0.382  Sum_probs=67.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeE-EEe--ecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVD-IDL--KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~-v~~--~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      ..++|||+|||+++++++|+++|+.||.|.. +.+  ..++.++|+|||+|.++++|.+|+..||+..|.|++|.|.++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            3456999999999999999999999998865 344  336788999999999999999999999999999999999875

>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=99.76  E-value=8.4e-19  Score=120.86  Aligned_cols=79  Identities=20%  Similarity=0.304  Sum_probs=69.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      .+.++|||+|||+++|+++|+++|..||.+ .|.++.  ++..+|||||+|.++++|.+|++ ||+..|.|+.|.|.++.
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~~~-~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~   90 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccCcc-eeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcC
Confidence            456799999999999999999999999855 455533  56778999999999999999997 89999999999999988


Q ss_pred             CCC
Q 023765           82 GGR   84 (277)
Q Consensus        82 ~~~   84 (277)
                      ...
T Consensus        91 ~~~   93 (102)
T d1weza_          91 TAG   93 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            644

>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=99.76  E-value=1.2e-18  Score=116.65  Aligned_cols=78  Identities=18%  Similarity=0.147  Sum_probs=70.4

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhc--CCcccCCceEEEEE
Q 023765            3 SRSSRTLYVGNLPGD-TRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGR--DGYNFDGYRLRVEL   79 (277)
Q Consensus         3 ~~~~~~l~V~nL~~~-~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l--~~~~~~g~~i~v~~   79 (277)
                      ..++++|||+|||.. +|++||.++|++||+|..|.+...   +++|||+|.+.++|..|++.|  ++..+.|++|.|.|
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~---k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~   81 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK---INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHL   81 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS---SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc---ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEE
Confidence            468999999999986 889999999999999999999753   679999999999999999865  67889999999999


Q ss_pred             ccCC
Q 023765           80 AHGG   83 (277)
Q Consensus        80 a~~~   83 (277)
                      ++..
T Consensus        82 s~~~   85 (89)
T d1x4da1          82 SQKY   85 (89)
T ss_dssp             ECCC
T ss_pred             CCCc
Confidence            9753

>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=99.75  E-value=1.3e-18  Score=119.11  Aligned_cols=77  Identities=26%  Similarity=0.297  Sum_probs=69.7

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHH--hcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGD-TRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIR--GRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~-~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~--~l~~~~~~g~~i~v~~a   80 (277)
                      .++++|||+|||.+ +|+++|.++|+.||.|..+.+..+   ++||||+|.+.++|..|++  .+++..|.|+.|.|.++
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~---k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s   92 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM---KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLS   92 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT---TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec---CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEc
Confidence            46789999999985 899999999999999999999743   7999999999999999997  57889999999999999


Q ss_pred             cCC
Q 023765           81 HGG   83 (277)
Q Consensus        81 ~~~   83 (277)
                      +..
T Consensus        93 ~~~   95 (99)
T d1x4fa1          93 EKY   95 (99)
T ss_dssp             CSC
T ss_pred             CCc
Confidence            754

>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=99.75  E-value=9.8e-19  Score=120.90  Aligned_cols=77  Identities=14%  Similarity=0.125  Sum_probs=68.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeE-EEee--cCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVD-IDLK--IPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~-v~~~--~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      ...+|||+|||+++|+++|.++|..||.|.. +.+.  .++.++|||||+|.++++|..|+. ||+..|.|+.|.|.++.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            4678999999999999999999999998876 4443  367889999999999999999997 99999999999999875


Q ss_pred             C
Q 023765           82 G   82 (277)
Q Consensus        82 ~   82 (277)
                      .
T Consensus        86 ~   86 (103)
T d2cpya1          86 L   86 (103)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=99.73  E-value=8.8e-20  Score=123.05  Aligned_cols=76  Identities=28%  Similarity=0.433  Sum_probs=67.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEee--------cCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEE
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLK--------IPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVE   78 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~--------~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~   78 (277)
                      ++|||+|||+.+|+++|+++|++||.|..+.+.        .++.++|||||+|.++++|..|++ |||..|.|+.|.|.
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            689999999999999999999999988776663        234678999999999999999996 99999999999997


Q ss_pred             EccCC
Q 023765           79 LAHGG   83 (277)
Q Consensus        79 ~a~~~   83 (277)
                      .++..
T Consensus        81 r~k~~   85 (90)
T d1u2fa_          81 RPHDY   85 (90)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            65543

>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=99.73  E-value=1.3e-18  Score=116.27  Aligned_cols=67  Identities=57%  Similarity=1.053  Sum_probs=61.4

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceee
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRS  179 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  179 (277)
                      ++|||+|||+.+++++|+++|.+||.|..+.+..+   +||||+|.+.++|++||..|||..+.|+.+..
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~---g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v   67 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGET   67 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT---SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCC
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc---ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEE
Confidence            47999999999999999999999999999998765   69999999999999999999999999965543

>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=99.72  E-value=1.6e-18  Score=121.47  Aligned_cols=78  Identities=21%  Similarity=0.263  Sum_probs=68.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEe---ecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDL---KIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~---~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      ...++|||+|||+++|+++|+++|+.||.|..+.+   ..++.++|||||+|.+.++|.+|++ ||+..|+|+.|.|..+
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEc
Confidence            46779999999999999999999999998865333   3467889999999999999999997 9999999999999887


Q ss_pred             cC
Q 023765           81 HG   82 (277)
Q Consensus        81 ~~   82 (277)
                      ..
T Consensus        95 ~~   96 (112)
T d1wela1          95 TK   96 (112)
T ss_dssp             CH
T ss_pred             Ch
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=99.70  E-value=5.3e-17  Score=107.22  Aligned_cols=76  Identities=25%  Similarity=0.310  Sum_probs=68.2

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      +++|||+|||+.+++++|.++|.+||.|..+.+..++.+    +||||+|.+.++|+.|+..|||..+.|    ..|.|.
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g----~~l~v~   77 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRN----KRLKVS   77 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETT----EECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECC----EEEEEE
Confidence            468999999999999999999999999999999887654    499999999999999999999999999    577777


Q ss_pred             ecCC
Q 023765          185 EYDS  188 (277)
Q Consensus       185 ~~~~  188 (277)
                      .+++
T Consensus        78 ~a~p   81 (82)
T d1b7fa1          78 YARP   81 (82)
T ss_dssp             ECCC
T ss_pred             EcCC
Confidence            6643

>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=99.69  E-value=1.1e-16  Score=105.87  Aligned_cols=69  Identities=19%  Similarity=0.230  Sum_probs=63.4

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                      .+.++|||+|||..+++++|+++|.+||.|..+.++.+..+    +||||+|.+.++|+.|+..|||..++|+
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr   79 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR   79 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCE
Confidence            34679999999999999999999999999999999887653    4999999999999999999999999994

>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=99.69  E-value=3.8e-17  Score=111.83  Aligned_cols=66  Identities=17%  Similarity=0.245  Sum_probs=60.5

Q ss_pred             CCCCCCeEEEcC--CCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCccc
Q 023765            2 SSRSSRTLYVGN--LPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNF   70 (277)
Q Consensus         2 ~~~~~~~l~V~n--L~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~   70 (277)
                      ++.++++|+|.|  ||+++|+++|+++|++||.|..|.+...   ++||||+|.+.++|..|+..|||..+
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~---k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN---KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT---CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC---ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            457899999955  9999999999999999999999998743   78999999999999999999999877

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=5.6e-17  Score=108.70  Aligned_cols=77  Identities=22%  Similarity=0.312  Sum_probs=69.6

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC--cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG--MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~--~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      ..+|||+|||+.+++++|+++|.+||.|..+.++.+..+  +||||+|.+.++|+.|++.|||..++|    ..|.|..+
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g----~~i~V~~a   83 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLND----RKVFVGRF   83 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETT----EEEEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECC----EEEEEEEC
Confidence            458999999999999999999999999999999877653  699999999999999999999999999    67888877


Q ss_pred             CCC
Q 023765          187 DSR  189 (277)
Q Consensus       187 ~~~  189 (277)
                      .++
T Consensus        84 ~~~   86 (89)
T d1cvja2          84 KSR   86 (89)
T ss_dssp             CCT
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=99.69  E-value=1.8e-16  Score=104.60  Aligned_cols=75  Identities=19%  Similarity=0.314  Sum_probs=67.0

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      .++|||+|||..+++++|.++|.+||.|..+.+..+...    +||||+|.+.++|+.|+..|||..+.|    ..|.|.
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g----~~l~v~   77 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQT----KTIKVS   77 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT----EECEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECC----EEEEEE
Confidence            357999999999999999999999999999999877544    499999999999999999999999999    567776


Q ss_pred             ecC
Q 023765          185 EYD  187 (277)
Q Consensus       185 ~~~  187 (277)
                      .++
T Consensus        78 ~Ak   80 (82)
T d1fxla1          78 YAR   80 (82)
T ss_dssp             ECC
T ss_pred             Eee
Confidence            654

>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=99.68  E-value=2.4e-16  Score=107.76  Aligned_cols=78  Identities=17%  Similarity=0.124  Sum_probs=69.3

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ..++|||+|||+.+++++|+++|.+||.|..+.++.+..+    +||||+|.+.++|+.||..|||..+.|    ..|.|
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~g----r~i~V   82 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQG----RMLHV   82 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSS----CEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECC----EEEEE
Confidence            3678999999999999999999999999999999876543    599999999999999999999999999    57777


Q ss_pred             eecCCC
Q 023765          184 REYDSR  189 (277)
Q Consensus       184 ~~~~~~  189 (277)
                      ..+..+
T Consensus        83 ~~a~~~   88 (99)
T d1whwa_          83 LPSTIK   88 (99)
T ss_dssp             EECCCC
T ss_pred             EECCCC
Confidence            776654

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=2.9e-16  Score=105.93  Aligned_cols=76  Identities=16%  Similarity=0.171  Sum_probs=68.4

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ..++|||+|||..+++++|.++|.+||+|..|.++.+..+    |||||+|.+.++|..|+..|||..++|    ..|.|
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g----r~i~V   81 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDD----RIIRT   81 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETT----EECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECC----EEEEE
Confidence            4679999999999999999999999999999999987655    499999999999999999999999999    56666


Q ss_pred             eecC
Q 023765          184 REYD  187 (277)
Q Consensus       184 ~~~~  187 (277)
                      ..+.
T Consensus        82 ~~a~   85 (93)
T d1h2vz_          82 DWDA   85 (93)
T ss_dssp             EEES
T ss_pred             EEcC
Confidence            6654

>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=99.68  E-value=3e-16  Score=105.29  Aligned_cols=77  Identities=10%  Similarity=0.088  Sum_probs=69.1

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC--cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG--MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~--~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      ..+|||+|||..+++++|.++|.+||.|..|.+..+..+  +||||+|.+.++|..|+..|||..+.|    ..|.+..+
T Consensus         8 ~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g----~~i~v~~a   83 (90)
T d2cqia1           8 PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILG----KEVKVNWA   83 (90)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETT----EEEEEEEC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECC----EEEEEEEc
Confidence            569999999999999999999999999999999876544  599999999999999999999999999    67778776


Q ss_pred             CCC
Q 023765          187 DSR  189 (277)
Q Consensus       187 ~~~  189 (277)
                      .+.
T Consensus        84 ~~~   86 (90)
T d2cqia1          84 TTP   86 (90)
T ss_dssp             CCT
T ss_pred             CCC
Confidence            543

>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=99.68  E-value=3e-16  Score=105.91  Aligned_cols=78  Identities=19%  Similarity=0.264  Sum_probs=70.2

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC--cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG--MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~--~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      ...+|||+|||+.+++++|.++|.+||+|..|.++.+..+  +||||+|.+.++|..|+..|||..++|    ..|.|..
T Consensus        10 ~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g----~~l~V~~   85 (93)
T d2cq3a1          10 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEG----RKIEVNN   85 (93)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETT----EECEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECC----EEEEEEe
Confidence            3668999999999999999999999999999999877553  699999999999999999999999999    6778887


Q ss_pred             cCCC
Q 023765          186 YDSR  189 (277)
Q Consensus       186 ~~~~  189 (277)
                      +.++
T Consensus        86 A~~r   89 (93)
T d2cq3a1          86 ATAR   89 (93)
T ss_dssp             CCSS
T ss_pred             cCcC
Confidence            7654

>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=99.68  E-value=3.8e-16  Score=107.23  Aligned_cols=78  Identities=22%  Similarity=0.276  Sum_probs=69.8

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      +.++|||+|||..+++++|.++|.+||.|..+.++.+..+    |||||+|.+.++|+.||..|||..+.|    ..|.|
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g----~~i~V   92 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGM----KRLKV   92 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETT----EECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECC----EEEEE
Confidence            4678999999999999999999999999999998887654    499999999999999999999999999    67778


Q ss_pred             eecCCC
Q 023765          184 REYDSR  189 (277)
Q Consensus       184 ~~~~~~  189 (277)
                      ....++
T Consensus        93 ~~a~~k   98 (102)
T d2cpza1          93 QLKRSK   98 (102)
T ss_dssp             ECCCCS
T ss_pred             EEeCCC
Confidence            776554

>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=99.68  E-value=2.5e-16  Score=105.20  Aligned_cols=76  Identities=16%  Similarity=0.196  Sum_probs=67.4

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      .+.+|||+|||..+++++|.++|.+||.|..+.+..+..+    +||||+|.+.++|+.|+..|||..+.|    ..|.|
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   81 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG----QTIQV   81 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETT----EECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECC----EEEEE
Confidence            3679999999999999999999999999999999987653    499999999999999999999999999    56666


Q ss_pred             eecC
Q 023765          184 REYD  187 (277)
Q Consensus       184 ~~~~  187 (277)
                      +.+.
T Consensus        82 ~~a~   85 (88)
T d1rk8a_          82 DWCF   85 (88)
T ss_dssp             EESE
T ss_pred             EEec
Confidence            6543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=2.2e-16  Score=103.57  Aligned_cols=72  Identities=18%  Similarity=0.160  Sum_probs=65.6

Q ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       111 ~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      .|||+|||+.+++++|.++|.+||+|..+.++.++.+    +||||+|.+.++|..|++.|||..+.|    ..|+|..+
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~g----r~i~v~~a   77 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKG----KPVRIMWS   77 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETT----EECEEEEC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECC----EEEEEEEe
Confidence            6999999999999999999999999999999987654    599999999999999999999999999    56666654

>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=99.67  E-value=3.8e-16  Score=105.92  Aligned_cols=80  Identities=21%  Similarity=0.278  Sum_probs=69.6

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC-CCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR-GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~-~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ...+.++|||+|||+.+++++|+++|.+||.|..+.+..+. ..+||||+|.+.++|+.||+.|||..+.|    ..|.|
T Consensus        10 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g----~~l~V   85 (95)
T d1x4aa1          10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDG----YRLRV   85 (95)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETT----EECEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECC----EEEEE
Confidence            34456789999999999999999999999999999887654 34699999999999999999999999999    67777


Q ss_pred             eecCC
Q 023765          184 REYDS  188 (277)
Q Consensus       184 ~~~~~  188 (277)
                      ..++.
T Consensus        86 ~~a~~   90 (95)
T d1x4aa1          86 EFPRS   90 (95)
T ss_dssp             ECCCC
T ss_pred             EeccC
Confidence            76654

>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=99.67  E-value=2.3e-16  Score=106.51  Aligned_cols=78  Identities=28%  Similarity=0.345  Sum_probs=68.9

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ...+|||+|||..+++++|+++|.+||.|..+.++.+..+    +||||+|.+.++|+.|+..|||..+.|    ..|.|
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g----~~l~V   83 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYG----KPIRV   83 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSS----CBCEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECC----EEEEE
Confidence            3579999999999999999999999999999999876543    599999999999999999999999999    56677


Q ss_pred             eecCCC
Q 023765          184 REYDSR  189 (277)
Q Consensus       184 ~~~~~~  189 (277)
                      ..+.++
T Consensus        84 ~~A~~~   89 (93)
T d1x5ua1          84 NKASAH   89 (93)
T ss_dssp             EETTTT
T ss_pred             EEcCCC
Confidence            766544

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

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

Probab=99.67  E-value=2.3e-16  Score=105.92  Aligned_cols=78  Identities=15%  Similarity=0.199  Sum_probs=69.8

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ...+|||+|||..+++++|.++|.+||.|..+.+..+..+    |||||+|.+.++|..|++.|||..+.|    ..|.|
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   82 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDH----LILNV   82 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETT----EECEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECC----EEEEE
Confidence            4678999999999999999999999999999999987654    499999999999999999999999999    67777


Q ss_pred             eecCCC
Q 023765          184 REYDSR  189 (277)
Q Consensus       184 ~~~~~~  189 (277)
                      ..++++
T Consensus        83 ~~akp~   88 (90)
T d2cq0a1          83 EWAKPS   88 (90)
T ss_dssp             EESSCC
T ss_pred             EeeeCC
Confidence            776543

>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=99.67  E-value=2.3e-16  Score=102.82  Aligned_cols=72  Identities=19%  Similarity=0.249  Sum_probs=64.1

Q ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC---cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG---MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       111 ~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      +|||+|||+.+++++|.++|.+||.|..+.+..+..+   +||||+|.+.++|+.|+..|||..+.|    ..|.|...
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g----~~l~V~~a   76 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDG----RPMNIQLV   76 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETT----EECEEEEE
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECC----EEEEEEEe
Confidence            6999999999999999999999999999999876543   599999999999999999999999999    45555443

>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=99.66  E-value=3.5e-16  Score=109.91  Aligned_cols=77  Identities=21%  Similarity=0.204  Sum_probs=67.7

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC-CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG-GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~-~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      ..+.+|||+|||..+++++|.++|.+||.|..|.+..+.. .|||||+|.+.++|..|++.|||..+.|    ..|.|..
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~g----r~l~V~~   80 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCN----RYLVVLY   80 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETT----EECEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECC----EEEEEEE
Confidence            3467999999999999999999999999999999886643 4799999999999999999999999999    5566655


Q ss_pred             cC
Q 023765          186 YD  187 (277)
Q Consensus       186 ~~  187 (277)
                      ..
T Consensus        81 a~   82 (114)
T d2f9da1          81 YN   82 (114)
T ss_dssp             CC
T ss_pred             cC
Confidence            43

>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=99.66  E-value=3.4e-16  Score=103.81  Aligned_cols=68  Identities=21%  Similarity=0.342  Sum_probs=62.7

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccc
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAF  176 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  176 (277)
                      +++|||+|||..+++++|+++|++||+|..+.++.++.+    +||||+|.+.++|..|++.|||..+.|..
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~   77 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGAT   77 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCC
Confidence            568999999999999999999999999999999987643    49999999999999999999999999854

>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=99.66  E-value=4.7e-16  Score=105.44  Aligned_cols=74  Identities=15%  Similarity=0.190  Sum_probs=67.1

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeecCC
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDS  188 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~~  188 (277)
                      .++|||+|||..+++++|.++|.+||.|..|.+..+  .+||||+|.+.++|..|+..|||..+.|    ..|+|...+.
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~--kg~afV~f~~~~~A~~Ai~~l~~~~i~g----~~l~v~~ak~   91 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE--KGYSFVRFSTHESAAHAIVSVNGTTIEG----HVVKCYWGKE   91 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT--TTEEEEEESSHHHHHHHHHHHTTCEETT----EECEEECCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec--ceEEEEEECCHHHHHHHHHHhCCCEECC----EEEEEEEcCC
Confidence            568999999999999999999999999999999866  4699999999999999999999999999    6677776543

>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=99.66  E-value=3e-16  Score=106.80  Aligned_cols=74  Identities=57%  Similarity=1.003  Sum_probs=65.5

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeE
Q 023765          104 VSRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSY  180 (277)
Q Consensus       104 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  180 (277)
                      +......+|||+|||..+++++|+++|.+||+|..+.+..+   +||||+|.+.++|+.||+.|||..+.|+.+.+.
T Consensus        10 ~~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~~---g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~   83 (98)
T d1wg4a_          10 PTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD---GMGMVEYLRKEDMEYALRKLDDTKFRSHEGETS   83 (98)
T ss_dssp             CCCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEETT---TEEEEEESSHHHHHHHHHHHSSEEEECTTSCEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhhccccccccccc---ceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            33455778999999999999999999999999999998754   699999999999999999999999999766543

>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=99.65  E-value=3.4e-16  Score=104.62  Aligned_cols=76  Identities=20%  Similarity=0.247  Sum_probs=67.0

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeec-ccceeeEEEEeec
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFR-NAFSRSYVRVREY  186 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~-g~~~~~~i~~~~~  186 (277)
                      +..+|||+|||..+++++|.++|.+||.|..+.+..+...+||||+|.+.++|.+|+..|||..+. |    ..|+|...
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 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGEN----HHLRVSFS   84 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSS----CBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCC----CEEEEEeC
Confidence            467999999999999999999999999999888887777789999999999999999999999884 6    45666554


Q ss_pred             C
Q 023765          187 D  187 (277)
Q Consensus       187 ~  187 (277)
                      +
T Consensus        85 k   85 (88)
T d2adca2          85 K   85 (88)
T ss_dssp             S
T ss_pred             C
Confidence            3

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=2.4e-16  Score=105.54  Aligned_cols=77  Identities=21%  Similarity=0.182  Sum_probs=69.2

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      ..+|||+|||..+++++|.++|.+||+|..+.++.+..    .|||||+|.+.++|+.|+..|||..++|    ..|.|.
T Consensus         5 ~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g----~~l~v~   80 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG----RTIRVN   80 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETT----EEEEEE
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECC----EEEEEE
Confidence            56999999999999999999999999999999987654    3599999999999999999999999999    677887


Q ss_pred             ecCCC
Q 023765          185 EYDSR  189 (277)
Q Consensus       185 ~~~~~  189 (277)
                      .+.+.
T Consensus        81 ~a~p~   85 (89)
T d2cqba1          81 LAKPM   85 (89)
T ss_dssp             ECCCC
T ss_pred             EeCCC
Confidence            77654

>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=99.64  E-value=2.8e-15  Score=109.02  Aligned_cols=79  Identities=20%  Similarity=0.216  Sum_probs=70.2

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      ...++|||+|||.++++++|.++|.+||.|..|.|+.+..+    |||||+|.+.++|..||+.|||..|+|    ..|.
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~g----r~l~  115 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN----KRLK  115 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSS----CEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECC----EEEE
Confidence            34568999999999999999999999999999999987654    499999999999999999999999999    5777


Q ss_pred             EeecCCC
Q 023765          183 VREYDSR  189 (277)
Q Consensus       183 ~~~~~~~  189 (277)
                      |..+..+
T Consensus       116 V~~a~~~  122 (139)
T d1u6fa1         116 VALAASG  122 (139)
T ss_dssp             EEESSCC
T ss_pred             EEEcCCC
Confidence            8776543

>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=99.64  E-value=6.2e-16  Score=105.23  Aligned_cols=75  Identities=13%  Similarity=0.160  Sum_probs=65.5

Q ss_pred             CCCceEEEeCCC-CCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          107 RSDYRVLVTGLP-SSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       107 ~~~~~l~v~~l~-~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      ....+|||+||+ ..+++++|+++|.+||.|..+.+.+    +||||+|++.++|++||..|||..+.|    ..|.|+.
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~r----g~aFV~f~~~~~A~~Ai~~lng~~~~g----~~l~V~~   84 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK----GFAFVQYVNERNARAAVAGEDGRMIAG----QVLDINL   84 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEET----EEEEEEESSHHHHHHHHHTTTTCEETT----EECEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEeC----CeEEEEECCHHHHHHHHHHcCCCEECC----EEEEEEE
Confidence            445789999997 5688999999999999999999954    499999999999999999999999999    6777777


Q ss_pred             cCCC
Q 023765          186 YDSR  189 (277)
Q Consensus       186 ~~~~  189 (277)
                      ....
T Consensus        85 a~~~   88 (98)
T d1wf2a_          85 AAEP   88 (98)
T ss_dssp             TTSC
T ss_pred             CCCC
Confidence            6543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=4.1e-16  Score=103.39  Aligned_cols=75  Identities=15%  Similarity=0.234  Sum_probs=66.7

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      .+|||+|||..+++++|.++|.+||+|..+.++.++.    .+||||+|.+.++|..|+..|||..+.|    ..|.|..
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g----~~l~V~~   77 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD----KKLLVQR   77 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSS----SCCEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECC----EEEEEEE
Confidence            4799999999999999999999999999999988754    3699999999999999999999999999    4566666


Q ss_pred             cCC
Q 023765          186 YDS  188 (277)
Q Consensus       186 ~~~  188 (277)
                      ...
T Consensus        78 A~~   80 (85)
T d2u2fa_          78 ASV   80 (85)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.64  E-value=5.9e-16  Score=104.62  Aligned_cols=78  Identities=18%  Similarity=0.285  Sum_probs=67.6

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC-----CCcEEEEEEechhHHHHHHHhc-CCCeecccceeeE
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR-----GGMTGIVDYTSYDDMKYAIRKL-DRSEFRNAFSRSY  180 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~-----~~~~~fv~f~~~~~a~~a~~~l-~g~~~~g~~~~~~  180 (277)
                      ....+|||+|||..+++++|.++|.+||.|..|.++.+.     ..|||||+|.+.++|..|+..| ||..+.|    ..
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~G----r~   81 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYG----RR   81 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSS----CB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECC----EE
Confidence            346789999999999999999999999999999997653     2469999999999999999998 8999999    56


Q ss_pred             EEEeecCC
Q 023765          181 VRVREYDS  188 (277)
Q Consensus       181 i~~~~~~~  188 (277)
                      |.|+.++.
T Consensus        82 l~V~~A~~   89 (94)
T d2cpha1          82 LVLEWADS   89 (94)
T ss_dssp             CEEEECCC
T ss_pred             EEEEEcCC
Confidence            66666654

>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=99.64  E-value=1e-15  Score=101.56  Aligned_cols=72  Identities=17%  Similarity=0.292  Sum_probs=64.3

Q ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC-------cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG-------MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       112 l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~-------~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      |||+|||..+++++|+++|.+||.|..+.+..+..+       |||||+|.+.++|..|+..|||..++|    ..|.|.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g----~~i~V~   76 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDG----HKLEVR   76 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETT----EECEEE
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECC----EEEEEE
Confidence            799999999999999999999999999998876432       489999999999999999999999999    567776


Q ss_pred             ecC
Q 023765          185 EYD  187 (277)
Q Consensus       185 ~~~  187 (277)
                      .++
T Consensus        77 ~a~   79 (85)
T d2cpfa1          77 ISE   79 (85)
T ss_dssp             CSS
T ss_pred             ECC
Confidence            653

>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=99.64  E-value=4.7e-16  Score=118.76  Aligned_cols=78  Identities=23%  Similarity=0.445  Sum_probs=71.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeec---CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            4 RSSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI---PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         4 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~---~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      ...++|||+|||+.+|+++|+++|+.||.|..+.+..   ++.++|||||+|.+.++|.+|+. +++..|.|+.|.|.+|
T Consensus        95 ~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A  173 (183)
T d1u1qa_          95 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA  173 (183)
T ss_dssp             CCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEEC
T ss_pred             cccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEec
Confidence            4678999999999999999999999999999998854   46778999999999999999998 7899999999999998


Q ss_pred             cC
Q 023765           81 HG   82 (277)
Q Consensus        81 ~~   82 (277)
                      .+
T Consensus       174 ~~  175 (183)
T d1u1qa_         174 LS  175 (183)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.63  E-value=5.6e-16  Score=101.88  Aligned_cols=74  Identities=18%  Similarity=0.291  Sum_probs=63.1

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEec----CCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEee
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD----RGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVRE  185 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~----~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~  185 (277)
                      ++|||+|||+.+++++|.++|.+||.|..+.+..+    ...+||||+|.+.++|.+|+..|||..+.|    ..|.|..
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g----~~i~V~~   77 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEG----YTLVTKV   77 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETT----EECEEEE
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECC----EEEEEEE
Confidence            58999999999999999999999999987766533    334699999999999999999999999999    5666665


Q ss_pred             cC
Q 023765          186 YD  187 (277)
Q Consensus       186 ~~  187 (277)
                      .+
T Consensus        78 a~   79 (81)
T d2ghpa1          78 SN   79 (81)
T ss_dssp             CC
T ss_pred             cc
Confidence            54

>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=99.62  E-value=5.5e-16  Score=108.41  Aligned_cols=72  Identities=18%  Similarity=0.182  Sum_probs=63.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcCh-HHHHHHHHhcCCcccCCceEEEEEcc
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDY-RDAEDAIRGRDGYNFDGYRLRVELAH   81 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~-~~a~~a~~~l~~~~~~g~~i~v~~a~   81 (277)
                      -.+||+|||+.+|+++|+++|++||+|..|.|+.   .++||||.|.+. ++|..|+..||+..+.+..+.|.++.
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~---~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR---GAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCT---TCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEec---CCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            3569999999999999999999999999999984   489999999996 68899999999998888877777654

>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=99.62  E-value=2.7e-15  Score=99.46  Aligned_cols=67  Identities=21%  Similarity=0.311  Sum_probs=61.8

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                      .++|||+|||..+++++|.++|++||.|..+.++.++.+    +||||+|.+.++|..|++.|||..+.|.
T Consensus         6 ~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   76 (85)
T d1b7fa2           6 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGG   76 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCC
Confidence            568999999999999999999999999999999987654    4999999999999999999999999873

>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=99.62  E-value=1.9e-15  Score=97.47  Aligned_cols=70  Identities=19%  Similarity=0.216  Sum_probs=62.3

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC--cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG--MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~--~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      ++|||+|||+.+++++|+++|..||.|..+.+..+..+  +||||+|.+.++|.+|+. +|+..++|+    .|.|.
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~----~i~V~   72 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQN----EIIVS   72 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTE----ECEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEECCE----EEEEE
Confidence            47999999999999999999999999999999877654  499999999999999995 899999994    55554

>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=99.62  E-value=2.5e-17  Score=113.30  Aligned_cols=72  Identities=18%  Similarity=0.263  Sum_probs=65.4

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeeEEEeec--CCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765            9 LYVGNLPGDTRMREVEDLFYKYGPIVDIDLKI--PPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus         9 l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      ++|.+++.++++++|.++|++||+|..|.|+.  ++.++|||||+|.+.++|.+|+..|||..|+|+.|.|+++
T Consensus        30 ~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          30 VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             HHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            56667777888999999999999999999954  5688999999999999999999999999999999999985

>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=99.61  E-value=3.7e-15  Score=99.57  Aligned_cols=76  Identities=24%  Similarity=0.336  Sum_probs=65.5

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      ...+|||+|||+.+++++|.++|.+||.|..|.++.++.+    |||||+|.+.++|++||+.++  .++|    ..|.+
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~~--~l~G----r~i~v   80 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH--MIDG----RWCDC   80 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCE--EETT----EEEEE
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcCC--ccCC----EEeEE
Confidence            3678999999999999999999999999999999987654    499999999999999998544  7888    56777


Q ss_pred             eecCCC
Q 023765          184 REYDSR  189 (277)
Q Consensus       184 ~~~~~~  189 (277)
                      ..+.++
T Consensus        81 ~~a~~k   86 (90)
T d2cqga1          81 KLPNSK   86 (90)
T ss_dssp             ECCCTT
T ss_pred             EeCCCC
Confidence            666544

>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=99.61  E-value=1.8e-15  Score=99.82  Aligned_cols=76  Identities=12%  Similarity=0.076  Sum_probs=64.8

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      +++.+|||+|||..+++++|.++|.+||.|..+.+..+. .+||||+|.+.++|..|+..|||..+.+.   ..|.+..+
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-~g~afV~f~~~~~A~~A~~~l~g~~~~~~---~~i~v~~a   81 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-HDIAFVEFTTELQSNAAKEALQGFKITPT---HAMKITFA   81 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-CSCEEEEESSHHHHHHHHHHHTTCBSSTT---CBCEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-ceeEEEecCCHHHHHHHHHHhCCcEeCCC---cEEEEEEe
Confidence            346799999999999999999999999999999987654 46999999999999999999999998542   34555544

>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=99.61  E-value=3.3e-15  Score=98.60  Aligned_cols=67  Identities=18%  Similarity=0.305  Sum_probs=61.1

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccc
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAF  176 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  176 (277)
                      ..+|||+|||.++++++|.++|.+||.|..+.+..+..+    |||||+|.+.++|++|++ +++..+.|+.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~   76 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRV   76 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEE
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEE
Confidence            568999999999999999999999999999999987654    599999999999999997 6899999943

>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=99.61  E-value=6.4e-16  Score=107.35  Aligned_cols=78  Identities=18%  Similarity=0.200  Sum_probs=68.1

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeecC
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYD  187 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~  187 (277)
                      +..+|||+|||+.+++++|.++|.+||.|..+.+..++..+||||+|.+.++|+.|+..|||..+.+..  ..|.+....
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~--~~l~v~~s~   83 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNAC--CTLRIDFSK   83 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTC--CCCEEEECS
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCC--cEEEEEecC
Confidence            467899999999999999999999999999999998888889999999999999999999999996533  345555443

>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=99.61  E-value=1.3e-15  Score=102.28  Aligned_cols=75  Identities=23%  Similarity=0.338  Sum_probs=65.4

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      ..+|||+|||+.+++++|+++|.+||.|..+.+..+..    .|||||+|.+.++|+.|+..|||..+.|+    .|.|.
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~----~l~V~   80 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGR----QIRVD   80 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSC----CCEEE
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCE----EEEEE
Confidence            56899999999999999999999999999998876543    35999999999999999999999999994    55555


Q ss_pred             ecC
Q 023765          185 EYD  187 (277)
Q Consensus       185 ~~~  187 (277)
                      .+.
T Consensus        81 ~a~   83 (90)
T d1x5sa1          81 QAG   83 (90)
T ss_dssp             EEE
T ss_pred             EcC
Confidence            543

>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=99.61  E-value=7.9e-16  Score=107.60  Aligned_cols=68  Identities=24%  Similarity=0.356  Sum_probs=61.5

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccce
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFS  177 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  177 (277)
                      ..++|||+|||+.+++++|+++|.+||+|..|.|..  ..+||||+|.+.++|..|+..|||..+.|+.+
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~--~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l   76 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE--GGITAIVEFLEPLEARKAFRHLAYSKFHHVPL   76 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS--SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBC
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec--cCceEEEEEcCHHHHHHHHHHHcCCccCCCeE
Confidence            467999999999999999999999999999988753  45799999999999999999999999999533

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=8.6e-16  Score=100.56  Aligned_cols=75  Identities=19%  Similarity=0.188  Sum_probs=65.2

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCC-eecccceeeEEEEeecCC
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRS-EFRNAFSRSYVRVREYDS  188 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~-~~~g~~~~~~i~~~~~~~  188 (277)
                      ++|||+|||..+++++|+++|.+||.|..+.+...  .+||||+|.+.++|..|++.|||. .+.|    ..|.|..+.+
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--SGYAFVDYPDQNWAIRAIETLSGKVELHG----KIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE--TTEEEECCSCHHHHHHHHHHHTTTCEETT----EECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc--cceEEEEECCHHHHHHHHHHhCCCeEECC----EEEEEEEcCC
Confidence            57999999999999999999999999887666654  359999999999999999999996 5898    6778877765


Q ss_pred             CC
Q 023765          189 RR  190 (277)
Q Consensus       189 ~r  190 (277)
                      +.
T Consensus        76 k~   77 (80)
T d2cqha1          76 KK   77 (80)
T ss_dssp             CC
T ss_pred             cC
Confidence            53

>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=99.60  E-value=1.5e-15  Score=98.07  Aligned_cols=65  Identities=17%  Similarity=0.251  Sum_probs=59.2

Q ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccc
Q 023765          111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAF  176 (277)
Q Consensus       111 ~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  176 (277)
                      +|||+|||+.+++++|.++|.+||.|..+.+..++.    .+||||+|.+.++|++|++ +++..++|+.
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~   69 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKV   69 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCE
Confidence            489999999999999999999999999999988654    3599999999999999997 7999999953

>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=99.60  E-value=1.7e-15  Score=102.76  Aligned_cols=80  Identities=13%  Similarity=0.172  Sum_probs=68.6

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      ....+|||+|||..+++++|.++|.+||.|..+.. .....+||||+|.+.++|+.|+..|||..+.|    ..|.|...
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g----r~i~V~~a   88 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG----RSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-TTEEEEEEEEEESSHHHHHHHHHHTTEEEETT----EEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-cCccccEEEEEeCCHHHHHHHHHHcCCCEECC----EEEEEEEe
Confidence            44789999999999999999999999998876643 23344699999999999999999999999999    78888887


Q ss_pred             CCCCc
Q 023765          187 DSRRS  191 (277)
Q Consensus       187 ~~~r~  191 (277)
                      .+++.
T Consensus        89 ~~k~~   93 (96)
T d1fjca_          89 GEKGG   93 (96)
T ss_dssp             SSSCC
T ss_pred             CCCCC
Confidence            76643

>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=99.60  E-value=1.8e-15  Score=99.84  Aligned_cols=74  Identities=16%  Similarity=0.229  Sum_probs=63.6

Q ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEE-EEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          112 VLVTGLPSSASWQDLKDHMRRAGDVCFS-QVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       112 l~v~~l~~~~~~~~l~~~f~~~g~v~~~-~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      |||+|||.++++++|.++|.+||.|..+ .++.+..    .+||||+|.+.++|..|++.|||..+.|    ..|.+..+
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~g----r~l~v~~a   76 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCN----RPITVSYA   76 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETT----EECEEEES
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECC----EEEEEEEe
Confidence            7999999999999999999999998664 5665543    3699999999999999999999999999    56777766


Q ss_pred             CCC
Q 023765          187 DSR  189 (277)
Q Consensus       187 ~~~  189 (277)
                      .++
T Consensus        77 ~~k   79 (83)
T d1x5ta1          77 FKK   79 (83)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            544

>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=99.60  E-value=8.7e-16  Score=105.01  Aligned_cols=74  Identities=19%  Similarity=0.245  Sum_probs=65.7

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      ..+|||+|||..+++++|+++|..||+|..|.++.+..+    |||||+|.+.++|.+|+. |||..+.|    ..|.|.
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~   92 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLG----VPIIVQ   92 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETT----EEEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECC----EEEEEE
Confidence            468999999999999999999999999999999987543    599999999999999995 99999999    567776


Q ss_pred             ecC
Q 023765          185 EYD  187 (277)
Q Consensus       185 ~~~  187 (277)
                      ...
T Consensus        93 ~a~   95 (101)
T d2cq4a1          93 ASQ   95 (101)
T ss_dssp             EHH
T ss_pred             ECC
Confidence            543

>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=99.60  E-value=6.7e-15  Score=101.07  Aligned_cols=75  Identities=19%  Similarity=0.162  Sum_probs=65.3

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      .++|||+|||..+++++|.++|.+||.|..|.++.+..    .+||||+|.+.++|+.|++.+|+ .+.|    ..|.|.
T Consensus        10 ~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~G----r~l~V~   84 (103)
T d2cqda1          10 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDG----RKANVN   84 (103)
T ss_dssp             SSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETT----EECEEE
T ss_pred             CcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCC----EEEEEE
Confidence            46799999999999999999999999999999987654    36999999999999999998876 6888    566776


Q ss_pred             ecCC
Q 023765          185 EYDS  188 (277)
Q Consensus       185 ~~~~  188 (277)
                      .+..
T Consensus        85 ~a~~   88 (103)
T d2cqda1          85 LAYL   88 (103)
T ss_dssp             ESTT
T ss_pred             EcCC
Confidence            6543

>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=99.60  E-value=1.7e-15  Score=100.50  Aligned_cols=74  Identities=19%  Similarity=0.241  Sum_probs=65.8

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeecCC
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDS  188 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~~  188 (277)
                      .++|||+|||..+++++|.++|.+||+|..|.+..+  .+||||+|.+.++|..|+..|||..+.|    ..|.|..+..
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--KGFGFIRLETRTLAEIAKVELDNMPLRG----KQLRVRFACH   81 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT--TTEEEEECSSSHHHHHHHHHHTTCCBTT----BCCEEEESSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc--cceEEEEECCHHHHHHHHHHhCCCEECC----EEEEEEECCC
Confidence            468999999999999999999999999999998865  4599999999999999999999999999    5666665543

>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=99.60  E-value=9e-16  Score=102.96  Aligned_cols=78  Identities=15%  Similarity=0.193  Sum_probs=66.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEe---cCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFR---DRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~---~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      +....+|||+|||..+++++|+++|.+||.|..+.++.   +...+||||+|.+.++|++||+ |||..+.|    ..|.
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g----~~i~   84 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFG----NEIK   84 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETT----EEEE
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECC----EEEE
Confidence            34567999999999999999999999999887766543   4455799999999999999996 99999999    6788


Q ss_pred             EeecCC
Q 023765          183 VREYDS  188 (277)
Q Consensus       183 ~~~~~~  188 (277)
                      |+.++.
T Consensus        85 V~~ak~   90 (91)
T d1fjeb1          85 LEKPKG   90 (91)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            876643

>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=99.59  E-value=1.1e-15  Score=99.17  Aligned_cols=68  Identities=18%  Similarity=0.257  Sum_probs=61.1

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeeccccee
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  178 (277)
                      ++|||+|||.++++++|+++|.+||.|..+.++.++.+    |||||+|.+.++|++|+. +++..++|+.+.
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~   72 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTID   72 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEE
Confidence            47999999999999999999999999999999877643    599999999999999997 799999996443

>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=99.59  E-value=8e-15  Score=97.37  Aligned_cols=76  Identities=16%  Similarity=0.096  Sum_probs=66.9

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeecC
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYD  187 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~  187 (277)
                      ...+|||+|||..+++++|.++|.+||.|..+.+...  .+||||+|.+.++|..|+..|||..+.|    ..|.|..+.
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~--rg~afV~f~~~~~A~~Ai~~l~~~~i~g----~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--RDYAFVHFSNREDAVEAMKALNGKVLDG----SPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--SSEEEEEESSHHHHHHHHHHHSSEEETT----EEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEccc--cEEEEEEeCCHHHHHHHHHHcCCCEECC----EEEEEEecc
Confidence            3578999999999999999999999999888777554  4699999999999999999999999999    678887765


Q ss_pred             CC
Q 023765          188 SR  189 (277)
Q Consensus       188 ~~  189 (277)
                      +.
T Consensus        81 P~   82 (86)
T d2cpda1          81 PV   82 (86)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.59  E-value=2.4e-15  Score=103.68  Aligned_cols=76  Identities=28%  Similarity=0.356  Sum_probs=67.3

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      ..+|||+|||..+++++|.++|++||+|..|.++.+..+    |||||+|.+.++|+.|+..|||..+.|    ..|.|.
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g----~~i~V~   83 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSG----RALRVD   83 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSS----SCBEEE
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECC----EEEEEE
Confidence            458999999999999999999999999999999887654    499999999999999999999999999    456666


Q ss_pred             ecCC
Q 023765          185 EYDS  188 (277)
Q Consensus       185 ~~~~  188 (277)
                      .+..
T Consensus        84 ~a~~   87 (104)
T d1p1ta_          84 NAAS   87 (104)
T ss_dssp             ETTC
T ss_pred             ECCC
Confidence            6543

>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=99.59  E-value=2.1e-15  Score=102.65  Aligned_cols=81  Identities=26%  Similarity=0.364  Sum_probs=69.6

Q ss_pred             CCCCCeEEEcCC--CCCCC---------HHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccC
Q 023765            3 SRSSRTLYVGNL--PGDTR---------MREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFD   71 (277)
Q Consensus         3 ~~~~~~l~V~nL--~~~~t---------~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~   71 (277)
                      .+.+++|+|.||  |.++.         .++|++.|++||.|..|.+.. +.++|+|||+|.++++|..|+..|||..|.
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~-~~~~G~~fV~f~~~e~A~~A~~~lng~~~~   83 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFD-RHPDGVASVSFRDPEEADYCIQTLDGRWFG   83 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEET-TCTTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccC-CCCccEEEEEECCHHHHHHHHHHhCCcEEC
Confidence            367899999999  55432         367899999999999998864 356899999999999999999999999999


Q ss_pred             CceEEEEEccCCC
Q 023765           72 GYRLRVELAHGGR   84 (277)
Q Consensus        72 g~~i~v~~a~~~~   84 (277)
                      |+.|.|.++.+..
T Consensus        84 gr~i~v~~~~g~~   96 (99)
T d2dita1          84 GRQITAQAWDGTT   96 (99)
T ss_dssp             TEECEEEECCSCC
T ss_pred             CEEEEEEEeCCcC
Confidence            9999999987543

>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=99.59  E-value=6.9e-16  Score=103.13  Aligned_cols=67  Identities=15%  Similarity=0.175  Sum_probs=61.0

Q ss_pred             CceEEEeCCCCCCCHHHH---HHHHHhcCCeeEEEEEecCCC-------cEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          109 DYRVLVTGLPSSASWQDL---KDHMRRAGDVCFSQVFRDRGG-------MTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l---~~~f~~~g~v~~~~~~~~~~~-------~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                      .++|||+|||+.+++++|   .++|.+||+|..|.+..++.+       +||||+|.+.++|..|++.|||..+.|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr   84 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   84 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCE
Confidence            568999999999999999   778999999999999876532       5999999999999999999999999994

>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=99.59  E-value=2.2e-15  Score=104.89  Aligned_cols=74  Identities=16%  Similarity=0.198  Sum_probs=65.2

Q ss_pred             CceEEEeCCCC-CCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeecC
Q 023765          109 DYRVLVTGLPS-SASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYD  187 (277)
Q Consensus       109 ~~~l~v~~l~~-~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~  187 (277)
                      ..+|||+||++ .+++++|.++|..||.|..|.|+.+. .+||||+|.+.++|..|++.|||..+.|+    .|.+...+
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-KENALVQMADGNQAQLAMSHLNGHKLHGK----PIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-SCCEEEEESCHHHHHHHHHHHTTCBCSSS----BCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-cceEEEEECCHHHHHHHHHHhCCCEECCE----EEEEEECC
Confidence            57999999965 59999999999999999999998875 46999999999999999999999999994    55666543

>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=99.59  E-value=4e-15  Score=101.11  Aligned_cols=78  Identities=21%  Similarity=0.210  Sum_probs=67.2

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeec
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREY  186 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~  186 (277)
                      .+..+|||+|||+++++++|+++|.+||.|..+.+..+  .+||||+|.+.++|+.|++.||+..+.|...  .|.++..
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~--~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~--~l~v~~a   90 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG--DSFAYIQYESLDAAQAACAKMRGFPLGGPDR--RLRVDFA   90 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS--SCCEEEEESSHHHHHHHHHHHTTCBCSSSSC--BCEEEEC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc--ccEEEeccCCHHHHHHHHHHhCCCEeCCCce--EEEEEeC
Confidence            34689999999999999999999999999999988765  3599999999999999999999999988433  4666665


Q ss_pred             CC
Q 023765          187 DS  188 (277)
Q Consensus       187 ~~  188 (277)
                      +.
T Consensus        91 k~   92 (97)
T d1whya_          91 KS   92 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.58  E-value=8.6e-15  Score=95.61  Aligned_cols=67  Identities=15%  Similarity=0.264  Sum_probs=60.5

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccc
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAF  176 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  176 (277)
                      ..+|||+|||+.+++++|+++|.+||.|..+.+..+..+    +||||+|.+.++|.+|+. +||..++|+.
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~   72 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHN   72 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEE
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEE
Confidence            468999999999999999999999999999999887654    499999999999999985 8999999943

>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=99.58  E-value=2e-15  Score=97.67  Aligned_cols=67  Identities=21%  Similarity=0.298  Sum_probs=59.8

Q ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeeccccee
Q 023765          111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       111 ~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  178 (277)
                      +|||+|||+++++++|.++|.+||.|..+.+..++.+    +||||+|.+.++|++|++ +||..++|+.+.
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~   71 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVE   71 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCE
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEE
Confidence            4899999999999999999999999999988766543    599999999999999996 999999995443

>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=99.58  E-value=3.6e-15  Score=97.32  Aligned_cols=72  Identities=13%  Similarity=0.128  Sum_probs=63.4

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeecC
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYD  187 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~  187 (277)
                      .+++|||+|++  +++++|+++|++||.|..+.+..+  .+||||+|.+.++|..|+..|||..+.|    ..|.|...+
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~--~~~afV~f~~~~~A~~Ai~~lng~~~~g----~~l~V~~a~   75 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP--RNCAFVTYEKMESADQAVAELNGTQVES----VQLKVNIAR   75 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT--TTEEEEECSSHHHHHHHHHHHTTCBCSS----CBCEEEECC
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC--CCEEEEEEcccHHHHHHHHHhCCCEECC----EEEEEEEec
Confidence            36799999985  899999999999999999988754  4599999999999999999999999999    566666654

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=7.2e-15  Score=100.66  Aligned_cols=76  Identities=17%  Similarity=0.241  Sum_probs=66.7

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      ..+|||+|||+++++++|+++|.+||.|..+.|..+..    .+||||+|.+.++|++|++ +++..|.|    ..|.|.
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G----~~i~V~   94 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDG----RVVEPK   94 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETT----EEEEEE
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECC----EEEEEE
Confidence            46899999999999999999999999999999988754    3699999999999999995 89999998    577776


Q ss_pred             ecCCC
Q 023765          185 EYDSR  189 (277)
Q Consensus       185 ~~~~~  189 (277)
                      .+.++
T Consensus        95 ~a~~k   99 (103)
T d1x4ba1          95 RAVAR   99 (103)
T ss_dssp             CCSSC
T ss_pred             ECccc
Confidence            65543

>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=99.57  E-value=3e-15  Score=97.60  Aligned_cols=73  Identities=16%  Similarity=0.214  Sum_probs=62.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCce-EEEEEccC
Q 023765            5 SSRTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYR-LRVELAHG   82 (277)
Q Consensus         5 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~-i~v~~a~~   82 (277)
                      +.+.|+|++||++++++. ..+|++||+|.++.+.   ..++||||+|.++++|.+|+. |||..|.|+. |.|..+..
T Consensus         3 ~~~wV~V~G~p~~~~~~i-l~~F~~~G~I~~~~~~---~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYI-LLQFAQYGNILKHVMS---NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GGGEEEEECCCGGGHHHH-HHHHHTTSCEEEEEEC---SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             cccEEEEECCChHHHHHH-HHHHHhhhhhheEEec---CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            457899999999998654 4689999999999885   347999999999999999997 9999999985 56887764

>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=99.57  E-value=8.3e-15  Score=100.27  Aligned_cols=70  Identities=19%  Similarity=0.319  Sum_probs=63.1

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC---cEEEEEEechhHHHHHHHhcCCCeecccce
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG---MTGIVDYTSYDDMKYAIRKLDRSEFRNAFS  177 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  177 (277)
                      ..++|||+|||..+++++|.++|.+||.|..+.+..+..+   +||||+|.+.++|.+|++.|||..+.|+.+
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~   89 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPG   89 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCC
Confidence            3578999999999999999999999999999988876543   599999999999999999999999999654

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=4.2e-15  Score=99.00  Aligned_cols=73  Identities=22%  Similarity=0.336  Sum_probs=61.5

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeecCC
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYDS  188 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~~  188 (277)
                      ..+|||+|||+++++++|+++|.+|| +..+.+  +...+||||+|.+.++|++|+..||+..+.|    ..|.|+..+.
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--DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRG----KDLIVQLQPT   77 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE--EGGGTEEEECCSCHHHHHHHHHHHTTEEETT----EEEEEEECCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeee--eccCCceEEEECCHHHHHHHHHHhCCCEECC----EEEEEEEcCC
Confidence            56899999999999999999999999 222333  2334699999999999999999999999999    6777776643

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

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

Probab=99.57  E-value=1.6e-14  Score=99.52  Aligned_cols=79  Identities=18%  Similarity=0.325  Sum_probs=64.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC-----CCcEEEEEEechhHHHHHHHhcCCCeecccceeeE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR-----GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSY  180 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~-----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  180 (277)
                      ..+..+|||+|||..+++++|+++|.+|| +..+.++.+.     ..+||||+|.+.++|++|+ .||+..+.|    ..
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~g----r~   85 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGN----KR   85 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETT----EE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECC----EE
Confidence            44568999999999999999999999999 6666665443     2359999999999998776 599999999    57


Q ss_pred             EEEeecCCCC
Q 023765          181 VRVREYDSRR  190 (277)
Q Consensus       181 i~~~~~~~~r  190 (277)
                      |.|..+....
T Consensus        86 l~V~~a~~~~   95 (104)
T d1wi8a_          86 IRVDVADQAQ   95 (104)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEECCCCC
Confidence            7777765543

>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=99.57  E-value=2.6e-15  Score=96.66  Aligned_cols=66  Identities=11%  Similarity=0.140  Sum_probs=58.7

Q ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC----cEEEEEEechhHHHHHHHhcCCCeecccce
Q 023765          111 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG----MTGIVDYTSYDDMKYAIRKLDRSEFRNAFS  177 (277)
Q Consensus       111 ~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  177 (277)
                      +|||+|||+.+++++|+++|.+||.|..|.++.++.+    |||||+|.+.++|++||+ +++..++|+.+
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i   70 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKC   70 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEe
Confidence            5899999999999999999999999999999877543    599999999999999996 57778888543

>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=99.56  E-value=1.3e-15  Score=97.67  Aligned_cols=65  Identities=22%  Similarity=0.306  Sum_probs=59.8

Q ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeecccc
Q 023765          112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNAF  176 (277)
Q Consensus       112 l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  176 (277)
                      |||+|||..+++++|.++|.+||.|..+.+..++.    .++|||+|.+.++|+.|+..|||..+.|+.
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~   69 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQM   69 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEES
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            79999999999999999999999999998887654    359999999999999999999999999853

>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=99.56  E-value=5.4e-15  Score=98.10  Aligned_cols=75  Identities=13%  Similarity=0.202  Sum_probs=63.7

Q ss_pred             CceEEEeCCCCCCC-HHHHHHHHHhcCCeeEEEEEecC-----CCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          109 DYRVLVTGLPSSAS-WQDLKDHMRRAGDVCFSQVFRDR-----GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       109 ~~~l~v~~l~~~~~-~~~l~~~f~~~g~v~~~~~~~~~-----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      ..+|||+|||..++ +++|+++|++||.|..|.+..+.     ..|||||+|.+.++|++|++ |||..++|    ..|.
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~g----r~l~   78 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGN----REIS   78 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETT----EEEE
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECC----EEEE
Confidence            57999999999876 56699999999999999986532     34599999999999999995 99999999    6777


Q ss_pred             EeecCC
Q 023765          183 VREYDS  188 (277)
Q Consensus       183 ~~~~~~  188 (277)
                      |..+++
T Consensus        79 V~~a~~   84 (86)
T d2ghpa3          79 VSLADK   84 (86)
T ss_dssp             EEECCC
T ss_pred             EEEcCC
Confidence            776654

>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=99.55  E-value=1.4e-14  Score=93.31  Aligned_cols=69  Identities=20%  Similarity=0.290  Sum_probs=59.3

Q ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeecC
Q 023765          112 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYD  187 (277)
Q Consensus       112 l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~  187 (277)
                      |||+|||+++++++|+++|.+|| +..+.  .+...+||||+|.+.++|++|+..|||..+.|    ..|.|....
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~--~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g----~~l~V~~a~   69 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCF--VDKYKGTAFVTLLNGEQAEAAINTFHQSRLRE----RELSVQLQP   69 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEE--EETTTTEEEEEESSHHHHHHHHHHHTTEESSS----CEEEEEECC
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-cccee--ecccceeEEEEECCHHHHHHHHHHhCCccCCC----CEEEEEEeC
Confidence            79999999999999999999999 43333  34566799999999999999999999999999    566776653

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=1.4e-14  Score=99.22  Aligned_cols=78  Identities=23%  Similarity=0.373  Sum_probs=65.6

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeE--------EEEEecCC----CcEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCF--------SQVFRDRG----GMTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~--------~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                      ...+|||+|||..+++++|+++|.+||.|..        +.+..+..    .+||||+|.+.++|..|+..|||..+.| 
T Consensus         7 ~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g-   85 (101)
T d2cpea1           7 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG-   85 (101)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT-
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC-
Confidence            4679999999999999999999999998743        44444432    3599999999999999999999999999 


Q ss_pred             ceeeEEEEeecCCC
Q 023765          176 FSRSYVRVREYDSR  189 (277)
Q Consensus       176 ~~~~~i~~~~~~~~  189 (277)
                         ..|.|..+..+
T Consensus        86 ---r~i~V~~a~~~   96 (101)
T d2cpea1          86 ---SKLKVSLARKK   96 (101)
T ss_dssp             ---EECEEECSSCC
T ss_pred             ---EEEEEEEcCCC
Confidence               67888777543

>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=99.55  E-value=1.6e-15  Score=104.25  Aligned_cols=78  Identities=8%  Similarity=0.037  Sum_probs=67.4

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEec----CCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEE
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD----RGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRV  183 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~----~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~  183 (277)
                      +.++|||+|||..+++++|.++|.+||.|..+.+..+    ...+||||+|.+.++|..|+..|||..+.|    ..|.|
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g----~~l~V   92 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYG----KILVI   92 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSS----CBCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECC----EEEEE
Confidence            4679999999999999999999999999887766543    345799999999999999999999999999    56777


Q ss_pred             eecCCC
Q 023765          184 REYDSR  189 (277)
Q Consensus       184 ~~~~~~  189 (277)
                      ..+..+
T Consensus        93 ~~ak~k   98 (102)
T d2cpxa1          93 EFGKNK   98 (102)
T ss_dssp             EECCCC
T ss_pred             EeCCCc
Confidence            776554

>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=99.55  E-value=2.1e-14  Score=97.83  Aligned_cols=77  Identities=9%  Similarity=0.154  Sum_probs=65.4

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC----CcEEEEEEechhHHHHHHHhcC------CCeecccce
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRG----GMTGIVDYTSYDDMKYAIRKLD------RSEFRNAFS  177 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~------g~~~~g~~~  177 (277)
                      ...+|||+|||+.+++++|+++|.+||.|..+.+..+..    .|||||+|.+.++|..|++.||      |..+.|   
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~g---   83 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG---   83 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS---
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECC---
Confidence            367899999999999999999999999999998876653    3699999999999999999887      455666   


Q ss_pred             eeEEEEeecCC
Q 023765          178 RSYVRVREYDS  188 (277)
Q Consensus       178 ~~~i~~~~~~~  188 (277)
                       ..|.|.....
T Consensus        84 -r~l~v~~a~~   93 (98)
T d1x4ha1          84 -RQLKVDLAVT   93 (98)
T ss_dssp             -CEEEEECCCC
T ss_pred             -EEEEEEECCC
Confidence             5777776644

>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=99.55  E-value=2.4e-14  Score=94.63  Aligned_cols=68  Identities=19%  Similarity=0.282  Sum_probs=61.2

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC---cEEEEEEechhHHHHHHHhcCCCeecccce
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG---MTGIVDYTSYDDMKYAIRKLDRSEFRNAFS  177 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  177 (277)
                      ..+|||+|||..+++++|.++|..||.|..|.+..+..+   |||||+|.+.++|.+||+ ++|..+.|+.+
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l   76 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDL   76 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEEC
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEE
Confidence            468999999999999999999999999999999877643   599999999999999995 89999999433

>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=99.55  E-value=3.8e-15  Score=102.45  Aligned_cols=79  Identities=24%  Similarity=0.412  Sum_probs=68.2

Q ss_pred             CCCCCeEEEcCC--CCCCC--------HHHHHHHhhccCCeeEEEeecC-----CCCCcEEEEEEcChHHHHHHHHhcCC
Q 023765            3 SRSSRTLYVGNL--PGDTR--------MREVEDLFYKYGPIVDIDLKIP-----PRPPGYAFLEFEDYRDAEDAIRGRDG   67 (277)
Q Consensus         3 ~~~~~~l~V~nL--~~~~t--------~~~l~~~F~~~G~v~~v~~~~~-----~~~~g~afV~f~~~~~a~~a~~~l~~   67 (277)
                      +.|+++|+|.||  |..+.        .++|++.|++||.|..|.|+.+     ....|++||+|.++++|.+|+..|||
T Consensus         1 g~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~G   80 (104)
T d1o0pa_           1 GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG   80 (104)
T ss_dssp             CCCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSS
T ss_pred             CCCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCC
Confidence            468999999999  55443        4578999999999999999542     23468999999999999999999999


Q ss_pred             cccCCceEEEEEcc
Q 023765           68 YNFDGYRLRVELAH   81 (277)
Q Consensus        68 ~~~~g~~i~v~~a~   81 (277)
                      ..|+|+.|.|.++.
T Consensus        81 r~f~gR~v~v~f~~   94 (104)
T d1o0pa_          81 RKFANRVVVTKYCD   94 (104)
T ss_dssp             CCSSSSCCEEEEEC
T ss_pred             CEECCeEEEEEEcC
Confidence            99999999999976

>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=99.54  E-value=5.3e-15  Score=98.61  Aligned_cols=76  Identities=11%  Similarity=0.104  Sum_probs=65.0

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEeecC
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVREYD  187 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~~~~  187 (277)
                      +..+|||+|||..+++++|+++|.+||.|..|.+... ..+||||+|.+.++|+.|+.  ++..++|    ..|.|..+.
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~-~~gfafV~f~~~~~a~~a~~--~~~~i~g----~~l~v~~a~   76 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-FRAFAFVTFADDQIAQSLCG--EDLIIKG----ISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-CCSCCEEECSCHHHHHHTTT--CEEEETT----EEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec-cCceEEEEECCHHHHHHHHh--CCCEECC----EEeEEEeCC
Confidence            3679999999999999999999999999999987654 34699999999999999985  7788888    677887765


Q ss_pred             CCC
Q 023765          188 SRR  190 (277)
Q Consensus       188 ~~r  190 (277)
                      ++.
T Consensus        77 ~k~   79 (88)
T d1wf0a_          77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.53  E-value=1.1e-14  Score=97.65  Aligned_cols=77  Identities=16%  Similarity=0.207  Sum_probs=64.8

Q ss_pred             CCceEEEeCCCCCCCHHHHHH----HHHhcCCeeEEEEEec-CCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          108 SDYRVLVTGLPSSASWQDLKD----HMRRAGDVCFSQVFRD-RGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~----~f~~~g~v~~~~~~~~-~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      |..+|||+|||..+++++|++    +|.+||+|..|.+... ...+||||+|.+.++|..|+..|||..+.|    ..|.
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g----~~l~   77 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYD----KPMR   77 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETT----EECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECC----EEEE
Confidence            367999999999999988864    5899999999888653 234699999999999999999999999999    5666


Q ss_pred             EeecCC
Q 023765          183 VREYDS  188 (277)
Q Consensus       183 ~~~~~~  188 (277)
                      +..++.
T Consensus        78 v~~ak~   83 (91)
T d1nu4a_          78 IQYAKT   83 (91)
T ss_dssp             EEECSS
T ss_pred             EEEeCC
Confidence            666543

>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=99.53  E-value=1.2e-14  Score=96.55  Aligned_cols=71  Identities=13%  Similarity=0.096  Sum_probs=60.1

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHHHhcCCeeE-EEEEecCC---CcEEEEEEechhHHHHHHHhcCCCeeccccee
Q 023765          108 SDYRVLVTGLPSSASWQDLKDHMRRAGDVCF-SQVFRDRG---GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       108 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~-~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  178 (277)
                      ..++|+|+|||+.+++++|.++|..||.+.. +.+..+..   .++|||+|.+.++|.+|+..||+..+.|+.+.
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~   82 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVK   82 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEE
Confidence            3678999999999999999999999998865 34444433   35999999999999999999999999995433

>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=99.53  E-value=2.4e-14  Score=98.15  Aligned_cols=76  Identities=17%  Similarity=0.222  Sum_probs=62.2

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC---cEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG---MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      .....+|||.|||+++++++|+++|..+|. ..+.+..+..+   +||||+|.+.++|++|++ ||+..|.|+    .|.
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR----~I~   85 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHR----YVE   85 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSS----CCE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCE----EEE
Confidence            344679999999999999999999999984 46666666543   599999999999999986 899999995    455


Q ss_pred             EeecC
Q 023765          183 VREYD  187 (277)
Q Consensus       183 ~~~~~  187 (277)
                      |....
T Consensus        86 V~~s~   90 (102)
T d1weza_          86 LFLNS   90 (102)
T ss_dssp             EEEEC
T ss_pred             EEEcC
Confidence            55443

>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=99.50  E-value=7.4e-14  Score=92.96  Aligned_cols=75  Identities=8%  Similarity=0.100  Sum_probs=64.3

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhc--CCCeecccceeeEEEEe
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKL--DRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l--~g~~~~g~~~~~~i~~~  184 (277)
                      .+..+|||+|||..+++++|.++|.+||.|..+.+..+.  +||||+|.+.++|+.|++.+  ++..+.|    ..|.+.
T Consensus         6 ~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~--~~afV~f~~~e~A~~a~~~~~~~~~~~~g----~~l~v~   79 (88)
T d2cq1a1           6 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK--NQAFLELATEEAAITMVNYYSAVTPHLRN----QPIYIQ   79 (88)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTT--TEEEEEESSHHHHHHHHHHHHHSCCEETT----EECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccc--eEEEEEeCCHHHHHHHHHHHccCCCccCC----CEEEEE
Confidence            457899999999999999999999999999999887554  59999999999999999865  5678888    566665


Q ss_pred             ecC
Q 023765          185 EYD  187 (277)
Q Consensus       185 ~~~  187 (277)
                      ...
T Consensus        80 ~sk   82 (88)
T d2cq1a1          80 YSN   82 (88)
T ss_dssp             ECS
T ss_pred             ECC
Confidence            543

>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=99.49  E-value=1.7e-13  Score=94.15  Aligned_cols=76  Identities=17%  Similarity=0.190  Sum_probs=63.8

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcC--CCeecccceeeEEEEe
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLD--RSEFRNAFSRSYVRVR  184 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~--g~~~~g~~~~~~i~~~  184 (277)
                      .+..+|||+|||..+++++|.++|.+||.|..+.+...  .++|||+|.+.++|+.|+..|+  +..+.|    ..|.|.
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~--k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g----~~l~v~   86 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF--KRQALVEFENIDSAKECVTFAADVPVYIAG----QQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT--TTEEEEEESSHHHHHHHHHHHHHSCCBSSS----SBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec--ceeEEEEeCCHHHHHHHHHHHcCCCcEEee----EEEEEE
Confidence            45789999999999999999999999999999988754  4599999999999999999874  556677    456666


Q ss_pred             ecCC
Q 023765          185 EYDS  188 (277)
Q Consensus       185 ~~~~  188 (277)
                      ..+.
T Consensus        87 ~s~~   90 (104)
T d1wexa_          87 YSTS   90 (104)
T ss_dssp             ECSS
T ss_pred             EcCC
Confidence            5543

>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=99.49  E-value=1.6e-13  Score=94.24  Aligned_cols=77  Identities=14%  Similarity=0.162  Sum_probs=62.2

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC----CCcEEEEEEechhHHHHHHHhcCCCeecccceeeEE
Q 023765          106 RRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDR----GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYV  181 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i  181 (277)
                      .....+|||.|||+++++++|+++|..+|.+..+.++...    ..+||||+|.+.++|++|++ +|+..|.|+    .|
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR----~i   86 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHR----YI   86 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSS----CC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcce----EE
Confidence            3456689999999999999999999999988775444332    23699999999999999995 999999995    45


Q ss_pred             EEeecC
Q 023765          182 RVREYD  187 (277)
Q Consensus       182 ~~~~~~  187 (277)
                      .|....
T Consensus        87 ~V~~~~   92 (104)
T d1wg5a_          87 EIFKSS   92 (104)
T ss_dssp             EEEEEC
T ss_pred             EEEECC
Confidence            555443

>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=99.46  E-value=1.4e-13  Score=93.16  Aligned_cols=77  Identities=17%  Similarity=0.238  Sum_probs=64.2

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCC-eeEEEEEecC-----CCcEEEEEEechhHHHHHHHhcCCCee--cccceeeEE
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRAGD-VCFSQVFRDR-----GGMTGIVDYTSYDDMKYAIRKLDRSEF--RNAFSRSYV  181 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~g~-v~~~~~~~~~-----~~~~~fv~f~~~~~a~~a~~~l~g~~~--~g~~~~~~i  181 (277)
                      ++|||+|||..+++++|.++|.+||+ |..+.++.+.     ..|||||+|.+.++|..|++.|++..+  .|    ..|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g----~~i   77 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWG----HQI   77 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTT----BCC
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECC----EEE
Confidence            57999999999999999999999996 8888887653     236999999999999999999976544  56    567


Q ss_pred             EEeecCCCC
Q 023765          182 RVREYDSRR  190 (277)
Q Consensus       182 ~~~~~~~~r  190 (277)
                      .|..+++..
T Consensus        78 ~V~~A~p~~   86 (96)
T d2disa1          78 AVDWAEPEI   86 (96)
T ss_dssp             EEEESCSSC
T ss_pred             EEEEcCCCC
Confidence            787776543

>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=99.44  E-value=1.9e-13  Score=92.91  Aligned_cols=75  Identities=13%  Similarity=0.112  Sum_probs=63.5

Q ss_pred             CCCCceEEEeCCCCC-CCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHH--hcCCCeecccceeeEEE
Q 023765          106 RRSDYRVLVTGLPSS-ASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIR--KLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       106 ~~~~~~l~v~~l~~~-~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~--~l~g~~~~g~~~~~~i~  182 (277)
                      ...+.+|||+|||.+ +++++|.++|.+||.|..+.+..+.  ++|||+|.+.++|..|++  .+++..+.|+    .|.
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k--~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr----~l~   88 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK--SQAFIEMETREDAMAMVDHCLKKALWFQGR----CVK   88 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTT--TEEEEECSSHHHHHHHHHHHHHSCCCSSSS----CCE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecC--CcEEEEecchHHHHHHHHHHhcCCceECCE----EEE
Confidence            345789999999985 8999999999999999999987654  599999999999999997  5788889994    455


Q ss_pred             Eeec
Q 023765          183 VREY  186 (277)
Q Consensus       183 ~~~~  186 (277)
                      |...
T Consensus        89 V~~s   92 (99)
T d1x4fa1          89 VDLS   92 (99)
T ss_dssp             EEEE
T ss_pred             EEEc
Confidence            5544

>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=3.8e-13  Score=91.56  Aligned_cols=65  Identities=17%  Similarity=0.166  Sum_probs=58.0

Q ss_pred             CCCceEEEeC--CCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeec
Q 023765          107 RSDYRVLVTG--LPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFR  173 (277)
Q Consensus       107 ~~~~~l~v~~--l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~  173 (277)
                      .+..+|+|.|  ||..+++++|+++|.+||.|..+.+..+.  +||||+|.+.++|..|+..|||..+.
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k--~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK--PYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTC--SCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCc--cEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            4467888855  99999999999999999999998887654  59999999999999999999999884

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.42  E-value=3e-13  Score=92.54  Aligned_cols=76  Identities=11%  Similarity=0.055  Sum_probs=64.9

Q ss_pred             CCceEEEeCCCCCC-C----HHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEE
Q 023765          108 SDYRVLVTGLPSSA-S----WQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVR  182 (277)
Q Consensus       108 ~~~~l~v~~l~~~~-~----~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~  182 (277)
                      +..+|||+||+..+ +    .++|+++|.+||.|..+.+...  .+||||+|.+.++|.+|+..|||..+.|    ..|.
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~--~~~afV~f~~~~~A~~Ai~~lng~~~~g----~~l~   77 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS--FKRVRINFSNPLSAADARLRLHKTEFLG----KEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT--TTEEEEECSSTTHHHHHHHTSTTSEETT----EECE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC--CCEEEEEECCHHHHHHHHHHhcccccCC----CEeE
Confidence            36799999999875 3    4679999999999999988754  4599999999999999999999999999    6777


Q ss_pred             EeecCCC
Q 023765          183 VREYDSR  189 (277)
Q Consensus       183 ~~~~~~~  189 (277)
                      |..+...
T Consensus        78 v~~a~~~   84 (104)
T d1weya_          78 LYFAQTL   84 (104)
T ss_dssp             EECCCCS
T ss_pred             EeecccC
Confidence            7776544

>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=99.42  E-value=2.3e-13  Score=90.50  Aligned_cols=75  Identities=11%  Similarity=0.084  Sum_probs=64.1

Q ss_pred             CCCceEEEeCCCCC-CCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhc--CCCeecccceeeEEEE
Q 023765          107 RSDYRVLVTGLPSS-ASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKL--DRSEFRNAFSRSYVRV  183 (277)
Q Consensus       107 ~~~~~l~v~~l~~~-~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l--~g~~~~g~~~~~~i~~  183 (277)
                      .+..+|||+|||.. +|++||.++|.+||.|..+.+..+.  ++|||+|++.++|..|++.|  ++..+.|    ..|.|
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k--~~afV~f~~~~~A~~A~~~l~~~~~~~~g----r~l~V   79 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI--NEAFIEMATTEDAQAAVDYYTTTPALVFG----KPVRV   79 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS--SCEEEEESSHHHHHHHHHHHHHSCCEETT----EECEE
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc--eEEEEEEcchhhHHHHHHHHhhCCCccCC----ceEEE
Confidence            34679999999986 7899999999999999999997664  48999999999999999966  6778999    56666


Q ss_pred             eecC
Q 023765          184 REYD  187 (277)
Q Consensus       184 ~~~~  187 (277)
                      ....
T Consensus        80 ~~s~   83 (89)
T d1x4da1          80 HLSQ   83 (89)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            6554

>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=99.42  E-value=1.8e-13  Score=95.28  Aligned_cols=73  Identities=21%  Similarity=0.266  Sum_probs=59.6

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEE-EEEecCC---CcEEEEEEechhHHHHHHHhcCCCeeccccee
Q 023765          105 SRRSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFS-QVFRDRG---GMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       105 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~-~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  178 (277)
                      +.....+|||+|||+.+++++|.++|..+|.+..+ .+..+..   .|||||+|.+.++|++|+. |||..|+|+.+.
T Consensus        14 ~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~   90 (112)
T d1wela1          14 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQ   90 (112)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBE
T ss_pred             CCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEE
Confidence            34457799999999999999999999999988654 3333332   3599999999999999995 999999996443

>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=99.38  E-value=4e-13  Score=92.15  Aligned_cols=73  Identities=19%  Similarity=0.181  Sum_probs=60.9

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeE-EEEEecC---CCcEEEEEEechhHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCF-SQVFRDR---GGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~-~~~~~~~---~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      ..+|||+|||+.+++++|.++|..||.+.. +.+..+.   ..|+|||+|.+.++|+.||. ||+..|+|    ..|.|.
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~g----r~i~V~   82 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNG----REAFVH   82 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETT----EEEEEE
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECC----cEEEEE
Confidence            568999999999999999999999998876 4444433   35699999999999999996 99999999    466665


Q ss_pred             ec
Q 023765          185 EY  186 (277)
Q Consensus       185 ~~  186 (277)
                      ..
T Consensus        83 ~~   84 (103)
T d2cpya1          83 VV   84 (103)
T ss_dssp             EE
T ss_pred             EC
Confidence            43

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.36  E-value=1.3e-12  Score=90.94  Aligned_cols=74  Identities=11%  Similarity=0.119  Sum_probs=64.3

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEech-hHHHHHHHhcCCCeecccceeeEEEEe
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSY-DDMKYAIRKLDRSEFRNAFSRSYVRVR  184 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~-~~a~~a~~~l~g~~~~g~~~~~~i~~~  184 (277)
                      ...+||+|||..+|+++|.++|.+||+|..|.|+.+  .+||||.|.+. ++|.+|+..|++..+.+......+.+.
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~--kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG--AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT--CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC--CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            456699999999999999999999999999999865  46999999986 689999999999999887766666553

>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=99.34  E-value=2.1e-12  Score=87.53  Aligned_cols=79  Identities=18%  Similarity=0.336  Sum_probs=67.2

Q ss_pred             CCCceEEEeCC--CCCCC---------HHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          107 RSDYRVLVTGL--PSSAS---------WQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       107 ~~~~~l~v~~l--~~~~~---------~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                      ....+|+|.||  |.++.         .++|++.|.+||.|..|.+..+...|+|||+|.+.++|..|+..|||..++| 
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~g-   84 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGG-   84 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETT-
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEECC-
Confidence            34679999998  44321         3689999999999999999998888999999999999999999999999999 


Q ss_pred             ceeeEEEEeecCCC
Q 023765          176 FSRSYVRVREYDSR  189 (277)
Q Consensus       176 ~~~~~i~~~~~~~~  189 (277)
                         ..|.+..++++
T Consensus        85 ---r~i~v~~~~g~   95 (99)
T d2dita1          85 ---RQITAQAWDGT   95 (99)
T ss_dssp             ---EECEEEECCSC
T ss_pred             ---EEEEEEEeCCc
Confidence               67777776543

>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=99.31  E-value=8.7e-14  Score=93.04  Aligned_cols=68  Identities=13%  Similarity=0.151  Sum_probs=56.8

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEE---------ecCCCcEEEEEEechhHHHHHHHhcCCCeeccccee
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVF---------RDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~---------~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  178 (277)
                      .+|||+|||..+++++|.++|.+||.+..+.+.         .....+||||+|.+.++|+.|+. |||..+.|+.+.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~   78 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLK   78 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEE
Confidence            479999999999999999999999977654432         23445799999999999999985 999999995433

>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=99.24  E-value=5.8e-13  Score=91.11  Aligned_cols=69  Identities=14%  Similarity=0.068  Sum_probs=60.1

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC---cEEEEEEechhHHHHHHHhcCCCeeccccee
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG---MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  178 (277)
                      ..++|.+++..+++++|+++|.+||+|..|.|+.+..+   |+|||+|.+.++|.+|+..|||.+++|+.+.
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~   99 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEE
Confidence            35777778888889999999999999999999876443   6999999999999999999999999995443

>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=99.23  E-value=1.3e-11  Score=79.96  Aligned_cols=63  Identities=21%  Similarity=0.186  Sum_probs=54.6

Q ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          109 DYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       109 ~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                      .+.|+|.|+|++++++.| ++|.+||+|..+.+..  ..+||||+|.+.++|++||. +||..++|+
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~--~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~   66 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN--TGNWMHIRYQSKLQARKALS-KDGRIFGES   66 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS--SSSEEEEEESSHHHHHHHHT-TTTCEETTT
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC--CCCEEEEEEcccHHHHHHHh-cCCCeECCc
Confidence            567999999999987655 5799999999887754  34699999999999999995 999999985

>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=99.17  E-value=9.1e-11  Score=80.04  Aligned_cols=72  Identities=21%  Similarity=0.235  Sum_probs=59.4

Q ss_pred             CCceEEEeCC--CCCCC--------HHHHHHHHHhcCCeeEEEEEecCCC------cEEEEEEechhHHHHHHHhcCCCe
Q 023765          108 SDYRVLVTGL--PSSAS--------WQDLKDHMRRAGDVCFSQVFRDRGG------MTGIVDYTSYDDMKYAIRKLDRSE  171 (277)
Q Consensus       108 ~~~~l~v~~l--~~~~~--------~~~l~~~f~~~g~v~~~~~~~~~~~------~~~fv~f~~~~~a~~a~~~l~g~~  171 (277)
                      ++.+|.|.|+  +..+.        .++|++.|.+||.|..|.|..+..+      +++||+|.+.++|.+|+..|||..
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            3678999999  44432        4579999999999999999765432      699999999999999999999999


Q ss_pred             ecccceee
Q 023765          172 FRNAFSRS  179 (277)
Q Consensus       172 ~~g~~~~~  179 (277)
                      ++|+.+..
T Consensus        83 f~gR~v~v   90 (104)
T d1o0pa_          83 FANRVVVT   90 (104)
T ss_dssp             SSSSCCEE
T ss_pred             ECCeEEEE
Confidence            99965443

>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=98.15  E-value=4.2e-06  Score=53.93  Aligned_cols=66  Identities=14%  Similarity=0.139  Sum_probs=56.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCC-----CCCcEEEEEEcChHHHHHHHHhcCCcccCC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPP-----RPPGYAFLEFEDYRDAEDAIRGRDGYNFDG   72 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~-----~~~g~afV~f~~~~~a~~a~~~l~~~~~~g   72 (277)
                      ++|.|..|||.+|++++.+.+..+|++........+     ..-.-|||.|.+.+++....+.++|..|.+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEc
Confidence            589999999999999999999999999888774321     223569999999999999999999988854

>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=98.08  E-value=4.3e-06  Score=52.93  Aligned_cols=54  Identities=22%  Similarity=0.402  Sum_probs=48.9

Q ss_pred             HHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEc
Q 023765           21 REVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELA   80 (277)
Q Consensus        21 ~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a   80 (277)
                      ++|.+.|..||+|.-|++.     .+-.+|+|.+-+.|.+|+. +++.++.|+.|.|...
T Consensus        39 ~~Llq~l~~~GeViLvRFv-----~d~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRIN-----QGQMLVTFADSHSALSVLD-VDGMKVKGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEE-----TTEEEEECSCSHHHHHHHH-GGGSEETTEEEEEECC
T ss_pred             HHHHHHHhhCCeEEEEEEe-----CCeEEEEECCcHHHHHHhc-cCCeEEcceEEEEecC
Confidence            4688899999999999998     4578999999999999999 9999999999999764

>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=98.05  E-value=1.7e-05  Score=47.54  Aligned_cols=60  Identities=22%  Similarity=0.361  Sum_probs=52.6

Q ss_pred             HHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCcccCCceEEEEEccC
Q 023765           23 VEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGYNFDGYRLRVELAHG   82 (277)
Q Consensus        23 l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~~~~g~~i~v~~a~~   82 (277)
                      |.+.|.++|.|..+.+.......-.|-|...+.++|..|+..|+-..|+++.|.|.++.+
T Consensus        13 L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          13 LQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            456889999999999965444567899999999999999999999999999999998763

>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=97.70  E-value=0.00025  Score=45.44  Aligned_cols=69  Identities=13%  Similarity=0.325  Sum_probs=58.9

Q ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCC------cEEEEEEechhHHHHHHHhcCCCeeccccee
Q 023765          110 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGG------MTGIVDYTSYDDMKYAIRKLDRSEFRNAFSR  178 (277)
Q Consensus       110 ~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~------~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  178 (277)
                      ++|.|..||+.+|++++.+.+...|++.......++..      --|+|.|.+.+++..-.+.++|..+-+....
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~   76 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQ   76 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCC
Confidence            57999999999999999999999999888877766433      1799999999999999999999998664443

>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=97.50  E-value=0.00024  Score=44.78  Aligned_cols=48  Identities=8%  Similarity=0.219  Sum_probs=43.6

Q ss_pred             HHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          123 WQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       123 ~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                      ..+|.+.|..||+|.-+.+..+    ..+|+|.+-+.|.+|+. ++|.++.|+
T Consensus        38 ~~~Llq~l~~~GeViLvRFv~d----~mwVTF~dG~SAL~al~-l~g~~v~G~   85 (95)
T d1ufwa_          38 RTELMQTLGSYGTIVLVRINQG----QMLVTFADSHSALSVLD-VDGMKVKGR   85 (95)
T ss_dssp             HHHHHHHHHHHSCCSEEEEETT----EEEEECSCSHHHHHHHH-GGGSEETTE
T ss_pred             HHHHHHHHhhCCeEEEEEEeCC----eEEEEECCcHHHHHHhc-cCCeEEcce
Confidence            3578899999999999999988    69999999999999997 999999994

>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=97.20  E-value=0.00084  Score=40.06  Aligned_cols=52  Identities=19%  Similarity=0.252  Sum_probs=44.5

Q ss_pred             HHHHHHHHhcCCeeEEEEEecCC-CcEEEEEEechhHHHHHHHhcCCCeeccc
Q 023765          124 QDLKDHMRRAGDVCFSQVFRDRG-GMTGIVDYTSYDDMKYAIRKLDRSEFRNA  175 (277)
Q Consensus       124 ~~l~~~f~~~g~v~~~~~~~~~~-~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  175 (277)
                      +.|...|.+++.|..+.+..... ...|-|...+.++|..|+..||...++++
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~K   63 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSK   63 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCe
Confidence            45777899999999998864433 34899999999999999999999999994

>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=97.09  E-value=0.00068  Score=43.43  Aligned_cols=55  Identities=15%  Similarity=0.196  Sum_probs=47.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcC
Q 023765            7 RTLYVGNLPGDTRMREVEDLFYKYGPIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRD   66 (277)
Q Consensus         7 ~~l~V~nL~~~~t~~~l~~~F~~~G~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~   66 (277)
                      .-||.-.+|..+...||.++|++||.|.--.|..     .-|||...+.++|..++..+.
T Consensus        16 dHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswIdd-----TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          16 DHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDD-----TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEEECCTTCCHHHHHHHHTTTCSCCCEEEET-----TEEEEECSCHHHHHHHHHHHH
T ss_pred             ceeEEEeCCcccchhHHHHHhcCCCceEEEEecC-----ceEEEEecCHHHHHHHHHHhc
Confidence            3588889999999999999999999887777753     389999999999999987543

>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=96.01  E-value=0.023  Score=36.18  Aligned_cols=58  Identities=16%  Similarity=0.188  Sum_probs=46.8

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCcEEEEEEechhHHHHHHHhcC
Q 023765          107 RSDYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLD  168 (277)
Q Consensus       107 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~  168 (277)
                      +.-..||.-.+|..+...||.++|..||.|.-..|...    -|||...+.++|..++..++
T Consensus        13 p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswIddT----Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          13 PKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDDT----SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEEETT----EEEEECSCHHHHHHHHHHHH
T ss_pred             CCcceeEEEeCCcccchhHHHHHhcCCCceEEEEecCc----eEEEEecCHHHHHHHHHHhc
Confidence            33557888889999999999999999998876555222    69999999999888886543

>d1vqos1 d.12.1.1 (S:1-81) Ribosomal protein L23 {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal proteins S24e, L23 and L15e
superfamily: Ribosomal proteins S24e, L23 and L15e
family: L23p
domain: Ribosomal protein L23
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=85.53  E-value=1  Score=27.33  Aligned_cols=55  Identities=13%  Similarity=0.133  Sum_probs=41.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhc-cC-CeeEEEeecCCCCCcEEEEEEcChHHHHHHH
Q 023765            8 TLYVGNLPGDTRMREVEDLFYK-YG-PIVDIDLKIPPRPPGYAFLEFEDYRDAEDAI   62 (277)
Q Consensus         8 ~l~V~nL~~~~t~~~l~~~F~~-~G-~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~   62 (277)
                      ..|+-.+++.++..+|++.++. || .|..|..+.......-|||.+.....|....
T Consensus        22 n~y~F~V~~~A~K~~IK~AVe~lf~VkV~~Vnt~~~~~~~KkA~V~L~~~~~a~dia   78 (81)
T d1vqos1          22 NKLQFAVDDRASKGEVADAVEEQYDVTVEQVNTQNTMDGEKKAVVRLSEDDDAQEVA   78 (81)
T ss_dssp             CEEEEEECTTCCHHHHHHHHHHHHCCCEEEEEEEECTTSSEEEEEEECTTSCHHHHH
T ss_pred             CEEEEEEcCcCCHHHHHHHHHHHcCCceeEEEEeEcCCCcEEEEEEeCCCCcHHHHH
Confidence            3455567889999999999985 66 8888887665544568999998887766543

>d1m1ha2 d.58.42.1 (A:5-50,A:132-186) N-utilization substance G protein NusG, N-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: N-utilization substance G protein NusG, N-terminal domain
family: N-utilization substance G protein NusG, N-terminal domain
domain: N-utilization substance G protein NusG, N-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=81.96  E-value=2.9  Score=26.41  Aligned_cols=47  Identities=13%  Similarity=0.089  Sum_probs=34.8

Q ss_pred             HHHHHhhccC---CeeEEEeecCCCCCcEEEEEEcChHHHHHHHHhcCCc
Q 023765           22 EVEDLFYKYG---PIVDIDLKIPPRPPGYAFLEFEDYRDAEDAIRGRDGY   68 (277)
Q Consensus        22 ~l~~~F~~~G---~v~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~l~~~   68 (277)
                      .|.......|   .|..+.++..+-..||.||.+.-.+++..++....|.
T Consensus        25 ~l~~~~~~~~l~~~i~~v~VP~~klfPGYvfV~~~~~~~~~~~Ir~t~gV   74 (101)
T d1m1ha2          25 NLLKVLELEGLKDLVDEVIVPANKIFPGYILIKAHMNDKLLMAIEKTPHV   74 (101)
T ss_dssp             HHHHHHHHTTCGGGEEEEECSSCSSSTTEEEEEECCCHHHHHHHHTSTTE
T ss_pred             HHHHHHHHcCchhhhHHHhccchhcCCCEEEEEEEeCchHHHHHhcCCCE
Confidence            4444444433   5777777766667899999999888988899878774