Citrus Sinensis ID: 022301

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------30
Protein Sequence
MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVREYDHRRDGSQSPSRGRSYSRGRSESRSRSRSRGRSYSRSRSQSKSPKAKSSRRSPDRSRSRSASRSRSGSKPRSLSRSRSRSRSPLPPKQISKSPKKRSVSRSPSGSRSRSRSLSR
Secondary Structure (PSIPRED)
cccccccEEEEccccccccHHHHHHHHHcccccEEEEEEcccccccEEEEEEccHHHHHHHHHHccccccccccEEEEEccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccEEEEEEEEcccccEEEEEEccHHHHHHHHHHHccccccccEEEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccEEEEccccccccHHHHHHHHHHcccEEEEEEccccccccEEEEEEccHccHHHHHHHcccccccccEEEEEEcccccccccccccccccccccccccccccEEEEEccccccccHHHHHHHHHHcccEEEEEEEEcccccEEEEEEccHHHHHHHHHHcccccccccEEEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mssrasrtlyvgnlpgdirEREVEDLfykygpiahidlkipprppgyafvefeeardaedairgrdgydfdgHRLRVELahggrgrsssdrhsshssgrgrgvsrrsEYRVLVTglpssaswQDLKDHMRRagdvcfsqvfrdgsgttgivdytnydDMKHAIKKLDDSEFRNAFSRAYVRVReydhrrdgsqspsrgrsysrgrsesrsrsrsrgrsysrsrsqskspkakssrrspdrsrsrsasrsrsgskprslsrsrsrsrsplppkqiskspkkrsvsrspsgsrsrsrslsr
Flexible Loop (DISEMBL)
mssrasrtlyvgnlpgdireREVEDLFYKYGPIahidlkipprPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELahggrgrsssdrhsshssgrgrgvsrrseyRVLVTGlpssaswqdLKDHMRRAGDVCfsqvfrdgsgttgivdytnYDDMKHAikklddsefrnAFSRAYVRvreydhrrdgsqspsrgrsysrgrsesrsrsrsrgrsysrsrsqskspkakssrrspdrsrsrsasrsrsgskprslsrsrsrsrsplppkqiskspkkrsvsrspsgsrsrsrslsr
Low Complexity Region (SEG)
MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAhggrgrsssdrhsshssgrgrgvsrrsEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVREYDHRRDgsqspsrgrsysrgrsesrsrsrsrgrsysrsrsqskspkakssrrspdrsrsrsasrsrsgskprslsrsrsrsrsplppkQIskspkkrsvsrspsgsrsrsrslsr
Disordered region (IsUnstruct)
********LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA*DAIRGRDGYDFDGHRLR*********************************RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVR********************************************************************************************************************
Disordered Region (DISOPRED)
*****SR**YVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDM********************************************************************************************************************************************
Disordered Region (DISEMBL)
********LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA*************************RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVRE*******************************************************************************************************************
Disordered Region (DISPRO)
*****SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH**********************SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVREY******************************************************************************************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVREYDHRRDGSQSPSRGRSYSRGRSESRSRSRSRGRSYSRSRSQSKSPKAKSSRRSPDRSRSRSASRSRSGSKPRSLSRSRSRSRSPLPPKQISKSPKKRSVSRSPSGSRSRSRSLSR
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	299	2.2.26 [Sep-21-2011]
O22315	303	Pre-mRNA-splicing factor	yes	no	0.973	0.960	0.693	8e-86
Q5ZML3	257	Serine/arginine-rich spli	yes	no	0.625	0.727	0.542	3e-48
Q6NYA0	245	Serine/arginine-rich spli	yes	no	0.575	0.702	0.553	2e-45
Q9NEW6	258	Probable splicing factor,	yes	no	0.575	0.666	0.531	6e-45
Q6DII2	267	Serine/arginine-rich spli	yes	no	0.575	0.644	0.505	7e-44
Q3YLA6	248	Serine/arginine-rich spli	yes	no	0.575	0.693	0.536	8e-44
Q6PDM2	248	Serine/arginine-rich spli	yes	no	0.575	0.693	0.536	8e-44
Q07955	248	Serine/arginine-rich spli	yes	no	0.575	0.693	0.536	8e-44
Q0VCY7	248	Serine/arginine-rich spli	yes	no	0.575	0.693	0.536	8e-44
Q7SXP4	257	Serine/arginine-rich spli	no	no	0.575	0.669	0.534	1e-43

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

 Score =  317 bits (812), Expect = 8e-86,   Method: Compositional matrix adjust.
 Identities = 213/307 (69%), Positives = 239/307 (77%), Gaps = 16/307 (5%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
           MSSR+SRT+YVGNLPGDIREREVEDLF KYGP+  IDLK+PPRPPGYAFVEF++ARDAED
Sbjct: 1   MSSRSSRTVYVGNLPGDIREREVEDLFSKYGPVVQIDLKVPPRPPGYAFVEFDDARDAED 60

Query: 61  AIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGV-----------SRRSEY 109
           AI GRDGYDFDGHRLRVELAHGGR RSS D   S + G   G            SRRSE+
Sbjct: 61  AIHGRDGYDFDGHRLRVELAHGGR-RSSDDTRGSFNGGGRGGGRGRGDGGSRGPSRRSEF 119

Query: 110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDS 169
           RVLVTGLPSSASWQDLKDHMR+ GDVCFSQV+RD  GTTG+VDYT Y+DMK+A+KKLDD+
Sbjct: 120 RVLVTGLPSSASWQDLKDHMRKGGDVCFSQVYRDARGTTGVVDYTCYEDMKYALKKLDDT 179

Query: 170 EFRNAFSRAYVRVREYDHRRDGSQSPSRGRSYSRGRSESRSRSRSRGRSYSRSRSQSKSP 229
           EFRNAFS  YVRVREYD R+D S+SPS  R  S  +S SRSR RS  RS SRSRS+S+SP
Sbjct: 180 EFRNAFSNGYVRVREYDSRKD-SRSPS--RGRSYSKSRSRSRGRSVSRSRSRSRSRSRSP 236

Query: 230 KAKSSRRSPDRSRSRS-ASRSRSGSKPRSLSRSRSRSRSPLPPKQISKSPKKRSVSRSPS 288
           KAKSSRRSP +S SRS   RS+S S     SRSRSRS  P   K+ SKSP K S ++SP 
Sbjct: 237 KAKSSRRSPAKSTSRSPGPRSKSRSPSPRRSRSRSRSPLPSVQKEGSKSPSKPSPAKSPI 296

Query: 289 GSRSRSR 295
            +RS SR
Sbjct: 297 HTRSPSR 303

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 =  192 bits (487), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 108/199 (54%), Positives = 136/199 (68%), Gaps = 12/199 (6%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
           +YVGNLP DIR +++ED+FYKYG I  IDLK     P +AFVEFE+ RDAEDA+ GRDGY
Sbjct: 18  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 77

Query: 69  DFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGV---SRRSEYRVLVTGLPSSASWQDL 125
           D+DG+RLRVE    GRG                     SRRSEYRV+V+GLP S SWQDL
Sbjct: 78  DYDGYRLRVEFPRSGRGTGRGGGGGGGGGAPRGRYGPPSRRSEYRVIVSGLPPSGSWQDL 137

Query: 126 KDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFR-NAFSRAYVRVRE 184
           KDHMR AGDVC++ VFRDG   TG+V++   +DM +A++KLD+++FR +    AY+RV  
Sbjct: 138 KDHMREAGDVCYADVFRDG---TGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV-- 192

Query: 185 YDHRRDGSQSPSRGRSYSR 203
              + DG +SPS GRS SR
Sbjct: 193 ---KVDGPRSPSYGRSRSR 208

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 =  182 bits (463), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 99/179 (55%), Positives = 125/179 (69%), Gaps = 7/179 (3%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
           +YVGNLP DIR ++VED+FYKYG I  IDLK     P +AFVEFE+ RDAEDA+ GRDGY
Sbjct: 17  IYVGNLPPDIRTKDVEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 76

Query: 69  DFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGV---SRRSEYRVLVTGLPSSASWQDL 125
           D+DG+RLRVE    GRG                     SRRSEYRV+V+GLP S SWQDL
Sbjct: 77  DYDGYRLRVEFPRSGRGGGRGGGGGGGVGAPRGRYGPPSRRSEYRVIVSGLPPSGSWQDL 136

Query: 126 KDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFR-NAFSRAYVRVR 183
           KDHMR AGDVC++ VFRDG   TG+V++   +DM +A++KLD+++FR +    AY+RV+
Sbjct: 137 KDHMREAGDVCYADVFRDG---TGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK 192

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

Danio rerio (taxid: 7955)

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

 Score =  181 bits (459), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 101/190 (53%), Positives = 131/190 (68%), Gaps = 18/190 (9%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
           +YVGNLPGD+RE+EVED+F+KYG I ++D+K   R P +AFVEFE+ RDAEDA+R RDGY
Sbjct: 11  VYVGNLPGDVREKEVEDIFHKYGRIKYVDIK-SGRGPAFAFVEFEDHRDAEDAVRARDGY 69

Query: 69  DFDGHRLRVELA-------------HGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTG 115
           +FDG R+RVE                 G      D       GRG G  RR+ YRV+V G
Sbjct: 70  EFDGRRIRVEFTRGVGPRGPGGRPLQDGGDHRGGDFRGGRGGGRGGGPQRRTGYRVIVEG 129

Query: 116 LPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFR-NA 174
           LP + SWQDLKDHMR AGDVC++ V RDG   TG+V++T Y+D+K+A++KLDD++FR + 
Sbjct: 130 LPPTGSWQDLKDHMRDAGDVCYADVARDG---TGVVEFTRYEDVKYAVRKLDDTKFRSHE 186

Query: 175 FSRAYVRVRE 184
              AY+RVRE
Sbjct: 187 GETAYIRVRE 196

Plays an essential role in embryogenesis.

Caenorhabditis elegans (taxid: 6239)

>sp|Q6DII2|SRSF1_XENTR Serine/arginine-rich splicing factor 1 OS=Xenopus tropicalis GN=srsf1 PE=2 SV=1

 Score =  177 bits (450), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 100/198 (50%), Positives = 127/198 (64%), Gaps = 26/198 (13%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
           +YVGNLP DIR +++ED+FYKYG I  IDLK     P +AFVEFE+ RDAEDA+ GRDGY
Sbjct: 18  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 77

Query: 69  DFDGHRLRVELAHGGRGRSSSDRHSSHSS----------------------GRGRGVSRR 106
           D+DG+RLRVE    GRG                                  GR    SRR
Sbjct: 78  DYDGYRLRVEFPRSGRGAGGRGGGGGGGGGGGGGGGGGGGGGGGGGGGAPRGRYGPPSRR 137

Query: 107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKL 166
           SEYRV+V+GLP S SWQDLKDHMR AGDVC++ VFRDG   TG+V++   +DM +A++KL
Sbjct: 138 SEYRVVVSGLPPSGSWQDLKDHMREAGDVCYADVFRDG---TGVVEFVRKEDMTYAVRKL 194

Query: 167 DDSEFR-NAFSRAYVRVR 183
           D+++FR +    AY+RV+
Sbjct: 195 DNTKFRSHEGETAYIRVK 212

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

Xenopus tropicalis (taxid: 8364)

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

 Score =  177 bits (449), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 96/179 (53%), Positives = 124/179 (69%), Gaps = 7/179 (3%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
           +YVGNLP DIR +++ED+FYKYG I  IDLK     P +AFVEFE+ RDAEDA+ GRDGY
Sbjct: 18  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 77

Query: 69  DFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGV---SRRSEYRVLVTGLPSSASWQDL 125
           D+DG+RLRVE    GRG                     SRRSE RV+V+GLP S SWQDL
Sbjct: 78  DYDGYRLRVEFPRSGRGTGRGGGGGGGGGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDL 137

Query: 126 KDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFR-NAFSRAYVRVR 183
           KDHMR AGDVC++ V+RDG   TG+V++   +DM +A++KLD+++FR +    AY+RV+
Sbjct: 138 KDHMREAGDVCYADVYRDG---TGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK 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 =  177 bits (449), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 96/179 (53%), Positives = 124/179 (69%), Gaps = 7/179 (3%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
           +YVGNLP DIR +++ED+FYKYG I  IDLK     P +AFVEFE+ RDAEDA+ GRDGY
Sbjct: 18  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 77

Query: 69  DFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGV---SRRSEYRVLVTGLPSSASWQDL 125
           D+DG+RLRVE    GRG                     SRRSE RV+V+GLP S SWQDL
Sbjct: 78  DYDGYRLRVEFPRSGRGTGRGGGGGGGGGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDL 137

Query: 126 KDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFR-NAFSRAYVRVR 183
           KDHMR AGDVC++ V+RDG   TG+V++   +DM +A++KLD+++FR +    AY+RV+
Sbjct: 138 KDHMREAGDVCYADVYRDG---TGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK 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 =  177 bits (449), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 96/179 (53%), Positives = 124/179 (69%), Gaps = 7/179 (3%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
           +YVGNLP DIR +++ED+FYKYG I  IDLK     P +AFVEFE+ RDAEDA+ GRDGY
Sbjct: 18  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 77

Query: 69  DFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGV---SRRSEYRVLVTGLPSSASWQDL 125
           D+DG+RLRVE    GRG                     SRRSE RV+V+GLP S SWQDL
Sbjct: 78  DYDGYRLRVEFPRSGRGTGRGGGGGGGGGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDL 137

Query: 126 KDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFR-NAFSRAYVRVR 183
           KDHMR AGDVC++ V+RDG   TG+V++   +DM +A++KLD+++FR +    AY+RV+
Sbjct: 138 KDHMREAGDVCYADVYRDG---TGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK 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 =  177 bits (449), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 96/179 (53%), Positives = 124/179 (69%), Gaps = 7/179 (3%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
           +YVGNLP DIR +++ED+FYKYG I  IDLK     P +AFVEFE+ RDAEDA+ GRDGY
Sbjct: 18  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 77

Query: 69  DFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGV---SRRSEYRVLVTGLPSSASWQDL 125
           D+DG+RLRVE    GRG                     SRRSE RV+V+GLP S SWQDL
Sbjct: 78  DYDGYRLRVEFPRSGRGTGRGGGGGGGGGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDL 137

Query: 126 KDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFR-NAFSRAYVRVR 183
           KDHMR AGDVC++ V+RDG   TG+V++   +DM +A++KLD+++FR +    AY+RV+
Sbjct: 138 KDHMREAGDVCYADVYRDG---TGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK 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|Q7SXP4|SRS1A_DANRE Serine/arginine-rich splicing factor 1A OS=Danio rerio GN=srsf1a PE=2 SV=2

 Score =  177 bits (448), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 101/189 (53%), Positives = 127/189 (67%), Gaps = 17/189 (8%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
           +YVGNLP DIR ++VED+FYKYG I  IDLK     P +AFVEFE+ RDAEDA+  RDGY
Sbjct: 17  IYVGNLPPDIRTKDVEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYARDGY 76

Query: 69  DFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGV-------------SRRSEYRVLVTG 115
           D+DG+RLRVE    GRG            G G G              SRRSEYRV+V+G
Sbjct: 77  DYDGYRLRVEFPRSGRGMGRGGFGGGGGGGGGGGGGGGGAPRGRYGPPSRRSEYRVIVSG 136

Query: 116 LPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFR-NA 174
           LP S SWQDLKDHMR AGDVC++ VFRDG   TG+V++   +DM +A++KLD+++FR + 
Sbjct: 137 LPPSGSWQDLKDHMREAGDVCYADVFRDG---TGVVEFVRKEDMTYAVRKLDNTKFRSHE 193

Query: 175 FSRAYVRVR 183
              AY+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	299
449436495	309	PREDICTED: pre-mRNA-splicing factor SF2-	0.933	0.902	0.810	4e-93
224068334	252	predicted protein [Populus trichocarpa]	0.692	0.821	0.884	8e-93
357511267	401	Pre-mRNA-splicing factor SF2 [Medicago t	0.926	0.690	0.778	2e-90
357516353	326	Pre-mRNA-splicing factor SF2 [Medicago t	0.926	0.849	0.778	3e-90
255564164	292	arginine/serine-rich splicing factor, pu	0.622	0.636	0.925	5e-89
357516357	347	Pre-mRNA-splicing factor SF2 [Medicago t	0.812	0.700	0.790	8e-89
357516355	329	Pre-mRNA-splicing factor SF2 [Medicago t	0.812	0.738	0.786	1e-88
147853033	720	hypothetical protein VITISV_000965 [Viti	0.622	0.258	0.888	2e-88
255646543	310	unknown [Glycine max]	0.826	0.796	0.797	5e-88
356572736	309	PREDICTED: pre-mRNA-splicing factor SF2-	0.826	0.799	0.813	6e-88

>gi|449436495|ref|XP_004136028.1| PREDICTED: pre-mRNA-splicing factor SF2-like [Cucumis sativus] gi|449498497|ref|XP_004160553.1| PREDICTED: pre-mRNA-splicing factor SF2-like [Cucumis sativus]

 Score =  347 bits (889), Expect = 4e-93,   Method: Compositional matrix adjust.
 Identities = 231/285 (81%), Positives = 248/285 (87%), Gaps = 6/285 (2%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
           MSSRASRT+YVGNLPGDIRE+EVEDLFYKYG IAHIDLK+PPRPPGYAFVEFE+A DA+D
Sbjct: 1   MSSRASRTVYVGNLPGDIREKEVEDLFYKYGRIAHIDLKVPPRPPGYAFVEFEDAEDAQD 60

Query: 61  AIRGRDGYDFDGHRLRVELAHGGRGRSSS-DRHSSHSSGRGRGVSRRS-EYRVLVTGLPS 118
           AIRGRDGYDFDGHRLRVELAHGGRG SSS DR+SSH   RG     R  +YRVLVTGLPS
Sbjct: 61  AIRGRDGYDFDGHRLRVELAHGGRGHSSSNDRYSSHGGSRGGRGVSRRSDYRVLVTGLPS 120

Query: 119 SASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA 178
           SASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMK+AIKKLDDSEFRNAFSRA
Sbjct: 121 SASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKYAIKKLDDSEFRNAFSRA 180

Query: 179 YVRVREYDHRRDGSQSPSRGRSYSRGRSESRSRSRSRGRSYSRSRSQSKSPKAKSSRRSP 238
           YVRVREYD +RD S+SPSRGR  S  R  S SRSRSRGRS S+S S+SKSPKAK S+RSP
Sbjct: 181 YVRVREYDSKRDLSRSPSRGR--SYSRGRSYSRSRSRGRSRSKSHSRSKSPKAKPSQRSP 238

Query: 239 DRSRSRSASRSRSGSKPRSLSRSRSRSRSPLP--PKQISKSPKKR 281
            +SRSRSAS  RS SK  SLS SRSRSRSP+P   K+ SKSPK+R
Sbjct: 239 VKSRSRSASPPRSRSKSSSLSGSRSRSRSPVPNREKRTSKSPKRR 283

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224068334|ref|XP_002302710.1| predicted protein [Populus trichocarpa] gi|222844436|gb|EEE81983.1| predicted protein [Populus trichocarpa]

 Score =  346 bits (887), Expect = 8e-93,   Method: Compositional matrix adjust.
 Identities = 184/208 (88%), Positives = 198/208 (95%), Gaps = 1/208 (0%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
           MSSRASRTLYVGNLPGDIRE+EVEDLFYKYGP+AHIDLKIPPRPPGYAFVEFEEARDAED
Sbjct: 1   MSSRASRTLYVGNLPGDIREKEVEDLFYKYGPVAHIDLKIPPRPPGYAFVEFEEARDAED 60

Query: 61  AIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRS-EYRVLVTGLPSS 119
           AIRGRDGYDFDGHRLRVELAHGGRG SSSDRHSS+S GRGRG + R  EYRV+VTGLPSS
Sbjct: 61  AIRGRDGYDFDGHRLRVELAHGGRGHSSSDRHSSYSGGRGRGGASRRSEYRVVVTGLPSS 120

Query: 120 ASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY 179
           ASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNY+DMK+AIKK+DDSEFRNAFS+AY
Sbjct: 121 ASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYEDMKYAIKKIDDSEFRNAFSQAY 180

Query: 180 VRVREYDHRRDGSQSPSRGRSYSRGRSE 207
           VRVREYD +RD S+SP R RS+SRGR++
Sbjct: 181 VRVREYDSKRDSSRSPGRDRSHSRGRND 208

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357511267|ref|XP_003625922.1| Pre-mRNA-splicing factor SF2 [Medicago truncatula] gi|355500937|gb|AES82140.1| Pre-mRNA-splicing factor SF2 [Medicago truncatula]

 Score =  338 bits (866), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 221/284 (77%), Positives = 243/284 (85%), Gaps = 7/284 (2%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
           MS  +SRT+YVGNLPGDIREREVEDLF KYG I HIDLK+PPRPPGYAFVEFE+ +DAED
Sbjct: 102 MSRHSSRTVYVGNLPGDIREREVEDLFMKYGHITHIDLKVPPRPPGYAFVEFEDVQDAED 161

Query: 61  AIRGRDGYDFDGHRLRVELAHGGRGRSSS-DRHSSHSSGRGRGVSRRS-EYRVLVTGLPS 118
           AIRGRDGYDFDGHRLRVE AHGGRG SSS DR+SSHS+GRG     R  EYRV+V GLPS
Sbjct: 162 AIRGRDGYDFDGHRLRVEAAHGGRGNSSSRDRYSSHSNGRGGRGVSRRSEYRVIVNGLPS 221

Query: 119 SASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA 178
           SASWQDLKDHMR+AGDVCFSQVF DG GTTGIVDYTNYDDMK+AIKKLDDSEFRNAFS++
Sbjct: 222 SASWQDLKDHMRKAGDVCFSQVFHDGRGTTGIVDYTNYDDMKYAIKKLDDSEFRNAFSKS 281

Query: 179 YVRVREYDHRRDGSQSPSRGRSYSRGRSESRSRSRSRGRSYSRS--RSQSKSPKAKSSRR 236
           YVRVREYD RRD S+SP RG S+SRGRS SRSRSRSR  S S S   S+SKSPK KSS+R
Sbjct: 282 YVRVREYDSRRD-SRSPGRGPSHSRGRSYSRSRSRSRSHSRSYSPGHSRSKSPKGKSSQR 340

Query: 237 SPDRSRSRSASRSRSGSKPRSLSRSRSRSRSPLPPKQISKSPKK 280
           SP +S ++S SRSRS S+ RSLS SRSRSRSPLP +  +KSPKK
Sbjct: 341 SPAKSPAKSVSRSRSRSRSRSLSGSRSRSRSPLPLR--NKSPKK 382

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357516353|ref|XP_003628465.1| Pre-mRNA-splicing factor SF2 [Medicago truncatula] gi|355522487|gb|AET02941.1| Pre-mRNA-splicing factor SF2 [Medicago truncatula]

 Score =  337 bits (865), Expect = 3e-90,   Method: Compositional matrix adjust.
 Identities = 221/284 (77%), Positives = 243/284 (85%), Gaps = 7/284 (2%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
           MS  +SRT+YVGNLPGDIREREVEDLF KYG I HIDLK+PPRPPGYAFVEFE+ +DAED
Sbjct: 27  MSRHSSRTVYVGNLPGDIREREVEDLFMKYGHITHIDLKVPPRPPGYAFVEFEDVQDAED 86

Query: 61  AIRGRDGYDFDGHRLRVELAHGGRGRSSS-DRHSSHSSGRGRGVSRRS-EYRVLVTGLPS 118
           AIRGRDGYDFDGHRLRVE AHGGRG SSS DR+SSHS+GRG     R  EYRV+V GLPS
Sbjct: 87  AIRGRDGYDFDGHRLRVEAAHGGRGNSSSRDRYSSHSNGRGGRGVSRRSEYRVIVNGLPS 146

Query: 119 SASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA 178
           SASWQDLKDHMR+AGDVCFSQVF DG GTTGIVDYTNYDDMK+AIKKLDDSEFRNAFS++
Sbjct: 147 SASWQDLKDHMRKAGDVCFSQVFHDGRGTTGIVDYTNYDDMKYAIKKLDDSEFRNAFSKS 206

Query: 179 YVRVREYDHRRDGSQSPSRGRSYSRGRSESRSRSRSRGRSYSRS--RSQSKSPKAKSSRR 236
           YVRVREYD RRD S+SP RG S+SRGRS SRSRSRSR  S S S   S+SKSPK KSS+R
Sbjct: 207 YVRVREYDSRRD-SRSPGRGPSHSRGRSYSRSRSRSRSHSRSYSPGHSRSKSPKGKSSQR 265

Query: 237 SPDRSRSRSASRSRSGSKPRSLSRSRSRSRSPLPPKQISKSPKK 280
           SP +S ++S SRSRS S+ RSLS SRSRSRSPLP +  +KSPKK
Sbjct: 266 SPAKSPAKSVSRSRSRSRSRSLSGSRSRSRSPLPLR--NKSPKK 307

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255564164|ref|XP_002523079.1| arginine/serine-rich splicing factor, putative [Ricinus communis] gi|223537641|gb|EEF39264.1| arginine/serine-rich splicing factor, putative [Ricinus communis]

 Score =  333 bits (854), Expect = 5e-89,   Method: Compositional matrix adjust.
 Identities = 173/187 (92%), Positives = 176/187 (94%), Gaps = 1/187 (0%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
           MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED
Sbjct: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60

Query: 61  AIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRS-EYRVLVTGLPSS 119
           AIRGRDGYDFDGH+LRVELAHGGRG SSSDRHSSHS G       R  EYRVLVTGLPSS
Sbjct: 61  AIRGRDGYDFDGHQLRVELAHGGRGHSSSDRHSSHSGGGRGRGVSRRSEYRVLVTGLPSS 120

Query: 120 ASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY 179
           ASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNY+DMKHAIKKLDDSEFRNAFSRAY
Sbjct: 121 ASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYEDMKHAIKKLDDSEFRNAFSRAY 180

Query: 180 VRVREYD 186
           VRV+EYD
Sbjct: 181 VRVKEYD 187

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357516357|ref|XP_003628467.1| Pre-mRNA-splicing factor SF2 [Medicago truncatula] gi|355522489|gb|AET02943.1| Pre-mRNA-splicing factor SF2 [Medicago truncatula]

 Score =  333 bits (853), Expect = 8e-89,   Method: Compositional matrix adjust.
 Identities = 196/248 (79%), Positives = 214/248 (86%), Gaps = 5/248 (2%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
           MS  +SRT+YVGNLPGDIREREVEDLF KYG I HIDLK+PPRPPGYAFVEFE+ +DAED
Sbjct: 27  MSRHSSRTVYVGNLPGDIREREVEDLFMKYGHITHIDLKVPPRPPGYAFVEFEDVQDAED 86

Query: 61  AIRGRDGYDFDGHRLRVELAHGGRGRSSS-DRHSSHSS-GRGRGVSRRSEYRVLVTGLPS 118
           AIRGRDGYDFDGHRLRVE AHGGRG SSS DR+SSHS+   GRGVSRRSEYRV+V GLPS
Sbjct: 87  AIRGRDGYDFDGHRLRVEAAHGGRGNSSSRDRYSSHSNGRGGRGVSRRSEYRVIVNGLPS 146

Query: 119 SASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA 178
           SASWQDLKDHMR+AGDVCFSQVF DG GTTGIVDYTNYDDMK+AIKKLDDSEFRNAFS++
Sbjct: 147 SASWQDLKDHMRKAGDVCFSQVFHDGRGTTGIVDYTNYDDMKYAIKKLDDSEFRNAFSKS 206

Query: 179 YVRVREYDHRRDGSQSPSRG--RSYSRGRSESRSRSRSRGRSYSRSRSQSKSPKAKSSRR 236
           YVRVREYD RRD S+SP RG   S  R  S SRSRSRS  RSYS   S+SKSPK KSS+R
Sbjct: 207 YVRVREYDSRRD-SRSPGRGPSHSRGRSYSRSRSRSRSHSRSYSPGHSRSKSPKGKSSQR 265

Query: 237 SPDRSRSR 244
           SP +S ++
Sbjct: 266 SPAKSPAK 273

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357516355|ref|XP_003628466.1| Pre-mRNA-splicing factor SF2 [Medicago truncatula] gi|355522488|gb|AET02942.1| Pre-mRNA-splicing factor SF2 [Medicago truncatula]

 Score =  332 bits (852), Expect = 1e-88,   Method: Compositional matrix adjust.
 Identities = 195/248 (78%), Positives = 214/248 (86%), Gaps = 5/248 (2%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
           MS  +SRT+YVGNLPGDIREREVEDLF KYG I HIDLK+PPRPPGYAFVEFE+ +DAED
Sbjct: 27  MSRHSSRTVYVGNLPGDIREREVEDLFMKYGHITHIDLKVPPRPPGYAFVEFEDVQDAED 86

Query: 61  AIRGRDGYDFDGHRLRVELAHGGRGRSSS-DRHSSHSSGRGRGVSRRS-EYRVLVTGLPS 118
           AIRGRDGYDFDGHRLRVE AHGGRG SSS DR+SSHS+GRG     R  EYRV+V GLPS
Sbjct: 87  AIRGRDGYDFDGHRLRVEAAHGGRGNSSSRDRYSSHSNGRGGRGVSRRSEYRVIVNGLPS 146

Query: 119 SASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA 178
           SASWQDLKDHMR+AGDVCFSQVF DG GTTGIVDYTNYDDMK+AIKKLDDSEFRNAFS++
Sbjct: 147 SASWQDLKDHMRKAGDVCFSQVFHDGRGTTGIVDYTNYDDMKYAIKKLDDSEFRNAFSKS 206

Query: 179 YVRVREYDHRRDGSQSPSRGRSYSRGRSESRSRSRSRGRSYSRS--RSQSKSPKAKSSRR 236
           YVRVREYD RRD S+SP RG S+SRGRS SRSRSRSR  S S S   S+SKSPK KSS+R
Sbjct: 207 YVRVREYDSRRD-SRSPGRGPSHSRGRSYSRSRSRSRSHSRSYSPGHSRSKSPKGKSSQR 265

Query: 237 SPDRSRSR 244
           SP +S ++
Sbjct: 266 SPAKSPAK 273

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147853033|emb|CAN81258.1| hypothetical protein VITISV_000965 [Vitis vinifera]

 Score =  331 bits (849), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 167/188 (88%), Positives = 170/188 (90%), Gaps = 2/188 (1%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
           MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEE+RDAED
Sbjct: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEESRDAED 60

Query: 61  AIRGRDGYDFDGHRLRVELAHGGRGRSSS--DRHSSHSSGRGRGVSRRSEYRVLVTGLPS 118
           AIRGRDGYDFDGHRLRVELAHGGRG SSS      S   G   G SRRSEYRVLVTGLPS
Sbjct: 61  AIRGRDGYDFDGHRLRVELAHGGRGHSSSIDRHSHSSGRGGRGGASRRSEYRVLVTGLPS 120

Query: 119 SASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA 178
           SASWQDLKDHMRRAGDVCFSQVF DG GT GIVDYTNYDDMK AI+KLDDSEFRNAFSRA
Sbjct: 121 SASWQDLKDHMRRAGDVCFSQVFHDGGGTVGIVDYTNYDDMKFAIRKLDDSEFRNAFSRA 180

Query: 179 YVRVREYD 186
           YVRV+EYD
Sbjct: 181 YVRVKEYD 188

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255646543|gb|ACU23746.1| unknown [Glycine max]

 Score =  330 bits (846), Expect = 5e-88,   Method: Compositional matrix adjust.
 Identities = 201/252 (79%), Positives = 218/252 (86%), Gaps = 5/252 (1%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
           MS R+SRT+YVGNLPGDIREREVEDLF KYG I HIDLK+PPRPPGYAFVEFE+A+DAED
Sbjct: 1   MSRRSSRTVYVGNLPGDIREREVEDLFLKYGHITHIDLKVPPRPPGYAFVEFEDAQDAED 60

Query: 61  AIRGRDGYDFDGHRLRVELAHGGRGRSSS-DRHSSHSSGRGRGVSRRS-EYRVLVTGLPS 118
           AIRGRDGYDFDGHRLRVE AHGGRG SSS DRH+SHS+GRG     R  EYRVLVTGLPS
Sbjct: 61  AIRGRDGYDFDGHRLRVEPAHGGRGHSSSKDRHNSHSNGRGGRGVSRRSEYRVLVTGLPS 120

Query: 119 SASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA 178
           SASWQDLKDHMR+AGDVCFSQVF DG GTTGIVDYTNYDDMK+AIKKLDDSEFRNAFS+ 
Sbjct: 121 SASWQDLKDHMRKAGDVCFSQVFHDGRGTTGIVDYTNYDDMKYAIKKLDDSEFRNAFSKG 180

Query: 179 YVRVREYDHRRDGSQSPSRGRSYSRGRSESRSRSRSRGRSYSRSRSQSKSPKAKSSRRSP 238
           YVRVREYD RRD S+SPS G S+S  R  S SRSRSR  SYSR RSQSKSPK KSS+RSP
Sbjct: 181 YVRVREYDSRRDSSRSPSHGPSHS--RGRSYSRSRSRSHSYSRDRSQSKSPKGKSSQRSP 238

Query: 239 DRS-RSRSASRS 249
            +S + +S+ RS
Sbjct: 239 AKSPKGKSSQRS 250

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356572736|ref|XP_003554522.1| PREDICTED: pre-mRNA-splicing factor SF2-like [Glycine max]

 Score =  330 bits (845), Expect = 6e-88,   Method: Compositional matrix adjust.
 Identities = 205/252 (81%), Positives = 222/252 (88%), Gaps = 5/252 (1%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
           MS R+SRT+YVGNLPGDIREREVEDLF KYG I HIDLK+PPRPPGYAFVEFE+A+DAED
Sbjct: 1   MSRRSSRTVYVGNLPGDIREREVEDLFLKYGHITHIDLKVPPRPPGYAFVEFEDAQDAED 60

Query: 61  AIRGRDGYDFDGHRLRVELAHGGRGRSSS-DRHSSHSS-GRGRGVSRRSEYRVLVTGLPS 118
           AIRGRDGYDFDGHRLRVE AHGGRG SSS DRH+SHS+   GRGVSRRSEYRVLVTGLPS
Sbjct: 61  AIRGRDGYDFDGHRLRVEPAHGGRGHSSSKDRHNSHSNGRGGRGVSRRSEYRVLVTGLPS 120

Query: 119 SASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA 178
           SASWQDLKDHMR+AGDVCFSQVF DG GTTGIVDYTNYDDMK+AIKKLDDSEFRNAFS+ 
Sbjct: 121 SASWQDLKDHMRKAGDVCFSQVFHDGRGTTGIVDYTNYDDMKYAIKKLDDSEFRNAFSKG 180

Query: 179 YVRVREYDHRRDGSQSPSRGRSYSRGRSESRSRSRSRGRSYSRSRSQSKSPKAKSSRRSP 238
           YVRVREYD RRD S+SPS G S+S  R  S SRSRSR  SYSR RSQSKSPK KSS+RSP
Sbjct: 181 YVRVREYDSRRDSSRSPSHGPSHS--RGRSYSRSRSRSHSYSRDRSQSKSPKGKSSQRSP 238

Query: 239 DRS-RSRSASRS 249
            +S + +S+ RS
Sbjct: 239 AKSPKGKSSQRS 250

Source: Glycine max

Species: Glycine max

Genus: Glycine

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	299
TAIR|locus:2024770	303	SR34 "Serine/Arginine-Rich Pro	0.635	0.627	0.685	8.9e-70
TAIR|locus:2133249	278	SR34b "Serine/Arginine-Rich Pr	0.625	0.672	0.681	1.9e-67
TAIR|locus:2195346	268	SR30 "Serine/Arginine-Rich Pro	0.628	0.701	0.686	5.1e-67
TAIR|locus:2114643	300	SR34a "Serine/Arginine-Rich Pr	0.632	0.63	0.579	9.3e-59
FB|FBgn0040284	255	SF2 "SF2" [Drosophila melanoga	0.247	0.290	0.628	1.2e-47
WB|WBGene00004700	258	rsp-3 [Caenorhabditis elegans	0.230	0.267	0.671	3.3e-47
UNIPROTKB|Q9NEW6	258	rsp-3 "Probable splicing facto	0.230	0.267	0.671	3.3e-47
ZFIN|ZDB-GENE-040426-1950	257	srsf1a "serine/arginine-rich s	0.234	0.272	0.671	1.1e-44
UNIPROTKB|Q5ZML3	257	SRSF1 "Serine/arginine-rich sp	0.575	0.669	0.508	4.5e-43
ZFIN|ZDB-GENE-040426-1467	258	srsf1b "serine/arginine-rich s	0.575	0.666	0.513	4.5e-43

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

 Score = 707 (253.9 bits), Expect = 8.9e-70, P = 8.9e-70
 Identities = 137/200 (68%), Positives = 152/200 (76%)

Query:     1 MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
             MSSR+SRT+YVGNLPGDIREREVEDLF KYGP+  IDLK+PPRPPGYAFVEF++ARDAED
Sbjct:     1 MSSRSSRTVYVGNLPGDIREREVEDLFSKYGPVVQIDLKVPPRPPGYAFVEFDDARDAED 60

Query:    61 AIRGRDGYDFDGHRLRVELAXXXXXXXXXXXXXXXXXXXXXXX----------XXXXEYR 110
             AI GRDGYDFDGHRLRVELA                                     E+R
Sbjct:    61 AIHGRDGYDFDGHRLRVELAHGGRRSSDDTRGSFNGGGRGGGRGRGDGGSRGPSRRSEFR 120

Query:   111 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSE 170
             VLVTGLPSSASWQDLKDHMR+ GDVCFSQV+RD  GTTG+VDYT Y+DMK+A+KKLDD+E
Sbjct:   121 VLVTGLPSSASWQDLKDHMRKGGDVCFSQVYRDARGTTGVVDYTCYEDMKYALKKLDDTE 180

Query:   171 FRNAFSRAYVRVREYDHRRD 190
             FRNAFS  YVRVREYD R+D
Sbjct:   181 FRNAFSNGYVRVREYDSRKD 200

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 = 685 (246.2 bits), Expect = 1.9e-67, P = 1.9e-67
 Identities = 137/201 (68%), Positives = 150/201 (74%)

Query:     1 MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
             MSSR+SRT+YVGNLPGDIREREVEDLF KYGP+  IDLKIPPRPPGYAFVEFE+ARDA+D
Sbjct:     1 MSSRSSRTIYVGNLPGDIREREVEDLFSKYGPVVQIDLKIPPRPPGYAFVEFEDARDADD 60

Query:    61 AIRGRDGYDFDGHRLRVELAXXXXXXXXXXXXXXXXXXXXXXX-----------XXXXEY 109
             AI GRDGYDFDGH LRVELA                                      EY
Sbjct:    61 AIYGRDGYDFDGHHLRVELAHGGRRSSHDARGSYSGRGRGGRGGGDGGGRERGPSRRSEY 120

Query:   110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDS 169
             RV+V+GLPSSASWQDLKDHMR+ G+VCFSQVFRDG GTTGIVDYT+Y+DMK+A   LDD+
Sbjct:   121 RVVVSGLPSSASWQDLKDHMRKGGEVCFSQVFRDGRGTTGIVDYTSYEDMKYA---LDDT 177

Query:   170 EFRNAFSRAYVRVREYDHRRD 190
             EFRNAFS  YVRVREYD RRD
Sbjct:   178 EFRNAFSHEYVRVREYDSRRD 198

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

 Score = 681 (244.8 bits), Expect = 5.1e-67, P = 5.1e-67
 Identities = 129/188 (68%), Positives = 146/188 (77%)

Query:     1 MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
             MSSR +RT+YVGNLPGDIR+ EVEDLFYKYGPI  IDLKIPPRPPGYAFVEFE+ RDA+D
Sbjct:     1 MSSRWNRTIYVGNLPGDIRKCEVEDLFYKYGPIVDIDLKIPPRPPGYAFVEFEDPRDADD 60

Query:    61 AIRGRDGYDFDGHRLRVELAXXXXXXXXXXXXXXXXXXXXXXXXXXXEYRVLVTGLPSSA 120
             AI GRDGYDFDG RLRVE+A                           +YRVLVTGLP SA
Sbjct:    61 AIYGRDGYDFDGCRLRVEIAHGGRRFSPSVDRYSSSYSASRAPSRRSDYRVLVTGLPPSA 120

Query:   121 SWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYV 180
             SWQDLKDHMR+AGDVCFS+VF D  G +G+VDY+NYDDMK+AI+KLD +EFRNAFS AY+
Sbjct:   121 SWQDLKDHMRKAGDVCFSEVFPDRKGMSGVVDYSNYDDMKYAIRKLDATEFRNAFSSAYI 180

Query:   181 RVREYDHR 188
             RVREY+ R
Sbjct:   181 RVREYESR 188

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

 Score = 603 (217.3 bits), Expect = 9.3e-59, P = 9.3e-59
 Identities = 117/202 (57%), Positives = 142/202 (70%)

Query:     1 MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
             MS R SR++YVGNLPGDIRE E+ED+FYKYG I  I+LK+PPRPP Y FVEFE +RDAED
Sbjct:     1 MSGRFSRSIYVGNLPGDIREHEIEDIFYKYGRIVDIELKVPPRPPCYCFVEFEHSRDAED 60

Query:    61 AIRGRDGYDFDGHRLRVELAXXXXXXXXXXXXXXXXX-------------XXXXXXXXXX 107
             AI+GRDGY+ DG RLRVELA                                        
Sbjct:    61 AIKGRDGYNLDGCRLRVELAHGGRGQSSSDRRGGYGGGGSGYGGGGGGGGSARFGVSRHS 120

Query:   108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLD 167
             E+RV+V GLPSSASWQDLKDHMR+AGDVCF++V RD  GT G+VDYTNYDDMK+AI+KLD
Sbjct:   121 EFRVIVRGLPSSASWQDLKDHMRKAGDVCFAEVTRDSDGTYGVVDYTNYDDMKYAIRKLD 180

Query:   168 DSEFRNAFSRAYVRVREYDHRR 189
             D+EFRN ++R ++RV++Y+  R
Sbjct:   181 DTEFRNPWARGFIRVKKYESSR 202

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

FB|FBgn0040284 SF2 "SF2" [Drosophila melanogaster (taxid:7227)]

 Score = 262 (97.3 bits), Expect = 1.2e-47, Sum P(2) = 1.2e-47
 Identities = 49/78 (62%), Positives = 63/78 (80%)

Query:   108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLD 167
             +YRV+VTGLP+S SWQDLKDHMR AGDVCF+  ++DGSG   +V++  ++DMK+AIKKLD
Sbjct:   114 QYRVMVTGLPASGSWQDLKDHMREAGDVCFADTYKDGSG---VVEFLRHEDMKYAIKKLD 170

Query:   168 DSEFRNAFSR-AYVRVRE 184
             DS FR+     AY+RVRE
Sbjct:   171 DSRFRSHEGEVAYIRVRE 188

GO:0005515 "protein binding" evidence=IPI

GO:0005681 "spliceosomal complex" evidence=ISS

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

GO:0003729 "mRNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=IDA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0071011 "precatalytic spliceosome" evidence=IDA

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

GO:0007095 "mitotic G2 DNA damage checkpoint" evidence=IGI

GO:0022008 "neurogenesis" evidence=IMP

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

 Score = 263 (97.6 bits), Expect = 3.3e-47, Sum P(2) = 3.3e-47
 Identities = 47/70 (67%), Positives = 60/70 (85%)

Query:     9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
             +YVGNLPGD+RE+EVED+F+KYG I ++D+K   R P +AFVEFE+ RDAEDA+R RDGY
Sbjct:    11 VYVGNLPGDVREKEVEDIFHKYGRIKYVDIK-SGRGPAFAFVEFEDHRDAEDAVRARDGY 69

Query:    69 DFDGHRLRVE 78
             +FDG R+RVE
Sbjct:    70 EFDGRRIRVE 79

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 = 263 (97.6 bits), Expect = 3.3e-47, Sum P(2) = 3.3e-47
 Identities = 47/70 (67%), Positives = 60/70 (85%)

Query:     9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
             +YVGNLPGD+RE+EVED+F+KYG I ++D+K   R P +AFVEFE+ RDAEDA+R RDGY
Sbjct:    11 VYVGNLPGDVREKEVEDIFHKYGRIKYVDIK-SGRGPAFAFVEFEDHRDAEDAVRARDGY 69

Query:    69 DFDGHRLRVE 78
             +FDG R+RVE
Sbjct:    70 EFDGRRIRVE 79

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

ZFIN|ZDB-GENE-040426-1950 srsf1a "serine/arginine-rich splicing factor 1a" [Danio rerio (taxid:7955)]

 Score = 248 (92.4 bits), Expect = 1.1e-44, Sum P(2) = 1.1e-44
 Identities = 47/70 (67%), Positives = 56/70 (80%)

Query:     9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
             +YVGNLP DIR ++VED+FYKYG I  IDLK     P +AFVEFE+ RDAEDA+  RDGY
Sbjct:    17 IYVGNLPPDIRTKDVEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYARDGY 76

Query:    69 DFDGHRLRVE 78
             D+DG+RLRVE
Sbjct:    77 DYDGYRLRVE 86

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

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

 Score = 455 (165.2 bits), Expect = 4.5e-43, P = 4.5e-43
 Identities = 91/179 (50%), Positives = 118/179 (65%)

Query:     9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
             +YVGNLP DIR +++ED+FYKYG I  IDLK     P +AFVEFE+ RDAEDA+ GRDGY
Sbjct:    18 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 77

Query:    69 DFDGHRLRVELAXXXXXXXXXXXXXXXXXXXXXXX---XXXXEYRVLVTGLPSSASWQDL 125
             D+DG+RLRVE                                EYRV+V+GLP S SWQDL
Sbjct:    78 DYDGYRLRVEFPRSGRGTGRGGGGGGGGGAPRGRYGPPSRRSEYRVIVSGLPPSGSWQDL 137

Query:   126 KDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR-AYVRVR 183
             KDHMR AGDVC++ VFRDG   TG+V++   +DM +A++KLD+++FR+     AY+RV+
Sbjct:   138 KDHMREAGDVCYADVFRDG---TGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK 193

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 = 455 (165.2 bits), Expect = 4.5e-43, P = 4.5e-43
 Identities = 92/179 (51%), Positives = 118/179 (65%)

Query:     9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
             +YVGNLP DIR ++VED+FYKYG I  IDLK     P +AFVEFE+ RDAEDA+ GRDGY
Sbjct:    17 IYVGNLPPDIRTKDVEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 76

Query:    69 DFDGHRLRVELAXXXXXXXXXXXXXXXXXXXXXXX---XXXXEYRVLVTGLPSSASWQDL 125
             D+DG+RLRVE                                EYRV+V+GLP S SWQDL
Sbjct:    77 DYDGYRLRVEFPRSGRGGGRGGGGGGGVGAPRGRYGPPSRRSEYRVIVSGLPPSGSWQDL 136

Query:   126 KDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR-AYVRVR 183
             KDHMR AGDVC++ VFRDG   TG+V++   +DM +A++KLD+++FR+     AY+RV+
Sbjct:   137 KDHMREAGDVCYADVFRDG---TGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK 192

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

---

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)
O22315	SRSF1_ARATH	No assigned EC number	0.6938	0.9732	0.9603	yes	no
Q5ZML3	SRSF1_CHICK	No assigned EC number	0.5427	0.6254	0.7276	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:
	gw1.II.749.1	hypothetical protein (252 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	gw1.II.4036.1	hypothetical protein (182 aa)			•						0.417

---

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	299
cd12602	76	cd12602, RRM2_SF2_plant_like, RNA recognition moti	8e-44
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	7e-43
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	2e-37
cd12601	74	cd12601, RRM2_SRSF1_like, RNA recognition motif 2	3e-29
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	3e-28
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	2e-27
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	1e-23
smart00360	73	smart00360, RRM, RNA recognition motif	8e-23
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	3e-21
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-21
cd12768	76	cd12768, RRM2_SRSF9, RNA recognition motif 2 in ve	2e-20
cd12767	76	cd12767, RRM2_SRSF1, RNA recognition motif 2 in se	1e-19
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-19
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	3e-18
cd12600	72	cd12600, RRM2_SRSF4_like, RNA recognition motif 2	7e-16
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-15
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-15
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	4e-15
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	4e-13
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	4e-13
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-12
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	1e-12
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	2e-12
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	2e-12
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	3e-12
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	5e-12
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	7e-12
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	8e-12
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	1e-11
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	1e-11
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	3e-11
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	3e-11
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	5e-11
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	5e-11
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	5e-11
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	6e-11
cd12764	72	cd12764, RRM2_SRSF4, RNA recognition motif 2 in ve	8e-11
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	1e-10
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-10
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-10
cd12765	75	cd12765, RRM2_SRSF5, RNA recognition motif 2 in ve	2e-10
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	3e-10
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	3e-10
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	4e-10
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	5e-10
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	6e-10
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	7e-10
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-09
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	2e-09
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-09
cd12766	73	cd12766, RRM2_SRSF6, RNA recognition motif 2 found	2e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	3e-09
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	3e-09
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-09
smart00360	73	smart00360, RRM, RNA recognition motif	4e-09
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	5e-09
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	6e-09
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	6e-09
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	7e-09
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	8e-09
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	8e-09
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	1e-08
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	1e-08
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	1e-08
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	1e-08
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-08
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	2e-08
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-08
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	2e-08
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	2e-08
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	2e-08
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-08
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	3e-08
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	3e-08
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	3e-08
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	4e-08
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	4e-08
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	5e-08
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	7e-08
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	7e-08
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	9e-08
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	9e-08
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	9e-08
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-07
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	1e-07
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	1e-07
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	1e-07
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	1e-07
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	1e-07
cd12420	79	cd12420, RRM_RBPMS_like, RNA recognition motif in	2e-07
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-07
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-07
cd12467	78	cd12467, RRM_Srp1p_like, RNA recognition motif 1 i	3e-07
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	3e-07
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	4e-07
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	4e-07
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	4e-07
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	4e-07
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	5e-07
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	7e-07
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	8e-07
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	8e-07
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	9e-07
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	9e-07
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	1e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	1e-06
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-06
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	1e-06
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-06
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	1e-06
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	1e-06
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	2e-06
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	2e-06
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-06
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	2e-06
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-06
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	2e-06
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	3e-06
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	4e-06
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	4e-06
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	4e-06
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	5e-06
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	5e-06
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	5e-06
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	6e-06
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	6e-06
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	7e-06
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	8e-06
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	9e-06
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	9e-06
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	1e-05
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	1e-05
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	1e-05
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	1e-05
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	1e-05
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	1e-05
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	1e-05
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	2e-05
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	2e-05
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-05
pfam06075	564	pfam06075, DUF936, Plant protein of unknown functi	2e-05
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-05
cd12658	76	cd12658, RRM1_MYEF2, RNA recognition motif 1 in ve	2e-05
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	2e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-05
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	2e-05
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	3e-05
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	3e-05
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	3e-05
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	3e-05
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	3e-05
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	3e-05
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	3e-05
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	3e-05
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	4e-05
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	4e-05
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	4e-05
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	5e-05
cd12250	82	cd12250, RRM2_hnRNPR_like, RNA recognition motif 2	5e-05
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	5e-05
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	5e-05
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	6e-05
cd12657	76	cd12657, RRM1_hnRNPM, RNA recognition motif 1 in v	6e-05
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	6e-05
cd12285	85	cd12285, RRM3_RBM39_like, RNA recognition motif 3	7e-05
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	7e-05
cd12533	84	cd12533, RRM_EWS, RNA recognition motif in vertebr	7e-05
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	8e-05
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	8e-05
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	9e-05
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	9e-05
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-04
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	1e-04
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-04
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	1e-04
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	1e-04
cd12281	92	cd12281, RRM1_TatSF1_like, RNA recognition motif 1	1e-04
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	1e-04
pfam00937	346	pfam00937, Corona_nucleoca, Coronavirus nucleocaps	1e-04
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	1e-04
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	1e-04
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	2e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-04
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	2e-04
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	2e-04
cd12253	79	cd12253, RRM_PIN4_like, RNA recognition motif in y	2e-04
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	2e-04
cd12724	92	cd12724, RRM1_CPEB2_like, RNA recognition motif 1	2e-04
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	2e-04
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	2e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	2e-04
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	3e-04
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	3e-04
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	3e-04
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	3e-04
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	3e-04
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	3e-04
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	3e-04
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	4e-04
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	4e-04
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	4e-04
cd12299	71	cd12299, RRM4_Prp24, RNA recognition motif 4 in fu	4e-04
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	5e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	5e-04
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	6e-04
cd12604	76	cd12604, RRM_RALY, RNA recognition motif in verteb	7e-04
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	7e-04
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	7e-04
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	7e-04
cd12439	79	cd12439, RRM_TRMT2A, RNA recognition motif in tRNA	9e-04
cd12434	75	cd12434, RRM_RCAN_like, RNA recognition motif in r	0.001
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	0.001
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	0.001
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	0.001
cd12461	81	cd12461, RRM_SCAF4, RNA recognition motif found in	0.001
cd12348	75	cd12348, RRM1_SHARP, RNA recognition motif 1 in SM	0.001
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	0.001
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	0.001
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	0.001
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	0.001
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	0.002
cd12478	91	cd12478, RRM1_U2B, RNA recognition motif 1 in U2 s	0.002
cd12388	70	cd12388, RRM1_RAVER, RNA recognition motif 1 in ri	0.002
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	0.002
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	0.002
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	0.002
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.003
cd12289	93	cd12289, RRM_LARP6, RNA recognition motif in La-re	0.003
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	0.003
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	0.003
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	0.003
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	0.003
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	0.003
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	0.003
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	0.004
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.004
pfam00937	346	pfam00937, Corona_nucleoca, Coronavirus nucleocaps	0.004
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	0.004
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	0.004
cd12569	72	cd12569, RRM4_RBM19, RNA recognition motif 4 in RN	0.004
pfam04484	313	pfam04484, DUF566, Family of unknown function (DUF	0.004
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	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 =  143 bits (363), Expect = 8e-44
 Identities = 68/76 (89%), Positives = 74/76 (97%)

Query: 109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDD 168
           +RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG GTTGIVD+TNYDDMK+AI+KLDD
Sbjct: 1   FRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGRGTTGIVDFTNYDDMKYAIRKLDD 60

Query: 169 SEFRNAFSRAYVRVRE 184
           +EFRN FSRAY+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 =  141 bits (357), Expect = 7e-43
 Identities = 65/72 (90%), Positives = 69/72 (95%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG 67
          T+YVGNLPGDIREREVEDLFYKYGPI  IDLK+PPRPPGYAF+EFE+ARDAEDAIRGRDG
Sbjct: 1  TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDG 60

Query: 68 YDFDGHRLRVEL 79
          YDFDG 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 =  127 bits (321), Expect = 2e-37
 Identities = 55/72 (76%), Positives = 62/72 (86%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG 67
           +YVGNLPGDIRER++EDLFYKYGPI  IDLK   R P +AFVEFE+ RDAEDA+RGRDG
Sbjct: 1  RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDAVRGRDG 60

Query: 68 YDFDGHRLRVEL 79
          YDFDG+RLRVE 
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|241045 cd12601, RRM2_SRSF1_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF9 and similar proteins

 Score =  106 bits (265), Expect = 3e-29
 Identities = 46/77 (59%), Positives = 63/77 (81%), Gaps = 4/77 (5%)

Query: 109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDD 168
           YRV+V+GLP + SWQDLKDHMR AGDVC++ V+RDG   TG+V++  Y+DMK+A+KKLDD
Sbjct: 1   YRVIVSGLPPTGSWQDLKDHMREAGDVCYADVYRDG---TGVVEFLRYEDMKYAVKKLDD 57

Query: 169 SEFRN-AFSRAYVRVRE 184
           S+FR+     +Y+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|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score =  103 bits (259), Expect = 3e-28
 Identities = 39/76 (51%), Positives = 54/76 (71%), Gaps = 5/76 (6%)

Query: 109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDD 168
           +RV+V+GLP  ASWQDLKD  R+AGDV ++ V RD  G  G+V++T+ +DM+ A++KLD 
Sbjct: 1   FRVVVSGLPEGASWQDLKDFGRQAGDVTYADVDRDQEG-EGVVEFTSQEDMERALRKLDG 59

Query: 169 SEFRNAFSRAYVRVRE 184
           +EFR       VRV E
Sbjct: 60  TEFRG----RRVRVEE 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|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score =  101 bits (253), Expect = 2e-27
 Identities = 49/70 (70%), Positives = 58/70 (82%), Gaps = 1/70 (1%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          +YVGNLP DIR +++EDLFYKYG I  IDLK    PP +AFVEFE+ RDAEDA+ GRDGY
Sbjct: 2  IYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRGPP-FAFVEFEDPRDAEDAVYGRDGY 60

Query: 69 DFDGHRLRVE 78
          D+DG+RLRVE
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 = 91.1 bits (227), Expect = 1e-23
 Identities = 39/74 (52%), Positives = 51/74 (68%), Gaps = 2/74 (2%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          +YVGNL     +RE+ED F KYGP+    + +   PPG+AFVEFE+ RDAEDA+R  DG 
Sbjct: 2  VYVGNLGPRATKRELEDEFEKYGPLR--SVWVARNPPGFAFVEFEDPRDAEDAVRALDGR 59

Query: 69 DFDGHRLRVELAHG 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 = 89.2 bits (222), Expect = 8e-23
 Identities = 31/73 (42%), Positives = 43/73 (58%), Gaps = 3/73 (4%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAIRG 64
          TL+VGNLP D  E E+ +LF K+G +  + L       +  G+AFVEFE   DAE A+  
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

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

Length = 73

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

 Score = 84.9 bits (210), Expect = 3e-21
 Identities = 43/70 (61%), Positives = 53/70 (75%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          +YVGNLP D+RE+++EDLFYKYG I  I+LK       +AFV FE+ RDAEDA+ GR+GY
Sbjct: 2  IYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVPFAFVRFEDPRDAEDAVFGRNGY 61

Query: 69 DFDGHRLRVE 78
          DF   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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 85.0 bits (211), Expect = 3e-21
 Identities = 32/70 (45%), Positives = 43/70 (61%), Gaps = 2/70 (2%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP--RPPGYAFVEFEEARDAEDAIRGRD 66
          L+VGNLP D  E +++DLF K+GPI  I +      R  G+AFVEFE+  DAE A+   +
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 67 GYDFDGHRLR 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|241212 cd12768, RRM2_SRSF9, RNA recognition motif 2 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 82.7 bits (204), Expect = 2e-20
 Identities = 39/77 (50%), Positives = 58/77 (75%), Gaps = 4/77 (5%)

Query: 109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDD 168
           +RV+V+GLP S SWQDLKDHMR AGDVC++ V +DG    G+V++   +DM++A++KLDD
Sbjct: 1   FRVIVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG---MGVVEFLRKEDMEYALRKLDD 57

Query: 169 SEFRNAFSR-AYVRVRE 184
           ++FR+     +Y+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|241211 cd12767, RRM2_SRSF1, RNA recognition motif 2 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 80.5 bits (198), Expect = 1e-19
 Identities = 42/75 (56%), Positives = 59/75 (78%), Gaps = 4/75 (5%)

Query: 110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDS 169
           RV+V+GLP S SWQDLKDHMR AGDVC++ VFRDG   TG+V++   +DM +A++KLD++
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREAGDVCYADVFRDG---TGVVEFVRKEDMTYAVRKLDNT 58

Query: 170 EFRN-AFSRAYVRVR 183
           +FR+     AY+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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 80.0 bits (198), Expect = 2e-19
 Identities = 29/72 (40%), Positives = 43/72 (59%), Gaps = 2/72 (2%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP--RPPGYAFVEFEEARDAEDAIRGRD 66
          L+VGNLP D  E ++ +LF K+G I  + +      +  G+AFVEFE   DAE A+   +
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 67 GYDFDGHRLRVE 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 = 76.9 bits (190), Expect = 3e-18
 Identities = 32/71 (45%), Positives = 40/71 (56%), Gaps = 7/71 (9%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHID-LKIPPRPPGYAFVEFEEARDAEDAIRGRDG 67
          L+VGNLP      E+  LF KYG +   D +K       Y FV  EE  DAEDAI+  +G
Sbjct: 2  LFVGNLPDATTSEELRALFEKYGTVTECDVVK------NYGFVHMEEEEDAEDAIKALNG 55

Query: 68 YDFDGHRLRVE 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 = 70.5 bits (173), Expect = 7e-16
 Identities = 29/63 (46%), Positives = 41/63 (65%), Gaps = 1/63 (1%)

Query: 109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDD 168
           YR++V  L S  SWQDLKD MR+AG+V ++   +      G+V++  Y DMK AI+KLD 
Sbjct: 1   YRLIVENLSSRVSWQDLKDFMRKAGEVTYADAHKQRPN-EGVVEFATYSDMKRAIEKLDG 59

Query: 169 SEF 171
           +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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 70.3 bits (173), Expect = 1e-15
 Identities = 29/76 (38%), Positives = 41/76 (53%), Gaps = 3/76 (3%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAIRG 64
           LYVGNLP ++ E +++DLF ++G +    +       R  G+ FVE E A +A  AI  
Sbjct: 1  NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 65 RDGYDFDGHRLRVELA 80
           +G DF 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|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 = 69.9 bits (172), Expect = 1e-15
 Identities = 27/76 (35%), Positives = 40/76 (52%), Gaps = 3/76 (3%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAIRG 64
           L+V  L     E+E+E LF K+G +  + L   P      G+ FV FE   DA+ AIR 
Sbjct: 3  KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 65 RDGYDFDGHRLRVELA 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|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 68.5 bits (168), Expect = 4e-15
 Identities = 34/74 (45%), Positives = 45/74 (60%), Gaps = 5/74 (6%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          +Y+G LP   RER+VE  F  YG I  I+LK      G+ FVEFE+ RDA+DA+   +G 
Sbjct: 2  VYIGRLPYRARERDVERFFKGYGRIREINLK-----NGFGFVEFEDPRDADDAVYELNGK 56

Query: 69 DFDGHRLRVELAHG 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|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 = 63.0 bits (154), Expect = 4e-13
 Identities = 29/74 (39%), Positives = 43/74 (58%), Gaps = 3/74 (4%)

Query: 10 YVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAIRGRD 66
          +VGN+P D  E ++ ++F + GP+    L       +P GY F EFE+   A  AIR  +
Sbjct: 2  FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 67 GYDFDGHRLRVELA 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|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 63.1 bits (153), Expect = 4e-13
 Identities = 35/74 (47%), Positives = 48/74 (64%), Gaps = 2/74 (2%)

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

Query: 69 DFDGHRLRVELAHG 82
             G R+RVEL++G
Sbjct: 65 TLCGCRVRVELSNG 78

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 61.8 bits (151), Expect = 1e-12
 Identities = 28/69 (40%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-RPPGYAFVEFEEARDAEDAIRGRDG 67
          LYV NLP  + E ++ + F  YG +  + L     RP G+AFVEF    DAE A++  +G
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

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

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

>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 = 61.8 bits (150), Expect = 1e-12
 Identities = 36/76 (47%), Positives = 47/76 (61%), Gaps = 7/76 (9%)

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

Query: 67 GYDF--DGHRLRVELA 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|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 61.6 bits (149), Expect = 2e-12
 Identities = 38/74 (51%), Positives = 48/74 (64%), Gaps = 2/74 (2%)

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

Query: 69 DFDGHRLRVELAHG 82
             G R+RVEL+ G
Sbjct: 60 VICGSRVRVELSTG 73

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|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 = 28/74 (37%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 8  TLYVGNL-PGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRD 66
          TL+V    PG  RE ++E LF  +GP+   D++       +AFVEFE++ DA  A+    
Sbjct: 1  TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDIRKT-----FAFVEFEDSEDATKALEALH 55

Query: 67 GYDFDGHRLRVELA 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|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 60.7 bits (148), Expect = 3e-12
 Identities = 27/74 (36%), Positives = 38/74 (51%), Gaps = 7/74 (9%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP-----GYAFVEFEEARDAEDAIR 63
          LYVG L  ++ E+ +   F  +G I   D++IP         G+AFVEFEE  DA  AI 
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDI--KDIQIPLDYETQKHRGFAFVEFEEPEDAAAAID 58

Query: 64 GRDGYDFDGHRLRV 77
            +  +  G  +RV
Sbjct: 59 NMNESELFGRTIRV 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|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 60.5 bits (147), Expect = 5e-12
 Identities = 34/82 (41%), Positives = 48/82 (58%), Gaps = 7/82 (8%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEARDAEDAI 62
          +LYV N+    R  ++  LF KYGPI  +D+ IP      RP G+A+V+FE+ RDAEDA+
Sbjct: 2  SLYVRNVADATRPDDLRRLFGKYGPI--VDVYIPLDFYTRRPRGFAYVQFEDVRDAEDAL 59

Query: 63 RGRDGYDFDGHRLRVELAHGGR 84
             D   F G  + ++ A G R
Sbjct: 60 YYLDRTRFLGREIEIQFAQGDR 81

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

 Score = 60.0 bits (146), Expect = 7e-12
 Identities = 30/80 (37%), Positives = 40/80 (50%), Gaps = 6/80 (7%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHID---LKIPP---RPPGYAFVEFEEARDAEDA 61
           L++GNL   + E  +  LF KYG I   D    K  P   +P GY FV FE   +AE A
Sbjct: 1  RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 62 IRGRDGYDFDGHRLRVELAH 81
          ++  +G    G +L V  AH
Sbjct: 61 LKSLNGKTALGKKLVVRWAH 80

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

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

 Score = 59.7 bits (145), Expect = 8e-12
 Identities = 22/73 (30%), Positives = 40/73 (54%)

Query: 5  ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRG 64
          A+RTL++GNL       ++ + F ++G I  ID+K     P YAF+++ +      A+R 
Sbjct: 1  ATRTLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRK 60

Query: 65 RDGYDFDGHRLRV 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|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 59.3 bits (144), Expect = 1e-11
 Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 7/78 (8%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEARDAED 60
          S  L+VGNLP DI E E+++ F ++G +  ++++I       R P + FV F++    + 
Sbjct: 3  SHQLFVGNLPHDITEDELKEFFKEFGNV--LEVRINSKGGGGRLPNFGFVVFDDPEAVQK 60

Query: 61 AIRGRDGYDFDGHRLRVE 78
           +  +  Y    HRL VE
Sbjct: 61 ILANKPIYFRGDHRLNVE 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|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 = 1e-11
 Identities = 30/82 (36%), Positives = 42/82 (51%), Gaps = 3/82 (3%)

Query: 6  SRTLYVGNLPGDIREREV-EDLFYKYGPIAHIDLKIPPR--PPGYAFVEFEEARDAEDAI 62
          SR L+V  LP   R+  +   LF + G      L I P   P G+AFVE+  A DAE+A 
Sbjct: 2  SRCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQ 61

Query: 63 RGRDGYDFDGHRLRVELAHGGR 84
          +  +G+   G  +RV   + GR
Sbjct: 62 QALNGHSLQGSPIRVSFGNPGR 83

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 57.5 bits (140), Expect = 3e-11
 Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 2/56 (3%)

Query: 25 DLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA 80
           LF  +G +    +K+  + PG+AFVEF     AE A++  +G  F G  LRV+ +
Sbjct: 3  KLFSPFGNV--EKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 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|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 57.6 bits (139), Expect = 3e-11
 Identities = 32/74 (43%), Positives = 46/74 (62%), Gaps = 5/74 (6%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          +Y+G L   +RE++++  F  YG +  IDLK      GY FVEFE++RDA+DA+   +G 
Sbjct: 2  VYIGRLSYHVREKDIQRFFGGYGKLLEIDLK-----NGYGFVEFEDSRDADDAVYELNGK 56

Query: 69 DFDGHRLRVELAHG 82
          D  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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 57.2 bits (139), Expect = 5e-11
 Identities = 16/66 (24%), Positives = 33/66 (50%), Gaps = 3/66 (4%)

Query: 111 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTT---GIVDYTNYDDMKHAIKKLD 167
           + V  LP   + +DLKD   + G +   ++ RD +G +     V++ + +D + A++ L+
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 168 DSEFRN 173
             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|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 57.2 bits (139), Expect = 5e-11
 Identities = 28/73 (38%), Positives = 42/73 (57%), Gaps = 3/73 (4%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
          L+VG L  ++ +  ++++F  YG +  +DL   +    P GYA+VEFE   DAE AI+  
Sbjct: 1  LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 66 DGYDFDGHRLRVE 78
          DG   DG  + VE
Sbjct: 61 DGGQIDGQEVTVE 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|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 57.2 bits (139), Expect = 5e-11
 Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 3/76 (3%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRG 64
          TL+V NLP D  + ++E+ F + GPI    +   K   +  G+ +V F    DA+ A+  
Sbjct: 1  TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 65 RDGYDFDGHRLRVELA 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|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 57.2 bits (139), Expect = 6e-11
 Identities = 28/72 (38%), Positives = 37/72 (51%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGR 65
          +R LYV NLP  I   E+ DLF KYG I  I +       G AFV +E+  DA++A    
Sbjct: 2  NRILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHL 61

Query: 66 DGYDFDGHRLRV 77
           G++     L V
Sbjct: 62 SGFNVANRYLVV 73

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

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

 Score = 57.0 bits (137), Expect = 8e-11
 Identities = 28/62 (45%), Positives = 44/62 (70%), Gaps = 1/62 (1%)

Query: 109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDD 168
           YR++V  L S  SWQDLKD+MR+AG+V ++   + G    G++++ +Y DMK A++KLD 
Sbjct: 1   YRLIVENLSSRCSWQDLKDYMRQAGEVTYADAHK-GRKNEGVIEFRSYSDMKRALEKLDG 59

Query: 169 SE 170
           +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|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins

 Score = 56.8 bits (138), Expect = 1e-10
 Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 3/75 (4%)

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

Query: 66 DGYDFDGHRLRVELA 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|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 = 22/75 (29%), Positives = 37/75 (49%), Gaps = 2/75 (2%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGR 65
           L+V  LP  + + E+E LF K+G +  + L      +P G A+VE+E    A  A+   
Sbjct: 4  KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 66 DGYDFDGHRLRVELA 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|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 56.4 bits (137), Expect = 1e-10
 Identities = 29/76 (38%), Positives = 41/76 (53%), Gaps = 3/76 (3%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRG 64
          T+ V NL  D  E ++ +LF  +GPI+ + L   K   +  G+AFV F    DAE AI  
Sbjct: 1  TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 65 RDGYDFDGHRLRVELA 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|241209 cd12765, RRM2_SRSF5, RNA recognition motif 2 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)

 Score = 55.5 bits (133), Expect = 2e-10
 Identities = 30/65 (46%), Positives = 43/65 (66%), Gaps = 1/65 (1%)

Query: 106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKK 165
           R+E R++V  L S  SWQDLKD MR+AG+V F+   R      G+V++ +Y D+K+AI+K
Sbjct: 1   RTENRLIVENLSSRVSWQDLKDFMRQAGEVTFADAHRPKL-NEGVVEFASYSDLKNAIEK 59

Query: 166 LDDSE 170
           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|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 55.7 bits (135), Expect = 3e-10
 Identities = 27/77 (35%), Positives = 37/77 (48%), Gaps = 10/77 (12%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-PRPP-------GYAFVEFEEARDAED 60
          LYVGNL   + E  +   F ++GP+A +  KI  PR            FV F    DAE 
Sbjct: 4  LYVGNLNPKVTEEVLCQEFGRFGPLASV--KIMWPRTEEERRRNRNCGFVAFMNRADAER 61

Query: 61 AIRGRDGYDFDGHRLRV 77
          A+   DG D  G+ 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|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 55.2 bits (134), Expect = 3e-10
 Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 3/77 (3%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
          LYVGNL     E ++ +LF + G I  I +   +    P G+ FVE+    DAE+A++  
Sbjct: 1  LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 66 DGYDFDGHRLRVELAHG 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|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 54.5 bits (132), Expect = 4e-10
 Identities = 27/71 (38%), Positives = 41/71 (57%), Gaps = 7/71 (9%)

Query: 6  SRTLYVGNLPGD-IREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRG 64
          SR ++VGNL  D + + ++E++F KYG I  I L       GY FV+F+   DA  A+ G
Sbjct: 1  SR-VFVGNLNTDKVSKEDLEEIFSKYGKILGISLH-----KGYGFVQFDNEEDARAAVAG 54

Query: 65 RDGYDFDGHRL 75
           +G +  G +L
Sbjct: 55 ENGREIAGQKL 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|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 = 5e-10
 Identities = 29/74 (39%), Positives = 38/74 (51%), Gaps = 7/74 (9%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEARDAEDAIR 63
          L V NL       ++  +F KYG +   D+ IP         G+AFV F + RDAEDA+ 
Sbjct: 1  LKVDNLTYRTTPDDLRRVFEKYGEVG--DVYIPRDRYTRESRGFAFVRFYDKRDAEDAMD 58

Query: 64 GRDGYDFDGHRLRV 77
            DG + DG  LRV
Sbjct: 59 AMDGKELDGRELRV 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|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 54.2 bits (131), Expect = 6e-10
 Identities = 26/74 (35%), Positives = 38/74 (51%), Gaps = 5/74 (6%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRD 66
          + LYV NLP    E ++ +LF +YG +  +          YAFV FEE  DA  A+   +
Sbjct: 2  KVLYVRNLPLSTTEEQLRELFSEYGEVERVKK-----IKDYAFVHFEERDDAVKAMEEMN 56

Query: 67 GYDFDGHRLRVELA 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|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 = 54.3 bits (131), Expect = 7e-10
 Identities = 24/58 (41%), Positives = 37/58 (63%), Gaps = 3/58 (5%)

Query: 5  ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAI 62
           S TL++G+L   + E ++++LF +YG I  ID+ IPPR  G A+V  E  +DA  A+
Sbjct: 1  CSTTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDM-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 = 53.4 bits (129), Expect = 2e-09
 Identities = 34/83 (40%), Positives = 46/83 (55%), Gaps = 6/83 (7%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIR 63
          +TL+V  L  D  E ++   F +YGPI  I L   K   +P GYAF+EFE  RD + A +
Sbjct: 2  KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61

Query: 64 GRDGYDFDGHRLRVELAHGGRGR 86
            DG   DG R+ V++    RGR
Sbjct: 62 YADGKKIDGRRVLVDVE---RGR 81

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

 Score = 52.7 bits (127), Expect = 2e-09
 Identities = 25/72 (34%), Positives = 36/72 (50%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          LYVGNL   + E  + +LF + GPI    L        YAFVE+ + R A  A++  +G 
Sbjct: 1  LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNGR 60

Query: 69 DFDGHRLRVELA 80
             G  ++V  A
Sbjct: 61 LILGQEIKVNWA 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|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 52.6 bits (127), Expect = 2e-09
 Identities = 25/72 (34%), Positives = 42/72 (58%), Gaps = 3/72 (4%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAIRGR 65
          LYVGNL  +I E ++  +F  +G I  + L+  P   R  GY F++F +A DA+ A+   
Sbjct: 1  LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 66 DGYDFDGHRLRV 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|241210 cd12766, RRM2_SRSF6, RNA recognition motif 2 found in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 52.7 bits (126), Expect = 2e-09
 Identities = 27/62 (43%), Positives = 43/62 (69%), Gaps = 1/62 (1%)

Query: 109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDD 168
           YR++V  L S  SWQDLKD MR+AG+V ++   ++     G++++ +Y DMK A++KLD 
Sbjct: 1   YRLIVENLSSRCSWQDLKDFMRQAGEVTYADAHKE-RANEGVIEFRSYSDMKRALEKLDG 59

Query: 169 SE 170
           +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|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 52.7 bits (127), Expect = 3e-09
 Identities = 28/72 (38%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIA--HIDL-KIPPRPPGYAFVEFEEARDAEDAIRGR 65
          L+V NLP    E E+ +LF  +G I+  H+ L K   R  G+AFV F     A  A    
Sbjct: 2  LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 66 DGYDFDGHRLRV 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|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  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          ++VGN+  D  + E+  LF  YG +    +        +AFV       A+ AI   +G 
Sbjct: 3  IFVGNVDEDTSQEELRALFEAYGAVLSCAVM-----RQFAFVHLRGEAAADRAIEELNGR 57

Query: 69 DFDGHRLRVELA 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|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 = 52.2 bits (126), Expect = 3e-09
 Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 3/70 (4%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG 67
          T+YVGNLP  + E E++  F  +G I   ++++     GYAFV F+    A  AI   +G
Sbjct: 2  TVYVGNLPHGLTEEELQRTFSPFGAIE--EVRVFKD-KGYAFVRFDTHEAAATAIVAVNG 58

Query: 68 YDFDGHRLRV 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|214636 smart00360, RRM, RNA recognition motif

 Score = 51.8 bits (125), Expect = 4e-09
 Identities = 14/68 (20%), Positives = 32/68 (47%), Gaps = 4/68 (5%)

Query: 110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD-GSGT---TGIVDYTNYDDMKHAIKK 165
            + V  LP   + ++L++   + G V   ++ RD  +G       V++ + +D + A++ 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 166 LDDSEFRN 173
           L+  E   
Sbjct: 61  LNGKELDG 68

Length = 73

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

 Score = 51.7 bits (124), Expect = 5e-09
 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRP-PGYAFVEFEEARDAEDAIRGRD 66
          T+Y G  P      +V+ LF   GP+    + +  R    +AF+ FE    A+ AI   +
Sbjct: 1  TVYAGPFPTSFCLSDVKRLFETCGPVR--KVTMLSRTVQPHAFITFENLEAAQLAIETLN 58

Query: 67 GYDFDGHRLRVE 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|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 51.6 bits (124), Expect = 6e-09
 Identities = 29/66 (43%), Positives = 40/66 (60%), Gaps = 5/66 (7%)

Query: 5  ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPG--YAFVEFEE---ARDAE 59
          A+RTL+VGNL   I E E+   F +YG +  +D+K PPR  G  YAFV+F     A  A+
Sbjct: 1  ATRTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAK 60

Query: 60 DAIRGR 65
           A+ G+
Sbjct: 61 VAMSGQ 66

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

 Score = 51.8 bits (125), Expect = 6e-09
 Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 8/82 (9%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAIR 63
          RT+++ NLP D  E E+++LF ++G + +  +          G AFV+F+    A+  + 
Sbjct: 1  RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

Query: 64 -----GRDGYDFDGHRLRVELA 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|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 51.1 bits (123), Expect = 7e-09
 Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 2/71 (2%)

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

Query: 67 GYDFDGHRLRV 77
          GYD +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|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 51.2 bits (123), Expect = 8e-09
 Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 3/77 (3%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIR 63
            L V  LP D+ + E+  LF   GPI    +   +I  +  GY FV++ +  DA+ AI 
Sbjct: 1  TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 64 GRDGYDFDGHRLRVELA 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|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 51.1 bits (123), Expect = 8e-09
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 3/72 (4%)

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

Query: 66 DGYDFDGHRLRV 77
          + +D  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|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 50.3 bits (121), Expect = 1e-08
 Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 3/64 (4%)

Query: 111 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGT---TGIVDYTNYDDMKHAIKKLD 167
           + V  LP S +WQDLKD  R  G+V  + V  D  G     G V + + +D + AI+  +
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 168 DSEF 171
             + 
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|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 50.8 bits (121), Expect = 1e-08
 Identities = 35/76 (46%), Positives = 45/76 (59%), Gaps = 5/76 (6%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          +Y+G L    RER+VE  F  YG I  +DLK      GY FVEF++ RDA+DA+   +G 
Sbjct: 2  VYIGRLSYQARERDVERFFKGYGKILEVDLK-----NGYGFVEFDDLRDADDAVYELNGK 56

Query: 69 DFDGHRLRVELAHGGR 84
          D  G R+ VE A G R
Sbjct: 57 DLCGERVIVEHARGPR 72

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|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 = 51.0 bits (122), Expect = 1e-08
 Identities = 25/75 (33%), Positives = 46/75 (61%), Gaps = 3/75 (4%)

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

Query: 66 DGYDFDGHRLRVELA 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|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 50.7 bits (122), Expect = 1e-08
 Identities = 27/71 (38%), Positives = 40/71 (56%), Gaps = 2/71 (2%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG 67
          TL V NL   I ++E+  LF ++G +   D++  P  P   FVEF + R AE A+   +G
Sbjct: 3  TLLVFNLDSPISDQELRSLFSQFGEVK--DIRETPLRPSQKFVEFYDIRAAEAALDALNG 60

Query: 68 YDFDGHRLRVE 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|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 55.3 bits (133), Expect = 1e-08
 Identities = 34/106 (32%), Positives = 44/106 (41%), Gaps = 1/106 (0%)

Query: 195 PSRGRSYSRGRSESRSRSRSRGRSYSRSRSQSKSPKAKS-SRRSPDRSRSRSASRSRSGS 253
           P R R  SRGR   RS  R R RS  RSR + +  +++  S R   R R R    SRS  
Sbjct: 5   PDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPR 64

Query: 254 KPRSLSRSRSRSRSPLPPKQISKSPKKRSVSRSPSGSRSRSRSLSR 299
             R  S  RSR R     + +    + R   R  S S    +   +
Sbjct: 65  SLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKK 110

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

 Score = 50.4 bits (121), Expect = 2e-08
 Identities = 27/69 (39%), Positives = 39/69 (56%), Gaps = 3/69 (4%)

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

Query: 69 DFDGHRLRV 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|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 50.4 bits (121), Expect = 2e-08
 Identities = 16/77 (20%), Positives = 37/77 (48%), Gaps = 5/77 (6%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRP---PGYAFVEFEEARDAEDAI 62
            +++VG L  D+ + E+ + F ++G I  +++ +  R      +AF++FE  + A  A+
Sbjct: 3  KYSIFVGQLSPDVTKEELNERFSRHGKI--LEVNLIKRANHTNAFAFIKFEREQAAARAV 60

Query: 63 RGRDGYDFDGHRLRVEL 79
             +        + V+ 
Sbjct: 61 ESENHSMLKNKTMHVQY 77

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

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

 Score = 50.0 bits (119), Expect = 2e-08
 Identities = 27/70 (38%), Positives = 38/70 (54%), Gaps = 5/70 (7%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          L+VGN+      +E+   F +YGP+   D+        YAFV  E A DA +AIRG D  
Sbjct: 3  LHVGNISSSCTNQELRAKFEEYGPVIECDIV-----KDYAFVHMERAEDAVEAIRGLDNT 57

Query: 69 DFDGHRLRVE 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|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 50.2 bits (120), Expect = 2e-08
 Identities = 27/75 (36%), Positives = 43/75 (57%), Gaps = 3/75 (4%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
          L++G L  D  E+ +E +F KYG I+ + +   +   R  G+ FV FE   DA+DA+   
Sbjct: 3  LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 66 DGYDFDGHRLRVELA 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|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 49.9 bits (119), Expect = 2e-08
 Identities = 24/70 (34%), Positives = 36/70 (51%), Gaps = 5/70 (7%)

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

Query: 69 DFDGHRLRVE 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|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP--RPPGYAFVEFEEARDAEDAIRGRD 66
          +YV NL  D+ + ++++LF KYG I    +      +  G+ FV FE    A+ A+   +
Sbjct: 4  VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELN 63

Query: 67 GYDFDGHRLRV 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|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins

 Score = 49.7 bits (119), Expect = 3e-08
 Identities = 20/69 (28%), Positives = 29/69 (42%), Gaps = 5/69 (7%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          LYV   P D  E  + ++F  YG +  + +        +AFVEFE    A  A     G 
Sbjct: 2  LYVRPFPPDTSESAIREIFSPYGAVKEVKMI-----SNFAFVEFESLESAIRAKDSVHGK 56

Query: 69 DFDGHRLRV 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|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 49.9 bits (120), Expect = 3e-08
 Identities = 24/79 (30%), Positives = 37/79 (46%), Gaps = 13/79 (16%)

Query: 11 VGNLPGDIREREVEDL-------FYKYGPIAHIDLKIPPRPP----GYAFVEFEEARDAE 59
          V  LP  + E ++E L       F K+G    + + +P        GYAFVEF    +A+
Sbjct: 6  VDGLP-VVGEEKLEKLKKVLRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAK 64

Query: 60 DAIRGRDGYDFD-GHRLRV 77
          +A++  +GY  D  H   V
Sbjct: 65 EAVKALNGYKLDKKHTFAV 83

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

 Score = 49.5 bits (119), Expect = 3e-08
 Identities = 26/75 (34%), Positives = 38/75 (50%), Gaps = 7/75 (9%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP----RPPGYAFVEFEEARDAEDAIRG 64
          ++VG +P D+ E E+  LF K GPI  + L +      R  GYAFV +     A+ A++ 
Sbjct: 4  VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNR--GYAFVTYTNKEAAQRAVKQ 61

Query: 65 RDGYDFD-GHRLRVE 78
             Y+   G RL V 
Sbjct: 62 LHNYEIRPGKRLGVC 76

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

 Score = 49.6 bits (118), Expect = 4e-08
 Identities = 30/82 (36%), Positives = 48/82 (58%), Gaps = 7/82 (8%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEARDAEDAI 62
          +L+V N+  D R  ++   F +YGPI  +D+ +P      RP G+A+V+FE+ RDAEDA+
Sbjct: 2  SLFVRNIADDTRSEDLRREFGRYGPI--VDVYVPLDFYTRRPRGFAYVQFEDVRDAEDAL 59

Query: 63 RGRDGYDFDGHRLRVELAHGGR 84
             D     G ++ ++ A G R
Sbjct: 60 HNLDRKWICGRQIEIQFAQGDR 81

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

 Score = 49.5 bits (119), Expect = 4e-08
 Identities = 24/59 (40%), Positives = 33/59 (55%), Gaps = 5/59 (8%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHI----DLKIPPRPPGYAFVEFEEARDAEDAIR 63
          LYVG+L  D+ E  + ++F   GP+  I    DL I  R  GYA+V F+   DAE A+ 
Sbjct: 2  LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDL-ITRRSLGYAYVNFQNPADAERALD 59

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

 Score = 49.2 bits (118), Expect = 5e-08
 Identities = 27/76 (35%), Positives = 41/76 (53%), Gaps = 6/76 (7%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP----GYAFVEFEEARDAEDAIRG 64
          L V NLP    E +++ LF  +G +   ++ IP +P     G+AFV+F    DAE AI+G
Sbjct: 2  LIVRNLPFKCTEADLKKLFSPFGFV--WEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKG 59

Query: 65 RDGYDFDGHRLRVELA 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|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 48.4 bits (116), Expect = 7e-08
 Identities = 22/55 (40%), Positives = 29/55 (52%), Gaps = 3/55 (5%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
           TLYVG L   + E+++ D FY++G I  I   + PR    AFV 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|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 52.6 bits (125), Expect = 7e-08
 Identities = 33/83 (39%), Positives = 49/83 (59%), Gaps = 3/83 (3%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARD 57
            S   + TL+VGNLP D+ E ++ +LF K+GP+  + L   +   +  G+AFVEFE    
Sbjct: 110 KSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEES 169

Query: 58  AEDAIRGRDGYDFDGHRLRVELA 80
           AE AI   +G + +G  LRV+ A
Sbjct: 170 AEKAIEELNGKELEGRPLRVQKA 192

Length = 306

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

 Score = 48.4 bits (116), Expect = 9e-08
 Identities = 25/81 (30%), Positives = 44/81 (54%), Gaps = 11/81 (13%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP--------GYAFVEFEEARDA 58
          R +YV NL   + E ++  +F K+G +  I  +IP +          G+AFV F++A  A
Sbjct: 1  REIYVRNLDFKLDEDDLRGIFSKFGEVESI--RIPKKQDEKQGRLNNGFAFVTFKDASSA 58

Query: 59 EDAIRGRDGYDFDGHRLRVEL 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|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 48.4 bits (116), Expect = 9e-08
 Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 12/81 (14%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAH---IDLKIPPRPPGYAFVEFEEARDAEDAIR 63
            ++VG LP    +  +   F ++G I     I  +   +  GY FV F++   AE A +
Sbjct: 1  TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 64 GRDGYD----FDGHRLRVELA 80
               D     DG +  V LA
Sbjct: 61 -----DPNPIIDGRKANVNLA 76

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

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

 Score = 48.0 bits (114), Expect = 9e-08
 Identities = 29/72 (40%), Positives = 42/72 (58%), Gaps = 5/72 (6%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          +++G L    RE++VE  F  YG I  IDLK      G+ FVEF++ RDA+DA+   DG 
Sbjct: 2  VFIGRLNPAAREKDVERFFKGYGRIRDIDLK-----RGFGFVEFDDPRDADDAVYELDGK 56

Query: 69 DFDGHRLRVELA 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 = 48.1 bits (115), Expect = 1e-07
 Identities = 14/66 (21%), Positives = 32/66 (48%), Gaps = 3/66 (4%)

Query: 111 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGT---TGIVDYTNYDDMKHAIKKLD 167
           + V  LP   + +DL++   + G++   ++ RD  G       V++ + +D + A++ L+
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 168 DSEFRN 173
             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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 47.5 bits (114), Expect = 1e-07
 Identities = 16/67 (23%), Positives = 31/67 (46%), Gaps = 2/67 (2%)

Query: 111 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTG--IVDYTNYDDMKHAIKKLDD 168
           + V  LP S + +DL++     G V   ++ R+     G   V++ + +D + A+KKL+ 
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 169 SEFRNAF 175
                  
Sbjct: 61  LVLDGRT 67

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

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

 Score = 48.2 bits (115), Expect = 1e-07
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 3/72 (4%)

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

Query: 66 DGYDFDGHRLRV 77
          DG  F G  + +
Sbjct: 65 DGKVFQGRLIHI 76

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

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

 Score = 47.8 bits (114), Expect = 1e-07
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 6/73 (8%)

Query: 9  LYVGNLPGD-IREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG 67
          L++GNLP   + + ++  +F  YG +A I LK       Y FV+F+      +AI    G
Sbjct: 2  LFIGNLPTKRVSKEDLFRIFSTYGELAQIVLK-----NAYGFVQFDSPESCANAINCEQG 56

Query: 68 YDFDGHRLRVELA 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|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 47.8 bits (114), Expect = 1e-07
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 3/72 (4%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAIRGR 65
          +YVG++  ++ E  +   F  +GPI  ID+   P   +  G+AFVE+E    A+ A+   
Sbjct: 3  VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 66 DGYDFDGHRLRV 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|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 47.7 bits (114), Expect = 1e-07
 Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 6/76 (7%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP----PRPPGYAFVEFEEARDAEDAI 62
          RTL+VGNL   + E  + +LF + GP+    +KIP     +P  +AFV F+       AI
Sbjct: 2  RTLFVGNLDARVTEEILYELFLQAGPL--EGVKIPKDPNGKPKSFAFVTFKHEVSVPYAI 59

Query: 63 RGRDGYDFDGHRLRVE 78
          +  +G    G  LR++
Sbjct: 60 QLLNGIRLFGRELRIK 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|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 47.8 bits (114), Expect = 1e-07
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 3/72 (4%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
          L++ NL     E ++E LF KYGP++ + L   K+  +P G+AFV +     A  A    
Sbjct: 5  LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 66 DGYDFDGHRLRV 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|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding protein with multiple splicing (RBP-MS)-like proteins

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 27/79 (34%), Positives = 37/79 (46%), Gaps = 7/79 (8%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPG----YAFVEFEEARDAEDAI 62
          RTL+V  LP D++ERE+  LF  +       L    +  G      FV+F  A+ A  A+
Sbjct: 1  RTLFVSGLPSDVKERELAHLFRPFPGYEASRLVFKEKKGGEKQPVGFVDFSSAQCAAAAM 60

Query: 63 RGRDGYDFDG---HRLRVE 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|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 47.5 bits (113), Expect = 2e-07
 Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 3/76 (3%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAIRG 64
          TL+V NL   + + ++ D F    PI H  +   P      GY FV F    DA++A+  
Sbjct: 1  TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 65 RDGYDFDGHRLRVELA 80
                 G  LR+++A
Sbjct: 61 LKNKKLHGRILRLDIA 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|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 47.6 bits (113), Expect = 2e-07
 Identities = 24/67 (35%), Positives = 34/67 (50%), Gaps = 3/67 (4%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
          LYV NLP  + E E+  +F  YG I   +L   K    P G AFV +++  +A+ AI   
Sbjct: 3  LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 66 DGYDFDG 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|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast pre-mRNA-splicing factor Srp1p and similar proteins

 Score = 47.1 bits (112), Expect = 3e-07
 Identities = 29/78 (37%), Positives = 38/78 (48%), Gaps = 6/78 (7%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPG---YAFVEFEEARDAEDAIRG 64
          TLYV     + R R++   F +YG +   D+  PPR      +AFVE+E  RDAEDA   
Sbjct: 1  TLYVTGFGAETRARDLAYEFERYGRLVRCDIP-PPRTFQSRPFAFVEYESHRDAEDAYEE 59

Query: 65 RDGYDFDGHR--LRVELA 80
            G  F      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|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 46.9 bits (112), Expect = 3e-07
 Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 7/77 (9%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI----PPRPPGYAFVEFEEARDAEDAIR 63
          TL+VGNL     + ++E+ F + G +   D++I      R  G+  VEF     A+ A+ 
Sbjct: 1  TLFVGNLSWSAEQDDLEEFFKECGEVV--DVRIAQDDDGRSKGFGHVEFATEEGAQKALE 58

Query: 64 GRDGYDFDGHRLRVELA 80
           + G +  G  +RV+LA
Sbjct: 59 -KSGEELLGREIRVDLA 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|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 50.7 bits (121), Expect = 4e-07
 Identities = 40/112 (35%), Positives = 47/112 (41%), Gaps = 10/112 (8%)

Query: 181 RVREYDHRRDGSQSPSRGRSYSRGRSESRSRSRSRGR---SYSRSRSQSKSPKAKSSRRS 237
           R  E D  R+ S+   R RS  R R  SR RSR R R   S  RS  +   P+ +    S
Sbjct: 1   RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDS 60

Query: 238 PDRSRSRSASRSRSGSKPRSLSRSRS-------RSRSPLPPKQISKSPKKRS 282
                 R +S  RS  +PR  SRS         R R   P  Q  K  KKRS
Sbjct: 61  RSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRS 112

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

 Score = 46.6 bits (111), Expect = 4e-07
 Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 9/63 (14%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP------GYAFVEFEEARDAEDA 61
          T+YV  LP +     ++ +F KYG + ++ 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|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 46.4 bits (110), Expect = 4e-07
 Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 5/71 (7%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          ++VGN+       E+  LF ++G +   D         YAFV  E   +A  AI   +G 
Sbjct: 3  IFVGNVSATCTSDELRGLFEEFGRVVECDKVK-----DYAFVHMEREEEALAAIEALNGK 57

Query: 69 DFDGHRLRVEL 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|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins

 Score = 46.6 bits (111), Expect = 4e-07
 Identities = 16/73 (21%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYA-FVEFEEARDAEDAIRGR 65
          R + + N+P  +R  +++ L   YG + + + ++P +       V +E    A+ A+   
Sbjct: 1  RKIQISNIPPHVRWEDLDSLLSTYGTVKNCE-QVPTKSETATVNVTYESPEQAQQAVNKL 59

Query: 66 DGYDFDGHRLRVE 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|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 46.0 bits (109), Expect = 5e-07
 Identities = 28/77 (36%), Positives = 42/77 (54%), Gaps = 8/77 (10%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAI 62
          S+ L V NL     E  ++++F K   I     +IP    RP GYAFVEFE A DA++A+
Sbjct: 1  SKVLVVNNLSYSASEDSLQEVFEKATSI-----RIPQNNGRPKGYAFVEFESAEDAKEAL 55

Query: 63 RGRDGYDFDGHRLRVEL 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|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 45.9 bits (109), Expect = 7e-07
 Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

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

Query: 65 RDGYDFDGHRLRV 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|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 45.6 bits (109), Expect = 8e-07
 Identities = 22/73 (30%), Positives = 41/73 (56%), Gaps = 4/73 (5%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGR 65
          ++ L++ NLP +  +  +E LF ++ P    ++++ PR  G AFVEFE    A  A++  
Sbjct: 2  NKILFLQNLPEETTKEMLEMLFNQF-P-GFKEVRLVPRR-GIAFVEFETEEQATVALQAL 58

Query: 66 DGYD-FDGHRLRV 77
           G+    GH +++
Sbjct: 59 QGFKITPGHAMKI 71

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

 Score = 45.4 bits (108), Expect = 8e-07
 Identities = 26/69 (37%), Positives = 36/69 (52%), Gaps = 3/69 (4%)

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

Query: 68 YDFDGHRLR 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|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 = 45.6 bits (109), Expect = 9e-07
 Identities = 29/84 (34%), Positives = 37/84 (44%), Gaps = 17/84 (20%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP----------GYAFVEFEEA 55
          +R LYVGNLP  I E E+ D F +   +    L   P  P           +AFVEF   
Sbjct: 1  ARRLYVGNLPPGITEEELVDFFNQA--MLAAGLNQAPGNPVLSVQINPEKNFAFVEF--- 55

Query: 56 RDAEDAIRG--RDGYDFDGHRLRV 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|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 50.2 bits (120), Expect = 9e-07
 Identities = 30/114 (26%), Positives = 41/114 (35%), Gaps = 1/114 (0%)

Query: 183 REYDHRRDGSQSPSRGRSYSRGRSESRSRSRSRGRSYSRSRSQSKSPKAKSSRRSPDRSR 242
                    S S  R RS S   S   S         S S S S+   + S+  S + SR
Sbjct: 278 PSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSR 337

Query: 243 SRSASRSRSGSKPRSLSRSRSRSRSPLPPKQISKSPKKRSVSRSPSGSRSRSRS 296
             + S   S S+  S SR    +    P K+   S    S + S  G  +R R+
Sbjct: 338 GAAVSPGPSPSRSPSPSRPPPPADPSSPRKRPRPSRAPSSPAASA-GRPTRRRA 390

Length = 1352

>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein MRN1 and similar proteins

 Score = 45.5 bits (108), Expect = 1e-06
 Identities = 22/59 (37%), Positives = 30/59 (50%), Gaps = 3/59 (5%)

Query: 5  ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIR 63
          ASR +Y+GNLP    E E+ +   K+GPI  I  KI  +    AFV 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|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 3/58 (5%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIR 63
          +YVGNL   + E  + +LF + GP+ ++ +   ++     GY FVEF    DA+ AI+
Sbjct: 1  VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIK 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|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 45.1 bits (107), Expect = 1e-06
 Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 7/78 (8%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI-----PPRPPGYAFVEFEEARDAEDAI 62
          TL+VGNL   + +  ++  F K+G +  +  ++       R  G+ +V+FE   DA+ AI
Sbjct: 1  TLFVGNLSWSVDDEWLKAEFEKFGTV--VGARVITDRETGRSRGFGYVDFESPEDAKKAI 58

Query: 63 RGRDGYDFDGHRLRVELA 80
             DG + DG  + V+ +
Sbjct: 59 EAMDGKELDGRPINVDFS 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|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 45.2 bits (107), Expect = 1e-06
 Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPG--YAFVEFEEARDAEDAIRGRD 66
          LYVGNL   + E  ++ +F   GP+ ++ +       G  Y FVE+ ++ DAE A++  +
Sbjct: 1  LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 67 GYDFDGHRLRVELA 80
          G   + + +RV  A
Sbjct: 61 GRQIENNEIRVNWA 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|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 26/76 (34%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIR 63
           TL+VG L     E  + ++F +YG I  + L    +     GYAFVE+E  RDA  A R
Sbjct: 4  LTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYR 63

Query: 64 GRDGYDFDGHRLRVEL 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|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 45.3 bits (107), Expect = 1e-06
 Identities = 21/62 (33%), Positives = 36/62 (58%), Gaps = 3/62 (4%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 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|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 44.9 bits (107), Expect = 1e-06
 Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 4/73 (5%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPG-YAFVEFEEARDAEDAIRGRD 66
          T+ V NLP D  E ++   F   G I   ++KI     G  A +EFE   +A  A+  +D
Sbjct: 2  TVKVKNLPKDTTENKIRQFFKDCGEI--REVKIVESEGGLVAVIEFETEDEALAALT-KD 58

Query: 67 GYDFDGHRLRVEL 79
               G+ + V  
Sbjct: 59 HKRLGGNEISVSR 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|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 44.6 bits (106), Expect = 2e-06
 Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 10/81 (12%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR----------PPGYAFVEFEEARDA 58
          +Y+  LP D+ E  + +LF   G I       PP           P G A V +++   A
Sbjct: 1  IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAA 60

Query: 59 EDAIRGRDGYDFDGHRLRVEL 79
          + AI   +GY+F G++++V L
Sbjct: 61 QAAIEWFNGYEFRGNKIKVSL 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|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 26/91 (28%), Positives = 47/91 (51%), Gaps = 21/91 (23%)

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

Query: 48 -AFVEFEEARDAEDAIRGRDGYDFDGHRLRV 77
           A+V F+E   AE A+   +G +F+GH +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|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 26/81 (32%), Positives = 38/81 (46%), Gaps = 8/81 (9%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPP-----GYAFVEFEEARDA 58
           TL+V NL     E  ++  F K G +  + +   K P  P      GY FVEF+    A
Sbjct: 1  TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 59 EDAIRGRDGYDFDGHRLRVEL 79
          + A++   G   DGH 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 48.6 bits (116), Expect = 2e-06
 Identities = 38/167 (22%), Positives = 76/167 (45%), Gaps = 10/167 (5%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP--RPPGYAFVEFEEARDAEDAIRGRD 66
           LYV NL   + E ++ +LF K+G I    +      R  G+AFV FE+  DA  A+   +
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMN 240

Query: 67  GYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGR-GRGVSRRSEYRVL---VTGLPSSASW 122
           G      +   +L + GR +  ++R +            R+ + + +   V  L  + + 
Sbjct: 241 GKKIGLAKEGKKL-YVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTD 299

Query: 123 QDLKDHMRRAGDVCFSQVFRDGSGTT---GIVDYTNYDDMKHAIKKL 166
           + L++     G++  ++V  D  G +   G V ++N ++   A+ ++
Sbjct: 300 EKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEM 346

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

 Score = 44.3 bits (105), Expect = 2e-06
 Identities = 19/68 (27%), Positives = 40/68 (58%), Gaps = 4/68 (5%)

Query: 110 RVLVTGLPSSASWQDLKDHMRR-AGDVCFSQVFRDGSGTT---GIVDYTNYDDMKHAIKK 165
           RV ++ +P    WQDLKD  R   G+V + ++F+D  G +   G+V++ + + ++ A++ 
Sbjct: 1   RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALET 60

Query: 166 LDDSEFRN 173
           ++  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|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 22/62 (35%), Positives = 36/62 (58%), Gaps = 3/62 (4%)

Query: 20 EREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLR 76
          ER++ ++F +YGPI  + +       R  G+ FV FE   DA++A    +G + DG R+R
Sbjct: 13 ERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRIR 72

Query: 77 VE 78
          V+
Sbjct: 73 VD 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|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 44.3 bits (105), Expect = 2e-06
 Identities = 24/81 (29%), Positives = 36/81 (44%), Gaps = 13/81 (16%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP-----GYAFVEFEEARDAEDAIR 63
          LY+GNL  D+ E ++  LF         + KIP         GYAFV+  +   A+ AI 
Sbjct: 1  LYIGNLSSDVNESDLRQLFE--------EHKIPVSSVLVKKGGYAFVDCPDQSWADKAIE 52

Query: 64 GRDGYDFDGHRLRVELAHGGR 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|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate

 Score = 44.2 bits (104), Expect = 3e-06
 Identities = 27/67 (40%), Positives = 40/67 (59%), Gaps = 5/67 (7%)

Query: 4  RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPG--YAFVEFEE---ARDA 58
          RA+R L++GNL  ++ E E+   F KYG I  + +K P R  G  YAF++F+    A  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|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 43.7 bits (104), Expect = 4e-06
 Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 4/78 (5%)

Query: 8  TLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIR 63
          TLY+ NL   I++ E++     LF ++GP+  I      +  G AFV F++   A +A+R
Sbjct: 1  TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNALR 60

Query: 64 GRDGYDFDGHRLRVELAH 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|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 44.0 bits (103), Expect = 4e-06
 Identities = 28/75 (37%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDL--KIPPRPPGYAFVEFEEARDAEDAIRGR 65
          TLYVGNL  D+ E  +  LF + GP     +  +     P Y FVEF E RDA  A+   
Sbjct: 1  TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-YCFVEFYEHRDAAAALAAM 59

Query: 66 DGYDFDGHRLRVELA 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|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins

 Score = 43.4 bits (103), Expect = 4e-06
 Identities = 18/74 (24%), Positives = 39/74 (52%), Gaps = 5/74 (6%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPI----AHIDLKIPPRPPGYAFVEFEEARDAEDAIRG 64
          L++ +LP +  ++++  LF  +G +      +D K   +   + FV ++    A+ AI+ 
Sbjct: 1  LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVD-KNTGQSKCFGFVSYDNPESAQAAIKA 59

Query: 65 RDGYDFDGHRLRVE 78
           +G+   G RL+V+
Sbjct: 60 MNGFQVGGKRLKVQ 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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 47.2 bits (112), Expect = 5e-06
 Identities = 26/87 (29%), Positives = 37/87 (42%), Gaps = 2/87 (2%)

Query: 197 RGRSYSRGRSESRSRSRSRGRSYSRSRSQSKSPKAKSSRRSPDRSRS-RSASRSRSG-SK 254
           R R   RGR  + +R   +GR  SR RS+S+    +   R   R R  RS SRS +   +
Sbjct: 1   RYRDRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYR 60

Query: 255 PRSLSRSRSRSRSPLPPKQISKSPKKR 281
           PR     R   R      +   +  +R
Sbjct: 61  PRGDRSYRRDDRRSGRNTKEPLTEAER 87

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

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

 Score = 43.1 bits (102), Expect = 5e-06
 Identities = 22/74 (29%), Positives = 32/74 (43%), Gaps = 4/74 (5%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRG 64
           L+VGNLP D    ++   F   G    + L   K   +  G AFVEF+ A     A++ 
Sbjct: 2  ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK- 60

Query: 65 RDGYDFDGHRLRVE 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|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 43.5 bits (102), Expect = 5e-06
 Identities = 27/82 (32%), Positives = 47/82 (57%), Gaps = 7/82 (8%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEARDAEDAI 62
          +L+V N+    R  ++   F +YGPI  +D+ +P      RP G+A+++FE+ RDAEDA+
Sbjct: 2  SLFVRNVADATRPEDLRREFGRYGPI--VDVYVPLDFYTRRPRGFAYIQFEDVRDAEDAL 59

Query: 63 RGRDGYDFDGHRLRVELAHGGR 84
             +     G ++ ++ A G R
Sbjct: 60 YNLNRKWVCGRQIEIQFAQGDR 81

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|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 43.3 bits (103), Expect = 6e-06
 Identities = 16/77 (20%), Positives = 37/77 (48%), Gaps = 4/77 (5%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFE-EARDAEDAIRG 64
          L+VG L   + E ++E+ F ++G ++ +++   K      G+A+++        +     
Sbjct: 2  LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 65 RDGYDFDGHRLRVELAH 81
           +G  + G  L++E A 
Sbjct: 62 LNGTKWKGSVLKIEEAK 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|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 43.4 bits (103), Expect = 6e-06
 Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 6/64 (9%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEF---EEARDAEDA 61
          TL++G+L   + E  +   F + G +  + +   K   +  GY FVEF   E A  A  +
Sbjct: 1  TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

Query: 62 IRGR 65
          + G+
Sbjct: 61 LNGK 64

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|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 43.0 bits (102), Expect = 7e-06
 Identities = 24/74 (32%), Positives = 34/74 (45%), Gaps = 5/74 (6%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          L+VG L       E+E  F ++G I  ID         YA++E+E    A+ A     G+
Sbjct: 1  LWVGGLGPWTSLAELEREFDRFGAIRRIDY---DPGRNYAYIEYESIEAAQAAKEALRGF 57

Query: 69 DF--DGHRLRVELA 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|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 43.0 bits (101), Expect = 8e-06
 Identities = 23/64 (35%), Positives = 37/64 (57%), Gaps = 3/64 (4%)

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

Query: 66 DGYD 69
          D Y+
Sbjct: 64 DNYE 67

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|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 46.7 bits (111), Expect = 9e-06
 Identities = 34/116 (29%), Positives = 46/116 (39%), Gaps = 2/116 (1%)

Query: 186 DHRRDGSQSPSRGRSYSR--GRSESRSRSRSRGRSYSRSRSQSKSPKAKSSRRSPDRSRS 243
              R  S SPS   S         S S S SR  S S + S S+S +  +    P  SRS
Sbjct: 291 PRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRS 350

Query: 244 RSASRSRSGSKPRSLSRSRSRSRSPLPPKQISKSPKKRSVSRSPSGSRSRSRSLSR 299
            S SR    + P S  +    SR+P  P   +  P +R    + +G   R  +  R
Sbjct: 351 PSPSRPPPPADPSSPRKRPRPSRAPSSPAASAGRPTRRRARAAVAGRARRRDATGR 406

Length = 1352

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

 Score = 42.6 bits (101), Expect = 9e-06
 Identities = 22/76 (28%), Positives = 32/76 (42%), Gaps = 3/76 (3%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDAEDAIRG 64
           L VGNLP +  + +  +L   +G +    L          GY FVE+     A  A   
Sbjct: 1  LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQ 60

Query: 65 RDGYDFDGHRLRVELA 80
           DG    G +L+V+ A
Sbjct: 61 LDGKQIGGRKLQVDWA 76

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

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

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 2/72 (2%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGR 65
          SRTL+V N+  ++ + E+  LF ++G I  +      R  G+  V + + R A  A R  
Sbjct: 1  SRTLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHR--GFIMVSYYDIRAARRAKRAL 58

Query: 66 DGYDFDGHRLRV 77
           G +  G +L +
Sbjct: 59 QGTELGGRKLDI 70

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|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 42.3 bits (99), Expect = 1e-05
 Identities = 22/62 (35%), Positives = 41/62 (66%), Gaps = 3/62 (4%)

Query: 20 EREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLR 76
          ER++ ++F +YGP+A +++   +   R  G+AFV FE   D+++A+   +G + DG R+R
Sbjct: 13 ERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRIR 72

Query: 77 VE 78
          V+
Sbjct: 73 VD 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|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 19/83 (22%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI----------PPRPPGYAFVEFEEARD 57
          T +VGNLP +  + +++ +F         DL +            +  G+ +VEFE+   
Sbjct: 3  TAFVGNLPFNTVQGDLDAIFK--------DLSVKSVRLVRDKETDKFKGFCYVEFEDVES 54

Query: 58 AEDAIRGRDGYDFDGHRLRVELA 80
           ++A+   DG  FD   LRV++A
Sbjct: 55 LKEALE-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|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 25/80 (31%), Positives = 38/80 (47%), Gaps = 4/80 (5%)

Query: 9  LYVGNLPGDIRERE----VEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRG 64
          ++V +LP    + E    V + F KYG +  + +    R   YAFV+F    DA++A+  
Sbjct: 5  VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQRPYAFVQFTNDDDAKNALAK 64

Query: 65 RDGYDFDGHRLRVELAHGGR 84
            G   DG  +R E A   R
Sbjct: 65 GQGTILDGRHIRCERAKVNR 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|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 42.3 bits (99), Expect = 1e-05
 Identities = 26/75 (34%), Positives = 36/75 (48%), Gaps = 3/75 (4%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP--RPPGYAFVEFEEARDAEDAIRGR 65
          TLYVGNL  D+ E  +  LF + GP     + +      P Y FVEF E R A  ++   
Sbjct: 1  TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDP-YCFVEFFEHRHAAASLAAM 59

Query: 66 DGYDFDGHRLRVELA 80
          +G    G  ++V  A
Sbjct: 60 NGRKIMGKEVKVNWA 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|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 27/78 (34%), Positives = 34/78 (43%), Gaps = 3/78 (3%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRD 66
          R +YVG +P D    E+   F  +G I  I L        Y FV +  A DA  AI    
Sbjct: 3  RVIYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDNYGFVTYRYACDAFRAI--EH 60

Query: 67 GYDFDGHRLRVELAHGGR 84
          G D D    + +L  GGR
Sbjct: 61 GND-DPTEPKYDLCFGGR 77

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

 Score = 42.3 bits (99), Expect = 1e-05
 Identities = 25/64 (39%), Positives = 40/64 (62%), Gaps = 3/64 (4%)

Query: 20 EREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLR 76
          ER++ ++F KYGPIA + +   +   R  G+AFV FE   DA++A    +G + DG R+R
Sbjct: 23 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 82

Query: 77 VELA 80
          V+ +
Sbjct: 83 VDFS 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|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2)

 Score = 41.9 bits (98), Expect = 2e-05
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 6/73 (8%)

Query: 9  LYVGNLPGD-IREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG 67
          +++GNL    +++ +VE +F KYG I    +       G+AFV++   R+A  A+ G DG
Sbjct: 4  VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-----KGFAFVQYVNERNARAAVAGEDG 58

Query: 68 YDFDGHRLRVELA 80
              G  L + LA
Sbjct: 59 RMIAGQVLDINLA 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|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 41.8 bits (98), Expect = 2e-05
 Identities = 27/69 (39%), Positives = 34/69 (49%), Gaps = 3/69 (4%)

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

Query: 69 DFDGHRLRV 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|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 3/73 (4%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAIRGR 65
          L+VGNL  D  E  + + F +YG I+ + L   P   RP G+ +VEF     A+ A+   
Sbjct: 1  LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 66 DGYDFDGHRLRVE 78
           G D  G  +R++
Sbjct: 61 GGTDLLGRPVRLD 73

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

>gnl|CDD|218883 pfam06075, DUF936, Plant protein of unknown function (DUF936)

 Score = 45.6 bits (108), Expect = 2e-05
 Identities = 33/121 (27%), Positives = 45/121 (37%), Gaps = 4/121 (3%)

Query: 174 AFSRAYVRVREYDHRRDGSQSPSRGRSYSRGRSESRSRSRSRGRSYSRSRSQSKSPKAKS 233
            FS A ++V +       S +P RG   S  +S S   S +      RS S+        
Sbjct: 123 FFSDAVIQVIKRKKA---SSAPRRGSWDSSSKSASIDSSPTVIGPRPRSFSELNLTDRTP 179

Query: 234 SRRSPDRSRSRSASRSRSGSKPRSLSRSRSRSRSPLPPKQISKSPKKRSVSRSPSGSRSR 293
           ++    RS   + S S   S P S    RS   S       S   KK +V  +P    SR
Sbjct: 180 AKVRSSRSELGAPSPSGGTSCPSSSGGRRSSIGSRRLRGSAS-LRKKVAVLSAPRKPGSR 238

Query: 294 S 294
           S
Sbjct: 239 S 239

This family consists of several hypothetical proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown. Length = 564

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

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 20/76 (26%), Positives = 34/76 (44%), Gaps = 7/76 (9%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEARDAEDAI 62
           +Y+G+LP    E E+   F ++G +    L++       +  GYAFVEFE    A+   
Sbjct: 1  VVYIGHLPHGFYEPELRKYFSQFGTV--TRLRLSRSKKTGKSKGYAFVEFESPEVAKIVA 58

Query: 63 RGRDGYDFDGHRLRVE 78
             + Y      L+ +
Sbjct: 59 ETMNNYLLFERLLKCK 74

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

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

 Score = 41.5 bits (97), Expect = 2e-05
 Identities = 18/62 (29%), Positives = 39/62 (62%), Gaps = 4/62 (6%)

Query: 110 RVLVTGLPSSASWQDLKDHMR-RAGDVCFSQVFRDGSGTT---GIVDYTNYDDMKHAIKK 165
           RV ++ +P    WQ +KD MR + G+V + ++F+D  G +   G+V++ + + +K A++ 
Sbjct: 1   RVFISNIPYDMKWQAIKDLMREKVGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALEV 60

Query: 166 LD 167
           ++
Sbjct: 61  MN 62

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|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 4/74 (5%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRD 66
          R ++VG L  D+ E ++   F ++G +   D+ IP     +AFV F +   A+      +
Sbjct: 1  RKVFVGRLTEDMTEEDLRQYFSQFGEV--TDVYIPKPFRAFAFVTFADPEVAQSLC--GE 56

Query: 67 GYDFDGHRLRVELA 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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 44.9 bits (106), Expect = 2e-05
 Identities = 45/172 (26%), Positives = 71/172 (41%), Gaps = 27/172 (15%)

Query: 6   SRT-LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDA 61
           S+T L V  LP  + + E+  LF   G I    L   K+  +  GY FV +    DAE A
Sbjct: 2   SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKA 61

Query: 62  IRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSAS 121
           +   +G       ++V  A     R SSD      S +G          + V+GLP + +
Sbjct: 62  VNSLNGLRLQNKTIKVSYA-----RPSSD------SIKGAN--------LYVSGLPKTMT 102

Query: 122 WQDLKDHMRRAGDVCFSQVFRDG----SGTTGIVDYTNYDDMKHAIKKLDDS 169
             +L+      G +  S++  D     S   G + +   D+   AIK L+ +
Sbjct: 103 QHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGT 154

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|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 21/60 (35%), Positives = 28/60 (46%), Gaps = 7/60 (11%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPG--YAFVEFEEARDAEDAIRG 64
            + V NLP    E E+ +LF K+G +  + L     PP    A VEF E  DA  A + 
Sbjct: 1  TVILVKNLPFGTTEEELRELFEKFGSLGRLLL-----PPSRTIALVEFLEPSDARKAFKS 55

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 41.4 bits (97), Expect = 3e-05
 Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 9/73 (12%)

Query: 4  RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP----PRPPGYAFVEFEEARDAE 59
          R +RTL+V NLP +I   E++++F        +D+++P        G A++EF+   +AE
Sbjct: 1  RDARTLFVKNLPYNITVDELKEVFED-----AVDIRLPSGKDGSSKGIAYIEFKTEAEAE 55

Query: 60 DAIRGRDGYDFDG 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|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 41.4 bits (98), Expect = 3e-05
 Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 15/81 (18%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL---------KIPPRPPGYAFVEFEEARDAE 59
          +++G LP  + E +V++L   +G +   +L         K      GYAF E+ +    +
Sbjct: 3  IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSK------GYAFCEYLDPSVTD 56

Query: 60 DAIRGRDGYDFDGHRLRVELA 80
           AI G +G      +L V+ A
Sbjct: 57 QAIAGLNGMQLGDKKLTVQRA 77

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

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

 Score = 41.2 bits (97), Expect = 3e-05
 Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 5/77 (6%)

Query: 5  ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPG-YAFVEFEEARDAEDAIR 63
          A R+++V        E ++ D F  +GP+ ++   I  +  G YA VEF+   +  D + 
Sbjct: 1  AERSVFVSGFKRGTSEEQLMDYFSAFGPVMNV---IMDKDKGVYAIVEFDSK-EGVDKVL 56

Query: 64 GRDGYDFDGHRLRVELA 80
              +  +GHRLRV   
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|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins

 Score = 41.4 bits (97), Expect = 3e-05
 Identities = 17/60 (28%), Positives = 34/60 (56%)

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

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

 Score = 41.3 bits (97), Expect = 3e-05
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL--KIPPRPPGYAFVEFEEARDAEDAIRGRD 66
          + V NLP +  +++V  LF  YG +  + +  K      G+AFVEF  A++A +A+    
Sbjct: 3  ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALK 62

Query: 67 GYDFDGHRLRVELA 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|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal EAR1-like proteins

 Score = 41.0 bits (96), Expect = 3e-05
 Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 2/71 (2%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG 67
          TL + NL   +    +  +F  YG +   +L+  P      FVEF + RDA  A+R  +G
Sbjct: 3  TLVIFNLDPTVSSETLRSIFQVYGDVK--ELRETPCKREQRFVEFFDVRDAAKALRAMNG 60

Query: 68 YDFDGHRLRVE 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|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 41.0 bits (96), Expect = 3e-05
 Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 6/76 (7%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP----RPPGYAFVEFEEARDAEDAI 62
          RTL+VGNL   + E  + +LF + GP+  I +KIP     +P  +AFV F+       A+
Sbjct: 2  RTLFVGNLDPKVTEELIFELFLQAGPV--IKVKIPKDKDGKPKQFAFVNFKHEVSVPYAM 59

Query: 63 RGRDGYDFDGHRLRVE 78
             +G    G  L ++
Sbjct: 60 NLLNGIKLYGRPLNIQ 75

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

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 20/72 (27%), Positives = 31/72 (43%), Gaps = 5/72 (6%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPI----AHIDLKIPPRPPGYAFVEFEEARDAEDAI 62
            +Y+  LP +  + ++E L   +G I    A +D K      GY FV+F+    A  AI
Sbjct: 1  TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNK-CKGYGFVDFDSPEAALKAI 59

Query: 63 RGRDGYDFDGHR 74
           G +G       
Sbjct: 60 EGLNGRGVQAQF 71

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

 Score = 41.0 bits (97), Expect = 4e-05
 Identities = 22/62 (35%), Positives = 31/62 (50%), Gaps = 3/62 (4%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
          L+VG LP    E +V  LF +YG I  + +   K   +  G AFV+F    +A+ AI   
Sbjct: 2  LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 66 DG 67
           G
Sbjct: 62 HG 63

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|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 40.8 bits (96), Expect = 4e-05
 Identities = 19/80 (23%), Positives = 33/80 (41%), Gaps = 8/80 (10%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIA--------HIDLKIPPRPPGYAFVEFEEARDAE 59
           +Y+ NL     E ++E+    + P++                RP G A+ EF     AE
Sbjct: 1  RVYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAE 60

Query: 60 DAIRGRDGYDFDGHRLRVEL 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|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 40.6 bits (95), Expect = 4e-05
 Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

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

Query: 68 YDFDGHRLRVE 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|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 4/72 (5%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
          L+VG L  D+ E ++ + F +YG +  +++   K   +  G+AFV F++  D  D I  +
Sbjct: 2  LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDD-YDPVDKIVLQ 60

Query: 66 DGYDFDGHRLRV 77
            +  +GHR+ V
Sbjct: 61 KYHTINGHRVEV 72

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

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 5/60 (8%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGP-----IAHIDLKIPPRPPGYAFVEFEEARDAEDAIR 63
          L+VG +P    + E+ + F K        I +       +  G+AFVE+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|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 27/74 (36%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP--RPPGYAFVEFEEARDAEDAIRGR 65
           L V NL  D+ E ++E+LF + G +  + +      R  G A V FE+  DAE AI+  
Sbjct: 2  RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQF 61

Query: 66 DGYDFDGHRLRVEL 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

>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 40.6 bits (95), Expect = 5e-05
 Identities = 25/82 (30%), Positives = 38/82 (46%), Gaps = 8/82 (9%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYG--PIAHIDLKIPPRPPG------YAFVEFEEARDAE 59
          TL+V NL      + + D F        A +  K  P+ PG      + FV F+    A+
Sbjct: 2  TLFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQ 61

Query: 60 DAIRGRDGYDFDGHRLRVELAH 81
           A++  DG+  DGH 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|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 40.5 bits (95), Expect = 6e-05
 Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR-PPGYAFVEFEEARDAEDAIRGR 65
          + L+V N+P   R+ ++  +F ++GPI  +++    R   G+ FV F  + DA+ A    
Sbjct: 1  KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKL 60

Query: 66 DGYDFDGHRLRVELA 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|241101 cd12657, RRM1_hnRNPM, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 40.4 bits (94), Expect = 6e-05
 Identities = 18/79 (22%), Positives = 42/79 (53%), Gaps = 8/79 (10%)

Query: 110 RVLVTGLPSSASWQDLKDHMR-RAGDVCFSQVFRDGSGTT---GIVDYTNYDDMKHAIKK 165
           R  ++ +P    WQ LKD ++ + G+V + ++  D  G +    +V++   + MK A++ 
Sbjct: 1   RAFISNIPFDVKWQSLKDLVKEKVGEVTYVELLMDAEGKSRGCAVVEFKMEESMKKAVEV 60

Query: 166 LDDSEFRNAFSRAYVRVRE 184
           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|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 40.0 bits (94), Expect = 6e-05
 Identities = 25/76 (32%), Positives = 34/76 (44%), Gaps = 10/76 (13%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP---GYAFVEFEEARDAEDAIRGR 65
          +YVG +P    E E+   F   G I  +DL   P      G AF+ F+     E+A +  
Sbjct: 1  VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFK----TEEAAKRA 56

Query: 66 ---DGYDFDGHRLRVE 78
             DG D  G  L+VE
Sbjct: 57 LALDGEDMGGRFLKVE 72

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

>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 40.6 bits (96), Expect = 7e-05
 Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 4/64 (6%)

Query: 17 DIREREVEDLFYKYGPIAHIDLKIPPRPP-GYAFVEFEEARDAEDAIRGRDGYDFDGHRL 75
          +I+E +V +   K+GP+ HI  K+    P G  +V+F+    A+  I+  +G  FDG ++
Sbjct: 23 EIKE-DVLEECSKFGPVEHI--KVDKNSPEGVVYVKFKTVEAAQKCIQALNGRWFDGRQI 79

Query: 76 RVEL 79
            E 
Sbjct: 80 TAEY 83

This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

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

 Score = 43.9 bits (103), Expect = 7e-05
 Identities = 37/167 (22%), Positives = 69/167 (41%), Gaps = 17/167 (10%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAIRGR 65
           +YVG++  ++RE  +   F  +GPI  I++   P   +  G+AFVE+E    A+ A+   
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 66  DGYDFDGHRLRVELAHG-GRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQD 124
           +G    G  ++V       + +   D     +         +   R+ V  +    S  D
Sbjct: 170 NGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEA---------KKFNRIYVASVHPDLSETD 220

Query: 125 LKDHMRRAGDVCFSQVFRDGSGTT----GIVDYTNYDDMKHAIKKLD 167
           +K      G++   Q+ R  +G      G ++Y N      AI  ++
Sbjct: 221 IKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMN 267

The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. Length = 612

>gnl|CDD|240977 cd12533, RRM_EWS, RNA recognition motif in vertebrate Ewing Sarcoma Protein (EWS)

 Score = 40.3 bits (94), Expect = 7e-05
 Identities = 26/83 (31%), Positives = 39/83 (46%), Gaps = 11/83 (13%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYG----------PIAHIDL-KIPPRPPGYAFVEFEEAR 56
          T+YV  L  ++   E+ D F   G          P+ +I   K   +P G A V +E+  
Sbjct: 2  TIYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPP 61

Query: 57 DAEDAIRGRDGYDFDGHRLRVEL 79
           A+ A+   DG DF 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|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 40.3 bits (94), Expect = 8e-05
 Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 2/69 (2%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP--PRPPGYAFVEFEEARDAEDAIRGRD 66
          +++G LP D+ E E+  L  K G I  + + +       GYAFV F   ++A++AI+  +
Sbjct: 4  IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLN 63

Query: 67 GYDFDGHRL 75
           Y+    RL
Sbjct: 64 NYEIRNGRL 72

This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 78

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

 Score = 40.0 bits (94), Expect = 8e-05
 Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 4/75 (5%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
          ++VG LP D+ E E ++ F ++G +    L       R  G+ FV F+    A + +   
Sbjct: 2  IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSE-SAVERVFSA 60

Query: 66 DGYDFDGHRLRVELA 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|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 40.0 bits (93), Expect = 9e-05
 Identities = 22/58 (37%), Positives = 33/58 (56%), Gaps = 3/58 (5%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRP---PGYAFVEFEEARDAEDAIR 63
          ++VG +P D+ E E+  LF K GPI  + L + P      GYAFV 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|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 39.9 bits (94), Expect = 9e-05
 Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 3/58 (5%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAI 62
          T++V  L   +RER++ + F K G +  + +   +   R  G A+VEF +      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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 43.0 bits (101), Expect = 1e-04
 Identities = 25/101 (24%), Positives = 47/101 (46%), Gaps = 3/101 (2%)

Query: 5   ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDA 61
               LYVGNL  +I E+E+  +F  +G I  + L   P   R  G+ F++F +A +A++A
Sbjct: 185 NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEA 244

Query: 62  IRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRG 102
           +   +G++  G  ++V  A        +         + + 
Sbjct: 245 LEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQM 285

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

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

 Score = 43.5 bits (102), Expect = 1e-04
 Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 3/78 (3%)

Query: 3   SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAE 59
           ++    +YV ++  D+ E +++ +F  +G I    L   P      GY F+E+   +   
Sbjct: 201 AKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQS 260

Query: 60  DAIRGRDGYDFDGHRLRV 77
           +AI   + +D  G  LRV
Sbjct: 261 EAIASMNLFDLGGQYLRV 278

The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. Length = 612

>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 3/76 (3%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRG 64
          T+YV NLP  +   ++  +F KYG +  + +   K   +  G AF+ F +  DA   ++ 
Sbjct: 3  TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62

Query: 65 RDGYDFDGHRLRVELA 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|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 24/84 (28%), Positives = 38/84 (45%), Gaps = 13/84 (15%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLK------------IPPRPPGYAFVEFEEAR 56
          ++V NLP +  E+++ + F   G I  ID K                P G A V +++  
Sbjct: 1  VFVSNLPPNTTEQDLAEHFGSIGII-KIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPH 59

Query: 57 DAEDAIRGRDGYDFDGHRLRVELA 80
           A  AI   +  DF G+ ++V LA
Sbjct: 60 AASAAIEWFNNKDFMGNTIKVSLA 83

This subgroup corresponds to the RRM in cabeza, also termed P19, or sarcoma-associated RNA-binding fly homolog (SARFH). It is a putative homolog of human RNA-binding proteins FUS (also termed TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1), TAF15 (also termed hTAFII68 or TAF2N or RPB56), and belongs to the 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 nuclear RNA binding protein that may play an important role in the regulation of RNA metabolism during fly development. Cabeza contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 3/73 (4%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
          +Y+G LP ++ E ++  +F +YG I  I+L   K   +  G+AF+ +E+ R    A+   
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 66 DGYDFDGHRLRVE 78
          +G    G  +RV+
Sbjct: 72 NGIKLLGRTIRVD 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|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins

 Score = 39.8 bits (94), Expect = 1e-04
 Identities = 23/83 (27%), Positives = 35/83 (42%), Gaps = 11/83 (13%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR----------PPGYAFVEFEEARDA 58
          +YV  LP DI   E  ++F K G I        P+            G A   + +    
Sbjct: 4  VYVSGLPLDITVEEFVEVFSKCGIIKEDPETGKPKIKLYRDENGNLKGDALCCYLKEESV 63

Query: 59 EDAIRGRDGYD-FDGHRLRVELA 80
          E AI+  DG +   G++++VE A
Sbjct: 64 ELAIQLLDGTEIGRGYKMKVERA 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|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 39.5 bits (92), Expect = 1e-04
 Identities = 20/53 (37%), Positives = 32/53 (60%), Gaps = 2/53 (3%)

Query: 3  SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR--PPGYAFVEFE 53
           RA+RTL++GNL   + E ++   F ++G I  +D+K P R     Y F++FE
Sbjct: 4  QRANRTLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFE 56

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|216205 pfam00937, Corona_nucleoca, Coronavirus nucleocapsid protein

 Score = 42.4 bits (100), Expect = 1e-04
 Identities = 26/85 (30%), Positives = 34/85 (40%)

Query: 203 RGRSESRSRSRSRGRSYSRSRSQSKSPKAKSSRRSPDRSRSRSASRSRSGSKPRSLSRSR 262
           R RS SRS SRS  R  SR  S++ S    SS      +   +A       K +S S+  
Sbjct: 155 RSRSSSRSSSRSNSRGPSRGSSRNNSRNRNSSSPDDLVAAVLAALAKLGFGKQKSSSKKP 214

Query: 263 SRSRSPLPPKQISKSPKKRSVSRSP 287
           SR       +   K   K    R+P
Sbjct: 215 SRVTKKSAAEAAKKQLNKPRWKRTP 239

Length = 346

>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 39.1 bits (91), Expect = 1e-04
 Identities = 26/69 (37%), Positives = 35/69 (50%), Gaps = 3/69 (4%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          L+VGNLP DI E E + LF KYG    + +    +  G+ F++ E    AE A    D  
Sbjct: 4  LFVGNLPADITEDEFKKLFAKYGEPGEVFIN---KGKGFGFIKLESRALAEIAKAELDDT 60

Query: 69 DFDGHRLRV 77
             G +LRV
Sbjct: 61 PMRGRQLRV 69

This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 71

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

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 4/71 (5%)

Query: 10 YVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRD 66
          +VGN+       E+++ F   G I  I +   K   +P G+A++EF +    E+A+   +
Sbjct: 3  FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LLN 61

Query: 67 GYDFDGHRLRV 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|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 42.9 bits (101), Expect = 2e-04
 Identities = 31/115 (26%), Positives = 37/115 (32%), Gaps = 6/115 (5%)

Query: 188 RRDGSQSPSRGRSYSRGRSESRSRSRSRGRSYSRSRSQSKSPKAKSSRRSPDRSRSRSAS 247
             + S             S S  R RS   S S   S       ++S  S     S S+S
Sbjct: 269 IWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSS 328

Query: 248 RSRSGSKPRSL------SRSRSRSRSPLPPKQISKSPKKRSVSRSPSGSRSRSRS 296
            S S    R        S SRS S S  PP     SP+KR        S + S  
Sbjct: 329 TSSSSESSRGAAVSPGPSPSRSPSPSRPPPPADPSSPRKRPRPSRAPSSPAASAG 383

Length = 1352

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

 Score = 42.5 bits (100), Expect = 2e-04
 Identities = 33/168 (19%), Positives = 70/168 (41%), Gaps = 19/168 (11%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP--RPPGYAFVEFEEARDAEDAIRGRD 66
           ++V NL   +  + + D F K+G I    +      +  GY FV FE+   A+ AI+  +
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVN 150

Query: 67  GYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLK 126
           G   +   + V             R           + + +   + V  L  S +   L+
Sbjct: 151 GMLLNDKEVYVG------------RFIKKHEREAAPLKKFTN--LYVKNLDPSVNEDKLR 196

Query: 127 DHMRRAGDVCFSQVFRDGSGTT---GIVDYTNYDDMKHAIKKLDDSEF 171
           +   + G++  + V +DGSG +     V++  ++D   A+++++  + 
Sbjct: 197 ELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKI 244

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

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

 Score = 42.1 bits (99), Expect = 2e-04
 Identities = 44/166 (26%), Positives = 74/166 (44%), Gaps = 23/166 (13%)

Query: 8   TLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRG 64
           +LYVG+L  D+ E ++ DLF  +GP+  + +    +  R  GY +V F+   DAE A+  
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61

Query: 65  RDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQD 124
            +     G  +R+  +     R  S R     SG G          + V  L  S   + 
Sbjct: 62  MNFKRLGGKPIRIMWSQ----RDPSLRR----SGVG---------NIFVKNLDKSVDNKA 104

Query: 125 LKDHMRRAGDVCFSQVFRDGSGTT---GIVDYTNYDDMKHAIKKLD 167
           L D   + G++   +V  D +G +   G V +   +  K AI+K++
Sbjct: 105 LFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVN 150

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

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

 Score = 42.2 bits (99), Expect = 2e-04
 Identities = 29/87 (33%), Positives = 34/87 (39%), Gaps = 11/87 (12%)

Query: 209 RSRSRSRGRSYSRSRSQSKSPKAKSSRRSPDRSRSRSASRSRSGSKPRSLSRSRSRSRSP 268
           R R R RGR  + +R        K   RS  RSRSR  SR R         R RSRSRSP
Sbjct: 1   RYRDRERGRLRNDTRRSD-----KGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSP 55

Query: 269 LPPKQISKSPKKRSVSRSPSGSRSRSR 295
                 ++  + R         R   R
Sbjct: 56  ------NRYYRPRGDRSYRRDDRRSGR 76

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

>gnl|CDD|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 = 39.1 bits (92), Expect = 2e-04
 Identities = 20/73 (27%), Positives = 28/73 (38%), Gaps = 4/73 (5%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIA---HIDLKIPPRPPGYAFVEFEEARDAEDAIRG 64
           + +  LP    E ++ D F          HI      RP G A+VEF    DA  A+R 
Sbjct: 1  VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALR- 59

Query: 65 RDGYDFDGHRLRV 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|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 16/61 (26%), Positives = 34/61 (55%), Gaps = 3/61 (4%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAIRGR 65
          +++G L  D  +++++D F K+G +    LK+ P   R  G+ FV F+E+   +  +  +
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|240699 cd12253, RRM_PIN4_like, RNA recognition motif in yeast RNA-binding protein PIN4, fission yeast RNA-binding post-transcriptional regulators cip1, cip2 and similar proteins

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 21/83 (25%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRP------------PGYAFVEFEEA 55
           + + N+P  +R+ ++ D+    G          P P             G AF  F   
Sbjct: 3  AIVIKNIPFSLRKEQLLDIIEDLGI---------PLPYAFNYHFDNGVFRGLAFANFRSP 53

Query: 56 RDAEDAIRGRDGYDFDGHRLRVE 78
           +A+  +   +GY+  G RLRVE
Sbjct: 54 EEAQTVVEALNGYEISGRRLRVE 76

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

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

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 3/73 (4%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRP---PGYAFVEFEEARDAEDAIRG 64
           ++V NLP D  E  +  LF  +G + ++ +          GY FV      +A  AI  
Sbjct: 3  CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62

Query: 65 RDGYDFDGHRLRV 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|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 = 39.4 bits (92), Expect = 2e-04
 Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 7/62 (11%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPP-GYAFVEFEEARDAED 60
          R ++VG LP DI E E+   F ++GP+  +D           PP GYAF+ F+E    + 
Sbjct: 1  RKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQA 59

Query: 61 AI 62
           I
Sbjct: 60 LI 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|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 22/80 (27%), Positives = 37/80 (46%), Gaps = 14/80 (17%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPG--------YAFVEFEEARDAE 59
          TL+V N P    + ++ DLF +YG I  I      R P         + +V+F     A 
Sbjct: 2  TLWVTNFPPSFDQSDIRDLFEQYGEILSI------RFPSLRFNKTRRFCYVQFTSPESAA 55

Query: 60 DAIRGRDGYDFDGHRLRVEL 79
           A+   +G   +G++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|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 39.1 bits (91), Expect = 2e-04
 Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 3/75 (4%)

Query: 9  LYVGNLPGDIRERE-VEDLFYKYGPIAHIDL--KIPPRPPGYAFVEFEEARDAEDAIRGR 65
          L + NLP  I++   ++ +F +YG +    +  K   +  G+AFV  ++ ++AE A+   
Sbjct: 3  LIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENT 62

Query: 66 DGYDFDGHRLRVELA 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|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 2/72 (2%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPG-YAFVEFEEARDAEDAIRGR 65
          RT++VG + G + E ++++ F   G +  + L    +    +AFVEF +A  A  A+   
Sbjct: 1  RTIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSALN-L 59

Query: 66 DGYDFDGHRLRV 77
           G    GH LRV
Sbjct: 60 SGTLLGGHPLRV 71

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 42.1 bits (99), Expect = 3e-04
 Identities = 24/77 (31%), Positives = 30/77 (38%)

Query: 192 SQSPSRGRSYSRGRSESRSRSRSRGRSYSRSRSQSKSPKAKSSRRSPDRSRSRSASRSRS 251
           S   SRG + S G S SRS S SR    +   S  K P+   +  SP  S  R   R   
Sbjct: 332 SSESSRGAAVSPGPSPSRSPSPSRPPPPADPSSPRKRPRPSRAPSSPAASAGRPTRRRAR 391

Query: 252 GSKPRSLSRSRSRSRSP 268
            +      R  +  R P
Sbjct: 392 AAVAGRARRRDATGRFP 408

Length = 1352

>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 7/79 (8%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP----RPPGYAFVEFEEARDAEDA 61
          SR L V NLP  I+E ++  LF  +G I  + LK       R   + FV ++   +A+ A
Sbjct: 1  SR-LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFR--KFGFVGYKTEEEAQKA 57

Query: 62 IRGRDGYDFDGHRLRVELA 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|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 38.7 bits (91), Expect = 3e-04
 Identities = 22/71 (30%), Positives = 30/71 (42%), Gaps = 17/71 (23%)

Query: 17 DIREREVEDLFYKYGPIAHIDLKIPPRPP---------GYAFVEFEEARDAEDAIRGRDG 67
          D++E E      KYG +  + + IP RP          G  FVEF +  DA+ A     G
Sbjct: 27 DVKE-ECG----KYGKV--LSVVIP-RPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAG 78

Query: 68 YDFDGHRLRVE 78
            FDG  +   
Sbjct: 79 RKFDGRTVVAS 89

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|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating protein-binding protein 2 (G3BP2) and similar proteins

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 17/53 (32%), Positives = 31/53 (58%), Gaps = 3/53 (5%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLK---IPPRPPGYAFVEFEEA 55
          S  L+VGNLP DI E E+++ F  +G +  + +    +  + P + FV F+++
Sbjct: 5  SHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDS 57

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|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 4/73 (5%)

Query: 11 VGNLPGDIREREVEDLFYK-YGPIAHIDLKIPP--RPPGYAFVEFEEARDAEDAIRGRDG 67
          V NLP D+ E ++ + F    GPI  + L      +  G A + F+ A DA  A    +G
Sbjct: 4  VSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDKFNG 63

Query: 68 YDFDGHR-LRVEL 79
             DG+R ++VE+
Sbjct: 64 RIDDGNRKMKVEV 76

This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p. . Length = 77

>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall integrity protein scw1 and similar proteins

 Score = 38.3 bits (90), Expect = 3e-04
 Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 1/54 (1%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
          TL+V NL  +  E E+  LF +      + +      P   FVEFE+   A  A
Sbjct: 4  TLFVANLGPNTTEEELRQLFSRQPGFRRLKMHNKGGGP-VCFVEFEDVSFATQA 56

This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins. Length = 79

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

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 3/69 (4%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG 67
          T+YVGN+P    + ++  LF  +G    ++ +  P   G+AFV+ +    A  AI    G
Sbjct: 2  TVYVGNIPPYTTQADLIPLFQNFG--YILEFRHQPDR-GFAFVKLDTHEQAAMAIVQLQG 58

Query: 68 YDFDGHRLR 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|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 2/68 (2%)

Query: 11 VGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDF 70
          V  LP     ++++D   + G + + D  +     G   VEF    D E A+R  DG +F
Sbjct: 5  VSGLPEGASWQDLKDFGRQAGDVTYAD--VDRDQEGEGVVEFTSQEDMERALRKLDGTEF 62

Query: 71 DGHRLRVE 78
           G R+RVE
Sbjct: 63 RGRRVRVE 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|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 5/76 (6%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPG----YAFVEFEEARDAEDAIRG 64
          L V NLP  + E E+++ F K+G     D+K+     G     AF+ ++   +A+ A   
Sbjct: 3  LIVKNLPASLTEAELKEHFSKHGGEI-TDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDY 61

Query: 65 RDGYDFDGHRLRVELA 80
           +    +  ++ VE A
Sbjct: 62 FNNTYINTSKISVEFA 77

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

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

 Score = 38.3 bits (89), Expect = 4e-04
 Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 4/75 (5%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
          L+VG L GD+ E ++ + F ++GP+   ++   K   +  G+ FV F+   D+ D     
Sbjct: 2  LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQN-HDSADKAAVV 60

Query: 66 DGYDFDGHRLRVELA 80
            +  +GHR+ V+ A
Sbjct: 61 KFHPINGHRVEVKKA 75

This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 8/74 (10%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGP-IAHIDLKIPPRPPGY--AFVEFEEARDAEDAIR 63
          RT+ + N+   + E +++  F K GP +  I+L      P +  A VEFE   DA  A  
Sbjct: 1  RTIGLFNVSDTVNEEQIKAFFEKIGPDVRKIELF-----PDHEGALVEFESPSDAGKASL 55

Query: 64 GRDGYDFDGHRLRV 77
            +G  F G  +++
Sbjct: 56 SLNGSQFGGKTIKI 69

This subfamily corresponds to the RRM4 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|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 38.0 bits (89), Expect = 5e-04
 Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 7/69 (10%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKI-----PPRPPGYAFVEFEEARDAEDAIR 63
          LYV  LP  + ++E+E LF  YG I  I  +I          G  F+ F++  +AE AI+
Sbjct: 3  LYVSGLPKTMTQQELEALFSPYGRI--ITSRILCDNVTGLSRGVGFIRFDKRIEAERAIK 60

Query: 64 GRDGYDFDG 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|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 37.6 bits (88), Expect = 5e-04
 Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 7/79 (8%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPG----YAFVEFEEARDAEDA 61
          SR + V NLP  + E  + + F   G +   D+K+     G    + FV F+   DA+ A
Sbjct: 1  SR-IIVKNLPKYVTEDRLREHFESKGEVT--DVKVMRTRDGKSRRFGFVGFKSEEDAQQA 57

Query: 62 IRGRDGYDFDGHRLRVELA 80
          ++  +    D  ++ VELA
Sbjct: 58 VKYFNKTFIDTSKISVELA 76

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 37.7 bits (87), Expect = 6e-04
 Identities = 21/62 (33%), Positives = 36/62 (58%), Gaps = 3/62 (4%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 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|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate RNA-binding protein Raly

 Score = 37.3 bits (86), Expect = 7e-04
 Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 6/73 (8%)

Query: 9  LYVGNL-PGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG 67
          +++GNL    +++ +VE +F KYG +    +       GYAFV++   R A  A+ G +G
Sbjct: 4  VFIGNLNTAVVKKSDVETIFSKYGRVVGCSVH-----KGYAFVQYSNERHARGAVIGENG 58

Query: 68 YDFDGHRLRVELA 80
              G  L + +A
Sbjct: 59 RVLAGQTLDINMA 71

This subgroup corresponds to the RRM of Raly, also termed autoantigen p542, or heterogeneous nuclear ribonucleoprotein C-like 2, or hnRNP core protein C-like 2, or hnRNP associated with lethal yellow protein homolog, an RNA-binding protein that may play a critical role in embryonic development. It is encoded by Raly, a ubiquitously expressed gene of unknown function. Raly shows a high degree of identity with the 5' sequences of p542 gene encoding autoantigen, which can cross-react with EBNA-1 of the Epstein Barr virus. Raly contains 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 a unique glycine/serine-rich stretch. . Length = 76

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 37.2 bits (86), Expect = 7e-04
 Identities = 25/69 (36%), Positives = 34/69 (49%), Gaps = 3/69 (4%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          L+VGNLP DI E + + LF KYG  + + +    R  G+ F+  E    AE A    DG 
Sbjct: 4  LFVGNLPTDITEEDFKKLFEKYGEPSEVFIN---RDRGFGFIRLESRTLAEIAKAELDGT 60

Query: 69 DFDGHRLRV 77
                LR+
Sbjct: 61 ILKNRPLRI 69

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 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|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)

 Score = 37.7 bits (87), Expect = 7e-04
 Identities = 23/79 (29%), Positives = 42/79 (53%), Gaps = 4/79 (5%)

Query: 4  RASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAE 59
          R + T+Y+ NL   I++ E++     +F ++G I  I +    +  G AFV F+E   A 
Sbjct: 1  RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 60

Query: 60 DAIRGRDGYDFDGHRLRVE 78
          +A+R   G+ F    +R++
Sbjct: 61 NALRSMQGFPFYDKPMRIQ 79

This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), 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 and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 89

>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 = 37.2 bits (87), Expect = 7e-04
 Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 6/77 (7%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP----GYAFVEFEEARDAEDAIR 63
           L V N+P +  ++E+ +LF  +G +    +++P +      G+AFVEF   ++A++A+ 
Sbjct: 2  KLIVRNVPFEATKKELRELFSPFGQV--KSVRLPKKFDGSHRGFAFVEFVTKQEAQNAME 59

Query: 64 GRDGYDFDGHRLRVELA 80
                  G  L +E A
Sbjct: 60 ALKSTHLYGRHLVLEYA 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|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins

 Score = 37.2 bits (87), Expect = 9e-04
 Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 11 VGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDF 70
          + NLP  I  ++++    K     H  +K+  R   +AFV F    + + A+   DG+ +
Sbjct: 10 IKNLPKYIGFKQLKKFLKKQLFKPH-KIKLLKRQD-FAFVTFRSEEERQKALEILDGFKW 67

Query: 71 DGHRLRVELA 80
           G  L   LA
Sbjct: 68 KGRVLSARLA 77

This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases. . Length = 79

>gnl|CDD|240880 cd12434, RRM_RCAN_like, RNA recognition motif in regulators of calcineurin (RCANs) and similar proteins

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 22/75 (29%), Positives = 30/75 (40%), Gaps = 10/75 (13%)

Query: 9  LYVGNLP------GDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAI 62
          L V N+P       +++   +E LF  YG IA     +       A V F    +A  A 
Sbjct: 1  LIVTNVPSEVFTNAELKA-ALESLFSSYGEIATF---VYLPSFRRARVVFSSPEEAALAR 56

Query: 63 RGRDGYDFDGHRLRV 77
              G  F+G  LRV
Sbjct: 57 IELHGTVFEGSVLRV 71

This subfamily corresponds to the RRM of RCANs, a novel family of calcineurin regulators that are key factors contributing to Down syndrome in humans. They can stimulate and inhibit the Ca2+/calmodulin-dependent phosphatase calcineurin (also termed PP2B or PP3C) signaling in vivo through direct interactions with its catalytic subunit. Overexpressed RCANs may bind and inhibit calcineurin. In contrast, low levels of phosphorylated RCANs may stimulate the calcineurin signaling. RCANs are characterized by harboring a central short, unique serine-proline motif containing FLIISPPxSPP box, which is strongly conserved from yeast to human but is absent in bacteria. They consist of an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a highly conserved SP repeat domain containing the phosphorylation site by GSK-3, a well-known PxIxIT motif responsible for docking many substrates to calcineurin, and an unrecognized C-terminal TxxP motif of unknown function. . Length = 75

>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 3/74 (4%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAIR 63
           T++VGN+P  + +  +  L  K G +        P   +   + F EFE+   A  A+R
Sbjct: 1  TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60

Query: 64 GRDGYDFDGHRLRV 77
            +G +  G +L V
Sbjct: 61 LLNGLELGGKKLLV 74

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

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

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 23/75 (30%), Positives = 34/75 (45%), Gaps = 3/75 (4%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
          L V  LP ++ + E+  LF   G I    L   K+  +  GY FV + +  DAE AI   
Sbjct: 4  LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTL 63

Query: 66 DGYDFDGHRLRVELA 80
          +G       ++V  A
Sbjct: 64 NGLRLQNKTIKVSYA 78

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

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

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 5/80 (6%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGY----AFVEFEEARDAEDAIR 63
           L +  LP  + + E   LF   GP+ +  + +  +  GY     FV+++ A DA+ AIR
Sbjct: 2  NLIINYLPQTLTDEEFRSLFLAVGPVKNCKI-VRDKRTGYSYGFGFVDYQSAEDAQRAIR 60

Query: 64 GRDGYDFDGHRLRVELAHGG 83
            +G      R++V  A  G
Sbjct: 61 TLNGLQLQNKRIKVAYARPG 80

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

>gnl|CDD|240907 cd12461, RRM_SCAF4, RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 22/61 (36%), Positives = 35/61 (57%), Gaps = 3/61 (4%)

Query: 3  SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAI 62
          S  S TL+VG L     +++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|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 36.7 bits (85), Expect = 0.001
 Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 4/72 (5%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL--KIPPRPPGYAFVEFEEARDAEDAIRGRD 66
          L+VGNLP ++RE  + + F +YG +  + +  K        AFV+F + + A+ A    +
Sbjct: 2  LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVAAFVDFVDIKSAQKAHNAVN 61

Query: 67 GYDFDGHRLRVE 78
                  LR +
Sbjct: 62 --KMGDRDLRTD 71

This subfamily corresponds to the RRM1 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 = 75

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

 Score = 36.7 bits (85), Expect = 0.001
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 6/75 (8%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGR 65
          L+VGNL  +  E E+   F + G I  + +       +  G+AFV+FEE   A +A++G+
Sbjct: 1  LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60

Query: 66 DGYDFDGHRLRVELA 80
               +G  LRVE  
Sbjct: 61 ---HLNGRALRVEYG 72

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPI--AHIDLKIPP--RPPGYAFVEFEEARDAEDAIRG 64
          ++VG+L  +I    +   F  +G I  A + +K     +  GY FV F +  DAE+AI+ 
Sbjct: 2  IFVGDLSPEIDTETLRAAFAPFGEISDARV-VKDMQTGKSKGYGFVSFVKKEDAENAIQS 60

Query: 65 RDGYDFDGHRLR 76
           +G    G  +R
Sbjct: 61 MNGQWLGGRAIR 72

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

>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 24/83 (28%), Positives = 34/83 (40%), Gaps = 8/83 (9%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYG--PIAHIDL---KIPPRPPGYAFVEFEEARDAE- 59
          + TL +  L     E ++          PI  + L   K+     G+AFVEF    DA  
Sbjct: 2  TNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQ 61

Query: 60 --DAIRGRDGYDFDGHRLRVELA 80
            DA+   D +  DG  +RV  A
Sbjct: 62 WMDALNNLDPFVIDGRVVRVSYA 84

This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 84

>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 36.4 bits (84), Expect = 0.001
 Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 4/77 (5%)

Query: 8  TLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIR 63
          T+Y+ NL   +++ E++     +F ++G I  I      +  G AFV F++   A +A+R
Sbjct: 1  TIYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVVFKDISSATNALR 60

Query: 64 GRDGYDFDGHRLRVELA 80
             G+ F    +R+  +
Sbjct: 61 SMQGFPFYDKPMRIAYS 77

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|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 36.6 bits (84), Expect = 0.002
 Identities = 21/62 (33%), Positives = 36/62 (58%), Gaps = 3/62 (4%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
          LYV  LP  + ++E+E LF +YG I    +   ++     G  F+ F++  +AE+AI+G 
Sbjct: 5  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64

Query: 66 DG 67
          +G
Sbjct: 65 NG 66

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|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear ribonucleoprotein B" (U2B") and similar proteins

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 4/79 (5%)

Query: 6  SRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
          + T+Y+ NL   I++ E++     LF ++G +  I      +  G AFV F+E   A +A
Sbjct: 1  NHTIYINNLNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELSSATNA 60

Query: 62 IRGRDGYDFDGHRLRVELA 80
          +R   G+ F G  +R++ A
Sbjct: 61 LRQLQGFPFYGKPMRIQYA 79

This subgroup corresponds to the RRM1 of U2B" (also termed U2 snRNP B") a unique protein that comprises the U2 snRNP. It was initially identified as binding to stem-loop IV (SLIV) at the 3' end of U2 snRNA. 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. In addition, the nuclear transport of U2B" is independent of U2 snRNA binding. U2B" contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B" to the nucleus. . Length = 91

>gnl|CDD|240834 cd12388, RRM1_RAVER, RNA recognition motif 1 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 17/70 (24%), Positives = 29/70 (41%), Gaps = 4/70 (5%)

Query: 11 VGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDF 70
          + NLP D+ ++EV DL   Y  + + D+    +    A V       A  AI       +
Sbjct: 4  IRNLPADVTKQEVHDLLSDYQ-VKYCDVD---KSKRTAQVTLLNGDQASRAIAKLHQSSY 59

Query: 71 DGHRLRVELA 80
             ++ V+L 
Sbjct: 60 KERKISVQLQ 69

This subfamily corresponds to the RRM1 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 = 70

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

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 20/74 (27%), Positives = 31/74 (41%), Gaps = 8/74 (10%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPI-----AHIDLKIPPRPPGYAFVEFEEARDAEDAIR 63
          +++ NL   I  + + D F  +G I     A  D     +  GY FV FE    A  AI 
Sbjct: 5  IFIKNLDKSIDNKALYDTFSAFGNILSCKVA-TDENGGSK--GYGFVHFETEEAAVRAIE 61

Query: 64 GRDGYDFDGHRLRV 77
            +G   +  ++ V
Sbjct: 62 KVNGMLLNDKKVFV 75

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

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

 Score = 36.0 bits (83), Expect = 0.002
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 8/64 (12%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHI-----DLKIPPRPPGYAFVEFEEARDAEDAIR 63
          L+VG L     E+EVE++F  YG +  I     ++K      G AFV++     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|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 21/69 (30%), Positives = 39/69 (56%), Gaps = 8/69 (11%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDAEDAIRGR 65
          LY+  LP  + +++VED+F ++G I +  + +        G AF+ F++  +AE+AI   
Sbjct: 3  LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAIT-- 60

Query: 66 DGYDFDGHR 74
              F+GH+
Sbjct: 61 ---SFNGHK 66

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

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

 Score = 38.3 bits (89), Expect = 0.003
 Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 3/75 (4%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
           +Y+GNLP  + E ++++L   +G +   +L          GYAF E+++    + AI   
Sbjct: 298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAAL 357

Query: 66  DGYDFDGHRLRVELA 80
           +G D   ++L V+ A
Sbjct: 358 NGKDTGDNKLHVQRA 372

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

>gnl|CDD|240735 cd12289, RRM_LARP6, RNA recognition motif in La-related protein 6 (LARP6) and similar proteins

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 25/75 (33%), Positives = 31/75 (41%), Gaps = 18/75 (24%)

Query: 7  RTLYVGNLPGDIRERE-VEDLFYKYGPIAHIDL-----KIPP-------RPPG-----YA 48
          RT+   NLP +    E V +LF   G IA I +      IPP       R P       A
Sbjct: 1  RTVVAVNLPEEESTIESVLELFSTCGVIALIRILRPGRTIPPDLKRYSSRHPQLGTKECA 60

Query: 49 FVEFEEARDAEDAIR 63
           VEFE+   A  A+ 
Sbjct: 61 VVEFEKLEAARKAVE 75

This subfamily corresponds to the RRM of LARP6, also termed Acheron (Achn), a novel member of the lupus antigen (La) family. It is expressed predominantly in neurons and muscle in vertebrates. LARP6 functions as a key regulatory protein that may play a role in mediating a variety of developmental and homeostatic processes in animals, including myogenesis, neurogenesis and possibly metastasis. LARP6 binds to Ca2+/calmodulin-dependent serine protein kinase (CASK), and forms a complex with inhibitor of differentiation transcription factors. It is structurally related to the La autoantigen and contains a La motif (LAM), nuclear localization and export (NLS and NES) signals, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 93

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

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 4/77 (5%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIR 63
          + ++VG +  D  E  + D F KYG I  I++   +   +  G+AFV F++  D  D I 
Sbjct: 1  KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDD-HDTVDKIV 59

Query: 64 GRDGYDFDGHRLRVELA 80
           +  +  +GH   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|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen B (HuB)

 Score = 35.9 bits (82), Expect = 0.003
 Identities = 21/62 (33%), Positives = 36/62 (58%), Gaps = 3/62 (4%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 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|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 35.4 bits (82), Expect = 0.003
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 3/49 (6%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEE 54
          ++VG L  +  E ++ + F K+G I  I+L +     +  G+ F+ F+ 
Sbjct: 2  IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDS 50

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|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 2/65 (3%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDL--KIPPRPPGYAFVEFEEARDAEDAIRG 64
            ++VG +P D+ E E+  LF + G I    L  +      GYAFV +    +A+ AIR 
Sbjct: 2  CEVFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAIRI 61

Query: 65 RDGYD 69
           + Y+
Sbjct: 62 LNNYE 66

This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

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

 Score = 36.1 bits (83), Expect = 0.003
 Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 5/61 (8%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAH----IDLKIPPRPPGYAFVEFEEARDAEDAIR 63
          TL+V NLP D  E  +   F K+G + +    ID K   R  G  FV F++       ++
Sbjct: 3  TLFVRNLPYDATEESLAPHFSKFGSVRYALPVID-KSTGRAKGTGFVCFKDQYTYNACLK 61

Query: 64 G 64
           
Sbjct: 62 N 62

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

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

 Score = 35.4 bits (82), Expect = 0.003
 Identities = 18/73 (24%), Positives = 30/73 (41%), Gaps = 3/73 (4%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPG---YAFVEFEEARDAEDAIRGR 65
          L+V  L    +  +++ LF KYG +    +    R PG   + FV      +A   I+  
Sbjct: 2  LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 66 DGYDFDGHRLRVE 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|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 38.6 bits (90), Expect = 0.004
 Identities = 34/138 (24%), Positives = 44/138 (31%), Gaps = 3/138 (2%)

Query: 162 AIKKLDDSEFRNAFSRAYVRVREYDHRRDGSQSPSRGRSYSRGRSESRSRSRSRGRSYSR 221
           A      +      S +     E      G ++       +     +R    S       
Sbjct: 221 APAPGRSAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASGWNG-PS 279

Query: 222 SRSQSKSPKAKSSRRSPDRSRSRSASRSRSGSKPRSLSRSRSRSRSPLPPKQISKSPKKR 281
           SR    S  +    RSP  S S   S     S   S S S SR  S       S+S +  
Sbjct: 280 SRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGA 339

Query: 282 SVSRSPSGSRSRSRSLSR 299
           +VS  PS   SRS S SR
Sbjct: 340 AVSPGPSP--SRSPSPSR 355

Length = 1352

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

 Score = 38.3 bits (89), Expect = 0.004
 Identities = 24/73 (32%), Positives = 32/73 (43%), Gaps = 2/73 (2%)

Query: 183 REYDHRRDGSQSPSRGRSYSRGRSESRSRSRSRGRSYSRSRSQSKSPKAKSSRRSPDR-S 241
           R  D  R   ++ +R     R RS  RSRSR R R   R R   +  + +S  RSP+R  
Sbjct: 1   RYRDRERGRLRNDTRRSDKGRERSRRRSRSRDRSRR-RRDRDYYRGRRGRSRSRSPNRYY 59

Query: 242 RSRSASRSRSGSK 254
           R R     R   +
Sbjct: 60  RPRGDRSYRRDDR 72

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

>gnl|CDD|216205 pfam00937, Corona_nucleoca, Coronavirus nucleocapsid protein

 Score = 38.1 bits (89), Expect = 0.004
 Identities = 20/63 (31%), Positives = 27/63 (42%)

Query: 236 RSPDRSRSRSASRSRSGSKPRSLSRSRSRSRSPLPPKQISKSPKKRSVSRSPSGSRSRSR 295
           RS  RS SRS SR  S    R+ SR+R+ S        +  +  K    +  S S+  SR
Sbjct: 157 RSSSRSSSRSNSRGPSRGSSRNNSRNRNSSSPDDLVAAVLAALAKLGFGKQKSSSKKPSR 216

Query: 296 SLS 298
              
Sbjct: 217 VTK 219

Length = 346

>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 = 35.2 bits (81), Expect = 0.004
 Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 3/54 (5%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAE 59
          ++VG L  D  ++++++ F K+G +    +KI P   R  G+ FV F++A   E
Sbjct: 1  MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVE 54

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

 Score = 35.5 bits (81), Expect = 0.004
 Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 3/75 (4%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
          L V  LP ++ + E++ LF   G I    L   KI  +  GY FV + + +DAE AI   
Sbjct: 7  LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 66

Query: 66 DGYDFDGHRLRVELA 80
          +G       ++V  A
Sbjct: 67 NGLRLQTKTIKVSYA 81

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

>gnl|CDD|241013 cd12569, RRM4_RBM19, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 35.0 bits (81), Expect = 0.004
 Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 7/55 (12%)

Query: 11 VGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPG--YAFVEFEEARDAEDAIR 63
          V NLP      E+ +LF K+G +  + L     PP    A VEF E  +A+ A R
Sbjct: 5  VKNLPAGTLTAELRELFSKFGSLGRVLL-----PPAGITAIVEFLEPSEAKLAFR 54

This subgroup corresponds to the RRM4 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|218107 pfam04484, DUF566, Family of unknown function (DUF566)

 Score = 38.0 bits (88), Expect = 0.004
 Identities = 36/118 (30%), Positives = 43/118 (36%), Gaps = 6/118 (5%)

Query: 188 RRDGSQSPSRGRSYSRGRSESRSRSRSRGRSYSRSRSQSKSPKAKSSRRSPDRSRSRSAS 247
           R     S S     S  RS SR R  S   S S S    +     S   S     + S+S
Sbjct: 1   RAASVSSGSTSGDASSPRSSSRRRLSSSFLSTSASSRPRRLNAPASPPSSSPARNTSSSS 60

Query: 248 -RSRSGSKPRSLSRSRSRSRSP-----LPPKQISKSPKKRSVSRSPSGSRSRSRSLSR 299
               S  +P SLSR R  SR        P    S +    + S S S S SRSR  + 
Sbjct: 61  SFGLSKQRPSSLSRGRLSSRFVSPSRGSPSAAASLNGSLATASTSGSSSPSRSRRTTS 118

Family of related proteins that is plant specific. Length = 313

>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate RNA-binding protein 26 (RBM26) and similar proteins

 Score = 34.8 bits (81), Expect = 0.004
 Identities = 16/59 (27%), Positives = 33/59 (55%), Gaps = 4/59 (6%)

Query: 6  SRTLYVGNLPGDI-REREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIR 63
          + TL V N+P ++    ++ + F K+G I  +++++   P   A V+F  + +A+ A R
Sbjct: 1  NTTLEVRNIPPELNNITKLNEHFSKFGTI--VNIQVNYNPES-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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	299
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.97
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	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	99.97
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.96
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.96
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.96
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.96
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.95
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.95
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.95
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.95
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.95
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.95
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.95
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.94
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.94
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.94
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.93
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.92
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.92
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	99.92
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.9
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.9
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.9
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.89
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.88
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.88
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.88
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.88
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.86
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.85
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.85
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.84
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.84
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.83
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.83
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.83
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.83
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.81
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.79
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.79
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.77
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.77
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.76
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.75
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.74
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.72
PLN03120	260	nucleic acid binding protein; Provisional	99.71
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.7
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.7
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.7
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.7
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.68
PLN03121	243	nucleic acid binding protein; Provisional	99.68
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.68
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.66
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.65
KOG0122	270	consensus Translation initiation factor 3, subunit	99.65
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.62
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.62
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.62
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.61
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.61
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.59
smart00362	72	RRM_2 RNA recognition motif.	99.57
PLN03213	759	repressor of silencing 3; Provisional	99.55
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.54
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.53
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.52
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.52
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.5
smart00360	71	RRM RNA recognition motif.	99.48
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.48
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.47
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.46
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.46
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.44
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.44
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.41
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.41
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.41
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.4
PLN03120	260	nucleic acid binding protein; Provisional	99.4
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.38
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.38
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	99.37
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.37
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.37
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.36
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.36
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.34
PLN03213	759	repressor of silencing 3; Provisional	99.33
PLN03121	243	nucleic acid binding protein; Provisional	99.33
smart00361	70	RRM_1 RNA recognition motif.	99.31
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	99.31
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.29
smart00362	72	RRM_2 RNA recognition motif.	99.29
KOG0122	270	consensus Translation initiation factor 3, subunit	99.28
smart00360	71	RRM RNA recognition motif.	99.2
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.19
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.17
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	99.15
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.13
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.11
KOG4660	549	consensus Protein Mei2, essential for commitment t	99.11
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.1
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.1
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.08
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.06
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.05
KOG0533	243	consensus RRM motif-containing protein [RNA proces	99.04
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.02
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.99
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.99
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.98
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.98
smart00361	70	RRM_1 RNA recognition motif.	98.94
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.93
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.92
KOG4210	285	consensus Nuclear localization sequence binding pr	98.91
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.91
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.87
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.87
KOG0151	877	consensus Predicted splicing regulator, contains R	98.85
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.81
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.8
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.69
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.67
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.59
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.59
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.58
KOG0226	290	consensus RNA-binding proteins [General function p	98.57
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.57
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.48
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.47
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.45
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	98.45
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.44
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.42
KOG0226	290	consensus RNA-binding proteins [General function p	98.41
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.36
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.32
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.3
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	98.26
KOG0151	877	consensus Predicted splicing regulator, contains R	98.24
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.21
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.21
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.19
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.18
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	98.17
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.13
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.07
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.99
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.96
KOG4210	285	consensus Nuclear localization sequence binding pr	97.93
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.93
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.92
KOG3152	278	consensus TBP-binding protein, activator of basal	97.85
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.82
KOG2314	698	consensus Translation initiation factor 3, subunit	97.81
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.75
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.71
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.65
KOG4368	757	consensus Predicted RNA binding protein, contains	97.64
KOG1996	378	consensus mRNA splicing factor [RNA processing and	97.63
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.58
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.58
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.53
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.51
KOG3152	278	consensus TBP-binding protein, activator of basal	97.39
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.39
KOG1996	378	consensus mRNA splicing factor [RNA processing and	97.34
KOG2591	684	consensus c-Mpl binding protein, contains La domai	97.34
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.33
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.33
KOG2314	698	consensus Translation initiation factor 3, subunit	97.3
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.25
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	97.24
KOG2135	526	consensus Proteins containing the RNA recognition	96.98
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.97
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	96.96
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.95
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.94
KOG2591	684	consensus c-Mpl binding protein, contains La domai	96.91
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.89
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	96.86
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.8
KOG2548	653	consensus SWAP mRNA splicing regulator [RNA proces	96.73
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.68
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	96.57
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	96.35
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	96.31
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	96.27
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	96.25
KOG2068	327	consensus MOT2 transcription factor [Transcription	96.15
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	95.91
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	95.89
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	95.79
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	95.72
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.69
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	95.49
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.38
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	95.08
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	94.93
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	94.8
KOG2888	453	consensus Putative RNA binding protein [General fu	94.58
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	94.38
KOG0835	367	consensus Cyclin L [General function prediction on	93.74
KOG4019	193	consensus Calcineurin-mediated signaling pathway i	93.6
KOG2068	327	consensus MOT2 transcription factor [Transcription	93.52
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	93.48
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	93.46
KOG2318	650	consensus Uncharacterized conserved protein [Funct	93.46
KOG0835	367	consensus Cyclin L [General function prediction on	93.04
KOG2888	453	consensus Putative RNA binding protein [General fu	92.8
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	92.77
KOG2135	526	consensus Proteins containing the RNA recognition	90.9
PF03468	116	XS: XS domain; InterPro: IPR005380 The XS (rice ge	88.1
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	87.81
KOG4483	528	consensus Uncharacterized conserved protein [Funct	86.59
KOG2318	650	consensus Uncharacterized conserved protein [Funct	86.02
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	84.82
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	84.62
KOG4008	261	consensus rRNA processing protein RRP7 [RNA proces	84.4
TIGR03636	77	L23_arch archaeal ribosomal protein L23. This mode	83.55
KOG1295	376	consensus Nonsense-mediated decay protein Upf3 [RN	83.52
PRK14548	84	50S ribosomal protein L23P; Provisional	82.22
KOG2295	648	consensus C2H2 Zn-finger protein [General function	81.43
PRK14548	84	50S ribosomal protein L23P; Provisional	80.94
TIGR02542	145	B_forsyth_147 Bacteroides forsythus 147-residue re	80.24

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=1e-32  Score=236.16  Aligned_cols=163  Identities=26%  Similarity=0.407  Sum_probs=141.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ...++|||+|||+++|+++|+++|..||+|+.|+|..   ++.++|||||+|.++++|..||..||+..|.+++|+|.++
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            4678999999999999999999999999999999954   4678899999999999999999999999999999999987


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecCh
Q 022301           81 HGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNY  156 (299)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~  156 (299)
                      .....                   ....++|||.|||..+++++|+++|.+||.|..+.|+.+..+    +||||+|.+.
T Consensus       185 ~p~~~-------------------~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~  245 (346)
T TIGR01659       185 RPGGE-------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKR  245 (346)
T ss_pred             ccccc-------------------ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCH
Confidence            54221                   123468999999999999999999999999999999988643    5999999999


Q ss_pred             hhHHHHHHhcCCCeecCceeeEEEEeccc
Q 022301          157 DDMKHAIKKLDDSEFRNAFSRAYVRVREY  185 (299)
Q Consensus       157 ~~a~~a~~~l~g~~~~g~~~~~~~~~~~~  185 (299)
                      ++|++||+.||+..+.+......+.+...
T Consensus       246 e~A~~Ai~~lng~~~~g~~~~l~V~~a~~  274 (346)
T TIGR01659       246 EEAQEAISALNNVIPEGGSQPLTVRLAEE  274 (346)
T ss_pred             HHHHHHHHHhCCCccCCCceeEEEEECCc
Confidence            99999999999999988644444444433

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).

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.97  E-value=8e-30  Score=229.24  Aligned_cols=169  Identities=22%  Similarity=0.356  Sum_probs=141.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ..++|||+|||+++++++|.++|..||+|..|.|..   +++++|||||+|.+.++|..|+..|||..|.|+.|.|.+..
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            468999999999999999999999999999999954   47889999999999999999999999999999999998643


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChh
Q 022301           82 GGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYD  157 (299)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~  157 (299)
                      ........        ............+|||+||+..+++++|+++|+.||.|..+.+..++.    .|||||+|.+.+
T Consensus       186 ~~p~a~~~--------~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e  257 (612)
T TIGR01645       186 NMPQAQPI--------IDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQ  257 (612)
T ss_pred             cccccccc--------cccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHH
Confidence            22110000        000011222457999999999999999999999999999999998754    469999999999


Q ss_pred             hHHHHHHhcCCCeecCceeeEEEEeccc
Q 022301          158 DMKHAIKKLDDSEFRNAFSRAYVRVREY  185 (299)
Q Consensus       158 ~a~~a~~~l~g~~~~g~~~~~~~~~~~~  185 (299)
                      +|..|++.|||..|+|+    .+.|...
T Consensus       258 ~A~kAI~amNg~elgGr----~LrV~kA  281 (612)
T TIGR01645       258 SQSEAIASMNLFDLGGQ----YLRVGKC  281 (612)
T ss_pred             HHHHHHHHhCCCeeCCe----EEEEEec
Confidence            99999999999999999    5555443

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.97  E-value=5.9e-29  Score=184.84  Aligned_cols=187  Identities=62%  Similarity=1.049  Sum_probs=160.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            1 MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         1 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      |+.+.+++|||+|||.++.+.+|++||-+||.|.+|.|+....+..||||+|+++.+|+.||..-+|-.++|..|.|+++
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            78899999999999999999999999999999999999877777789999999999999999999999999999999999


Q ss_pred             cCCCCCCCCCCC-------CCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEe
Q 022301           81 HGGRGRSSSDRH-------SSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDY  153 (299)
Q Consensus        81 ~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f  153 (299)
                      ............       .........++.....+.+.|.+||...++++|+++|.+.|.|+...+..+.   ++.|+|
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            876522111110       0111112345677788999999999999999999999999999999999885   899999


Q ss_pred             cChhhHHHHHHhcCCCeecCceeeEEEEecccccCCC
Q 022301          154 TNYDDMKHAIKKLDDSEFRNAFSRAYVRVREYDHRRD  190 (299)
Q Consensus       154 ~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~~~~~~~~  190 (299)
                      ...++.+.|+.+|+...+...-.+++|.+........
T Consensus       158 ~r~eDMkYAvr~ld~~~~~seGe~~yirv~~~~~~~~  194 (241)
T KOG0105|consen  158 LRKEDMKYAVRKLDDQKFRSEGETAYIRVRGDENRDQ  194 (241)
T ss_pred             eehhhHHHHHHhhccccccCcCcEeeEEecccCCCcc
Confidence            9999999999999999998877888998877655543

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.97  E-value=1.3e-29  Score=221.84  Aligned_cols=153  Identities=24%  Similarity=0.426  Sum_probs=137.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      +.++|||+|||.++|+++|+++|+.||+|.+|.|..   ++.++|||||+|.+.++|+.||..|||..|.|+.|.|.++.
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            578999999999999999999999999999999954   46788999999999999999999999999999999999986


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC----CCCEEEEEecChh
Q 022301           82 GGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG----SGTTGIVDYTNYD  157 (299)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~----~~~~~fv~f~~~~  157 (299)
                      +...                   .....+|||+|||..+++++|.++|..||.|..+.++.+.    ..|||||+|.+.+
T Consensus        82 ~~~~-------------------~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~  142 (352)
T TIGR01661        82 PSSD-------------------SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRD  142 (352)
T ss_pred             cccc-------------------ccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHH
Confidence            4321                   1234689999999999999999999999999999988764    3469999999999


Q ss_pred             hHHHHHHhcCCCeecCcee
Q 022301          158 DMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       158 ~a~~a~~~l~g~~~~g~~~  176 (299)
                      +|+.|++.|||..+.|...
T Consensus       143 ~A~~ai~~l~g~~~~g~~~  161 (352)
T TIGR01661       143 EADRAIKTLNGTTPSGCTE  161 (352)
T ss_pred             HHHHHHHHhCCCccCCCce
Confidence            9999999999999988654

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.97  E-value=4.9e-29  Score=225.34  Aligned_cols=166  Identities=21%  Similarity=0.317  Sum_probs=140.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .+.++|||+|||..+++++|+++|..||+|.+|.|+.   ++.++|||||+|.+.++|.+||. |+|..|.|.+|.|.++
T Consensus        87 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~  165 (457)
T TIGR01622        87 RDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSS  165 (457)
T ss_pred             cCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeec
Confidence            4678999999999999999999999999999999965   46789999999999999999998 9999999999999887


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecCh
Q 022301           81 HGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNY  156 (299)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~  156 (299)
                      .............       .....+...+|||+|||..+++++|.++|..||.|..|.++.+..+    |||||+|.+.
T Consensus       166 ~~~~~~~~~~~~~-------~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~  238 (457)
T TIGR01622       166 QAEKNRAAKAATH-------QPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDA  238 (457)
T ss_pred             chhhhhhhhcccc-------cCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCH
Confidence            5433221110000       0011123689999999999999999999999999999999987654    6999999999


Q ss_pred             hhHHHHHHhcCCCeecCceee
Q 022301          157 DDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       157 ~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      ++|..|+..|+|..|.|+.+.
T Consensus       239 e~A~~A~~~l~g~~i~g~~i~  259 (457)
T TIGR01622       239 EEAKEALEVMNGFELAGRPIK  259 (457)
T ss_pred             HHHHHHHHhcCCcEECCEEEE
Confidence            999999999999999998543

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=99.97  E-value=2.7e-28  Score=213.50  Aligned_cols=172  Identities=24%  Similarity=0.352  Sum_probs=136.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCC--ceEEEEE
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDG--HRLRVEL   79 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g--~~i~v~~   79 (299)
                      ..++|||+|||.++++++|.++|..||.|..+.+..   ++.++|||||+|.+.++|..|+..|||..+.|  .+|.|.+
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            467899999999999999999999999999999854   35678999999999999999999999998877  5788888


Q ss_pred             ccCCCCCCCC--------------CC-CCC-----------------C--------------------------CCC-C-
Q 022301           80 AHGGRGRSSS--------------DR-HSS-----------------H--------------------------SSG-R-   99 (299)
Q Consensus        80 ~~~~~~~~~~--------------~~-~~~-----------------~--------------------------~~~-~-   99 (299)
                      +.........              .. ...                 .                          ... . 
T Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  247 (352)
T TIGR01661       168 ANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPP  247 (352)
T ss_pred             CCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCc
Confidence            7533310000              00 000                 0                          000 0 


Q ss_pred             -------------CCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC----CCCEEEEEecChhhHHHH
Q 022301          100 -------------GRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG----SGTTGIVDYTNYDDMKHA  162 (299)
Q Consensus       100 -------------~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~----~~~~~fv~f~~~~~a~~a  162 (299)
                                   ........+.+|||+|||..+++++|.++|.+||.|..+.|+.+.    ..|||||+|.+.++|..|
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                         000001234479999999999999999999999999999999886    346999999999999999


Q ss_pred             HHhcCCCeecCcee
Q 022301          163 IKKLDDSEFRNAFS  176 (299)
Q Consensus       163 ~~~l~g~~~~g~~~  176 (299)
                      |..|||..|+|+.+
T Consensus       328 i~~lnG~~~~gr~i  341 (352)
T TIGR01661       328 ILSLNGYTLGNRVL  341 (352)
T ss_pred             HHHhCCCEECCeEE
Confidence            99999999999944

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>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=2.4e-29  Score=197.62  Aligned_cols=166  Identities=20%  Similarity=0.349  Sum_probs=142.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCCC
Q 022301            8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGR   84 (299)
Q Consensus         8 ~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~~   84 (299)
                      -|||+.|.+.++-|+|++.|.+||+|.+++|..   +++++||+||-|.+.++|+.||..|||.+|.++.|..+|+.-+.
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   57999999999999999999999999999999999999997554


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHH
Q 022301           85 GRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIK  164 (299)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~  164 (299)
                      .......   ..-+....-..+.++++||+|++..+++++|++.|..||.|..|.+++++.  |+||.|++.|.|..||.
T Consensus       144 ~e~n~~~---ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~qG--YaFVrF~tkEaAahAIv  218 (321)
T KOG0148|consen  144 SEMNGKP---LTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQG--YAFVRFETKEAAAHAIV  218 (321)
T ss_pred             cccCCCC---ccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecccc--eEEEEecchhhHHHHHH
Confidence            1111100   000111223456789999999999999999999999999999999998875  99999999999999999


Q ss_pred             hcCCCeecCceeeE
Q 022301          165 KLDDSEFRNAFSRA  178 (299)
Q Consensus       165 ~l~g~~~~g~~~~~  178 (299)
                      .+||.+|.|+.+..
T Consensus       219 ~mNntei~G~~VkC  232 (321)
T KOG0148|consen  219 QMNNTEIGGQLVRC  232 (321)
T ss_pred             HhcCceeCceEEEE
Confidence            99999999986643

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.96  E-value=2.7e-28  Score=220.24  Aligned_cols=162  Identities=17%  Similarity=0.231  Sum_probs=136.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhc--CCCCCCCceEEEEEccC
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGR--DGYDFDGHRLRVELAHG   82 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l--~~~~~~g~~i~v~~~~~   82 (299)
                      |+++|||+|||+++|+++|.++|+.||+|..|.|..   .++||||+|.+.++|+.|+..|  ++..|.|+.|.|.|+..
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            689999999999999999999999999999999973   4689999999999999999864  77899999999999875


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHH
Q 022301           83 GRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHA  162 (299)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a  162 (299)
                      ........    .  . ...........|+|.||+..+++++|.++|..||.|..|.++.+...++|||+|.+.++|.+|
T Consensus        78 ~~~~~~~~----~--~-~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~~~~afVef~~~~~A~~A  150 (481)
T TIGR01649        78 QEIKRDGN----S--D-FDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNVFQALVEFESVNSAQHA  150 (481)
T ss_pred             cccccCCC----C--c-ccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCCceEEEEEECCHHHHHHH
Confidence            43211110    0  0 000111234579999999999999999999999999999998887767999999999999999


Q ss_pred             HHhcCCCeecCcee
Q 022301          163 IKKLDDSEFRNAFS  176 (299)
Q Consensus       163 ~~~l~g~~~~g~~~  176 (299)
                      ++.|||..|.|...
T Consensus       151 ~~~Lng~~i~~~~~  164 (481)
T TIGR01649       151 KAALNGADIYNGCC  164 (481)
T ss_pred             HHHhcCCcccCCce
Confidence            99999999977543

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=99.96  E-value=7.1e-28  Score=222.67  Aligned_cols=152  Identities=25%  Similarity=0.425  Sum_probs=134.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCCC
Q 022301            8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGR   84 (299)
Q Consensus         8 ~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~~   84 (299)
                      +|||+|||+++|+++|.++|..||+|..|.|..   ++.++|||||+|.+.++|..|+..||+..|.|+.|.|.|+....
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            799999999999999999999999999999955   36788999999999999999999999999999999999975322


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC---CCEEEEEecChhhHHH
Q 022301           85 GRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS---GTTGIVDYTNYDDMKH  161 (299)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~---~~~~fv~f~~~~~a~~  161 (299)
                      .                 .......+|||+|||.++++++|.++|+.||.|..|.+..+..   .|||||+|.+.++|..
T Consensus        82 ~-----------------~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~  144 (562)
T TIGR01628        82 S-----------------LRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKA  144 (562)
T ss_pred             c-----------------ccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHH
Confidence            1                 0111235799999999999999999999999999999988754   4799999999999999


Q ss_pred             HHHhcCCCeecCcee
Q 022301          162 AIKKLDDSEFRNAFS  176 (299)
Q Consensus       162 a~~~l~g~~~~g~~~  176 (299)
                      |++.|+|..+.|+.+
T Consensus       145 Ai~~lng~~~~~~~i  159 (562)
T TIGR01628       145 AIQKVNGMLLNDKEV  159 (562)
T ss_pred             HHHHhcccEecCceE
Confidence            999999999999843

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.96  E-value=3.4e-27  Score=213.10  Aligned_cols=170  Identities=18%  Similarity=0.263  Sum_probs=136.4

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            4 RASRTLYVGNLPG-DIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         4 ~~~~~l~V~nLp~-~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      .++++|||+|||+ .+|+++|.++|+.||.|..|+|..+.  +|||||+|.+.++|..|+..|||..|.|+.|.|.+++.
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            4678999999998 69999999999999999999997653  68999999999999999999999999999999999865


Q ss_pred             CCCCCCCCCC--------CCCCCC--CCC--------CCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCC--eeEEEEEe
Q 022301           83 GRGRSSSDRH--------SSHSSG--RGR--------GVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGD--VCFSQVFR  142 (299)
Q Consensus        83 ~~~~~~~~~~--------~~~~~~--~~~--------~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~--v~~~~~~~  142 (299)
                      ..........        ..+...  ...        .....+..+|||.|||..+++++|+++|..||.  |..+.+..
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            4322111000        000000  000        011245678999999999999999999999998  77777765


Q ss_pred             CC--CCCEEEEEecChhhHHHHHHhcCCCeecCce
Q 022301          143 DG--SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAF  175 (299)
Q Consensus       143 ~~--~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  175 (299)
                      ..  ..++|||+|.+.++|..|+..|||..|.++.
T Consensus       431 ~~~~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~  465 (481)
T TIGR01649       431 KDNERSKMGLLEWESVEDAVEALIALNHHQLNEPN  465 (481)
T ss_pred             CCCCcceeEEEEcCCHHHHHHHHHHhcCCccCCCC
Confidence            43  2369999999999999999999999999874

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.95  E-value=4.6e-27  Score=215.33  Aligned_cols=170  Identities=20%  Similarity=0.304  Sum_probs=132.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhc------------CCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCC
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKY------------GPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDF   70 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~------------G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~   70 (299)
                      +...++|||+|||+.+|+++|.++|..|            +.|..+.+.   ..+|||||+|.+.++|..||. |||+.|
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            345555554   457999999999999999996 999999


Q ss_pred             CCceEEEEEccCCCCCCCCCCCCCC------CCC----CCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEE
Q 022301           71 DGHRLRVELAHGGRGRSSSDRHSSH------SSG----RGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQV  140 (299)
Q Consensus        71 ~g~~i~v~~~~~~~~~~~~~~~~~~------~~~----~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~  140 (299)
                      .|..|.|.........+........      ...    ...........+|||+|||..+++++|.++|+.||.|..+.+
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            9999999765433311110000000      000    011112335679999999999999999999999999999999


Q ss_pred             EeCC----CCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          141 FRDG----SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       141 ~~~~----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      +.+.    ..|||||+|.+.++|..|++.|+|..|.|..+
T Consensus       328 ~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l  367 (509)
T TIGR01642       328 IKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKL  367 (509)
T ss_pred             EecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            8775    34699999999999999999999999999854

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.95  E-value=2e-27  Score=198.94  Aligned_cols=178  Identities=22%  Similarity=0.290  Sum_probs=140.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCC-CceEEEEEcc
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFD-GHRLRVELAH   81 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~-g~~i~v~~~~   81 (299)
                      -|-|||+.||.++.|++|..||+..|+|-++.|+++   |.++|||||.|.+.++|++|++.||+..|. |+.|.|..+.
T Consensus        83 G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Sv  162 (506)
T KOG0117|consen   83 GCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSV  162 (506)
T ss_pred             CceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEee
Confidence            478999999999999999999999999999999665   789999999999999999999999999885 8888887654


Q ss_pred             CCCCC---------------------------------CCC---------------------------CCCCCCCCC---
Q 022301           82 GGRGR---------------------------------SSS---------------------------DRHSSHSSG---   98 (299)
Q Consensus        82 ~~~~~---------------------------------~~~---------------------------~~~~~~~~~---   98 (299)
                      .+...                                 +..                           .....+...   
T Consensus       163 an~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tV  242 (506)
T KOG0117|consen  163 ANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITV  242 (506)
T ss_pred             ecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCccee
Confidence            22110                                 000                           000000000   


Q ss_pred             ----C---CCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCee
Q 022301           99 ----R---GRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEF  171 (299)
Q Consensus        99 ----~---~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~  171 (299)
                          .   ........-..|||.||+..+|++.|+++|.+||.|..|+.+.|    ||||+|.+.++|.+|++.+||++|
T Consensus       243 dWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD----YaFVHf~eR~davkAm~~~ngkel  318 (506)
T KOG0117|consen  243 DWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD----YAFVHFAEREDAVKAMKETNGKEL  318 (506)
T ss_pred             eccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc----eeEEeecchHHHHHHHHHhcCcee
Confidence                0   01112224467999999999999999999999999999999987    999999999999999999999999


Q ss_pred             cCceeeEEEEeccccc
Q 022301          172 RNAFSRAYVRVREYDH  187 (299)
Q Consensus       172 ~g~~~~~~~~~~~~~~  187 (299)
                      +|..+++.+.....+.
T Consensus       319 dG~~iEvtLAKP~~k~  334 (506)
T KOG0117|consen  319 DGSPIEVTLAKPVDKK  334 (506)
T ss_pred             cCceEEEEecCChhhh
Confidence            9997766555444333

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.95  E-value=6.1e-27  Score=210.48  Aligned_cols=167  Identities=22%  Similarity=0.340  Sum_probs=129.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCC-CceEEEEEccC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFD-GHRLRVELAHG   82 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~-g~~i~v~~~~~   82 (299)
                      .++|||+|||.++++++|.++|..||+|.+|+|+.  ++.++|||||+|.+.++|++||..||+..|. |+.|.|.++..
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            58999999999999999999999999999999965  4788999999999999999999999998875 66665554321


Q ss_pred             CCCC-------------------C---------------CCCCCCC-------------------CCCC-----------
Q 022301           83 GRGR-------------------S---------------SSDRHSS-------------------HSSG-----------   98 (299)
Q Consensus        83 ~~~~-------------------~---------------~~~~~~~-------------------~~~~-----------   98 (299)
                      ....                   .               .......                   ....           
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            1000                   0               0000000                   0000           


Q ss_pred             ---CC---CCCCCCCccEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCe
Q 022301           99 ---RG---RGVSRRSEYRVLVTGLPSSASWQDLKDHMRRA--GDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSE  170 (299)
Q Consensus        99 ---~~---~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~--G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~  170 (299)
                         ..   .........+|||+||+..+++++|+++|..|  |.|..|.++.+    ||||+|.+.++|++|++.|||..
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               00   00011234689999999999999999999999  99999988754    99999999999999999999999


Q ss_pred             ecCcee
Q 022301          171 FRNAFS  176 (299)
Q Consensus       171 ~~g~~~  176 (299)
                      |+|+.+
T Consensus       294 i~Gr~I  299 (578)
T TIGR01648       294 LEGSEI  299 (578)
T ss_pred             ECCEEE
Confidence            999944

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=1.3e-26  Score=212.33  Aligned_cols=174  Identities=19%  Similarity=0.340  Sum_probs=136.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .+.++|||+|||..+|+++|.++|..||.|..+.|..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
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            3468999999999999999999999999999999854   4778999999999999999999999999999999999998


Q ss_pred             cCCCCCCCCCCCCC------CCCCC---CCCCCCCCccEEEEeCCCCCC----------CHHHHHHHHHhcCCeeEEEEE
Q 022301           81 HGGRGRSSSDRHSS------HSSGR---GRGVSRRSEYRVLVTGLPSSA----------SWQDLKDHMRRAGDVCFSQVF  141 (299)
Q Consensus        81 ~~~~~~~~~~~~~~------~~~~~---~~~~~~~~~~~l~v~nl~~~~----------~~~~l~~~f~~~G~v~~~~~~  141 (299)
                      ..............      .....   .......+..+|+|.||....          ..++|+++|.+||.|..|.|+
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            75543322111110      00000   011123356788999985421          236899999999999999998


Q ss_pred             eCC-------CCCEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          142 RDG-------SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       142 ~~~-------~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      .+.       ..|+|||+|.+.++|++|+..|||..|+|+.+.
T Consensus       453 ~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~  495 (509)
T TIGR01642       453 RPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVV  495 (509)
T ss_pred             ccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            652       236999999999999999999999999998553

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.95  E-value=9.6e-28  Score=190.50  Aligned_cols=145  Identities=28%  Similarity=0.531  Sum_probs=134.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCCCCC
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGRGR   86 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~~~~   86 (299)
                      -.|||+|||.++++.+|+.||++||+|.+|.|.     ++||||..++...|..||..|||-.|.|..|+|+.++.+.. 
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIv-----KNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKsk-   76 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIV-----KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKSK-   76 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeee-----cccceEEeecccccHHHHhhcccceecceEEEEEeccccCC-
Confidence            479999999999999999999999999999998     77999999999999999999999999999999999876532 


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhc
Q 022301           87 SSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKL  166 (299)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l  166 (299)
                                          ..++|+|+||.+..+.+||+..|++||+|+.++|.++    |+||.|+-.++|..|+..|
T Consensus        77 --------------------~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd----y~fvh~d~~eda~~air~l  132 (346)
T KOG0109|consen   77 --------------------ASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD----YAFVHFDRAEDAVEAIRGL  132 (346)
T ss_pred             --------------------CccccccCCCCccccCHHHhhhhcccCCceeeeeecc----eeEEEEeeccchHHHHhcc
Confidence                                3478999999999999999999999999999999998    9999999999999999999


Q ss_pred             CCCeecCceeeEEEE
Q 022301          167 DDSEFRNAFSRAYVR  181 (299)
Q Consensus       167 ~g~~~~g~~~~~~~~  181 (299)
                      ++.++.|+...+.+.
T Consensus       133 ~~~~~~gk~m~vq~s  147 (346)
T KOG0109|consen  133 DNTEFQGKRMHVQLS  147 (346)
T ss_pred             cccccccceeeeeee
Confidence            999999996644443

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.95  E-value=3.4e-27  Score=175.24  Aligned_cols=165  Identities=22%  Similarity=0.352  Sum_probs=141.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      +...||||+||+..++++.|++||-+.|+|++++|..   +...+|||||+|.++|+|+-|++.||...|.|++|+|..+
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            5678999999999999999999999999999999955   3567899999999999999999999999999999999887


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeE-EEEEeCCCC----CEEEEEecC
Q 022301           81 HGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCF-SQVFRDGSG----TTGIVDYTN  155 (299)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~-~~~~~~~~~----~~~fv~f~~  155 (299)
                      ....                  .....+.+|||+||.+.+++..|.+.|+.||.+.. .+++.++.+    +||||.|.+
T Consensus        87 s~~~------------------~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~s  148 (203)
T KOG0131|consen   87 SAHQ------------------KNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYAS  148 (203)
T ss_pred             cccc------------------ccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechh
Confidence            5211                  12223479999999999999999999999998876 466666553    499999999


Q ss_pred             hhhHHHHHHhcCCCeecCceeeEEEEecccc
Q 022301          156 YDDMKHAIKKLDDSEFRNAFSRAYVRVREYD  186 (299)
Q Consensus       156 ~~~a~~a~~~l~g~~~~g~~~~~~~~~~~~~  186 (299)
                      .+.+..|+..|+|..++.+.++..+...+..
T Consensus       149 feasd~ai~s~ngq~l~nr~itv~ya~k~~~  179 (203)
T KOG0131|consen  149 FEASDAAIGSMNGQYLCNRPITVSYAFKKDT  179 (203)
T ss_pred             HHHHHHHHHHhccchhcCCceEEEEEEecCC
Confidence            9999999999999999999776666554443

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.95  E-value=7.1e-27  Score=182.83  Aligned_cols=154  Identities=23%  Similarity=0.411  Sum_probs=139.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEee---cCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLK---IPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~---~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ...+.|.|.-||.++|+|+|+.||..+|+|++|++.   .+|++.||+||.|-++++|++|+..|||..+..+.|+|.|+
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            445779999999999999999999999999999994   46899999999999999999999999999999999999999


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecCh
Q 022301           81 HGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNY  156 (299)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~  156 (299)
                      .+..                   ....+.+|||.+||..+++.||+++|.+||.|+...|..|..+    |.+||.|...
T Consensus       119 RPSs-------------------~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr  179 (360)
T KOG0145|consen  119 RPSS-------------------DSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKR  179 (360)
T ss_pred             cCCh-------------------hhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecch
Confidence            7533                   2445679999999999999999999999999999888888655    4899999999


Q ss_pred             hhHHHHHHhcCCCeecCcee
Q 022301          157 DDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       157 ~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .+|+.||..|||..--|...
T Consensus       180 ~EAe~AIk~lNG~~P~g~te  199 (360)
T KOG0145|consen  180 IEAEEAIKGLNGQKPSGCTE  199 (360)
T ss_pred             hHHHHHHHhccCCCCCCCCC
Confidence            99999999999999888755

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

Probab=99.94  E-value=3.1e-26  Score=211.74  Aligned_cols=173  Identities=22%  Similarity=0.354  Sum_probs=140.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCC----CceEEEE
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFD----GHRLRVE   78 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~----g~~i~v~   78 (299)
                      ..++|||+|||.++|+++|+++|..||+|..+.+..  ++..+|||||+|.+.++|..|+..|||..|.    |..|.|.
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            457899999999999999999999999999999954  3567899999999999999999999999999    9999998


Q ss_pred             EccCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC---CCEEEEEecC
Q 022301           79 LAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS---GTTGIVDYTN  155 (299)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~---~~~~fv~f~~  155 (299)
                      ++........... .................+|||+||+..+++++|.++|..||.|..+.++.+..   .|||||+|.+
T Consensus       257 ~a~~k~er~~~~~-~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~  335 (562)
T TIGR01628       257 RAQKRAEREAELR-RKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSN  335 (562)
T ss_pred             cccChhhhHHHHH-hhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCC
Confidence            8754432110000 00000001112234567899999999999999999999999999999998853   3699999999


Q ss_pred             hhhHHHHHHhcCCCeecCceeeE
Q 022301          156 YDDMKHAIKKLDDSEFRNAFSRA  178 (299)
Q Consensus       156 ~~~a~~a~~~l~g~~~~g~~~~~  178 (299)
                      .++|.+|+..|||..++|+.+.+
T Consensus       336 ~~~A~~A~~~~~g~~~~gk~l~V  358 (562)
T TIGR01628       336 PEEANRAVTEMHGRMLGGKPLYV  358 (562)
T ss_pred             HHHHHHHHHHhcCCeeCCceeEE
Confidence            99999999999999999995533

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.94  E-value=3.7e-25  Score=200.13  Aligned_cols=176  Identities=21%  Similarity=0.341  Sum_probs=137.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      +++|||+|||.++|+++|+++|+.||.|..|.|..+   +.++|||||+|.+.++|..|+..|||..|.|+.|.|.|+..
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            589999999999999999999999999999999643   46789999999999999999999999999999999999653


Q ss_pred             CCCCCCCC-------------------------------C------CCCCCC-------------------------C--
Q 022301           83 GRGRSSSD-------------------------------R------HSSHSS-------------------------G--   98 (299)
Q Consensus        83 ~~~~~~~~-------------------------------~------~~~~~~-------------------------~--   98 (299)
                      ........                               .      ......                         .  
T Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  345 (457)
T TIGR01622       266 STYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALA  345 (457)
T ss_pred             CCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhccccccccccccccccccccccc
Confidence            21100000                               0      000000                         0  


Q ss_pred             ----CCCCC---CCCCccEEEEeCCCCCCC----------HHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHH
Q 022301           99 ----RGRGV---SRRSEYRVLVTGLPSSAS----------WQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKH  161 (299)
Q Consensus        99 ----~~~~~---~~~~~~~l~v~nl~~~~~----------~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~  161 (299)
                          ....+   ......+|+|.||....+          .++|.+.|.+||.|+.+.+......|++||+|.+.++|..
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                00000   123556888899855443          3789999999999999999877777899999999999999


Q ss_pred             HHHhcCCCeecCceeeEEEE
Q 022301          162 AIKKLDDSEFRNAFSRAYVR  181 (299)
Q Consensus       162 a~~~l~g~~~~g~~~~~~~~  181 (299)
                      |++.|||..++|+.+.+...
T Consensus       426 A~~~lnGr~f~gr~i~~~~~  445 (457)
T TIGR01622       426 AFQALNGRYFGGKMITAAFV  445 (457)
T ss_pred             HHHHhcCcccCCeEEEEEEE
Confidence            99999999999997655443

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.

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

Probab=99.94  E-value=2.6e-26  Score=191.41  Aligned_cols=162  Identities=23%  Similarity=0.440  Sum_probs=136.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCC-CCC--ceEEEE
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYD-FDG--HRLRVE   78 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~-~~g--~~i~v~   78 (299)
                      ..-+|||+.||..++|.||+++|++||.|.+|.|..   ++.++|||||.|.+.++|.+|+..||+.. |.|  .+|.|.
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            456899999999999999999999999999999955   57889999999999999999999999854 444  578888


Q ss_pred             EccCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC---CEEEEEecC
Q 022301           79 LAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG---TTGIVDYTN  155 (299)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv~f~~  155 (299)
                      ++.....                  ....+.+|||+-|+..+++.+|+++|.+||.|++|.|+.+..+   |||||.|.+
T Consensus       113 ~Ad~E~e------------------r~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fst  174 (510)
T KOG0144|consen  113 YADGERE------------------RIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFST  174 (510)
T ss_pred             ccchhhh------------------ccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEeh
Confidence            8764432                  1133578999999999999999999999999999999998754   799999999


Q ss_pred             hhhHHHHHHhcCCCe-ecCceeeEEEEecc
Q 022301          156 YDDMKHAIKKLDDSE-FRNAFSRAYVRVRE  184 (299)
Q Consensus       156 ~~~a~~a~~~l~g~~-~~g~~~~~~~~~~~  184 (299)
                      .+.|..||+.|||.. +.|+..-..+++.+
T Consensus       175 ke~A~~Aika~ng~~tmeGcs~PLVVkFAD  204 (510)
T KOG0144|consen  175 KEMAVAAIKALNGTQTMEGCSQPLVVKFAD  204 (510)
T ss_pred             HHHHHHHHHhhccceeeccCCCceEEEecc
Confidence            999999999999985 56665433444433

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.93  E-value=3.1e-25  Score=173.64  Aligned_cols=174  Identities=24%  Similarity=0.364  Sum_probs=140.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEe---ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCC--ceEEEEEc
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDG--HRLRVELA   80 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~---~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g--~~i~v~~~   80 (299)
                      ...|||.+||..+|..+|.++|++||.|..-.|   ..++.++|.+||.|...++|+.||..|||..-.|  .+|.|+|+
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            457999999999999999999999999988877   3468899999999999999999999999987665  58999998


Q ss_pred             cCCCCCCCCC-------------------CCC---------------CCCCC----------CCCCCCCCCccEEEEeCC
Q 022301           81 HGGRGRSSSD-------------------RHS---------------SHSSG----------RGRGVSRRSEYRVLVTGL  116 (299)
Q Consensus        81 ~~~~~~~~~~-------------------~~~---------------~~~~~----------~~~~~~~~~~~~l~v~nl  116 (299)
                      ..........                   ...               .+.+.          ...+.....+|+|||.||
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            7553221100                   000               00000          011223346899999999


Q ss_pred             CCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCceeeEE
Q 022301          117 PSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY  179 (299)
Q Consensus       117 ~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  179 (299)
                      .+++++..|+++|.+||.|..|+++.|..    .|||||.+.+.++|..||..|||+.++++.+.+.
T Consensus       287 spd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVs  353 (360)
T KOG0145|consen  287 SPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVS  353 (360)
T ss_pred             CCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEE
Confidence            99999999999999999999999999865    4699999999999999999999999999965433

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.92  E-value=1.6e-24  Score=185.63  Aligned_cols=172  Identities=20%  Similarity=0.335  Sum_probs=142.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ...||||++||+.++.++|.++|+.+|+|..+.+..+   +..+|||||.|.-.|+++.|+..+++..|.|+.|.|.++.
T Consensus         4 ~g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~   83 (678)
T KOG0127|consen    4 SGATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAK   83 (678)
T ss_pred             CCceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccc
Confidence            4489999999999999999999999999999999543   3568999999999999999999999999999999999987


Q ss_pred             CCCCCCCCCCCCC--CCCCCC---C--CCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC---CEEEE
Q 022301           82 GGRGRSSSDRHSS--HSSGRG---R--GVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG---TTGIV  151 (299)
Q Consensus        82 ~~~~~~~~~~~~~--~~~~~~---~--~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv  151 (299)
                      .............  ......   .  .....+.+.|+|.|||..+...+|+.+|+.||.|..|.|+....+   |||||
T Consensus        84 ~R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV  163 (678)
T KOG0127|consen   84 KRARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFV  163 (678)
T ss_pred             ccccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEE
Confidence            6554331111100  000000   0  111234799999999999999999999999999999999977665   59999


Q ss_pred             EecChhhHHHHHHhcCCCeecCcee
Q 022301          152 DYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       152 ~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      +|....+|..|++.|||.+|+|+.+
T Consensus       164 ~fk~~~dA~~Al~~~N~~~i~gR~V  188 (678)
T KOG0127|consen  164 QFKEKKDAEKALEFFNGNKIDGRPV  188 (678)
T ss_pred             EEeeHHHHHHHHHhccCceecCcee
Confidence            9999999999999999999999944

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.92  E-value=1.2e-23  Score=180.37  Aligned_cols=177  Identities=21%  Similarity=0.360  Sum_probs=139.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEee--cCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLK--IPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~--~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      .-.|+|.|||+.|.+.+|+.+|+.||.|.+|.|+  .++...|||||+|.+..+|..|+..||+..|.|++|-|.|+-..
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            4579999999999999999999999999999994  45677799999999999999999999999999999999998643


Q ss_pred             CCCCCCC-----------------------C------------CCCC--CC---------C---------CCC-------
Q 022301           84 RGRSSSD-----------------------R------------HSSH--SS---------G---------RGR-------  101 (299)
Q Consensus        84 ~~~~~~~-----------------------~------------~~~~--~~---------~---------~~~-------  101 (299)
                      .......                       .            ....  ..         .         ...       
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            3211100                       0            0000  00         0         000       


Q ss_pred             ---------CCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhc--
Q 022301          102 ---------GVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKL--  166 (299)
Q Consensus       102 ---------~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l--  166 (299)
                               .....-+.+|||.|||+++++++|.++|.+||.|.++.+..++.+    |.|||.|.+..+|+.||...  
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                     001112368999999999999999999999999999999988766    59999999999999999876  


Q ss_pred             ---CC-CeecCceeeEEEEe
Q 022301          167 ---DD-SEFRNAFSRAYVRV  182 (299)
Q Consensus       167 ---~g-~~~~g~~~~~~~~~  182 (299)
                         .| ..|+|+.+.+...|
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 67788876555544

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=99.92  E-value=4.5e-26  Score=187.68  Aligned_cols=167  Identities=16%  Similarity=0.168  Sum_probs=122.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC------CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP------PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRV   77 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~------~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v   77 (299)
                      .....|.|.||.+++|.++|+.||+.+|+|.++.|..+      +.....|||.|.+...+..|++ |.+++|-++.|.|
T Consensus         5 ~~~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv   83 (479)
T KOG4676|consen    5 SSLGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIV   83 (479)
T ss_pred             CCCceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEE
Confidence            44558999999999999999999999999999999653      2334689999999999999999 7777777777777


Q ss_pred             EEccCCCCCCC---------CCCC------CCCCCCCC------------CCCCCC----------CccEEEEeCCCCCC
Q 022301           78 ELAHGGRGRSS---------SDRH------SSHSSGRG------------RGVSRR----------SEYRVLVTGLPSSA  120 (299)
Q Consensus        78 ~~~~~~~~~~~---------~~~~------~~~~~~~~------------~~~~~~----------~~~~l~v~nl~~~~  120 (299)
                      .+......+..         ...+      ...++...            ..|+.+          ...+++|++|+..+
T Consensus        84 ~p~~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~  163 (479)
T KOG4676|consen   84 RPYGDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAA  163 (479)
T ss_pred             EecCCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhh
Confidence            66543322100         0000      00000000            000000          12458899999999


Q ss_pred             CHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeec
Q 022301          121 SWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFR  172 (299)
Q Consensus       121 ~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~  172 (299)
                      ...++.+.|..+|.|.+..+.......+|.|.|........|+. ++|.++.
T Consensus       164 ~l~e~~e~f~r~Gev~ya~~ask~~s~~c~~sf~~qts~~halr-~~gre~k  214 (479)
T KOG4676|consen  164 ILPESGESFERKGEVSYAHTASKSRSSSCSHSFRKQTSSKHALR-SHGRERK  214 (479)
T ss_pred             cchhhhhhhhhcchhhhhhhhccCCCcchhhhHhhhhhHHHHHH-hcchhhh
Confidence            99999999999999999999888777799999999888888887 6666655

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.90  E-value=1.9e-23  Score=163.30  Aligned_cols=163  Identities=38%  Similarity=0.658  Sum_probs=134.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCCCCC
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGRGR   86 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~~~~   86 (299)
                      ..|||++||+.+.+.+|..||..||.|.++.|+     .||+||+|.+..+|..|+..||+..|.|..+.|+|+......
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            468999999999999999999999999999997     689999999999999999999999999999999988754332


Q ss_pred             CCCCCCCCCCC-CCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHh
Q 022301           87 SSSDRHSSHSS-GRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKK  165 (299)
Q Consensus        87 ~~~~~~~~~~~-~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~  165 (299)
                      ......+.... .....++....+.++|.+++..+.+++|.++|.++|.+....+    ..+++||+|.+.++|..|+..
T Consensus        77 ~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~----~~~~~~v~Fs~~~da~ra~~~  152 (216)
T KOG0106|consen   77 RGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA----RRNFAFVEFSEQEDAKRALEK  152 (216)
T ss_pred             cCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh----hccccceeehhhhhhhhcchh
Confidence            21111111111 2233455678889999999999999999999999999955444    223899999999999999999


Q ss_pred             cCCCeecCceeeE
Q 022301          166 LDDSEFRNAFSRA  178 (299)
Q Consensus       166 l~g~~~~g~~~~~  178 (299)
                      |+|..+.++.++.
T Consensus       153 l~~~~~~~~~l~~  165 (216)
T KOG0106|consen  153 LDGKKLNGRRISV  165 (216)
T ss_pred             ccchhhcCceeee
Confidence            9999999995543

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.90  E-value=3.8e-22  Score=151.28  Aligned_cols=75  Identities=17%  Similarity=0.144  Sum_probs=68.9

Q ss_pred             CCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          102 GVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       102 ~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ++.....+.|.|.||.+.++.++|..+|++||.|.+|.|..+..+    |||||.|....+|++|++.|+|..|+|+.+
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            355567789999999999999999999999999999999999755    599999999999999999999999999944

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.90  E-value=2.3e-22  Score=173.33  Aligned_cols=142  Identities=26%  Similarity=0.380  Sum_probs=129.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCCCCC
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGRGR   86 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~~~~   86 (299)
                      ..||||   +++|+..|.++|+.+|+|..+.+..+-.+.|||||.|.++++|..||..||...+.|++|.+.|+....  
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~tslgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~--   76 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDATSLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDP--   76 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecCCccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCC--
Confidence            479998   999999999999999999999994332389999999999999999999999999999999999986433  


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC--CEEEEEecChhhHHHHHH
Q 022301           87 SSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG--TTGIVDYTNYDDMKHAIK  164 (299)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~--~~~fv~f~~~~~a~~a~~  164 (299)
                                            ..|||.||++.++..+|.++|+.||.|+.|++..+..+  || ||+|++.++|.+|++
T Consensus        77 ----------------------~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~  133 (369)
T KOG0123|consen   77 ----------------------SLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIE  133 (369)
T ss_pred             ----------------------ceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHH
Confidence                                  22999999999999999999999999999999999766  58 999999999999999


Q ss_pred             hcCCCeecCcee
Q 022301          165 KLDDSEFRNAFS  176 (299)
Q Consensus       165 ~l~g~~~~g~~~  176 (299)
                      .+||..+.|+.+
T Consensus       134 ~~ng~ll~~kki  145 (369)
T KOG0123|consen  134 KLNGMLLNGKKI  145 (369)
T ss_pred             HhcCcccCCCee
Confidence            999999999843

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.89  E-value=3.2e-23  Score=169.74  Aligned_cols=162  Identities=22%  Similarity=0.362  Sum_probs=136.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      |.||||.|.+.+.|+.|...|..||+|++|.|.+   +++.+|||||+|+-+|.|+.|++.|||..+.|+.|+|....+-
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNm  193 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM  193 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCC
Confidence            7899999999999999999999999999999955   5789999999999999999999999999999999999743211


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhH
Q 022301           84 RGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDM  159 (299)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a  159 (299)
                      ....        +-..........-+.|||..+.++++++||+.+|+-||+|+.|.+..++.+    ||+||+|.+....
T Consensus       194 pQAQ--------piID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~  265 (544)
T KOG0124|consen  194 PQAQ--------PIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQ  265 (544)
T ss_pred             cccc--------hHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccch
Confidence            1000        000000112224578999999999999999999999999999999998754    5999999999999


Q ss_pred             HHHHHhcCCCeecCcee
Q 022301          160 KHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       160 ~~a~~~l~g~~~~g~~~  176 (299)
                      ..|+..||=..++|.++
T Consensus       266 ~eAiasMNlFDLGGQyL  282 (544)
T KOG0124|consen  266 SEAIASMNLFDLGGQYL  282 (544)
T ss_pred             HHHhhhcchhhcccceE
Confidence            99999999999999954

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.88  E-value=3.5e-21  Score=149.05  Aligned_cols=170  Identities=22%  Similarity=0.321  Sum_probs=138.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHH----HhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEE
Q 022301            2 SSRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRV   77 (299)
Q Consensus         2 ~~~~~~~l~V~nLp~~~t~~~l~~----~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v   77 (299)
                      +-+++.||||.||+..+..++|+.    ||++||.|.+|....+.+.+|.|||.|.+.+.|..|+..|+|..|.|+++.|
T Consensus         5 ~~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mri   84 (221)
T KOG4206|consen    5 SVNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRI   84 (221)
T ss_pred             ccCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhhe
Confidence            346667999999999999999887    9999999999999999999999999999999999999999999999999999


Q ss_pred             EEccCCCCCCCCCC------------------------CCCC---CCCC---CC-CCCCCCccEEEEeCCCCCCCHHHHH
Q 022301           78 ELAHGGRGRSSSDR------------------------HSSH---SSGR---GR-GVSRRSEYRVLVTGLPSSASWQDLK  126 (299)
Q Consensus        78 ~~~~~~~~~~~~~~------------------------~~~~---~~~~---~~-~~~~~~~~~l~v~nl~~~~~~~~l~  126 (299)
                      .||+.....-....                        ....   ....   .. .....+...+++.|||..++.+.|.
T Consensus        85 qyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~  164 (221)
T KOG4206|consen   85 QYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLS  164 (221)
T ss_pred             ecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHH
Confidence            99975542111100                        0000   0000   00 1235677899999999999999999


Q ss_pred             HHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeec
Q 022301          127 DHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFR  172 (299)
Q Consensus       127 ~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~  172 (299)
                      .+|.+|.....+.++.... +.|||+|.+...|..|...++|..|-
T Consensus       165 ~lf~qf~g~keir~i~~~~-~iAfve~~~d~~a~~a~~~lq~~~it  209 (221)
T KOG4206|consen  165 DLFEQFPGFKEIRLIPPRS-GIAFVEFLSDRQASAAQQALQGFKIT  209 (221)
T ss_pred             HHHhhCcccceeEeccCCC-ceeEEecchhhhhHHHhhhhccceec
Confidence            9999999888888776543 48999999999999999999998886

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.88  E-value=5.7e-22  Score=175.23  Aligned_cols=160  Identities=23%  Similarity=0.401  Sum_probs=135.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CC----CCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PP----RPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~----~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ++|||.||++.+|.++|..+|..+|.|..+.|..  ++    .+.|||||+|.++++|+.|++.|+|+.|.|..|.|.++
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            3499999999999999999999999999998833  22    24599999999999999999999999999999999999


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC----CCCEEEEEecCh
Q 022301           81 HGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG----SGTTGIVDYTNY  156 (299)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~----~~~~~fv~f~~~  156 (299)
                      .........          ..-.....++.|+|.|||..++..+++++|..||.|..|.++...    ..|||||+|.++
T Consensus       596 ~~k~~~~~g----------K~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~  665 (725)
T KOG0110|consen  596 ENKPASTVG----------KKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTP  665 (725)
T ss_pred             cCccccccc----------cccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCc
Confidence            722211111          111223347899999999999999999999999999999998772    236999999999


Q ss_pred             hhHHHHHHhcCCCeecCcee
Q 022301          157 DDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       157 ~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .+|..|+++|.+..|.|+.+
T Consensus       666 ~ea~nA~~al~STHlyGRrL  685 (725)
T KOG0110|consen  666 REAKNAFDALGSTHLYGRRL  685 (725)
T ss_pred             HHHHHHHHhhcccceechhh
Confidence            99999999999999999865

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.88  E-value=4.4e-21  Score=145.53  Aligned_cols=80  Identities=35%  Similarity=0.588  Sum_probs=73.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      +...+|.|-||.+.++.++|..+|++||.|.+|.|..   +.+++|||||.|....+|+.|+..|+|.+|+|+.|.|++|
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            3467899999999999999999999999999999954   5788999999999999999999999999999999999988


Q ss_pred             cCC
Q 022301           81 HGG   83 (299)
Q Consensus        81 ~~~   83 (299)
                      ...
T Consensus        91 ryg   93 (256)
T KOG4207|consen   91 RYG   93 (256)
T ss_pred             hcC
Confidence            643

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.88  E-value=3.5e-21  Score=142.43  Aligned_cols=73  Identities=21%  Similarity=0.274  Sum_probs=65.9

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEE
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYV  180 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~  180 (299)
                      ..+.|||+||+..+++.||+.+|..||.|..|+|..+ +.|||||+|++..+|++|+..|+|..|+|..+.+++
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~   81 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVEL   81 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-CCCceEEeccCcccHHHHHhhcCCccccCceEEEEe
Confidence            3689999999999999999999999999999999995 557999999999999999999999999998443333

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.86  E-value=3.4e-20  Score=137.29  Aligned_cols=79  Identities=49%  Similarity=0.832  Sum_probs=73.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      +-.+.|||+||+.++++.||..+|..||+|..|+|..  .+.|||||+|+++.+|..|+..|+|..|.|..|.|+++...
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvAr--nPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~   85 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVAR--NPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGR   85 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEee--cCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCC
Confidence            4578999999999999999999999999999999965  44799999999999999999999999999999999998754


Q ss_pred             C
Q 022301           84 R   84 (299)
Q Consensus        84 ~   84 (299)
                      .
T Consensus        86 ~   86 (195)
T KOG0107|consen   86 P   86 (195)
T ss_pred             c
Confidence            4

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

Probab=99.85  E-value=6.9e-21  Score=159.27  Aligned_cols=181  Identities=23%  Similarity=0.334  Sum_probs=142.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCC-CC--CceEEEEE
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYD-FD--GHRLRVEL   79 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~-~~--g~~i~v~~   79 (299)
                      ..++|||+.|+..+||++|.++|.+||.|++|.|..  ++.++|||||+|.+.|.|..||+.|||.. +.  ..+|.|.|
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            367899999999999999999999999999999965  46889999999999999999999999954 44  45899999


Q ss_pred             ccCCCCCCC-----------------------------------------------------------------------
Q 022301           80 AHGGRGRSS-----------------------------------------------------------------------   88 (299)
Q Consensus        80 ~~~~~~~~~-----------------------------------------------------------------------   88 (299)
                      +........                                                                       
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            863322100                                                                       


Q ss_pred             --------CCCCCC--------CC----C---------C-----------------------------------------
Q 022301           89 --------SDRHSS--------HS----S---------G-----------------------------------------   98 (299)
Q Consensus        89 --------~~~~~~--------~~----~---------~-----------------------------------------   98 (299)
                              ......        ..    .         .                                         
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                    000000        00    0         0                                         


Q ss_pred             ----------------------------------------------------CCCCCCCCCccEEEEeCCCCCCCHHHHH
Q 022301           99 ----------------------------------------------------RGRGVSRRSEYRVLVTGLPSSASWQDLK  126 (299)
Q Consensus        99 ----------------------------------------------------~~~~~~~~~~~~l~v~nl~~~~~~~~l~  126 (299)
                                                                          .......+.+.+|||.+||.+.-+.+|-
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                                                                0000001156789999999999999999


Q ss_pred             HHHHhcCCeeEEEEEeCCCCC----EEEEEecChhhHHHHHHhcCCCeecCceeeEEEEeccc
Q 022301          127 DHMRRAGDVCFSQVFRDGSGT----TGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVREY  185 (299)
Q Consensus       127 ~~f~~~G~v~~~~~~~~~~~~----~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~~~  185 (299)
                      ..|..||.|+..++..|+.++    |+||.|++..+|..||..|||..|+.+..++-.+++..
T Consensus       443 ~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk~~~~  505 (510)
T KOG0144|consen  443 ATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLKRDRN  505 (510)
T ss_pred             HHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEeeeccC
Confidence            999999999999999999887    89999999999999999999999999976655554443

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.85  E-value=1.7e-20  Score=161.78  Aligned_cols=160  Identities=26%  Similarity=0.424  Sum_probs=136.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC-CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~-~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      +++...|||.||++.++..+|.++|+.||+|.+|++..+ ..++|| ||+|.++++|.+|+..|||..+.|++|.|....
T Consensus        73 ~rd~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~  151 (369)
T KOG0123|consen   73 QRDPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFE  151 (369)
T ss_pred             ccCCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeecc
Confidence            456666999999999999999999999999999999554 348899 999999999999999999999999999998775


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC---CEEEEEecChhh
Q 022301           82 GGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG---TTGIVDYTNYDD  158 (299)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv~f~~~~~  158 (299)
                      ..........           .....-+.++|.|++.+++++.|.++|..+|.|..+.++.+..+   +|+||+|++.++
T Consensus       152 ~~~er~~~~~-----------~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~  220 (369)
T KOG0123|consen  152 RKEEREAPLG-----------EYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPED  220 (369)
T ss_pred             chhhhccccc-----------chhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhH
Confidence            4432111110           12234578999999999999999999999999999999987544   699999999999


Q ss_pred             HHHHHHhcCCCeecCc
Q 022301          159 MKHAIKKLDDSEFRNA  174 (299)
Q Consensus       159 a~~a~~~l~g~~~~g~  174 (299)
                      |..|++.|+|..+.+.
T Consensus       221 a~~av~~l~~~~~~~~  236 (369)
T KOG0123|consen  221 AKKAVETLNGKIFGDK  236 (369)
T ss_pred             HHHHHHhccCCcCCcc
Confidence            9999999999999976

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.84  E-value=2.4e-20  Score=146.91  Aligned_cols=172  Identities=22%  Similarity=0.336  Sum_probs=135.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCC-CCC--ceEEEEE
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYD-FDG--HRLRVEL   79 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~-~~g--~~i~v~~   79 (299)
                      ..++|||+-|...-.|||+..+|..||+|.+|.+..  ++.++|+|||+|.+..+|..||..|||.. +.|  -.|.|+|
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            467899999999999999999999999999999954  67889999999999999999999999954 333  4688888


Q ss_pred             ccCCCCC-------------------------------------------------------------------------
Q 022301           80 AHGGRGR-------------------------------------------------------------------------   86 (299)
Q Consensus        80 ~~~~~~~-------------------------------------------------------------------------   86 (299)
                      +......                                                                         
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            6511100                                                                         


Q ss_pred             CCC-----CCC-----------------C------CCCCC----------------------------------------
Q 022301           87 SSS-----DRH-----------------S------SHSSG----------------------------------------   98 (299)
Q Consensus        87 ~~~-----~~~-----------------~------~~~~~----------------------------------------   98 (299)
                      +..     ..+                 .      ..+.+                                        
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            000     000                 0      00000                                        


Q ss_pred             ------------------CCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCC----EEEEEecCh
Q 022301           99 ------------------RGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGT----TGIVDYTNY  156 (299)
Q Consensus        99 ------------------~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~----~~fv~f~~~  156 (299)
                                        .......+.+++|||..||.+..+.||.++|-.||.|+..+++.|.-+.    |+||.|.++
T Consensus       258 paays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp  337 (371)
T KOG0146|consen  258 PAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNP  337 (371)
T ss_pred             chhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCc
Confidence                              0000112268999999999999999999999999999999999887554    999999999


Q ss_pred             hhHHHHHHhcCCCeecCcee
Q 022301          157 DDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       157 ~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..|+.||..|||.+|+-+.+
T Consensus       338 ~SaQaAIqAMNGFQIGMKRL  357 (371)
T KOG0146|consen  338 ASAQAAIQAMNGFQIGMKRL  357 (371)
T ss_pred             hhHHHHHHHhcchhhhhhhh
Confidence            99999999999999998844

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.84  E-value=8.2e-20  Score=140.28  Aligned_cols=169  Identities=23%  Similarity=0.379  Sum_probs=130.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCC----CceEEEEecChHHHHHHHHhcCCCCCC---CceEEE
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRP----PGYAFVEFEEARDAEDAIRGRDGYDFD---GHRLRV   77 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~----~g~afV~F~~~e~A~~A~~~l~~~~~~---g~~i~v   77 (299)
                      .-+||||.+||.++...+|..||..|--.+.+.++.+.+.    +.+|||.|.+.++|..|++.|||+.|+   +..|.+
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            3589999999999999999999999988888888776544    379999999999999999999999997   778999


Q ss_pred             EEccCCCCCCCCCCCCCC----------------------------------CCC-------------------------
Q 022301           78 ELAHGGRGRSSSDRHSSH----------------------------------SSG-------------------------   98 (299)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~----------------------------------~~~-------------------------   98 (299)
                      ++++..............                                  ...                         
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            998754321110000000                                  000                         


Q ss_pred             --------CCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCe
Q 022301           99 --------RGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSE  170 (299)
Q Consensus        99 --------~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~  170 (299)
                              .........+.+|||.||..++++++|+++|+.|-....++|........||++|++.+.|.+||..|+|..
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                    000011114568999999999999999999999988877777655544589999999999999999999988


Q ss_pred             ecC
Q 022301          171 FRN  173 (299)
Q Consensus       171 ~~g  173 (299)
                      |-.
T Consensus       273 ~s~  275 (284)
T KOG1457|consen  273 LSS  275 (284)
T ss_pred             ecc
Confidence            753

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.83  E-value=7.4e-19  Score=158.81  Aligned_cols=78  Identities=24%  Similarity=0.483  Sum_probs=72.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ..++|||+|||+++++++|+++|+.||+|..+.|..   ++..+|||||+|.+.++|..|+..||+..|.|+.|.|.++.
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   35689999999999999999999999999999999998865


Q ss_pred             C
Q 022301           82 G   82 (299)
Q Consensus        82 ~   82 (299)
                      .
T Consensus       283 ~  283 (612)
T TIGR01645       283 T  283 (612)
T ss_pred             C
Confidence            3

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.83  E-value=3.5e-20  Score=146.29  Aligned_cols=128  Identities=25%  Similarity=0.415  Sum_probs=109.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            1 MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         1 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      |.+...+||||+||...+||+-|..||.++|.|..++|+.+                                .|+|.|+
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            45788999999999999999999999999999999999854                                4666666


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecCh
Q 022301           81 HGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNY  156 (299)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~  156 (299)
                      .....+..              +.......+||+.|...++-++|++.|.+||+|..++|++|..+    ||+||.|.+.
T Consensus        49 ~~p~nQsk--------------~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k  114 (321)
T KOG0148|consen   49 TAPGNQSK--------------PTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNK  114 (321)
T ss_pred             cCcccCCC--------------CccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccch
Confidence            54322111              22233578999999999999999999999999999999999765    5999999999


Q ss_pred             hhHHHHHHhcCCCeecCc
Q 022301          157 DDMKHAIKKLDDSEFRNA  174 (299)
Q Consensus       157 ~~a~~a~~~l~g~~~~g~  174 (299)
                      ++|+.||..|||..|+++
T Consensus       115 ~dAEnAI~~MnGqWlG~R  132 (321)
T KOG0148|consen  115 EDAENAIQQMNGQWLGRR  132 (321)
T ss_pred             HHHHHHHHHhCCeeeccc
Confidence            999999999999999998

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.83  E-value=5.1e-20  Score=158.78  Aligned_cols=171  Identities=22%  Similarity=0.348  Sum_probs=128.9

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCCCC
Q 022301            9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGRG   85 (299)
Q Consensus         9 l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~~~   85 (299)
                      |||+||..++|+++|..+|+.||.|..|.+..   +|..+|||||+|.+.++|.+|+..|||..|.|+.|+|........
T Consensus       281 l~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~  360 (549)
T KOG0147|consen  281 LYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERVD  360 (549)
T ss_pred             hhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeecc
Confidence            89999999999999999999999999999944   588999999999999999999999999999999999977553332


Q ss_pred             CCCCCC---C------CCCC--CC------------------------------------------CCCCCCC-------
Q 022301           86 RSSSDR---H------SSHS--SG------------------------------------------RGRGVSR-------  105 (299)
Q Consensus        86 ~~~~~~---~------~~~~--~~------------------------------------------~~~~~~~-------  105 (299)
                      ......   .      ....  ..                                          .....+.       
T Consensus       361 ~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~  440 (549)
T KOG0147|consen  361 TKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADASPAFD  440 (549)
T ss_pred             cccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCccccccccC
Confidence            221100   0      0000  00                                          0011111       


Q ss_pred             CCccEEEEeCCCCC--CC--------HHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCce
Q 022301          106 RSEYRVLVTGLPSS--AS--------WQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAF  175 (299)
Q Consensus       106 ~~~~~l~v~nl~~~--~~--------~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  175 (299)
                      .+.-++.+.|+-..  .|        .+++.+.+.+||+|+.|.+..+.. |+.||.|.+.+.|..|+..|||.++.|+.
T Consensus       441 i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~ns~-g~VYvrc~s~~~A~~a~~alhgrWF~gr~  519 (549)
T KOG0147|consen  441 IPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKNSA-GCVYVRCPSAEAAGTAVKALHGRWFAGRM  519 (549)
T ss_pred             CccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccCCC-ceEEEecCcHHHHHHHHHHHhhhhhccce
Confidence            23334445553221  11        477888889999999888877765 89999999999999999999999999998


Q ss_pred             eeEEE
Q 022301          176 SRAYV  180 (299)
Q Consensus       176 ~~~~~  180 (299)
                      +++.+
T Consensus       520 Ita~~  524 (549)
T KOG0147|consen  520 ITAKY  524 (549)
T ss_pred             eEEEE
Confidence            76554

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.83  E-value=5.2e-21  Score=164.83  Aligned_cols=168  Identities=20%  Similarity=0.297  Sum_probs=138.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      +..+|||+-.|+..+++.+|.+||+.+|+|.+|.|+.+   +.++|.|||+|.+.+.+..||. |.|..+.|.+|.|...
T Consensus       177 Rd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq~s  255 (549)
T KOG0147|consen  177 RDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQLS  255 (549)
T ss_pred             HhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEeccc
Confidence            56788999999999999999999999999999999554   5688999999999999999997 9999999999999887


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecCh
Q 022301           81 HGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNY  156 (299)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~  156 (299)
                      ............. ..    ...-..+...|||+||..++++++|..+|+.||.|..|++..+..+    |||||+|.+.
T Consensus       256 Eaeknr~a~~s~a-~~----~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~  330 (549)
T KOG0147|consen  256 EAEKNRAANASPA-LQ----GKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNK  330 (549)
T ss_pred             HHHHHHHHhcccc-cc----ccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecH
Confidence            5444321111110 00    0011112223999999999999999999999999999999988633    5999999999


Q ss_pred             hhHHHHHHhcCCCeecCceee
Q 022301          157 DDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       157 ~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      ++|..|+.+|||.+|.|..+.
T Consensus       331 ~~ar~a~e~lngfelAGr~ik  351 (549)
T KOG0147|consen  331 EDARKALEQLNGFELAGRLIK  351 (549)
T ss_pred             HHHHHHHHHhccceecCceEE
Confidence            999999999999999999765

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.81  E-value=1.6e-19  Score=150.43  Aligned_cols=162  Identities=20%  Similarity=0.360  Sum_probs=135.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEE
Q 022301            1 MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRV   77 (299)
Q Consensus         1 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v   77 (299)
                      |+....++|||++|++++++|.|.+.|.+||+|.+|.++.   ++..+||+||+|++++.+..+|. .....|.|+.|.+
T Consensus         1 ~~~~~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~   79 (311)
T KOG4205|consen    1 SESGESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEP   79 (311)
T ss_pred             CCccCCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccc
Confidence            3455789999999999999999999999999999999955   46788999999999999999988 6677899999988


Q ss_pred             EEccCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEe
Q 022301           78 ELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDY  153 (299)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f  153 (299)
                      +.+.+...+......             .....|||++||.++++++|++.|.+||.|..+.++.+...    +|+||.|
T Consensus        80 k~av~r~~~~~~~~~-------------~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~  146 (311)
T KOG4205|consen   80 KRAVSREDQTKVGRH-------------LRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTF  146 (311)
T ss_pred             eeccCcccccccccc-------------cceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEe
Confidence            877655433222111             14569999999999999999999999999999988888654    5999999


Q ss_pred             cChhhHHHHHHhcCCCeecCceee
Q 022301          154 TNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       154 ~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      ...+.+.+++. ..-..|+|+.++
T Consensus       147 ~~e~sVdkv~~-~~f~~~~gk~ve  169 (311)
T KOG4205|consen  147 DSEDSVDKVTL-QKFHDFNGKKVE  169 (311)
T ss_pred             ccccccceecc-cceeeecCceee
Confidence            99999998887 777788888443

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.79  E-value=7.7e-19  Score=132.34  Aligned_cols=82  Identities=26%  Similarity=0.510  Sum_probs=75.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ..+++|||+|||+++|+++|+++|.+||+|..|.|..   ++.++|||||+|.+.++|+.|+..||+..|.|+.|+|.++
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            4578999999999999999999999999999999954   4678999999999999999999999999999999999998


Q ss_pred             cCCCC
Q 022301           81 HGGRG   85 (299)
Q Consensus        81 ~~~~~   85 (299)
                      .....
T Consensus       112 ~~~~~  116 (144)
T PLN03134        112 NDRPS  116 (144)
T ss_pred             CcCCC
Confidence            75543

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.79  E-value=9.7e-18  Score=136.92  Aligned_cols=180  Identities=21%  Similarity=0.270  Sum_probs=140.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCee--------EEEe--ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIA--------HIDL--KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGH   73 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~--------~i~~--~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~   73 (299)
                      .-++.|||.|||.++|.+++.++|++||.|.        .|+|  ...|+.+|-|+|.|...|++..|+..|++..|.|+
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            3466799999999999999999999999773        2444  33578899999999999999999999999999999


Q ss_pred             eEEEEEccCCCCCCCCCCCCC-------------------CCCCCCCCCCCCCccEEEEeCCCCC----CC-------HH
Q 022301           74 RLRVELAHGGRGRSSSDRHSS-------------------HSSGRGRGVSRRSEYRVLVTGLPSS----AS-------WQ  123 (299)
Q Consensus        74 ~i~v~~~~~~~~~~~~~~~~~-------------------~~~~~~~~~~~~~~~~l~v~nl~~~----~~-------~~  123 (299)
                      .|.|+.|+.............                   +......+.-.....+|+|.|+-..    .+       ++
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            999998875443222211110                   0111111122235578888886331    12       57


Q ss_pred             HHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEec
Q 022301          124 DLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVR  183 (299)
Q Consensus       124 ~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~  183 (299)
                      +|.+.+.+||.|..|.|....+.|.+.|.|.+.++|..||+.|+|..++|+.+++.+--.
T Consensus       292 dl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG  351 (382)
T KOG1548|consen  292 DLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDG  351 (382)
T ss_pred             HHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCC
Confidence            788889999999999999999999999999999999999999999999999888777533

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.77  E-value=4.4e-17  Score=130.63  Aligned_cols=80  Identities=39%  Similarity=0.708  Sum_probs=74.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEe---ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~---~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..|=+||||+-|+++++|..|+..|..||+|+.|.|   +.+++++|||||+|.++.+...|.+..+|..|+|+.|.|.+
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            467899999999999999999999999999999999   45789999999999999999999999999999999999988


Q ss_pred             ccC
Q 022301           80 AHG   82 (299)
Q Consensus        80 ~~~   82 (299)
                      -..
T Consensus       178 ERg  180 (335)
T KOG0113|consen  178 ERG  180 (335)
T ss_pred             ccc
Confidence            653

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.77  E-value=7.4e-18  Score=149.43  Aligned_cols=175  Identities=20%  Similarity=0.277  Sum_probs=136.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      ...+.|+|+|||..+..++|..+|..||+|..|.|+..|   ..|+|+|.++.+|..|+..|....+...++.+.|+...
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 RSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPPGG---TGAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWAPED  459 (725)
T ss_pred             hhcceeeeccCccccccHHHHHHhhcccccceeecCccc---ceeeeeecCccchHHHHHHhchhhhccCccccccChhh
Confidence            346889999999999999999999999999999665222   25899999999999999999999999999999887644


Q ss_pred             CCC--CCCCC------CC----------CCCCCCCCC-------------CCCCCccEEEEeCCCCCCCHHHHHHHHHhc
Q 022301           84 RGR--SSSDR------HS----------SHSSGRGRG-------------VSRRSEYRVLVTGLPSSASWQDLKDHMRRA  132 (299)
Q Consensus        84 ~~~--~~~~~------~~----------~~~~~~~~~-------------~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~  132 (299)
                      ...  +....      ..          .........             ......+.|||.||+..++.++|..+|..+
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            433  11000      00          000000000             011123349999999999999999999999


Q ss_pred             CCeeEEEEEeCCCC-------CEEEEEecChhhHHHHHHhcCCCeecCceeeEEEE
Q 022301          133 GDVCFSQVFRDGSG-------TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVR  181 (299)
Q Consensus       133 G~v~~~~~~~~~~~-------~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~  181 (299)
                      |.|..+.|...+..       |||||+|.+.++|+.|+..|+|..|+|+.+...+.
T Consensus       540 G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S  595 (725)
T KOG0110|consen  540 GTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKIS  595 (725)
T ss_pred             CeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEec
Confidence            99999988777654       79999999999999999999999999996644443

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.76  E-value=2.4e-17  Score=137.34  Aligned_cols=167  Identities=16%  Similarity=0.265  Sum_probs=136.6

Q ss_pred             CCeEEEcCCCCC-CCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCCC
Q 022301            6 SRTLYVGNLPGD-IREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGR   84 (299)
Q Consensus         6 ~~~l~V~nLp~~-~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~~   84 (299)
                      +++|.|.||.+. +|.+.|..+|+-||+|..|+|...++  ..|+|+|.+...|+.|++.|+|..+.|++|.|.+++...
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk--d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~  374 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK--DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTN  374 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC--cceeeeecchhHHHHHHHHhhcceecCceEEEeeccCcc
Confidence            789999999665 99999999999999999999976653  689999999999999999999999999999999998766


Q ss_pred             CCCCCCCCCCC--CCC--------------CCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCE
Q 022301           85 GRSSSDRHSSH--SSG--------------RGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTT  148 (299)
Q Consensus        85 ~~~~~~~~~~~--~~~--------------~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~  148 (299)
                      .+...+.....  ..+              .......++..+|++.|+|..+++++|+++|...|..+.......+...+
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            54333222110  000              01112335667999999999999999999999999887766666666669


Q ss_pred             EEEEecChhhHHHHHHhcCCCeecCc
Q 022301          149 GIVDYTNYDDMKHAIKKLDDSEFRNA  174 (299)
Q Consensus       149 ~fv~f~~~~~a~~a~~~l~g~~~~g~  174 (299)
                      |++++++.++|..|+..++...+++.
T Consensus       455 al~q~~sveeA~~ali~~hnh~lgen  480 (492)
T KOG1190|consen  455 ALPQLESVEEAIQALIDLHNHYLGEN  480 (492)
T ss_pred             eecccCChhHhhhhccccccccCCCC
Confidence            99999999999999999999888765

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.75  E-value=6.4e-17  Score=135.89  Aligned_cols=170  Identities=24%  Similarity=0.354  Sum_probs=134.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhh-hcCCeeEEEeecC--CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFY-KYGPIAHIDLKIP--PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~-~~G~v~~i~~~~~--~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ..+.+||+|||+++.+.+|++||. +.|+|.+|.+..+  ++++|+|.|+|+++|.+++|++.||...+.|++|.|+...
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            356799999999999999999998 7899999999665  7899999999999999999999999999999999998755


Q ss_pred             CCCCCCCC------------------------------------------CCC------CCCCCC---------------
Q 022301           82 GGRGRSSS------------------------------------------DRH------SSHSSG---------------   98 (299)
Q Consensus        82 ~~~~~~~~------------------------------------------~~~------~~~~~~---------------   98 (299)
                      ........                                          ...      .+....               
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            32110000                                          000      000000               


Q ss_pred             ---CCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC---CEEEEEecChhhHHHHHHhcCCCeec
Q 022301           99 ---RGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG---TTGIVDYTNYDDMKHAIKKLDDSEFR  172 (299)
Q Consensus        99 ---~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~  172 (299)
                         ....+..+-..++||.||.+.+....|.+.|.-.|+|..+.+-.++.+   ++|.|+|.++-+|-+||..|++.-+.
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               001123345568999999999999999999999999999988877644   69999999999999999999986655


Q ss_pred             Cc
Q 022301          173 NA  174 (299)
Q Consensus       173 g~  174 (299)
                      ..
T Consensus       283 ~~  284 (608)
T KOG4212|consen  283 DR  284 (608)
T ss_pred             cc
Confidence            54

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.74  E-value=4.2e-18  Score=119.54  Aligned_cols=80  Identities=38%  Similarity=0.572  Sum_probs=73.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEe---ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~---~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ..++||||+||+..++||+|.+||+.+|+|..|.|   ..+..+.|||||+|.+.++|..|+..++|+.++.++|.+.|.
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            56899999999999999999999999999999999   334567899999999999999999999999999999999987


Q ss_pred             cCC
Q 022301           81 HGG   83 (299)
Q Consensus        81 ~~~   83 (299)
                      ...
T Consensus       114 ~GF  116 (153)
T KOG0121|consen  114 AGF  116 (153)
T ss_pred             ccc
Confidence            543

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.72  E-value=2.4e-16  Score=134.62  Aligned_cols=161  Identities=20%  Similarity=0.273  Sum_probs=124.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC-CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCCC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGR   84 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~-~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~~   84 (299)
                      .-.|.+.+||++||++||.++|+.|+ |..+.+..+ ++..|-|||+|.++|++.+|++ .+-..+..+.|.|..+....
T Consensus        10 ~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~~e   87 (510)
T KOG4211|consen   10 AFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGGAE   87 (510)
T ss_pred             ceEEEecCCCccccHHHHHHHHhcCc-eeEEEEeccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCCcc
Confidence            34677889999999999999999985 788877554 8999999999999999999999 88888999999998775444


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeE-EEEEeC---CCCCEEEEEecChhhHH
Q 022301           85 GRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCF-SQVFRD---GSGTTGIVDYTNYDDMK  160 (299)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~-~~~~~~---~~~~~~fv~f~~~~~a~  160 (299)
                      ..-......        +........|-+.+||..++++||.++|.-.-.|.. +.+..+   +.++-|||+|++.+.|+
T Consensus        88 ~d~~~~~~g--------~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae  159 (510)
T KOG4211|consen   88 ADWVMRPGG--------PNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAE  159 (510)
T ss_pred             ccccccCCC--------CCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHH
Confidence            321111111        011135568899999999999999999998765554 333333   34568999999999999


Q ss_pred             HHHHhcCCCeecCceee
Q 022301          161 HAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       161 ~a~~~l~g~~~~g~~~~  177 (299)
                      +|+. -|...|+.++++
T Consensus       160 ~Al~-rhre~iGhRYIE  175 (510)
T KOG4211|consen  160 IALG-RHRENIGHRYIE  175 (510)
T ss_pred             HHHH-HHHHhhccceEE
Confidence            9998 566677777443

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.71  E-value=7.9e-17  Score=129.63  Aligned_cols=79  Identities=22%  Similarity=0.323  Sum_probs=73.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCCCC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGRG   85 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~~~   85 (299)
                      .++|||+|||+.+|+++|+++|+.||+|.+|.|..++...|||||+|.++++|..||. |||..|.|+.|.|.++.....
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~~~~   82 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAEDYQL   82 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccCCCC
Confidence            6899999999999999999999999999999998777778999999999999999997 999999999999999875543

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.70  E-value=4.3e-17  Score=135.81  Aligned_cols=178  Identities=17%  Similarity=0.239  Sum_probs=136.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCC--CCCCCceEEEEEc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG--YDFDGHRLRVELA   80 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~--~~~~g~~i~v~~~   80 (299)
                      ..++..|+++|||++++|++|.+|+.+||.|..+.+.   +.+..|||+|.++++|...+..+..  -.+.|.+|.|.|+
T Consensus        25 ~~pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~l---kGknQAflem~d~~sAvtmv~~y~~~~p~lr~~~~yiq~s  101 (492)
T KOG1190|consen   25 AEPSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLML---KGKNQAFLEMADEESAVTMVNYYTSVTPVLRGQPIYIQYS  101 (492)
T ss_pred             cCCcceeEeccCCccccHHHHHHhcccccceeeeeee---ccchhhhhhhcchhhhhheeecccccCccccCcceeehhh
Confidence            4689999999999999999999999999999999997   4466999999999999886664444  3466889999886


Q ss_pred             cCCCCCCCCCCCC------------------CCCC-C--CCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEE
Q 022301           81 HGGRGRSSSDRHS------------------SHSS-G--RGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQ  139 (299)
Q Consensus        81 ~~~~~~~~~~~~~------------------~~~~-~--~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~  139 (299)
                      .............                  .... .  .+.......-..++|.|+-+.++-+.|.++|+.||.|..+.
T Consensus       102 n~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~VlKIi  181 (492)
T KOG1190|consen  102 NHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVLKII  181 (492)
T ss_pred             hHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcceeEEEE
Confidence            5332211111100                  0000 0  01122233445788899999999999999999999999988


Q ss_pred             EEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEec
Q 022301          140 VFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVR  183 (299)
Q Consensus       140 ~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~  183 (299)
                      .+....+-.|.|+|.+.+.|+.|...|+|..|...+++..|...
T Consensus       182 TF~Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~S  225 (492)
T KOG1190|consen  182 TFTKNNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFS  225 (492)
T ss_pred             EEecccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehh
Confidence            88777766899999999999999999999999887777666543

>PF00076 RRM_1: RNA recognition motif

Probab=99.70  E-value=2.9e-17  Score=108.92  Aligned_cols=68  Identities=44%  Similarity=0.826  Sum_probs=63.6

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEE
Q 022301            9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLR   76 (299)
Q Consensus         9 l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~   76 (299)
                      |||+|||+++|+++|.++|..||.|..+.+..  .+..+++|||+|.+.++|..|+..|||..|.|..|+
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            79999999999999999999999999999955  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 ....

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.70  E-value=1.1e-16  Score=108.14  Aligned_cols=81  Identities=36%  Similarity=0.510  Sum_probs=75.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            2 SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         2 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ....+..|||.|||.++|.|++.+||+.||.|..|.|-.+...+|.|||.|++..+|.+|+..|+|..+.+..|.|-+..
T Consensus        14 ppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   14 PPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             ChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            34568899999999999999999999999999999997777889999999999999999999999999999999998875


Q ss_pred             C
Q 022301           82 G   82 (299)
Q Consensus        82 ~   82 (299)
                      .
T Consensus        94 ~   94 (124)
T KOG0114|consen   94 P   94 (124)
T ss_pred             H
Confidence            4

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.70  E-value=1.4e-16  Score=143.93  Aligned_cols=127  Identities=21%  Similarity=0.285  Sum_probs=100.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhc--CCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKY--GPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~--G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      ..++|||+||+.++|+++|+++|+.|  |+|..|.+.     ++||||+|.+.++|.+|+..||+..|.|+.|.|.|+++
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            35789999999999999999999999  999999886     57999999999999999999999999999999999976


Q ss_pred             CCCCCCCCCCCC---------CCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCee
Q 022301           83 GRGRSSSDRHSS---------HSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVC  136 (299)
Q Consensus        83 ~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~  136 (299)
                      ............         ...........+...++++.|++..++.+-+.++|..+|.|.
T Consensus       307 ~~~~~~~~~~rg~gg~~~~~~~~~~~~g~~~sp~s~~~~~g~~~~~~~~~~~~~~f~~~g~~~  369 (578)
T TIGR01648       307 VDKKSYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAYEDYYYHPPYAPSLHFPRMPGPIR  369 (578)
T ss_pred             CCcccccccccccCCCcccccccccccCcccCccccccccccccccccccchhhccccCcccc
Confidence            543211100000         000001112333567899999999999999999999998765

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.

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.68  E-value=2.6e-16  Score=137.66  Aligned_cols=182  Identities=20%  Similarity=0.351  Sum_probs=134.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ...+.|||+|||..+++.++.+++..||++....+..   ++.++||||.+|.+...+..|+..|||+.+.++.|.|..+
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            3567899999999999999999999999999988843   4678999999999999999999999999999999999988


Q ss_pred             cCCCCCCCCCCC--C-CCCCCC--CCCCCCCCccEEEEeCC--CCCC-C-------HHHHHHHHHhcCCeeEEEEEeC-C
Q 022301           81 HGGRGRSSSDRH--S-SHSSGR--GRGVSRRSEYRVLVTGL--PSSA-S-------WQDLKDHMRRAGDVCFSQVFRD-G  144 (299)
Q Consensus        81 ~~~~~~~~~~~~--~-~~~~~~--~~~~~~~~~~~l~v~nl--~~~~-~-------~~~l~~~f~~~G~v~~~~~~~~-~  144 (299)
                      ............  + ......  ..+....+...|.+.|+  |.+. .       .++++..|.+||.|..|.+... .
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            765543332222  1 011111  11233334444555442  1111 1       2556677888999999999887 2


Q ss_pred             ------CCCEEEEEecChhhHHHHHHhcCCCeecCceee-EEEEeccc
Q 022301          145 ------SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR-AYVRVREY  185 (299)
Q Consensus       145 ------~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~-~~~~~~~~  185 (299)
                            ..|..||+|.+.++++.|+..|+|.+++|+.+. .|+-++.+
T Consensus       447 ~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeDkY  494 (500)
T KOG0120|consen  447 DENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDEDKY  494 (500)
T ss_pred             CCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHHHh
Confidence                  235899999999999999999999999998743 34444444

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.68  E-value=1.1e-15  Score=121.03  Aligned_cols=81  Identities=23%  Similarity=0.272  Sum_probs=74.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      ....||||+||++.+|+++|+++|+.||+|.+|.|..++...++|||+|.++++|..|+. |||..|.+..|.|..+...
T Consensus         3 ~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~~y   81 (243)
T PLN03121          3 PGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWGQY   81 (243)
T ss_pred             CCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCccc
Confidence            455899999999999999999999999999999998888888999999999999999997 9999999999999987654


Q ss_pred             CC
Q 022301           84 RG   85 (299)
Q Consensus        84 ~~   85 (299)
                      ..
T Consensus        82 ~~   83 (243)
T PLN03121         82 ED   83 (243)
T ss_pred             cc
Confidence            43

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.68  E-value=1.1e-15  Score=129.54  Aligned_cols=141  Identities=30%  Similarity=0.530  Sum_probs=111.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      .++|||+|||..+|+++|.++|..||.|..+.+..   ++..+|||||+|.+.++|..|+..|+|..|.|+.|.|.++..
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            59999999999999999999999999999998854   478899999999999999999999999999999999999753


Q ss_pred             --CCCCCCCC---CCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC
Q 022301           83 --GRGRSSSD---RHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG  146 (299)
Q Consensus        83 --~~~~~~~~---~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~  146 (299)
                        ........   ....................+++.+++..+...++...|..+|.+..+.+......
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  263 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDG  263 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCCCC
Confidence              11111110   00000111222344556788999999999999999999999999977666655543

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.66  E-value=6.2e-15  Score=121.46  Aligned_cols=75  Identities=25%  Similarity=0.518  Sum_probs=68.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      =+.|||..+.++++++||+.+|+-||+|..|.+..   ....+||+||+|.+.+....|+..||-..+.|..|.|-.+
T Consensus       210 fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~  287 (544)
T KOG0124|consen  210 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC  287 (544)
T ss_pred             hheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccc
Confidence            36899999999999999999999999999999943   3567999999999999999999999999999999999654

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.65  E-value=1.6e-14  Score=116.05  Aligned_cols=71  Identities=20%  Similarity=0.229  Sum_probs=65.7

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .+-.+|||.-|++++++..|+..|..||+|..|.|+.+..+    |||||+|++..+...|.+..+|.+|+|+.+
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri  173 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRI  173 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEE
Confidence            45579999999999999999999999999999999988544    599999999999999999999999999955

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

Probab=99.65  E-value=7e-16  Score=120.48  Aligned_cols=80  Identities=40%  Similarity=0.642  Sum_probs=75.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEe---ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~---~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .++++|-|.||+.++++++|.+||.+||.|..|.|   +.+|.++|||||.|...++|..||..|||.-++.-.|.|+|+
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            46889999999999999999999999999999999   446899999999999999999999999999999999999999


Q ss_pred             cCC
Q 022301           81 HGG   83 (299)
Q Consensus        81 ~~~   83 (299)
                      ++.
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            753

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.62  E-value=1.1e-15  Score=108.51  Aligned_cols=79  Identities=27%  Similarity=0.498  Sum_probs=73.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      .-.|||+++.+.+|+++|.+.|..||+|++|.++.   +|-.+|||+|+|++.++|+.|+..|||..|.|+.|.|.|+..
T Consensus        72 GwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv  151 (170)
T KOG0130|consen   72 GWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFV  151 (170)
T ss_pred             eEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEe
Confidence            34799999999999999999999999999999955   577899999999999999999999999999999999999875


Q ss_pred             CC
Q 022301           83 GR   84 (299)
Q Consensus        83 ~~   84 (299)
                      ..
T Consensus       152 ~g  153 (170)
T KOG0130|consen  152 KG  153 (170)
T ss_pred             cC
Confidence            44

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.62  E-value=1.1e-15  Score=101.21  Aligned_cols=68  Identities=34%  Similarity=0.727  Sum_probs=60.5

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC--CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEE
Q 022301            9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP--PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLR   76 (299)
Q Consensus         9 l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~--~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~   76 (299)
                      |||+|||+++++++|.++|..||.|..+.+...  +..+++|||+|.++++|..|+..+++..|.|+.|.
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            799999999999999999999999999999543  55679999999999999999999888999999874

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 ....

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.62  E-value=2.6e-14  Score=107.72  Aligned_cols=73  Identities=22%  Similarity=0.324  Sum_probs=66.4

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .....++|||.|||..+++++|+++|.+||.|..+.++.+..    .+||||+|.+.++|+.|++.|+|..|+|+.+
T Consensus        30 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l  106 (144)
T PLN03134         30 LRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHI  106 (144)
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            345667999999999999999999999999999999998864    4699999999999999999999999999844

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.61  E-value=4.1e-15  Score=127.87  Aligned_cols=81  Identities=32%  Similarity=0.529  Sum_probs=72.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCC--ceEEEEE
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDG--HRLRVEL   79 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g--~~i~v~~   79 (299)
                      ..++|||+|||.++|+++|+++|++||+|+.|.|..   ++.+++||||+|.+.++|++||..||+..|.+  .+|.|.+
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            467899999999999999999999999999999954   46778999999999999999999999998876  6899998


Q ss_pred             ccCCCC
Q 022301           80 AHGGRG   85 (299)
Q Consensus        80 ~~~~~~   85 (299)
                      +.....
T Consensus       272 a~~~~~  277 (346)
T TIGR01659       272 AEEHGK  277 (346)
T ss_pred             CCcccc
Confidence            876543

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=6.2e-14  Score=115.92  Aligned_cols=170  Identities=17%  Similarity=0.203  Sum_probs=134.8

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            4 RASRTLYVGNLPGD-IREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         4 ~~~~~l~V~nLp~~-~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      -+.+.++|.+|... ++-+-|.++|+.||.|..|+++.+.  .|.|+|++.+..+++.|+..||+..+.|.+|.|.+++.
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            46789999999775 7888899999999999999998765  57899999999999999999999999999999999875


Q ss_pred             CCCCCCCC--------CCCCCCC----------CCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcC-CeeEEEEEeC
Q 022301           83 GRGRSSSD--------RHSSHSS----------GRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAG-DVCFSQVFRD  143 (299)
Q Consensus        83 ~~~~~~~~--------~~~~~~~----------~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G-~v~~~~~~~~  143 (299)
                      ........        ....+..          .....-...+.+.|+..|.|..+|++.|.++|...+ ....++++..
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            54322210        0000000          011223455788999999999999999999999877 3455677666


Q ss_pred             CCCC--EEEEEecChhhHHHHHHhcCCCeecCce
Q 022301          144 GSGT--TGIVDYTNYDDMKHAIKKLDDSEFRNAF  175 (299)
Q Consensus       144 ~~~~--~~fv~f~~~~~a~~a~~~l~g~~~~g~~  175 (299)
                      +...  .+.++|++.++|..||..+|...|.+..
T Consensus       443 kserSssGllEfe~~s~Aveal~~~NH~pi~~p~  476 (494)
T KOG1456|consen  443 KSERSSSGLLEFENKSDAVEALMKLNHYPIEGPN  476 (494)
T ss_pred             cccccccceeeeehHHHHHHHHHHhccccccCCC
Confidence            5433  7999999999999999999999998864

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.59  E-value=1.7e-16  Score=118.35  Aligned_cols=84  Identities=26%  Similarity=0.504  Sum_probs=77.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEee---cCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLK---IPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~---~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .++.-|||+|||..+||.||.-+|++||+|++|.+.   .||+++||||+.|+++-+...|+..|||..|.|+.|.|.+.
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            467789999999999999999999999999999994   46899999999999999999999999999999999999998


Q ss_pred             cCCCCCC
Q 022301           81 HGGRGRS   87 (299)
Q Consensus        81 ~~~~~~~   87 (299)
                      .....+.
T Consensus       113 ~~Yk~pk  119 (219)
T KOG0126|consen  113 SNYKKPK  119 (219)
T ss_pred             ccccCCc
Confidence            7666543

>smart00362 RRM_2 RNA recognition motif

Probab=99.57  E-value=2.3e-14  Score=95.01  Aligned_cols=70  Identities=46%  Similarity=0.848  Sum_probs=64.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC-CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEE
Q 022301            8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRV   77 (299)
Q Consensus         8 ~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~-~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v   77 (299)
                      +|||+|||.++++++|.++|..||+|..+.+..+ +.+.++|||+|.+.++|..|+..|++..+.|..|.|
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            6899999999999999999999999999998654 456799999999999999999999999999998876

>PLN03213 repressor of silencing 3; Provisional

Probab=99.55  E-value=2e-14  Score=122.87  Aligned_cols=78  Identities=19%  Similarity=0.385  Sum_probs=71.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecCh--HHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEA--RDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~--e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ....+||||||++.+|+++|..+|..||.|..|.|+... .+|||||+|.+.  .++.+||..|||..+.|+.|+|+.++
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRET-GRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAK   86 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTK-GRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAK   86 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeccc-CCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeecc
Confidence            456789999999999999999999999999999997543 399999999987  78999999999999999999999886


Q ss_pred             C
Q 022301           82 G   82 (299)
Q Consensus        82 ~   82 (299)
                      +
T Consensus        87 P   87 (759)
T PLN03213         87 E   87 (759)
T ss_pred             H
Confidence            3

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.54  E-value=2.4e-14  Score=116.45  Aligned_cols=81  Identities=23%  Similarity=0.458  Sum_probs=74.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC-CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~-~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      ...+.|+|.|||...-+.||...|.+||+|.+|.|+.+ ..+||||||+|++.++|++|-.+|||..|.|++|.|+-+..
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            56789999999999999999999999999999999654 57899999999999999999999999999999999998865


Q ss_pred             CC
Q 022301           83 GR   84 (299)
Q Consensus        83 ~~   84 (299)
                      ..
T Consensus       174 rV  175 (376)
T KOG0125|consen  174 RV  175 (376)
T ss_pred             hh
Confidence            43

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.53  E-value=1.1e-14  Score=111.93  Aligned_cols=84  Identities=35%  Similarity=0.612  Sum_probs=77.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      +..+||||++|...+|+.-|...|-+||.|.+|.++.+   .+.+|||||+|...|+|..||..||+..|.|+.|.|+++
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            56789999999999999999999999999999999654   678999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 022301           81 HGGRGRS   87 (299)
Q Consensus        81 ~~~~~~~   87 (299)
                      .+.....
T Consensus        88 kP~kike   94 (298)
T KOG0111|consen   88 KPEKIKE   94 (298)
T ss_pred             CCccccC
Confidence            8776543

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.52  E-value=2.6e-14  Score=111.37  Aligned_cols=75  Identities=25%  Similarity=0.430  Sum_probs=67.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEee---cCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLK---IPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~---~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      ++|||++|++.++.|.|+.+|++||+|++..|+   .++.++|||||+|.+.+.|..|++. -+-.|+|++..|+++.-
T Consensus        13 TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   13 TKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLASL   90 (247)
T ss_pred             EEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhhh
Confidence            689999999999999999999999999999884   4578999999999999999999994 44678999999999865

>PF00076 RRM_1: RNA recognition motif

Probab=99.52  E-value=1e-13  Score=91.70  Aligned_cols=66  Identities=20%  Similarity=0.383  Sum_probs=60.4

Q ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC---CCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          111 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG---SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       111 l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~---~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      |||+|||..+++++|.++|.+||.|..+.+..+.   ..++|||+|.+.++|+.|++.|+|..++|+.+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~i   69 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKI   69 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCc
Confidence            7999999999999999999999999999999862   22599999999999999999999999999843

(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 ....

>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=2.1e-13  Score=90.88  Aligned_cols=72  Identities=42%  Similarity=0.815  Sum_probs=65.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCC--CCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP--RPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         8 ~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~--~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      +|+|+|||..+++++|.++|..||+|..+.+..+.  .+.++|||+|.+.++|..|+..+++..+.|..|.|.+
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            58999999999999999999999999999996543  4578999999999999999999999999999998864

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).

>smart00360 RRM RNA recognition motif

Probab=99.48  E-value=2e-13  Score=90.07  Aligned_cols=67  Identities=45%  Similarity=0.804  Sum_probs=61.6

Q ss_pred             EcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEE
Q 022301           11 VGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRV   77 (299)
Q Consensus        11 V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v   77 (299)
                      |+|||..+++++|+++|..||.|..+.+..   ++.++++|||+|.+.++|..|+..|++..+.|..|.|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v   70 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV   70 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEe
Confidence            689999999999999999999999999954   3567899999999999999999999999999998887

>PF13893 RRM_5: RNA recognition motif

Probab=99.48  E-value=1.9e-13  Score=86.07  Aligned_cols=56  Identities=38%  Similarity=0.661  Sum_probs=51.0

Q ss_pred             HHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301           23 VEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus        23 l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      |.++|++||+|..|.+..+.  .++|||+|.+.++|..|+..|||..|.|+.|.|.|+
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            68999999999999997554  589999999999999999999999999999999985

(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 ....

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.47  E-value=3.6e-12  Score=107.68  Aligned_cols=75  Identities=21%  Similarity=0.390  Sum_probs=63.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEe--ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL--KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~--~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      -...+||.||...+..+.|++.|.-.|.|+.|.+  ...+.++|+|.|+|.++-+|..||..|++.-++..+..+.+
T Consensus       214 l~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~~~g~~~~~~~~Rl  290 (608)
T KOG4212|consen  214 LHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLDRQGLFDRRMTVRL  290 (608)
T ss_pred             ccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHHHHHHhhccCCCccccceeec
Confidence            3468999999999999999999999999998888  44567889999999999999999998887666655555543

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.46  E-value=2.4e-14  Score=117.56  Aligned_cols=81  Identities=23%  Similarity=0.392  Sum_probs=75.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEee---cCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLK---IPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~---~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .|.++|||..|++-+|.++|.-+|+.||+|..|.|+   .+|.+..||||+|.+.++|.+|+..|++..|..+.|.|.|+
T Consensus       237 PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFS  316 (479)
T KOG0415|consen  237 PPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFS  316 (479)
T ss_pred             CCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehh
Confidence            588999999999999999999999999999999994   46788899999999999999999999999999999999998


Q ss_pred             cCCC
Q 022301           81 HGGR   84 (299)
Q Consensus        81 ~~~~   84 (299)
                      +...
T Consensus       317 QSVs  320 (479)
T KOG0415|consen  317 QSVS  320 (479)
T ss_pred             hhhh
Confidence            6543

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.46  E-value=1.7e-12  Score=107.57  Aligned_cols=166  Identities=15%  Similarity=0.199  Sum_probs=129.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHh--cCCCCCCCceEEEEEcc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRG--RDGYDFDGHRLRVELAH   81 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~--l~~~~~~g~~i~v~~~~   81 (299)
                      .++-.|.|.+|-..+++.+|.+.++.||+|..+.+..   .+..|+|+|++.+.|+.|+..  -+...+.|+...++++.
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 NPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMP---HKRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNYST  105 (494)
T ss_pred             CCCceEEEeccccccchhHHHHHHhcCCceEEEEecc---ccceeeeeeccccchhhheehhccCcccccCchhhcccch
Confidence            5677899999999999999999999999999999863   256899999999999999873  23466778888887774


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCccEEE--EeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhH
Q 022301           82 GGRGRSSSDRHSSHSSGRGRGVSRRSEYRVL--VTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDM  159 (299)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~--v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a  159 (299)
                      .......            ......++..|.  |.|--+.+|.+.|..++...|+|..|.|+.. ++-.|.|+|++.+.|
T Consensus       106 sq~i~R~------------g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk-ngVQAmVEFdsv~~A  172 (494)
T KOG1456|consen  106 SQCIERP------------GDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK-NGVQAMVEFDSVEVA  172 (494)
T ss_pred             hhhhccC------------CCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec-cceeeEEeechhHHH
Confidence            3321110            011222333343  4455667899999999999999999998877 445899999999999


Q ss_pred             HHHHHhcCCCeecCceeeEEEEeccc
Q 022301          160 KHAIKKLDDSEFRNAFSRAYVRVREY  185 (299)
Q Consensus       160 ~~a~~~l~g~~~~g~~~~~~~~~~~~  185 (299)
                      ++|...|||..|....++..|...+.
T Consensus       173 qrAk~alNGADIYsGCCTLKIeyAkP  198 (494)
T KOG1456|consen  173 QRAKAALNGADIYSGCCTLKIEYAKP  198 (494)
T ss_pred             HHHHhhcccccccccceeEEEEecCc
Confidence            99999999999988777777765543

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.44  E-value=5.2e-13  Score=110.85  Aligned_cols=175  Identities=17%  Similarity=0.209  Sum_probs=119.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcC----CeeEEEe--ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYG----PIAHIDL--KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRV   77 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G----~v~~i~~--~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v   77 (299)
                      .+.-.|-+.+||.++|+.||.++|..-.    .++.|.+  ..++...|-|||.|..+++|+.|+. -|...+..+.|.+
T Consensus       159 ~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~-khrq~iGqRYIEl  237 (508)
T KOG1365|consen  159 ENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALR-KHRQNIGQRYIEL  237 (508)
T ss_pred             ccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHH-HHHHHHhHHHHHH
Confidence            3456778899999999999999996322    2334443  3478899999999999999999998 4544444444443


Q ss_pred             EEccCCC------------CCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCC-eeE--EEEEe
Q 022301           78 ELAHGGR------------GRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGD-VCF--SQVFR  142 (299)
Q Consensus        78 ~~~~~~~------------~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~-v~~--~~~~~  142 (299)
                      .-+....            -.+...............+......+|-+.+||+.++.++|.++|..|.. |..  |++..
T Consensus       238 FRSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~  317 (508)
T KOG1365|consen  238 FRSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVL  317 (508)
T ss_pred             HHHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEE
Confidence            2211000            00000000000011122234445678999999999999999999999873 333  66666


Q ss_pred             CCC---CCEEEEEecChhhHHHHHHhcCCCeecCceeeEE
Q 022301          143 DGS---GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY  179 (299)
Q Consensus       143 ~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  179 (299)
                      +..   .|-|||+|.+.+.|..|..+.+.+....++++++
T Consensus       318 N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvf  357 (508)
T KOG1365|consen  318 NGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVF  357 (508)
T ss_pred             cCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEe
Confidence            643   4689999999999999999999888888865544

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=99.44  E-value=4.7e-12  Score=109.42  Aligned_cols=158  Identities=22%  Similarity=0.293  Sum_probs=108.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEe-ecC----CCCCc---eEEEEecChHHHHHHHHhcCCCCCCCceEE
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL-KIP----PRPPG---YAFVEFEEARDAEDAIRGRDGYDFDGHRLR   76 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~-~~~----~~~~g---~afV~F~~~e~A~~A~~~l~~~~~~g~~i~   76 (299)
                      =++.||||+||++++|++|...|..||.+.--+- +..    -.++|   |+|+.|+++..+...+..+..   ....+.
T Consensus       258 ~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~---~~~~~y  334 (520)
T KOG0129|consen  258 YSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE---GEGNYY  334 (520)
T ss_pred             cccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh---cccceE
Confidence            3678999999999999999999999997643222 111    13455   999999999999887775443   333333


Q ss_pred             EEEccCCCCCCCCCC----CCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHH-hcCCeeEEEEEeCCC----CC
Q 022301           77 VELAHGGRGRSSSDR----HSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMR-RAGDVCFSQVFRDGS----GT  147 (299)
Q Consensus        77 v~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~-~~G~v~~~~~~~~~~----~~  147 (299)
                      +..+........-+.    .....-.......-.+..+|||++||-.++.++|..+|. .||.|..+.|-.|+.    .|
T Consensus       335 f~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkG  414 (520)
T KOG0129|consen  335 FKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKG  414 (520)
T ss_pred             EEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCC
Confidence            333322222111000    000000001112334568999999999999999999999 699999999998853    46


Q ss_pred             EEEEEecChhhHHHHHHh
Q 022301          148 TGIVDYTNYDDMKHAIKK  165 (299)
Q Consensus       148 ~~fv~f~~~~~a~~a~~~  165 (299)
                      -|=|+|.+.....+||.+
T Consensus       415 aGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  415 AGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cceeeecccHHHHHHHhh
Confidence            799999999999999975

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.41  E-value=4.7e-13  Score=113.28  Aligned_cols=76  Identities=32%  Similarity=0.569  Sum_probs=70.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCCCCC
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGRGR   86 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~~~~   86 (299)
                      ..|||.||+.++|+|.|+++|++||.|..|+..     +.||||.|.+.++|.+|++.|||+.|.|..|.|.++++....
T Consensus       260 KvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~-----rDYaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~  334 (506)
T KOG0117|consen  260 KVLYVRNLMESTTEETLKKLFNEFGKVERVKKP-----RDYAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKK  334 (506)
T ss_pred             eeeeeeccchhhhHHHHHHHHHhccceEEeecc-----cceeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhh
Confidence            579999999999999999999999999999887     569999999999999999999999999999999999876544


Q ss_pred             C
Q 022301           87 S   87 (299)
Q Consensus        87 ~   87 (299)
                      .
T Consensus       335 k  335 (506)
T KOG0117|consen  335 K  335 (506)
T ss_pred             c
Confidence            3

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.41  E-value=1.2e-12  Score=88.70  Aligned_cols=75  Identities=16%  Similarity=0.200  Sum_probs=67.4

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC-CEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG-TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~-~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      .++..+..|||.|||..+|.+++-++|.+||+|..+.+-..+.+ |.|||.|++..+|.+|+++|.|..+++.++.
T Consensus        13 lppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~   88 (124)
T KOG0114|consen   13 LPPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLV   88 (124)
T ss_pred             CChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEE
Confidence            34456678999999999999999999999999999999877655 6999999999999999999999999998543

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.41  E-value=8.4e-13  Score=115.25  Aligned_cols=78  Identities=33%  Similarity=0.672  Sum_probs=73.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      ++|||||||+++++++|.++|+..|.|.++++..   +|.++||||++|.+.++|..|+..|||..+.|++|+|.|+...
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   4789999999999999999999999999999999999998754


Q ss_pred             C
Q 022301           84 R   84 (299)
Q Consensus        84 ~   84 (299)
                      .
T Consensus        99 ~   99 (435)
T KOG0108|consen   99 K   99 (435)
T ss_pred             c
Confidence            4

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.40  E-value=1.4e-12  Score=114.50  Aligned_cols=172  Identities=21%  Similarity=0.321  Sum_probs=134.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhc-----------C-CeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKY-----------G-PIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFD   71 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-----------G-~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~   71 (299)
                      .....++|++||..++++.+..+|..-           | .|..+.++   ..+++|||+|.+.++|..|+. +++..+.
T Consensus       173 ~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n---~~~nfa~ie~~s~~~at~~~~-~~~~~f~  248 (500)
T KOG0120|consen  173 RQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLN---LEKNFAFIEFRSISEATEAMA-LDGIIFE  248 (500)
T ss_pred             hhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeec---ccccceeEEecCCCchhhhhc-ccchhhC
Confidence            345679999999999999999999754           2 36667665   457899999999999999999 9999999


Q ss_pred             CceEEEEEccCCCCCCCCCCCC----CCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC-
Q 022301           72 GHRLRVELAHGGRGRSSSDRHS----SHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG-  146 (299)
Q Consensus        72 g~~i~v~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~-  146 (299)
                      |..+++.-.......+......    .................++|++||..+++.++.|+...||.+....+..+... 
T Consensus       249 g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g  328 (500)
T KOG0120|consen  249 GRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATG  328 (500)
T ss_pred             CCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccc
Confidence            9998886544433322221111    11222222334456789999999999999999999999999999888888664 


Q ss_pred             ---CEEEEEecChhhHHHHHHhcCCCeecCceeeEE
Q 022301          147 ---TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY  179 (299)
Q Consensus       147 ---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  179 (299)
                         ||||.+|.+......|+..|||..+++..+.+.
T Consensus       329 ~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq  364 (500)
T KOG0120|consen  329 NSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQ  364 (500)
T ss_pred             cccceeeeeeeCCcchhhhhcccchhhhcCceeEee
Confidence               599999999999999999999999999865433

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.40  E-value=2.4e-12  Score=103.95  Aligned_cols=69  Identities=14%  Similarity=0.242  Sum_probs=63.7

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC-CCCEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG-SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~-~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      ..+|||+|||+.+++++|+++|+.||+|..|.|..+. ..+||||+|.+.++|+.|+. |+|..|.|+.+.
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~   73 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVT   73 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEE
Confidence            4699999999999999999999999999999999886 45799999999999999995 999999999553

>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=5.1e-13  Score=107.12  Aligned_cols=76  Identities=42%  Similarity=0.716  Sum_probs=71.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      ++++++|+|+||.+.|+.++|++.|++||+|++|.|.     ++|+||.|.-.++|..|+..|||..|.|+.++|+.+..
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     78999999999999999999999999999999999764


Q ss_pred             C
Q 022301           83 G   83 (299)
Q Consensus        83 ~   83 (299)
                      .
T Consensus       150 r  150 (346)
T KOG0109|consen  150 R  150 (346)
T ss_pred             c
Confidence            4

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.38  E-value=2e-12  Score=92.01  Aligned_cols=74  Identities=19%  Similarity=0.301  Sum_probs=68.0

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCC----EEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGT----TGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~----~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      ....+|.|||+++...+++++|.+.|..||+|..+++..+..+|    ||+|+|++..+|+.|+..|||..|.|..+.
T Consensus        68 rSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~  145 (170)
T KOG0130|consen   68 RSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVS  145 (170)
T ss_pred             cceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCcee
Confidence            34567999999999999999999999999999999999998765    999999999999999999999999998543

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=99.37  E-value=1e-13  Score=106.64  Aligned_cols=142  Identities=20%  Similarity=0.278  Sum_probs=115.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ...+||||+||...++++-|.+||-+-|+|..|.|..  ++..+ ||||.|.++..+..|+..|||..+.+..|+|.+-.
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            4568999999999999999999999999999999954  44555 99999999999999999999999999999997653


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC---CCEEEEEecChhh
Q 022301           82 GGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS---GTTGIVDYTNYDD  158 (299)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~---~~~~fv~f~~~~~  158 (299)
                      ....                            .-|...++.+.+.+.|...|.+..+.+..+..   ..++|+.+.-...
T Consensus        86 G~sh----------------------------apld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~  137 (267)
T KOG4454|consen   86 GNSH----------------------------APLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCA  137 (267)
T ss_pred             CCCc----------------------------chhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhc
Confidence            2211                            01455678888888999999998888877655   3489999888888


Q ss_pred             HHHHHHhcCCCeecCc
Q 022301          159 MKHAIKKLDDSEFRNA  174 (299)
Q Consensus       159 a~~a~~~l~g~~~~g~  174 (299)
                      ...++...++.++.-+
T Consensus       138 ~P~~~~~y~~l~~~~~  153 (267)
T KOG4454|consen  138 VPFALDLYQGLELFQK  153 (267)
T ss_pred             CcHHhhhhcccCcCCC
Confidence            8888888777766543

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.37  E-value=2.8e-12  Score=84.82  Aligned_cols=65  Identities=23%  Similarity=0.412  Sum_probs=58.8

Q ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC---CCEEEEEecChhhHHHHHHhcCCCeecCce
Q 022301          111 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS---GTTGIVDYTNYDDMKHAIKKLDDSEFRNAF  175 (299)
Q Consensus       111 l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  175 (299)
                      |+|.|||..+++++|.++|..||.|..+.+..++.   .++|||+|.+.++|..|++.++|..++|+.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~   68 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRK   68 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEE
Confidence            78999999999999999999999999999999865   359999999999999999999999999984

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 ....

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.37  E-value=1.6e-12  Score=116.92  Aligned_cols=79  Identities=30%  Similarity=0.558  Sum_probs=73.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      ..++||||+.|+.++++.||.++|+.||+|+.|.|+   .+.++|||.+..-.+|.+|+.+|++..|.++.|+|.|+...
T Consensus       419 V~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li---~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~  495 (894)
T KOG0132|consen  419 VCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILI---PPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGK  495 (894)
T ss_pred             EeeeeeeeccccchhhHHHHHHHHHhcccceeEeec---cCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccC
Confidence            468999999999999999999999999999999997   56899999999999999999999999999999999999765


Q ss_pred             CC
Q 022301           84 RG   85 (299)
Q Consensus        84 ~~   85 (299)
                      ..
T Consensus       496 G~  497 (894)
T KOG0132|consen  496 GP  497 (894)
T ss_pred             Cc
Confidence            43

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.36  E-value=6.3e-12  Score=102.58  Aligned_cols=74  Identities=20%  Similarity=0.238  Sum_probs=67.2

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC--CEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG--TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~--~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      .......|+|.|||....+-||..+|.+||.|.+|+|+.+..+  |||||+|++.++|++|-++|||..|.|+.++
T Consensus        92 s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIE  167 (376)
T KOG0125|consen   92 SKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIE  167 (376)
T ss_pred             CCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEE
Confidence            3445678999999999999999999999999999999988654  7999999999999999999999999999544

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.36  E-value=9e-12  Score=93.60  Aligned_cols=78  Identities=17%  Similarity=0.229  Sum_probs=67.9

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC-CCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEeccc
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS-GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVREY  185 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~~~  185 (299)
                      ....|||+|||.++.+.+|+++|-+||.|..|.+...+. ..||||+|+++.+|+.||..-+|..++|.    .++|+..
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~----rLRVEfp   80 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGC----RLRVEFP   80 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcc----eEEEEec
Confidence            347899999999999999999999999999999876654 35999999999999999999999999999    5555555


Q ss_pred             ccC
Q 022301          186 DHR  188 (299)
Q Consensus       186 ~~~  188 (299)
                      +..
T Consensus        81 rgg   83 (241)
T KOG0105|consen   81 RGG   83 (241)
T ss_pred             cCC
Confidence            444

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.34  E-value=4.6e-12  Score=89.40  Aligned_cols=77  Identities=16%  Similarity=0.181  Sum_probs=68.1

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEe
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRV  182 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~  182 (299)
                      ..++|||+||..-+++++|.++|.++|+|..|.+-.+..+    |||||+|...++|..|+..++|..++.+    .|.+
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr----~ir~  110 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDR----PIRI  110 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCccccc----ceee
Confidence            5689999999999999999999999999999988777654    5999999999999999999999999998    5665


Q ss_pred             ccccc
Q 022301          183 REYDH  187 (299)
Q Consensus       183 ~~~~~  187 (299)
                      +....
T Consensus       111 D~D~G  115 (153)
T KOG0121|consen  111 DWDAG  115 (153)
T ss_pred             ecccc
Confidence            54433

>PLN03213 repressor of silencing 3; Provisional

Probab=99.33  E-value=9.3e-12  Score=106.83  Aligned_cols=71  Identities=15%  Similarity=0.227  Sum_probs=65.6

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecCh--hhHHHHHHhcCCCeecCcee
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNY--DDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~--~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .....|||+||++.+++++|..+|..||.|..|.|+.....|||||+|...  .++.+||..|||..+.|+.+
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~L   80 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRL   80 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCcee
Confidence            345799999999999999999999999999999999887788999999987  68999999999999999944

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.33  E-value=1.4e-11  Score=97.91  Aligned_cols=69  Identities=20%  Similarity=0.312  Sum_probs=63.4

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC-CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG-TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~-~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .+++|+|+||++.+++++|+++|..||+|..|.|+.+... ++|||+|++.++|+.|+. |+|..|.+..+
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I   73 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVL-LSGATIVDQRV   73 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHh-cCCCeeCCceE
Confidence            4589999999999999999999999999999999988654 599999999999999995 99999999853

>smart00361 RRM_1 RNA recognition motif

Probab=99.31  E-value=8.2e-12  Score=82.33  Aligned_cols=58  Identities=28%  Similarity=0.546  Sum_probs=51.3

Q ss_pred             HHHHHHHhh----hcCCeeEEE-eec---C--CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEE
Q 022301           20 EREVEDLFY----KYGPIAHID-LKI---P--PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRV   77 (299)
Q Consensus        20 ~~~l~~~F~----~~G~v~~i~-~~~---~--~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v   77 (299)
                      +++|.++|.    .||.|..|. |..   +  +.++|||||+|.+.++|..|+..|||..+.|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            578999998    999999985 422   3  678999999999999999999999999999999976

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.31  E-value=1.6e-12  Score=118.61  Aligned_cols=151  Identities=21%  Similarity=0.316  Sum_probs=129.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC--CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP--PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~--~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ..+.|||++||+..+++.+|...|..+|.|..|.|..+  +....||||.|.+...+-.|...+.+..|....+++.+..
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            46899999999999999999999999999999999554  4455799999999999999999899988876666655442


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHH
Q 022301           82 GGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKH  161 (299)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~  161 (299)
                      .                     .....+.++|++|+.-+....|..+|..||.|..|.+-....  ||+|+|++...|+.
T Consensus       450 ~---------------------kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq~--yayi~yes~~~aq~  506 (975)
T KOG0112|consen  450 P---------------------KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQP--YAYIQYESPPAAQA  506 (975)
T ss_pred             c---------------------ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccCCc--ceeeecccCccchh
Confidence            1                     233457899999999999999999999999999987766554  99999999999999


Q ss_pred             HHHhcCCCeecCceee
Q 022301          162 AIKKLDDSEFRNAFSR  177 (299)
Q Consensus       162 a~~~l~g~~~~g~~~~  177 (299)
                      |+..|-|..|+|....
T Consensus       507 a~~~~rgap~G~P~~r  522 (975)
T KOG0112|consen  507 ATHDMRGAPLGGPPRR  522 (975)
T ss_pred             hHHHHhcCcCCCCCcc
Confidence            9999999999986543

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.29  E-value=1.9e-11  Score=100.73  Aligned_cols=80  Identities=19%  Similarity=0.255  Sum_probs=72.5

Q ss_pred             CCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCC----EEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          101 RGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGT----TGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       101 ~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~----~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .+...++.+.|||+.|.+-++.++|.-+|+.||+|..|.|+.+..+|    ||||+|++.+++++|.-+|++..|+.+  
T Consensus       232 dAd~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDr--  309 (479)
T KOG0415|consen  232 DADVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDR--  309 (479)
T ss_pred             ccccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccc--
Confidence            34456688999999999999999999999999999999999999887    999999999999999999999999998  


Q ss_pred             eEEEEecc
Q 022301          177 RAYVRVRE  184 (299)
Q Consensus       177 ~~~~~~~~  184 (299)
                        .|.|+.
T Consensus       310 --RIHVDF  315 (479)
T KOG0415|consen  310 --RIHVDF  315 (479)
T ss_pred             --eEEeeh
Confidence              555443

>smart00362 RRM_2 RNA recognition motif

Probab=99.29  E-value=3.8e-11  Score=79.28  Aligned_cols=66  Identities=21%  Similarity=0.365  Sum_probs=60.5

Q ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC--CCCEEEEEecChhhHHHHHHhcCCCeecCce
Q 022301          110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG--SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAF  175 (299)
Q Consensus       110 ~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~--~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  175 (299)
                      +|+|.|||..+++++|.++|.+||+|..+.+..+.  ..++|||+|.+.++|+.|+..++|..+.|..
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~   68 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRP   68 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEE
Confidence            48999999999999999999999999999888765  3469999999999999999999999999874

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

Probab=99.28  E-value=2e-11  Score=95.87  Aligned_cols=72  Identities=26%  Similarity=0.320  Sum_probs=66.4

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCC----EEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGT----TGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~----~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ....++|-|.||+.++++.+|+++|.+||.|..+.+..++.+|    ||||.|.+.++|.+||+.|||.-++.-++
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 RDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLIL  261 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEE
Confidence            3366789999999999999999999999999999999998775    99999999999999999999999988744

>smart00360 RRM RNA recognition motif

Probab=99.20  E-value=1.6e-10  Score=76.01  Aligned_cols=63  Identities=19%  Similarity=0.374  Sum_probs=57.9

Q ss_pred             EeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCce
Q 022301          113 VTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAF  175 (299)
Q Consensus       113 v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  175 (299)
                      |.|||..+++++|.++|.+||.|..+.+..+..    .++|||+|.+.++|..|+..|++..+.|..
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~   67 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRP   67 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcE
Confidence            578999999999999999999999999988765    469999999999999999999999998874

>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=99.19  E-value=2.7e-10  Score=75.53  Aligned_cols=67  Identities=21%  Similarity=0.380  Sum_probs=61.7

Q ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC---CCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS---GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       110 ~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      +|+|.|||..+++++|.++|..+|.|..+.+..++.   .++|||+|.+.++|..|++.+++..+.|..+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~   70 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPL   70 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEE
Confidence            478999999999999999999999999999998764   5799999999999999999999999998744

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=99.17  E-value=5.2e-11  Score=89.41  Aligned_cols=72  Identities=21%  Similarity=0.212  Sum_probs=65.7

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC----CCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG----SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .....+|||+||+..++++.|.++|-+.|+|+.++++.+.    ..|||||+|.+.++|+.|++.|+...|.|+.+
T Consensus         6 rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpI   81 (203)
T KOG0131|consen    6 RNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPI   81 (203)
T ss_pred             cCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCcee
Confidence            3456899999999999999999999999999999999885    45799999999999999999999999999944

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=99.15  E-value=5.5e-12  Score=105.10  Aligned_cols=64  Identities=17%  Similarity=0.163  Sum_probs=54.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFD   71 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~   71 (299)
                      .+||+|++|+..+-..++.++|..+|+|....+.- +....+|.|+|....+...|+. ++|..+.
T Consensus       151 rRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~as-k~~s~~c~~sf~~qts~~halr-~~gre~k  214 (479)
T KOG4676|consen  151 RRTREVQSLISAAILPESGESFERKGEVSYAHTAS-KSRSSSCSHSFRKQTSSKHALR-SHGRERK  214 (479)
T ss_pred             Hhhhhhhcchhhhcchhhhhhhhhcchhhhhhhhc-cCCCcchhhhHhhhhhHHHHHH-hcchhhh
Confidence            37899999999999999999999999998888732 2334588999999999999999 7777665

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.13  E-value=2.1e-10  Score=94.56  Aligned_cols=77  Identities=31%  Similarity=0.584  Sum_probs=68.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHh-cCCCCCCCceEEEEEcc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRG-RDGYDFDGHRLRVELAH   81 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~-l~~~~~~g~~i~v~~~~   81 (299)
                      +....||||++|...+++.+|.+.|.+||+|..|.+.   ..+++|||+|.+.+.|+.|... +|...|.|+.|+|.|..
T Consensus       225 D~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~---~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~  301 (377)
T KOG0153|consen  225 DTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRIL---PRKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGR  301 (377)
T ss_pred             ccceeEEEecccccchhHHHHHHHHhhcCCeeeEEee---cccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCC
Confidence            3566899999999999999999999999999999996   3367999999999999998776 56677899999999987


Q ss_pred             C
Q 022301           82 G   82 (299)
Q Consensus        82 ~   82 (299)
                      .
T Consensus       302 ~  302 (377)
T KOG0153|consen  302 P  302 (377)
T ss_pred             C
Confidence            6

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=99.11  E-value=3e-10  Score=87.19  Aligned_cols=80  Identities=28%  Similarity=0.440  Sum_probs=71.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhc-CCeeEEEe---ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKY-GPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-G~v~~i~~---~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      .....+||.-||.-+-+.+|..+|.+| |.|..+.+   ..||.++|||||+|.+++.|.-|.+.||+-.|+|+.|.|.+
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            345678999999999999999999988 77888888   56899999999999999999999999999999999999998


Q ss_pred             ccCC
Q 022301           80 AHGG   83 (299)
Q Consensus        80 ~~~~   83 (299)
                      ..+.
T Consensus       127 mppe  130 (214)
T KOG4208|consen  127 MPPE  130 (214)
T ss_pred             eCch
Confidence            7654

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=99.11  E-value=6e-11  Score=103.54  Aligned_cols=166  Identities=19%  Similarity=0.180  Sum_probs=104.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      +-++.+|+|.|||..|++++|..+|+.||+|..|.+  +....|.+||+|.+.-+|+.|++.|++..+.|+.|+......
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~--t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~~~~~~  149 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE--TPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIKRPGGAR  149 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc--ccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcCCCccc
Confidence            457899999999999999999999999999999665  334578999999999999999999999999999998221111


Q ss_pred             CCCCCCCCC--CCCCCCCCCCCCCCCC-ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhH
Q 022301           83 GRGRSSSDR--HSSHSSGRGRGVSRRS-EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDM  159 (299)
Q Consensus        83 ~~~~~~~~~--~~~~~~~~~~~~~~~~-~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a  159 (299)
                      .........  ...........++..+ ...++ +.|++..+..-++.++..+|.+..-.......  .-|+.|.+..++
T Consensus       150 ~~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~-g~l~P~~s~~~~~~~~~~~~~~~~~~~~~~~h--q~~~~~~~~~s~  226 (549)
T KOG4660|consen  150 RAMGLQSGTSFLNHFGSPLANSPPGGWPRGQLF-GMLSPTRSSILLEHISSVDGSSPGRETPLLNH--QRFVEFADNRSY  226 (549)
T ss_pred             ccchhcccchhhhhccchhhcCCCCCCcCCcce-eeeccchhhhhhhcchhccCccccccccchhh--hhhhhhccccch
Confidence            100000000  0000000111111111 12222 23888888877777888888766511111111  567778887777


Q ss_pred             HHHHHhcCCCeecCc
Q 022301          160 KHAIKKLDDSEFRNA  174 (299)
Q Consensus       160 ~~a~~~l~g~~~~g~  174 (299)
                      ..++..+ |..+.+.
T Consensus       227 a~~~~~~-G~~~s~~  240 (549)
T KOG4660|consen  227 AFSEPRG-GFLISNS  240 (549)
T ss_pred             hhcccCC-ceecCCC
Confidence            4444422 4444443

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.10  E-value=1.2e-11  Score=92.72  Aligned_cols=73  Identities=16%  Similarity=0.238  Sum_probs=66.8

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCC----EEEEEecChhhHHHHHHhcCCCeecCceeeEEEEec
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGT----TGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVR  183 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~----~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~  183 (299)
                      ..-|||+|||+.+|+-||.-+|++||.|+.|.++.+..+|    |||+.|++.....-|+..|||..|.|+    .|+|+
T Consensus        35 sA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gR----tirVD  110 (219)
T KOG0126|consen   35 SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGR----TIRVD  110 (219)
T ss_pred             ceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecce----eEEee
Confidence            3579999999999999999999999999999999998775    999999999999999999999999999    55554


Q ss_pred             c
Q 022301          184 E  184 (299)
Q Consensus       184 ~  184 (299)
                      .
T Consensus       111 H  111 (219)
T KOG0126|consen  111 H  111 (219)
T ss_pred             e
Confidence            3

>PF13893 RRM_5: RNA recognition motif

Probab=99.10  E-value=6.3e-10  Score=69.89  Aligned_cols=52  Identities=19%  Similarity=0.381  Sum_probs=46.3

Q ss_pred             HHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          125 LKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       125 l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      |.++|++||+|..+.+..+. .++|||+|.+.++|..|+..|||..++|+.+.
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~   52 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLK   52 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-TTEEEEEESSHHHHHHHHHHHTTSEETTEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-CCEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            67899999999999998777 57999999999999999999999999998543

(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 ....

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.08  E-value=4.3e-09  Score=90.82  Aligned_cols=174  Identities=18%  Similarity=0.227  Sum_probs=118.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeE-EEee--cCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAH-IDLK--IPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-i~~~--~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      +.-+|-+.+||+.||++||.++|+.+-.|.. |.|.  ..+.+.|-|||+|++.+.|++|+. -|...|.-+.|.|..+.
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            5678999999999999999999998766655 3343  345678999999999999999998 66677777777775532


Q ss_pred             CCCC-------------CCCCCC-----C-------------C-----------------------C---CCCC--CCCC
Q 022301           82 GGRG-------------RSSSDR-----H-------------S-----------------------S---HSSG--RGRG  102 (299)
Q Consensus        82 ~~~~-------------~~~~~~-----~-------------~-----------------------~---~~~~--~~~~  102 (299)
                      ....             +.....     .             .                       .   ....  ...+
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            0000             000000     0             0                       0   0000  0000


Q ss_pred             ----C-----------CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC---CCCEEEEEecChhhHHHHHH
Q 022301          103 ----V-----------SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG---SGTTGIVDYTNYDDMKHAIK  164 (299)
Q Consensus       103 ----~-----------~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~---~~~~~fv~f~~~~~a~~a~~  164 (299)
                          +           ....+..++..+||...+..+|..+|...-.+ .|+|...+   .++-|+|+|.+.++|..|+.
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           00122567778999999999999999886555 55555444   34689999999999999997


Q ss_pred             hcCCCeecCceeeEEEE
Q 022301          165 KLDDSEFRNAFSRAYVR  181 (299)
Q Consensus       165 ~l~g~~~~g~~~~~~~~  181 (299)
                       -++..+..++++.+..
T Consensus       340 -kd~anm~hrYVElFln  355 (510)
T KOG4211|consen  340 -KDGANMGHRYVELFLN  355 (510)
T ss_pred             -cCCcccCcceeeeccc
Confidence             6777788886555544

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.06  E-value=1.7e-10  Score=91.67  Aligned_cols=80  Identities=23%  Similarity=0.493  Sum_probs=73.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      -+.|.|||.-||.+..+.+|.+.|-.||.|++.++..   +..++.|+||.|.++.+|+.||..|||..|.-+.|+|.+.
T Consensus       283 PeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLK  362 (371)
T KOG0146|consen  283 PEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLK  362 (371)
T ss_pred             CCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhc
Confidence            5679999999999999999999999999999999955   4788999999999999999999999999999999999876


Q ss_pred             cCC
Q 022301           81 HGG   83 (299)
Q Consensus        81 ~~~   83 (299)
                      .++
T Consensus       363 RPk  365 (371)
T KOG0146|consen  363 RPK  365 (371)
T ss_pred             Ccc
Confidence            543

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.05  E-value=7.5e-10  Score=86.74  Aligned_cols=76  Identities=14%  Similarity=0.219  Sum_probs=63.5

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceeeEEE
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYV  180 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~  180 (299)
                      ...-++|||++|++.+..+.|..+|++||+|+.+.|+.|+.+    |||||+|.+.+.|..|++..+ -.|+|+...+.+
T Consensus         9 DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~-piIdGR~aNcnl   87 (247)
T KOG0149|consen    9 DTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN-PIIDGRKANCNL   87 (247)
T ss_pred             CceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC-Ccccccccccch
Confidence            345579999999999999999999999999999999999766    499999999999999998544 456776544344


Q ss_pred             E
Q 022301          181 R  181 (299)
Q Consensus       181 ~  181 (299)
                      .
T Consensus        88 A   88 (247)
T KOG0149|consen   88 A   88 (247)
T ss_pred             h
Confidence            3

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=99.04  E-value=1.1e-09  Score=88.23  Aligned_cols=81  Identities=26%  Similarity=0.498  Sum_probs=71.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ....+|+|.|||+.|+++||++||..||.+..+.|++  .+.+.|.|-|.|...++|..|++.|||..+.|+.|++....
T Consensus        81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~  160 (243)
T KOG0533|consen   81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIIS  160 (243)
T ss_pred             CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEec
Confidence            3457899999999999999999999999888888855  47788999999999999999999999999999999998765


Q ss_pred             CCC
Q 022301           82 GGR   84 (299)
Q Consensus        82 ~~~   84 (299)
                      ...
T Consensus       161 ~~~  163 (243)
T KOG0533|consen  161 SPS  163 (243)
T ss_pred             Ccc
Confidence            443

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.02  E-value=3.1e-10  Score=87.70  Aligned_cols=70  Identities=21%  Similarity=0.242  Sum_probs=64.5

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC----CCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG----SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ...+|||++|...+++..|...|-+||.|..|+++.+-    ..+||||+|+..++|..||+.||+.+|.|+.+
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~Grti   82 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTI   82 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeE
Confidence            44799999999999999999999999999999998884    44699999999999999999999999999944

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.99  E-value=1.2e-09  Score=95.64  Aligned_cols=80  Identities=26%  Similarity=0.485  Sum_probs=72.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      .+.|||.+|...+-..+|++||++||+|+..+|..+   +....|+||+|.+.++|.+||..||-+.|.|+.|.|+.+++
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            468999999999999999999999999999999543   45578999999999999999999999999999999999876


Q ss_pred             CCC
Q 022301           83 GRG   85 (299)
Q Consensus        83 ~~~   85 (299)
                      .+.
T Consensus       485 Ep~  487 (940)
T KOG4661|consen  485 EPG  487 (940)
T ss_pred             Ccc
Confidence            554

>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=98.99  E-value=3.2e-09  Score=69.59  Aligned_cols=71  Identities=27%  Similarity=0.416  Sum_probs=49.7

Q ss_pred             CeEEEcCCCCCCCHHH----HHHHhhhcC-CeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            7 RTLYVGNLPGDIRERE----VEDLFYKYG-PIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~----l~~~F~~~G-~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ..|||.|||.+.+...    |++|+..|| .|..|.       .+.|+|.|.+++.|..|++.|+|..++|.+|.|.|..
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            4699999999999876    566777887 666662       4689999999999999999999999999999999985


Q ss_pred             CCC
Q 022301           82 GGR   84 (299)
Q Consensus        82 ~~~   84 (299)
                      ...
T Consensus        76 ~~r   78 (90)
T PF11608_consen   76 KNR   78 (90)
T ss_dssp             -S-
T ss_pred             Ccc
Confidence            443

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.98  E-value=4.2e-11  Score=109.12  Aligned_cols=136  Identities=23%  Similarity=0.317  Sum_probs=115.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEe---ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~---~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ..+++||.||++.+.+++|...|..+|.|..+.+   ...+..+|+|||+|..+++|.+|+. ++...+.|+        
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            3468999999999999999999999998877766   3457789999999999999999999 555555552        


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC---CCCEEEEEecChhh
Q 022301           82 GGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG---SGTTGIVDYTNYDD  158 (299)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~---~~~~~fv~f~~~~~  158 (299)
                                                 ..++|.|+|...|.++|+.+|..+|.+..+.++...   +.|.|+|.|.+..+
T Consensus       737 ---------------------------~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~  789 (881)
T KOG0128|consen  737 ---------------------------ISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEAD  789 (881)
T ss_pred             ---------------------------hhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcch
Confidence                                       367899999999999999999999999887665554   45799999999999


Q ss_pred             HHHHHHhcCCCeecCcee
Q 022301          159 MKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       159 a~~a~~~l~g~~~~g~~~  176 (299)
                      |..++...++..+.....
T Consensus       790 ~s~~~~s~d~~~~rE~~~  807 (881)
T KOG0128|consen  790 ASRKVASVDVAGKRENNG  807 (881)
T ss_pred             hhhhcccchhhhhhhcCc
Confidence            999999888887776643

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=98.98  E-value=5.7e-09  Score=88.14  Aligned_cols=69  Identities=22%  Similarity=0.359  Sum_probs=64.0

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC----CCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG----SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..+|||+|||..+++++|.++|..||.|..+.+..+.    ..|||||+|.+.++|..|+..++|..|.|+.+
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~  187 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPL  187 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCcee
Confidence            6899999999999999999999999999999998875    33699999999999999999999999999944

>smart00361 RRM_1 RNA recognition motif

Probab=98.94  E-value=5.8e-09  Score=68.64  Aligned_cols=55  Identities=16%  Similarity=0.237  Sum_probs=46.4

Q ss_pred             HHHHHHHHH----hcCCeeEEE-EEeCC------CCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          122 WQDLKDHMR----RAGDVCFSQ-VFRDG------SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       122 ~~~l~~~f~----~~G~v~~~~-~~~~~------~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      +++|.++|.    +||.|..+. +..++      ..|||||+|.+.++|..|+..|||..++|+.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l   67 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTV   67 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            567888888    999999985 54443      24699999999999999999999999999854

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.93  E-value=8e-09  Score=71.38  Aligned_cols=75  Identities=20%  Similarity=0.317  Sum_probs=61.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhh--cCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCC----CceEEE
Q 022301            7 RTLYVGNLPGDIREREVEDLFYK--YGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFD----GHRLRV   77 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~--~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~----g~~i~v   77 (299)
                      +||+|.|||...|.++|.+++..  .|...-+.++.+   +.+.|||||.|.+++.|......++|..+.    .+.+.|
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            79999999999999999998874  356666666443   567899999999999999999999998775    556677


Q ss_pred             EEcc
Q 022301           78 ELAH   81 (299)
Q Consensus        78 ~~~~   81 (299)
                      .||.
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            7764

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.92  E-value=1.4e-10  Score=97.89  Aligned_cols=143  Identities=24%  Similarity=0.423  Sum_probs=115.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhc--CCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCC-CCCCCceEEEEEccCC
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKY--GPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG-YDFDGHRLRVELAHGG   83 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~--G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~-~~~~g~~i~v~~~~~~   83 (299)
                      +.|||+||.+.++..+|..+|...  |--..+.|.     .|||||...+..-|.+|++.|+| ..+.|+.+.|.+.-..
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            579999999999999999999743  222333333     58999999999999999999999 5688999999876432


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEE-eCCCCCEEEEEecChhhHHHH
Q 022301           84 RGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVF-RDGSGTTGIVDYTNYDDMKHA  162 (299)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~-~~~~~~~~fv~f~~~~~a~~a  162 (299)
                      .                     .....+-|.|+|+...++.|..++..||.+..|... .+..+...-|+|.+.+.+..|
T Consensus        77 k---------------------qrsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~etavvnvty~~~~~~~~a  135 (584)
T KOG2193|consen   77 K---------------------QRSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETAVVNVTYSAQQQHRQA  135 (584)
T ss_pred             H---------------------HHhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHHHHHHHHHHHHHHHHH
Confidence            2                     233568899999999999999999999999887553 333333555789999999999


Q ss_pred             HHhcCCCeecCce
Q 022301          163 IKKLDDSEFRNAF  175 (299)
Q Consensus       163 ~~~l~g~~~~g~~  175 (299)
                      |.+|+|..+...-
T Consensus       136 i~kl~g~Q~en~~  148 (584)
T KOG2193|consen  136 IHKLNGPQLENQH  148 (584)
T ss_pred             HHhhcchHhhhhh
Confidence            9999999998753

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.91  E-value=2.5e-09  Score=89.53  Aligned_cols=159  Identities=20%  Similarity=0.248  Sum_probs=120.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCC-CCCCceEEEEEc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGY-DFDGHRLRVELA   80 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~-~~~g~~i~v~~~   80 (299)
                      ..+++|++++..++.+.++..+|..+|.+....+..   ....+++++|.|...+++..|+. +.+. .+.+..+...+.
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~-~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALE-ESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHH-hhhccccccccccCccc
Confidence            467899999999999999999999999877776622   35678999999999999999999 6664 555555444333


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCccEEE-EeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCC----EEEEEecC
Q 022301           81 HGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVL-VTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGT----TGIVDYTN  155 (299)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~----~~fv~f~~  155 (299)
                      .........         ...........+++ |.+|+..++.++|..+|..+|.|..+.+......+    ||||.|..
T Consensus       166 ~~~~~~~~n---------~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~  236 (285)
T KOG4210|consen  166 TRRGLRPKN---------KLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSA  236 (285)
T ss_pred             ccccccccc---------hhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhh
Confidence            322210000         01112222334455 99999999999999999999999999999887764    89999999


Q ss_pred             hhhHHHHHHhcCCCeecCc
Q 022301          156 YDDMKHAIKKLDDSEFRNA  174 (299)
Q Consensus       156 ~~~a~~a~~~l~g~~~~g~  174 (299)
                      ...+..++.. +...+.+.
T Consensus       237 ~~~~~~~~~~-~~~~~~~~  254 (285)
T KOG4210|consen  237 GNSKKLALND-QTRSIGGR  254 (285)
T ss_pred             chhHHHHhhc-ccCcccCc
Confidence            9999999987 78788776

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.91  E-value=1.1e-09  Score=91.91  Aligned_cols=82  Identities=26%  Similarity=0.540  Sum_probs=72.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      .+.+|||++||.++++++|++.|.+||.|..+.++.+   ...+||+||.|.+++.+.+++. +.-+.|.|+.+.|..|.
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            3569999999999999999999999999988888554   5678999999999999999998 88899999999999887


Q ss_pred             CCCCCC
Q 022301           82 GGRGRS   87 (299)
Q Consensus        82 ~~~~~~   87 (299)
                      +.....
T Consensus       175 pk~~~~  180 (311)
T KOG4205|consen  175 PKEVMQ  180 (311)
T ss_pred             chhhcc
Confidence            665443

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.87  E-value=5.2e-09  Score=91.18  Aligned_cols=75  Identities=32%  Similarity=0.606  Sum_probs=65.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      .+|||.|||.++++.+|+++|..||+|+...|..   .++...||||+|.+.++++.||. -+-..+.++.|.|+.-..
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            4599999999999999999999999999888833   24444899999999999999999 678889999999987654

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.87  E-value=6.2e-09  Score=91.30  Aligned_cols=68  Identities=22%  Similarity=0.313  Sum_probs=64.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCC----EEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGT----TGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~----~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..+||+|+|+++++++|.++|...|.|..++++.|..+|    |||++|.+.++|..|+..|||.++.|+.+
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l   90 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKL   90 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceE
Confidence            799999999999999999999999999999999997664    99999999999999999999999999944

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.85  E-value=9.4e-09  Score=92.25  Aligned_cols=79  Identities=27%  Similarity=0.454  Sum_probs=71.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC------CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP------PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRV   77 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~------~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v   77 (299)
                      -.++.|||+||++.++++.|...|+.||+|..|+|++.      .....+|||.|-+-.+|+.|+..|+|..+.+..+++
T Consensus       172 P~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~  251 (877)
T KOG0151|consen  172 PQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKL  251 (877)
T ss_pred             CcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeee
Confidence            45788999999999999999999999999999999663      234579999999999999999999999999999999


Q ss_pred             EEccC
Q 022301           78 ELAHG   82 (299)
Q Consensus        78 ~~~~~   82 (299)
                      -|.+.
T Consensus       252 gWgk~  256 (877)
T KOG0151|consen  252 GWGKA  256 (877)
T ss_pred             ccccc
Confidence            99853

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.81  E-value=7.5e-09  Score=83.78  Aligned_cols=79  Identities=25%  Similarity=0.411  Sum_probs=71.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .+...+||+|+...+|.++|...|..||.|..+.|..   .++++|||||+|.+.+.+..|+. |||..|.|..+.|.+.
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            5678999999999999999999999999998777743   46789999999999999999999 9999999999999887


Q ss_pred             cCC
Q 022301           81 HGG   83 (299)
Q Consensus        81 ~~~   83 (299)
                      ...
T Consensus       178 r~~  180 (231)
T KOG4209|consen  178 RTN  180 (231)
T ss_pred             eee
Confidence            644

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.80  E-value=3.3e-08  Score=86.76  Aligned_cols=80  Identities=20%  Similarity=0.321  Sum_probs=69.9

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC-C---EEEEEecChhhHHHHHHhcCCCeecCceeeEEE
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG-T---TGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYV  180 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~-~---~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~  180 (299)
                      ...+.+|+|.+|...+...+|+.+|.+||+|+-++|+.+... |   |+||+|.+.++|.++|+.||..+|.|+    +|
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGr----mI  477 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGR----MI  477 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcce----ee
Confidence            345678999999999999999999999999999999888533 2   999999999999999999999999999    77


Q ss_pred             EecccccC
Q 022301          181 RVREYDHR  188 (299)
Q Consensus       181 ~~~~~~~~  188 (299)
                      .|......
T Consensus       478 SVEkaKNE  485 (940)
T KOG4661|consen  478 SVEKAKNE  485 (940)
T ss_pred             eeeecccC
Confidence            77665543

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.69  E-value=3.7e-07  Score=76.60  Aligned_cols=166  Identities=17%  Similarity=0.212  Sum_probs=110.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCee---EEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIA---HIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~---~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .++..|-..+||+..++.+|..+|.-.-...   .+-+...+.-.|.|.|.|.++|.-+.|++ -+...+.++.|.|.-+
T Consensus        58 ~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~Rdlalk-Rhkhh~g~ryievYka  136 (508)
T KOG1365|consen   58 DDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALK-RHKHHMGTRYIEVYKA  136 (508)
T ss_pred             CcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhH-hhhhhccCCceeeecc
Confidence            5677788899999999999999997543221   12223345557899999999999999999 6777888888888765


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHh---c-C---CeeEEEEEeCCCCCEEEEEe
Q 022301           81 HGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRR---A-G---DVCFSQVFRDGSGTTGIVDY  153 (299)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~---~-G---~v~~~~~~~~~~~~~~fv~f  153 (299)
                      .....-.......   ..............|-..+||.+.++.++.++|..   . |   .|..|.-..+..+|-|||.|
T Consensus       137 ~ge~f~~iagg~s---~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlf  213 (508)
T KOG1365|consen  137 TGEEFLKIAGGTS---NEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLF  213 (508)
T ss_pred             CchhheEecCCcc---ccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEe
Confidence            4332211110000   00001112223345666799999999999999963   1 2   33344444556678999999


Q ss_pred             cChhhHHHHHHhcCCCeecCc
Q 022301          154 TNYDDMKHAIKKLDDSEFRNA  174 (299)
Q Consensus       154 ~~~~~a~~a~~~l~g~~~~g~  174 (299)
                      ..+++|+.|+.+ |...|+-+
T Consensus       214 a~ee~aq~aL~k-hrq~iGqR  233 (508)
T KOG1365|consen  214 ACEEDAQFALRK-HRQNIGQR  233 (508)
T ss_pred             cCHHHHHHHHHH-HHHHHhHH
Confidence            999999999974 33444444

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.67  E-value=1.1e-07  Score=74.53  Aligned_cols=69  Identities=13%  Similarity=0.172  Sum_probs=62.2

Q ss_pred             ccEEEEeCCCCCCCHHHHHH----HHHhcCCeeEEEEEeC-CCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          108 EYRVLVTGLPSSASWQDLKD----HMRRAGDVCFSQVFRD-GSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~----~f~~~G~v~~~~~~~~-~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..+|||.||+..+..++|+.    +|++||+|..|.+... +-.|.|||.|.+.+.|-.|+..|+|..+.|+..
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~m   82 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPM   82 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchh
Confidence            34999999999999999888    9999999999888755 455799999999999999999999999999854

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.59  E-value=5.1e-08  Score=75.89  Aligned_cols=66  Identities=29%  Similarity=0.440  Sum_probs=56.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDF   70 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~   70 (299)
                      ..-.||||.||.++|||++|+++|+.|-...-++|...+. ...||++|.+.+.|..|+..|+|..|
T Consensus       208 ~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g-~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  208 RACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGG-MPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             hhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCC-cceEeecHHHHHHHHHHHHHhhccee
Confidence            3456899999999999999999999998888888854333 45899999999999999999998665

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.59  E-value=2.5e-07  Score=83.13  Aligned_cols=168  Identities=11%  Similarity=-0.006  Sum_probs=115.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEe--ec-CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL--KI-PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~--~~-~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      +.+.+-+.+++.+....++.++|... .|..+.|  .. .+-..|-++|+|....++++|+. -|...+-.+.+.|-.+-
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            34556667899999999999999643 2444444  22 23337899999999999999998 67777778888886543


Q ss_pred             CCCCCCCCCCC---------------CCC-----CCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeE-EEE
Q 022301           82 GGRGRSSSDRH---------------SSH-----SSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCF-SQV  140 (299)
Q Consensus        82 ~~~~~~~~~~~---------------~~~-----~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~-~~~  140 (299)
                      ...........               ...     ..+.....+...+.+|||..||..++..++..+|...-.|++ |.+
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            32211111000               000     011112245557789999999999999999999999888877 555


Q ss_pred             EeCCC---CCEEEEEecChhhHHHHHHhcCCCeecCc
Q 022301          141 FRDGS---GTTGIVDYTNYDDMKHAIKKLDDSEFRNA  174 (299)
Q Consensus       141 ~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  174 (299)
                      ...+.   .+.|||.|...+++..|...-+...++.+
T Consensus       468 t~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r  504 (944)
T KOG4307|consen  468 TRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHR  504 (944)
T ss_pred             ccCCcccccchhhheeccccccchhhhcccccccCce
Confidence            44443   34899999999988888875555555555

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.58  E-value=2.4e-07  Score=74.96  Aligned_cols=74  Identities=24%  Similarity=0.301  Sum_probs=65.9

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC---CEEEEEecChhhHHHHHHhcCCCeecCceeeEEE
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG---TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYV  180 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~  180 (299)
                      ....|+|.|||+.|.++||+++|..||.+..+.+..++.+   |.|-|.|...++|..|++.++|..++|......+
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            3478999999999999999999999999988888888766   6999999999999999999999999999654333

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.57  E-value=1.4e-07  Score=74.85  Aligned_cols=154  Identities=14%  Similarity=0.196  Sum_probs=109.1

Q ss_pred             EEEcCCCCCCCHHH---HHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            9 LYVGNLPGDIRERE---VEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         9 l~V~nLp~~~t~~~---l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      +++.|+-..+..+-   +...|+.|-.+....+..  .+.-.+++|+.|.....-.++...-+++.+.-.+|++  +...
T Consensus        99 p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~--a~gt  176 (290)
T KOG0226|consen   99 PFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRL--AAGT  176 (290)
T ss_pred             ccccccccccCCCCCCcchhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceee--cccc
Confidence            34555545444443   256666665555555532  2455689999999888777787766777766655443  2221


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhH
Q 022301           84 RGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDM  159 (299)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a  159 (299)
                      ....           .....-......||.+.|..+++.+.|...|.+|-.....+++.+..+    ||+||.|.+..++
T Consensus       177 swed-----------Psl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~  245 (290)
T KOG0226|consen  177 SWED-----------PSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADY  245 (290)
T ss_pred             ccCC-----------cccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHH
Confidence            1110           011122345579999999999999999999999999988888888655    5999999999999


Q ss_pred             HHHHHhcCCCeecCce
Q 022301          160 KHAIKKLDDSEFRNAF  175 (299)
Q Consensus       160 ~~a~~~l~g~~~~g~~  175 (299)
                      ..|+..|+|+.++.+.
T Consensus       246 ~rAmrem~gkyVgsrp  261 (290)
T KOG0226|consen  246 VRAMREMNGKYVGSRP  261 (290)
T ss_pred             HHHHHhhcccccccch
Confidence            9999999999999874

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.57  E-value=1.1e-07  Score=75.06  Aligned_cols=63  Identities=22%  Similarity=0.334  Sum_probs=59.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCce
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAF  175 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  175 (299)
                      ..+||++||+.+.+.+|+.+|..||.|..+.+...    |+||+|++..+|..|+..|||..|.|..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~g----f~fv~fed~rda~Dav~~l~~~~l~~e~   64 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKNG----FGFVEFEDPRDADDAVHDLDGKELCGER   64 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeecc----cceeccCchhhhhcccchhcCceeccee
Confidence            46899999999999999999999999999888765    9999999999999999999999999985

>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=98.48  E-value=3.9e-07  Score=64.59  Aligned_cols=69  Identities=17%  Similarity=0.343  Sum_probs=43.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCC-----CCCCceEEEE
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY-----DFDGHRLRVE   78 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~-----~~~g~~i~v~   78 (299)
                      +.|+|.+++..++-++|+++|..||+|..|.+..   .-..|||-|.+++.|+.|+..+...     .+.+..+.+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~---G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSR---GDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--T---T-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecC---CCCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            5799999999999999999999999999999963   3458999999999999998876544     4445554443

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.47  E-value=7e-07  Score=74.12  Aligned_cols=75  Identities=16%  Similarity=0.204  Sum_probs=63.3

Q ss_pred             CCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHh-cCCCeecCcee
Q 022301          100 GRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKK-LDDSEFRNAFS  176 (299)
Q Consensus       100 ~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~-l~g~~~~g~~~  176 (299)
                      ..++....-.+|||++|...+++.+|.++|.+||+|..+.+.....  +|||+|.+.+.|+.|.++ ++-..|+|..+
T Consensus       220 lepPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~~--CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl  295 (377)
T KOG0153|consen  220 LEPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRKG--CAFVTFTTREAAEKAAEKSFNKLVINGFRL  295 (377)
T ss_pred             cCCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecccc--cceeeehhhHHHHHHHHhhcceeeecceEE
Confidence            3456666778999999999999999999999999999998887654  999999999999877766 56667788733

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.45  E-value=7.2e-07  Score=81.30  Aligned_cols=70  Identities=16%  Similarity=0.252  Sum_probs=62.9

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ....++|+|++|+..+++.||..+|+.||.|..|.++...  ++|||.+....+|.+|+.+|....+.++.+
T Consensus       418 sV~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R--~cAfI~M~~RqdA~kalqkl~n~kv~~k~I  487 (894)
T KOG0132|consen  418 SVCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPR--GCAFIKMVRRQDAEKALQKLSNVKVADKTI  487 (894)
T ss_pred             eEeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccCC--ceeEEEEeehhHHHHHHHHHhcccccceee
Confidence            3467899999999999999999999999999998887654  599999999999999999999988888754

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=98.45  E-value=1.5e-06  Score=76.94  Aligned_cols=75  Identities=12%  Similarity=0.228  Sum_probs=64.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhh-hcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCC---CCceEEEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFY-KYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDF---DGHRLRVEL   79 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~-~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~---~g~~i~v~~   79 (299)
                      .+++.|||.||-.-.|..+|++|+. .+|.|.+.+|.   +-+..|||.|.+.++|.+..+.|||..+   .++.|.+.|
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 78888888773   2266999999999999999999999876   367888888


Q ss_pred             cc
Q 022301           80 AH   81 (299)
Q Consensus        80 ~~   81 (299)
                      ..
T Consensus       519 ~~  520 (718)
T KOG2416|consen  519 VR  520 (718)
T ss_pred             cc
Confidence            54

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.44  E-value=9.5e-07  Score=68.24  Aligned_cols=78  Identities=15%  Similarity=0.155  Sum_probs=65.5

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhc-CCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRA-GDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~-G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      +.......++|..+|..+.+.+|..+|.++ |.|..+.+..+..+    |||||+|++.+.|+-|.+.||++-+.|+.+.
T Consensus        44 p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~  123 (214)
T KOG4208|consen   44 PEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLE  123 (214)
T ss_pred             CccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheee
Confidence            445556789999999999999999999998 56667777677655    4999999999999999999999999999775


Q ss_pred             EEE
Q 022301          178 AYV  180 (299)
Q Consensus       178 ~~~  180 (299)
                      +.+
T Consensus       124 c~v  126 (214)
T KOG4208|consen  124 CHV  126 (214)
T ss_pred             eEE
Confidence            444

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.42  E-value=1.2e-07  Score=73.55  Aligned_cols=73  Identities=15%  Similarity=0.108  Sum_probs=65.4

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC--CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG--TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~--~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..+...+|||.|+...++++-|.++|-+.|+|+.|.|..+...  .||||.|+++....-|++.+||..+.+..+
T Consensus         5 aae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~l~~~e~   79 (267)
T KOG4454|consen    5 AAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDDLEEDEE   79 (267)
T ss_pred             CcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccchhhhhhhcccchhccchh
Confidence            3445679999999999999999999999999999999887654  399999999999999999999999998754

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.41  E-value=3.3e-07  Score=72.86  Aligned_cols=76  Identities=18%  Similarity=0.411  Sum_probs=67.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEe---ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~---~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      +.-.||.+.|..+++++.|...|.+|-.....++   ..+++++||+||-|.+.+++..|+..|||..++.++|++..+
T Consensus       189 ~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  189 DDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             ccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            4567999999999999999999999987766666   557899999999999999999999999999999999988654

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.36  E-value=3.1e-06  Score=74.08  Aligned_cols=67  Identities=18%  Similarity=0.281  Sum_probs=55.9

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeC----CCCCEEEEEecChhhHHHHHHhcCCCeecCc
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD----GSGTTGIVDYTNYDDMKHAIKKLDDSEFRNA  174 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~----~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  174 (299)
                      ....|||.|||.+++..+|+++|..||.|....|..-    ....||||+|++..+++.||++- -..|+++
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As-p~~ig~~  357 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS-PLEIGGR  357 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC-ccccCCe
Confidence            3445999999999999999999999999987666553    23359999999999999999955 6677777

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.32  E-value=6.4e-07  Score=78.85  Aligned_cols=71  Identities=18%  Similarity=0.179  Sum_probs=62.1

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .....+|+|.|||..|+.++|.++|+.||+|..+...... .+.+||+|.+..+|+.|++.|++.+|.|+.+
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~-~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~  142 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNK-RGIVFVEFYDVRDAERALKALNRREIAGKRI  142 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccccc-CceEEEEEeehHhHHHHHHHHHHHHhhhhhh
Confidence            4456799999999999999999999999999986554443 3599999999999999999999999999854

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.30  E-value=5e-06  Score=69.12  Aligned_cols=85  Identities=25%  Similarity=0.443  Sum_probs=70.5

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeE--------EEEEeCCCC---CEEEEEecChhhHHHHHHhcCCCee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCF--------SQVFRDGSG---TTGIVDYTNYDDMKHAIKKLDDSEF  171 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~--------~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~  171 (299)
                      +....++.|||.|||.++|.+++.++|.+||.|..        |++..+..+   |=|.|.|...+...-|++.|++..+
T Consensus       129 ~~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~  208 (382)
T KOG1548|consen  129 PEPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDEL  208 (382)
T ss_pred             cccccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccc
Confidence            34556778999999999999999999999997743        677777654   4699999999999999999999999


Q ss_pred             cCceeeEEEEecccccCCCC
Q 022301          172 RNAFSRAYVRVREYDHRRDG  191 (299)
Q Consensus       172 ~g~~~~~~~~~~~~~~~~~~  191 (299)
                      .|+    .++|..+.....+
T Consensus       209 rg~----~~rVerAkfq~Kg  224 (382)
T KOG1548|consen  209 RGK----KLRVERAKFQMKG  224 (382)
T ss_pred             cCc----EEEEehhhhhhcc
Confidence            999    7777766665443

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=98.26  E-value=5.8e-07  Score=71.74  Aligned_cols=61  Identities=25%  Similarity=0.432  Sum_probs=52.5

Q ss_pred             HHHHHHhh-hcCCeeEEEee--cCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301           21 REVEDLFY-KYGPIAHIDLK--IPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus        21 ~~l~~~F~-~~G~v~~i~~~--~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ++|...|. +||+|+++.|-  ...+..|.+||+|..+++|++|+..||+.+|.|++|.++++.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            55666666 99999999883  334667999999999999999999999999999999998874

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.24  E-value=4.1e-06  Score=75.76  Aligned_cols=73  Identities=18%  Similarity=0.165  Sum_probs=65.4

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC-------CCEEEEEecChhhHHHHHHhcCCCeecCce
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS-------GTTGIVDYTNYDDMKHAIKKLDDSEFRNAF  175 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-------~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  175 (299)
                      ...+..++|||+||++.++++.|...|..||+|..++|+....       ..+|||.|-+..+|+.|++.|+|..+.+..
T Consensus       169 dgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e  248 (877)
T KOG0151|consen  169 DGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYE  248 (877)
T ss_pred             CCCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeee
Confidence            3456778999999999999999999999999999999988753       249999999999999999999999998763

>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=98.21  E-value=1.3e-05  Score=52.90  Aligned_cols=67  Identities=19%  Similarity=0.269  Sum_probs=45.9

Q ss_pred             cEEEEeCCCCCCCHHH----HHHHHHhcC-CeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEec
Q 022301          109 YRVLVTGLPSSASWQD----LKDHMRRAG-DVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVR  183 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~----l~~~f~~~G-~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~  183 (299)
                      ..|+|.|||.+.+...    |++++..+| +|..+.      ++.|+|.|.+.+.|..|.+.|+|..+.|.    .|.+.
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------GGTAILRFPNQEFAERAQKRMEGEDVFGN----KISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE--------TT-EEEEESSHHHHHHHHHHHTT--SSSS------EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe------CCEEEEEeCCHHHHHHHHHhhcccccccc----eEEEE
Confidence            5799999999988654    566777787 665552      35899999999999999999999999999    55555


Q ss_pred             cc
Q 022301          184 EY  185 (299)
Q Consensus       184 ~~  185 (299)
                      ..
T Consensus        73 ~~   74 (90)
T PF11608_consen   73 FS   74 (90)
T ss_dssp             SS
T ss_pred             Ec
Confidence            44

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=98.21  E-value=1.7e-05  Score=54.91  Aligned_cols=66  Identities=15%  Similarity=0.155  Sum_probs=57.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCc
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRA--GDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNA  174 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~--G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  174 (299)
                      ++|.|.|||...+.++|.+++...  |....+.++.|-.    .|||||.|.+++.|..-.+.++|..+..-
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~   73 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNF   73 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccC
Confidence            689999999999999999998773  6666777777743    47999999999999999999999999753

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.19  E-value=1.8e-06  Score=72.23  Aligned_cols=81  Identities=31%  Similarity=0.472  Sum_probs=69.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCee--------EEEe---ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIA--------HIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDG   72 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~--------~i~~---~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g   72 (299)
                      ..+.+|||-+||.++++++|.++|.+||.|.        .|+|   +.|+.+++-|.|.|.+...|+.|+..++++.|.+
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~g  143 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCG  143 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccC
Confidence            3467999999999999999999999999773        2223   3467889999999999999999999999999999


Q ss_pred             ceEEEEEccCCC
Q 022301           73 HRLRVELAHGGR   84 (299)
Q Consensus        73 ~~i~v~~~~~~~   84 (299)
                      ..|+|.++....
T Consensus       144 n~ikvs~a~~r~  155 (351)
T KOG1995|consen  144 NTIKVSLAERRT  155 (351)
T ss_pred             CCchhhhhhhcc
Confidence            999998876544

>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=98.18  E-value=3.6e-06  Score=59.67  Aligned_cols=59  Identities=22%  Similarity=0.449  Sum_probs=39.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCC
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDS  169 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~  169 (299)
                      +.|+|.+++..++.++|+++|..||.|.+|.+.....  .|||.|.+.+.|+.|+.++...
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            5788999999999999999999999999998877654  8999999999999999887544

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=98.17  E-value=5.7e-06  Score=50.73  Aligned_cols=53  Identities=28%  Similarity=0.553  Sum_probs=44.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHH
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAI   62 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~   62 (299)
                      ++.|-|.+.+++..+ +|...|..||+|..+.+.   .....+||.|.+..+|+.||
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            467899999988774 455588899999999886   33569999999999999985

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.13  E-value=7.2e-06  Score=67.91  Aligned_cols=76  Identities=24%  Similarity=0.445  Sum_probs=61.5

Q ss_pred             CCeEEEcCCCCCCCHHH----H--HHHhhhcCCeeEEEeecCC----CCCceE--EEEecChHHHHHHHHhcCCCCCCCc
Q 022301            6 SRTLYVGNLPGDIRERE----V--EDLFYKYGPIAHIDLKIPP----RPPGYA--FVEFEEARDAEDAIRGRDGYDFDGH   73 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~----l--~~~F~~~G~v~~i~~~~~~----~~~g~a--fV~F~~~e~A~~A~~~l~~~~~~g~   73 (299)
                      .+-+||-+||+.+..|+    |  .++|++||.|..|.|+...    ...+.+  ||.|.+.|+|..||...+|..++|+
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            45689999999887776    2  3799999999999994321    112233  9999999999999999999999999


Q ss_pred             eEEEEEcc
Q 022301           74 RLRVELAH   81 (299)
Q Consensus        74 ~i~v~~~~   81 (299)
                      .|+..|..
T Consensus       194 ~lkatYGT  201 (480)
T COG5175         194 VLKATYGT  201 (480)
T ss_pred             eEeeecCc
Confidence            99998743

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.07  E-value=2.1e-05  Score=71.18  Aligned_cols=76  Identities=22%  Similarity=0.379  Sum_probs=65.2

Q ss_pred             CCCC-eEEEcCCCCCCCHHHHHHHhhhcCCe-eEEEe--ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            4 RASR-TLYVGNLPGDIREREVEDLFYKYGPI-AHIDL--KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         4 ~~~~-~l~V~nLp~~~t~~~l~~~F~~~G~v-~~i~~--~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      .+-+ +|-+.|+|.+++.+||.++|.-|-.+ .+|.+  ..+|...|-|.|.|++.++|..|+..|++..|..++|.|.+
T Consensus       864 ~pGp~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  864 SPGPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CCCCeEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            3444 88999999999999999999999765 33444  55688999999999999999999999999999999988754

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.99  E-value=7.2e-06  Score=68.21  Aligned_cols=74  Identities=16%  Similarity=0.218  Sum_probs=62.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcC--CeeEEEe---ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYG--PIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G--~v~~i~~---~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      -++||+||-+++|++||.+.+...|  .|.++++   ..+|+++|||+|...+...+++.++.|-.+.|.|+.-.|..+
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~  159 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSY  159 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeecc
Confidence            4689999999999999999998777  4566666   335899999999999999999999999999999987777543

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.96  E-value=1.1e-05  Score=68.90  Aligned_cols=73  Identities=29%  Similarity=0.281  Sum_probs=58.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC--------CC--------CCceEEEEecChHHHHHHHHhcCCC
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP--------PR--------PPGYAFVEFEEARDAEDAIRGRDGY   68 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~--------~~--------~~g~afV~F~~~e~A~~A~~~l~~~   68 (299)
                      +++||.+.|||.+-.-+.|.+||+.||.|..|.|...        +.        .+-+|||+|.+.+.|.+|.+.|+..
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            6899999999999888999999999999999999443        11        2467999999999999999977664


Q ss_pred             CCCCceEEE
Q 022301           69 DFDGHRLRV   77 (299)
Q Consensus        69 ~~~g~~i~v   77 (299)
                      ..+-.-|+|
T Consensus       310 ~~wr~glkv  318 (484)
T KOG1855|consen  310 QNWRMGLKV  318 (484)
T ss_pred             hhhhhcchh
Confidence            443333333

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.93  E-value=7.5e-06  Score=68.76  Aligned_cols=80  Identities=24%  Similarity=0.426  Sum_probs=69.8

Q ss_pred             CCCCCeEE-EcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEE
Q 022301            3 SRASRTLY-VGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVE   78 (299)
Q Consensus         3 ~~~~~~l~-V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~   78 (299)
                      ..++-++| |+||+.+++.++|+.+|..+|.|..+.+..   ++..+|||||.|.+...+..|+.. +...+.+.++.|.
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            35566677 999999999999999999999999999943   467889999999999999999996 8889999999998


Q ss_pred             EccCC
Q 022301           79 LAHGG   83 (299)
Q Consensus        79 ~~~~~   83 (299)
                      +....
T Consensus       260 ~~~~~  264 (285)
T KOG4210|consen  260 EDEPR  264 (285)
T ss_pred             cCCCC
Confidence            87543

>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=97.93  E-value=3.3e-05  Score=53.88  Aligned_cols=75  Identities=17%  Similarity=0.261  Sum_probs=54.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEe-e---------cCCCCCceEEEEecChHHHHHHHHhcCCCCCCCc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL-K---------IPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGH   73 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~-~---------~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~   73 (299)
                      ...+.|.|-+.|+. ....|.++|++||+|.+..- .         ......+...|+|.++.+|.+||. .||..|.|.
T Consensus         4 ~~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~   81 (100)
T PF05172_consen    4 DSETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGS   81 (100)
T ss_dssp             GGCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTC
T ss_pred             cCCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCc
Confidence            35677889999999 55788899999999988751 0         011335689999999999999999 899999886


Q ss_pred             eE-EEEEc
Q 022301           74 RL-RVELA   80 (299)
Q Consensus        74 ~i-~v~~~   80 (299)
                      .| -|.++
T Consensus        82 ~mvGV~~~   89 (100)
T PF05172_consen   82 LMVGVKPC   89 (100)
T ss_dssp             EEEEEEE-
T ss_pred             EEEEEEEc
Confidence            55 46665

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.

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=97.92  E-value=1.6e-05  Score=64.53  Aligned_cols=72  Identities=19%  Similarity=0.230  Sum_probs=63.6

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      ......++|+|+...++.++++.+|+.||.|..+.+..+...    +|+||+|.+.+.++.|+. |+|..|.|..+.
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~  173 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIE  173 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccce
Confidence            345579999999999999999999999999988888777544    499999999999999999 999999998543

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.85  E-value=1e-05  Score=64.60  Aligned_cols=70  Identities=17%  Similarity=0.315  Sum_probs=59.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCC-----------CCCc----eEEEEecChHHHHHHHHhcCCCC
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----------RPPG----YAFVEFEEARDAEDAIRGRDGYD   69 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~-----------~~~g----~afV~F~~~e~A~~A~~~l~~~~   69 (299)
                      .+-+|||.|||+.+....|.++|..||.|-.|.|....           ...+    -|.|+|.....|..+...|||..
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            45689999999999999999999999999999995431           2221    26799999999999999999999


Q ss_pred             CCCce
Q 022301           70 FDGHR   74 (299)
Q Consensus        70 ~~g~~   74 (299)
                      |.|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99875

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.82  E-value=8.6e-05  Score=65.25  Aligned_cols=61  Identities=23%  Similarity=0.412  Sum_probs=56.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhh-hcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHh
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFY-KYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRG   64 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~-~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~   64 (299)
                      ++.+|||||+||--++.++|..+|. -||.|..+-|..+   +-++|-|=|.|.+..+-.+||..
T Consensus       368 DprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  368 DPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            6889999999999999999999999 8999999999766   35789999999999999999983

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.81  E-value=5.1e-05  Score=67.19  Aligned_cols=74  Identities=28%  Similarity=0.423  Sum_probs=58.9

Q ss_pred             CCeEEEcCCCCCCC--HH----HHHHHhhhcCCeeEEEeecC--CCCCceEEEEecChHHHHHHHHhcCCCCCC-CceEE
Q 022301            6 SRTLYVGNLPGDIR--ER----EVEDLFYKYGPIAHIDLKIP--PRPPGYAFVEFEEARDAEDAIRGRDGYDFD-GHRLR   76 (299)
Q Consensus         6 ~~~l~V~nLp~~~t--~~----~l~~~F~~~G~v~~i~~~~~--~~~~g~afV~F~~~e~A~~A~~~l~~~~~~-g~~i~   76 (299)
                      ...|+|.|+|.--.  .+    -|..+|+++|+|..+.++.+  +..+||+|++|.+..+|+.|++.|||..|+ ...+.
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            45788999987422  22    36679999999999999654  568999999999999999999999998876 44556


Q ss_pred             EEE
Q 022301           77 VEL   79 (299)
Q Consensus        77 v~~   79 (299)
                      |..
T Consensus       138 v~~  140 (698)
T KOG2314|consen  138 VRL  140 (698)
T ss_pred             eeh
Confidence            654

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.75  E-value=8.9e-05  Score=45.44  Aligned_cols=52  Identities=17%  Similarity=0.310  Sum_probs=41.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHH
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAI  163 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~  163 (299)
                      ..|.|.+.+.... +++..+|..||+|..+.+...  ..+.+|.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~~~--~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVPES--TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcCCC--CcEEEEEECCHHHHHhhC
Confidence            4677888887655 445558999999999888733  339999999999999985

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.71  E-value=0.00011  Score=58.82  Aligned_cols=93  Identities=27%  Similarity=0.287  Sum_probs=77.6

Q ss_pred             HHHHHHHhcCCCCCCCceEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCee
Q 022301           57 DAEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVC  136 (299)
Q Consensus        57 ~A~~A~~~l~~~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~  136 (299)
                      -|..|...|++....|+.|.|.|+..                          ..|+|.||...+..+.|.+.|..||+|.
T Consensus         6 ~ae~ak~eLd~~~~~~~~lr~rfa~~--------------------------a~l~V~nl~~~~sndll~~~f~~fg~~e   59 (275)
T KOG0115|consen    6 LAEIAKRELDGRFPKGRSLRVRFAMH--------------------------AELYVVNLMQGASNDLLEQAFRRFGPIE   59 (275)
T ss_pred             HHHHHHHhcCCCCCCCCceEEEeecc--------------------------ceEEEEecchhhhhHHHHHhhhhcCccc
Confidence            46667777999999999999999853                          5899999999999999999999999998


Q ss_pred             EEEEEeCC---CCCEEEEEecChhhHHHHHHhcCCCeecCce
Q 022301          137 FSQVFRDG---SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAF  175 (299)
Q Consensus       137 ~~~~~~~~---~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  175 (299)
                      ...+..|.   .++-++|.|...-.|.+|+..+.-.-+.+..
T Consensus        60 ~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~  101 (275)
T KOG0115|consen   60 RAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGFGGTT  101 (275)
T ss_pred             hheeeecccccccccchhhhhcchhHHHHHHHhccCccccCC
Confidence            86666653   3358999999999999999988655555543

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.65  E-value=0.00011  Score=68.66  Aligned_cols=81  Identities=28%  Similarity=0.436  Sum_probs=71.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCC--ceEEEEEc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDG--HRLRVELA   80 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g--~~i~v~~~   80 (299)
                      ..+++.|||++|.+++....|...|..||.|..|.+.   +...||||+|.+...|+.|++.|-|..|.|  +.|.|.|+
T Consensus       452 st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~---hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla  528 (975)
T KOG0112|consen  452 STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR---HGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLA  528 (975)
T ss_pred             cccceeeccCCCCCCChHHHHHHHhhccCcceeeecc---cCCcceeeecccCccchhhHHHHhcCcCCCCCcccccccc
Confidence            3578899999999999999999999999999999986   446699999999999999999999999975  56888888


Q ss_pred             cCCCCC
Q 022301           81 HGGRGR   86 (299)
Q Consensus        81 ~~~~~~   86 (299)
                      ......
T Consensus       529 ~~~~~~  534 (975)
T KOG0112|consen  529 SPPGAT  534 (975)
T ss_pred             cCCCCC
Confidence            755443

>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]

Probab=97.64  E-value=0.00013  Score=64.84  Aligned_cols=12  Identities=67%  Similarity=0.614  Sum_probs=4.6

Q ss_pred             CCCCCCCCCCCC
Q 022301          218 SYSRSRSQSKSP  229 (299)
Q Consensus       218 srsr~rsrsr~~  229 (299)
                      +++|++|++++.
T Consensus       607 skSRSRSpS~~~  618 (757)
T KOG4368|consen  607 SKSRSRSPSRSN  618 (757)
T ss_pred             ccccCCCccccc
Confidence            333333333333

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=97.63  E-value=0.00015  Score=59.14  Aligned_cols=77  Identities=25%  Similarity=0.404  Sum_probs=57.6

Q ss_pred             CCCeEEEcCC--CCCCC---HHHHHHHhhhcCCeeEEEeecCC----CCCceEEEEecChHHHHHHHHhcCCCCCCCceE
Q 022301            5 ASRTLYVGNL--PGDIR---EREVEDLFYKYGPIAHIDLKIPP----RPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRL   75 (299)
Q Consensus         5 ~~~~l~V~nL--p~~~t---~~~l~~~F~~~G~v~~i~~~~~~----~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i   75 (299)
                      +++.|.+.|+  +-.++   ++++++..++||.|..|.|....    +-.--.||+|...++|.+|+-.|||.+|.|+.+
T Consensus       280 ptkvlllrnmVg~gevd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v  359 (378)
T KOG1996|consen  280 PTKVLLLRNMVGAGEVDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVV  359 (378)
T ss_pred             chHHHHhhhhcCcccccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceee
Confidence            3444555555  33344   34688899999999999884321    223457999999999999999999999999999


Q ss_pred             EEEEcc
Q 022301           76 RVELAH   81 (299)
Q Consensus        76 ~v~~~~   81 (299)
                      ...|.+
T Consensus       360 ~A~Fyn  365 (378)
T KOG1996|consen  360 SACFYN  365 (378)
T ss_pred             eheecc
Confidence            887754

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.58  E-value=0.00021  Score=59.46  Aligned_cols=72  Identities=17%  Similarity=0.243  Sum_probs=58.4

Q ss_pred             CCccEEEEeCCCCCCCHHH------HHHHHHhcCCeeEEEEEeCCCC-----C--EEEEEecChhhHHHHHHhcCCCeec
Q 022301          106 RSEYRVLVTGLPSSASWQD------LKDHMRRAGDVCFSQVFRDGSG-----T--TGIVDYTNYDDMKHAIKKLDDSEFR  172 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~------l~~~f~~~G~v~~~~~~~~~~~-----~--~~fv~f~~~~~a~~a~~~l~g~~~~  172 (299)
                      ...+-+||.+|++.+..++      -.++|.+||+|..+.|.+....     +  -.||.|...++|..||.+.+|..++
T Consensus       112 vQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~D  191 (480)
T COG5175         112 VQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLD  191 (480)
T ss_pred             eecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcccccc
Confidence            3556789999999886665      2479999999999888665421     1  3599999999999999999999999


Q ss_pred             Cceee
Q 022301          173 NAFSR  177 (299)
Q Consensus       173 g~~~~  177 (299)
                      |+.+.
T Consensus       192 Gr~lk  196 (480)
T COG5175         192 GRVLK  196 (480)
T ss_pred             CceEe
Confidence            98664

>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=97.58  E-value=0.00034  Score=48.85  Aligned_cols=67  Identities=21%  Similarity=0.229  Sum_probs=48.7

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEE-E----------EeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQ-V----------FRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~-~----------~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..-|.|.+.|+. ....|.++|++||+|.... +          .......+..|.|.+..+|++||. .||..+.|...
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEE
Confidence            356889999887 5667888999999997764 1          112233499999999999999999 89999998754

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.

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=97.53  E-value=0.00056  Score=45.24  Aligned_cols=56  Identities=16%  Similarity=0.275  Sum_probs=44.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG   67 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~   67 (299)
                      ....+|+ +|......||.+||+.||.|.--.|.     -.-|||...+.+.|..|+..+.-
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi~-----dTSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWIN-----DTSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEEEEEEC-----TTEEEEEECCCHHHHHHHHHHTT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEEEEEEc-----CCcEEEEeecHHHHHHHHHHhcc
Confidence            3566776 99999999999999999999877776     34899999999999999997753

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.51  E-value=0.00048  Score=51.06  Aligned_cols=55  Identities=24%  Similarity=0.463  Sum_probs=46.1

Q ss_pred             HHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301           22 EVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus        22 ~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      +|.+.|..||+|.-+++.     -+.-.|+|.+-+.|.+|+. |+|..+.|..|+|....+
T Consensus        52 ~ll~~~~~~GevvLvRfv-----~~~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtp  106 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFV-----GDTMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTP  106 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEE-----TTCEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE---
T ss_pred             HHHHHHHhCCceEEEEEe-----CCeEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCc
Confidence            577889999999988887     3467999999999999999 999999999999988643

; PDB: 1UFW_A 2DNR_A.

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.39  E-value=0.00011  Score=58.97  Aligned_cols=69  Identities=13%  Similarity=0.173  Sum_probs=60.4

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC---------C-------EEEEEecChhhHHHHHHhcCCCe
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG---------T-------TGIVDYTNYDDMKHAIKKLDDSE  170 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~---------~-------~~fv~f~~~~~a~~a~~~l~g~~  170 (299)
                      ..-.||+.+||+.+...-|.++|..||.|-.|.+......         +       -|+|+|.....|..+...||+..
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            3458999999999999999999999999999888765432         2       38999999999999999999999


Q ss_pred             ecCce
Q 022301          171 FRNAF  175 (299)
Q Consensus       171 ~~g~~  175 (299)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99974

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.39  E-value=0.0003  Score=65.48  Aligned_cols=78  Identities=18%  Similarity=0.218  Sum_probs=68.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEe--ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL--KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~--~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      ...|+|.|+|+..|.++|+.+|..+|.+.++.+  ...|+++|.|||.|.++.+|..++..+++..+....+.|..+++.
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            457899999999999999999999999999887  456899999999999999999999988888888777777776553

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=97.34  E-value=0.00083  Score=54.97  Aligned_cols=58  Identities=17%  Similarity=0.204  Sum_probs=50.2

Q ss_pred             HHHHHHHHHhcCCeeEEEEEeCCCCC-----EEEEEecChhhHHHHHHhcCCCeecCceeeEE
Q 022301          122 WQDLKDHMRRAGDVCFSQVFRDGSGT-----TGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY  179 (299)
Q Consensus       122 ~~~l~~~f~~~G~v~~~~~~~~~~~~-----~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  179 (299)
                      +.++++.|.+||+|..|.|+..+...     -.||+|+..++|.+|+-.|||..++|+.+.+.
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~  362 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSAC  362 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeehe
Confidence            56788999999999999888876442     68999999999999999999999999976544

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=97.34  E-value=0.00033  Score=62.08  Aligned_cols=70  Identities=16%  Similarity=0.241  Sum_probs=56.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhh--hcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCC--CCCCCceEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFY--KYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG--YDFDGHRLRV   77 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~--~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~--~~~~g~~i~v   77 (299)
                      ..-|.|+|.-||..+..|+|+.||.  .|-++++|.+..+   - -=||+|++.+||+.|++.|..  +.|.|++|..
T Consensus       173 ~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N---~-nWyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  173 HKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHN---D-NWYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             cceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeec---C-ceEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            4568899999999999999999998  5889999999532   2 349999999999999887665  5566766544

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.33  E-value=0.00037  Score=58.73  Aligned_cols=72  Identities=19%  Similarity=0.261  Sum_probs=60.7

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCee--------EEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeec
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVC--------FSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFR  172 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~--------~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~  172 (299)
                      .....+|||-+||..++.++|.++|.++|.|.        .|++..+..+    +-|.|.|+++..|+.|+.-++++.+.
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            45667999999999999999999999999773        3555555433    48999999999999999999999999


Q ss_pred             Ccee
Q 022301          173 NAFS  176 (299)
Q Consensus       173 g~~~  176 (299)
                      +..+
T Consensus       143 gn~i  146 (351)
T KOG1995|consen  143 GNTI  146 (351)
T ss_pred             CCCc
Confidence            9643

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.33  E-value=8.4e-05  Score=63.75  Aligned_cols=69  Identities=13%  Similarity=0.266  Sum_probs=57.8

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeC---CCC--------------CEEEEEecChhhHHHHHHh
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD---GSG--------------TTGIVDYTNYDDMKHAIKK  165 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~---~~~--------------~~~fv~f~~~~~a~~a~~~  165 (299)
                      .+..+..+|.+.|||.+-.-+.|.++|..+|.|..|.|...   +..              .+|+|+|+..+.|.+|.+.
T Consensus       226 ~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~  305 (484)
T KOG1855|consen  226 EEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKAREL  305 (484)
T ss_pred             ccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHh
Confidence            34457789999999999999999999999999999998776   211              1799999999999999998


Q ss_pred             cCCCee
Q 022301          166 LDDSEF  171 (299)
Q Consensus       166 l~g~~~  171 (299)
                      |+....
T Consensus       306 ~~~e~~  311 (484)
T KOG1855|consen  306 LNPEQN  311 (484)
T ss_pred             hchhhh
Confidence            865443

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.30  E-value=0.00084  Score=59.78  Aligned_cols=68  Identities=24%  Similarity=0.306  Sum_probs=56.1

Q ss_pred             CccEEEEeCCCCCCC------HHHHHHHHHhcCCeeEEEEEeCCCC---CEEEEEecChhhHHHHHHhcCCCeecCc
Q 022301          107 SEYRVLVTGLPSSAS------WQDLKDHMRRAGDVCFSQVFRDGSG---TTGIVDYTNYDDMKHAIKKLDDSEFRNA  174 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~------~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~  174 (299)
                      -...|+|.|+|---.      ...|..+|+++|+|+.+.++.+..+   ||.|++|.+..+|+.|++.|||+.|+-+
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldkn  133 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKN  133 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceeccc
Confidence            346788888776322      4567789999999999999977665   4999999999999999999999999754

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=97.25  E-value=0.00084  Score=54.07  Aligned_cols=59  Identities=14%  Similarity=0.169  Sum_probs=46.4

Q ss_pred             HHHHHHHH-hcCCeeEEEEEeCC---CCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEE
Q 022301          123 QDLKDHMR-RAGDVCFSQVFRDG---SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVR  181 (299)
Q Consensus       123 ~~l~~~f~-~~G~v~~~~~~~~~---~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~  181 (299)
                      ++|...|. +||+|..+.|-.+-   -.|.+||.|...++|+.|++.||+..+.|+.+.+...
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeec
Confidence            45555555 79999888665543   2368999999999999999999999999997765543

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=97.24  E-value=0.0029  Score=46.33  Aligned_cols=74  Identities=19%  Similarity=0.249  Sum_probs=57.3

Q ss_pred             CCCCCeEEEcCCCCCCCH----HHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEE
Q 022301            3 SRASRTLYVGNLPGDIRE----REVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVE   78 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~----~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~   78 (299)
                      +-|-.||.|.=|..++..    ..|...++.||+|+.|.+.    ++..|.|.|.+..+|.+|+.+++. ...|.-+++.
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c----GrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCs  157 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC----GRQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCS  157 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec----CCceEEEEehhhHHHHHHHHhhcC-CCCCceEEee
Confidence            345568888777666543    2366677899999999985    356899999999999999997766 6677888887


Q ss_pred             Ecc
Q 022301           79 LAH   81 (299)
Q Consensus        79 ~~~   81 (299)
                      |-.
T Consensus       158 Wqq  160 (166)
T PF15023_consen  158 WQQ  160 (166)
T ss_pred             ccc
Confidence            754

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=96.98  E-value=0.00066  Score=59.14  Aligned_cols=77  Identities=16%  Similarity=0.229  Sum_probs=64.9

Q ss_pred             CCCCeEEEcCCCCCC-CHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            4 RASRTLYVGNLPGDI-REREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~-t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      ..++.|-+.-+|..+ |.++|...|.+||+|..|.+-..   .-.|.|+|.+..+|-.|.. .++..|.++.|+|.|-+.
T Consensus       370 ~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~---~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  370 VDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS---SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             cccchhhhhccCCCCchHhhhhhhhhhcCccccccccCc---hhhheeeeeccccccchhc-cccceecCceeEEEEecC
Confidence            566777777777774 56789999999999999999644   3479999999999988888 899999999999999876


Q ss_pred             CC
Q 022301           83 GR   84 (299)
Q Consensus        83 ~~   84 (299)
                      ..
T Consensus       446 s~  447 (526)
T KOG2135|consen  446 SP  447 (526)
T ss_pred             Cc
Confidence            43

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.97  E-value=0.0035  Score=41.55  Aligned_cols=54  Identities=19%  Similarity=0.220  Sum_probs=41.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcC
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLD  167 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~  167 (299)
                      ...+|+ .|..+...||.++|..||.|.-..|...    .|||.....+.|..|+..+.
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi~dT----SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWINDT----SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEEEEEECTT----EEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEEEEEEcCC----cEEEEeecHHHHHHHHHHhc
Confidence            445555 9999999999999999999875554333    89999999999999998775

; 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.

>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=96.96  E-value=0.0077  Score=42.91  Aligned_cols=66  Identities=14%  Similarity=0.106  Sum_probs=47.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcC-CeeEEEeecCCC-CCceEEEEecChHHHHHHHHhcCCCCCC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYG-PIAHIDLKIPPR-PPGYAFVEFEEARDAEDAIRGRDGYDFD   71 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G-~v~~i~~~~~~~-~~g~afV~F~~~e~A~~A~~~l~~~~~~   71 (299)
                      +..+.+...|..++.++|..+...+- .|..++|..++. ++-.++|+|.+.++|......+||+.|.
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            34444444455566666766666554 577888877765 4557889999999999999999998875

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.95  E-value=0.0093  Score=37.47  Aligned_cols=55  Identities=16%  Similarity=0.129  Sum_probs=45.3

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhc---CCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhc
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRA---GDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKL  166 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~---G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l  166 (299)
                      ...|+|.|+. +++.++|+.+|..|   .....+.++.|.   .|-|.|.+.+.|..|+.+|
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            3589999985 47889999999999   245567777775   6889999999999999865

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.94  E-value=0.0066  Score=45.10  Aligned_cols=53  Identities=17%  Similarity=0.251  Sum_probs=44.1

Q ss_pred             HHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEE
Q 022301          123 QDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYV  180 (299)
Q Consensus       123 ~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~  180 (299)
                      .+|.+.|..||.+.-+.+..+    .-+|+|.+-+.|.+|+. ++|.+++|+.+....
T Consensus        51 ~~ll~~~~~~GevvLvRfv~~----~mwVTF~dg~sALaals-~dg~~v~g~~l~i~L  103 (146)
T PF08952_consen   51 DELLQKFAQYGEVVLVRFVGD----TMWVTFRDGQSALAALS-LDGIQVNGRTLKIRL  103 (146)
T ss_dssp             HHHHHHHHCCS-ECEEEEETT----CEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE
T ss_pred             HHHHHHHHhCCceEEEEEeCC----eEEEEECccHHHHHHHc-cCCcEECCEEEEEEe
Confidence            477888999999998887765    67999999999999998 999999999654443

; PDB: 1UFW_A 2DNR_A.

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=96.91  E-value=0.0055  Score=54.70  Aligned_cols=91  Identities=12%  Similarity=0.167  Sum_probs=68.3

Q ss_pred             HHHHHHHhcCCCCCCCceEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHh--cCC
Q 022301           57 DAEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRR--AGD  134 (299)
Q Consensus        57 ~A~~A~~~l~~~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~--~G~  134 (299)
                      -..++|...-+..++.+-++|...                         ..-+.|++..||..+..++++.+|+.  +-+
T Consensus       149 LI~Evlresp~VqvDekgekVrp~-------------------------~kRcIvilREIpettp~e~Vk~lf~~encPk  203 (684)
T KOG2591|consen  149 LIVEVLRESPNVQVDEKGEKVRPN-------------------------HKRCIVILREIPETTPIEVVKALFKGENCPK  203 (684)
T ss_pred             HHHHHHhcCCCceeccCccccccC-------------------------cceeEEEEeecCCCChHHHHHHHhccCCCCC
Confidence            334556656666666666666332                         33467888999999999999999987  778


Q ss_pred             eeEEEEEeCCCCCEEEEEecChhhHHHHHHhc-------CCCeecCce
Q 022301          135 VCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKL-------DDSEFRNAF  175 (299)
Q Consensus       135 v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l-------~g~~~~g~~  175 (299)
                      ++.|.+..+.   ..||+|++..||++|.+.|       .|+.|.-++
T Consensus       204 ~iscefa~N~---nWyITfesd~DAQqAykylreevk~fqgKpImARI  248 (684)
T KOG2591|consen  204 VISCEFAHND---NWYITFESDTDAQQAYKYLREEVKTFQGKPIMARI  248 (684)
T ss_pred             ceeeeeeecC---ceEEEeecchhHHHHHHHHHHHHHhhcCcchhhhh
Confidence            9999988776   5899999999999998664       566555443

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.89  E-value=0.0085  Score=37.65  Aligned_cols=54  Identities=17%  Similarity=0.349  Sum_probs=41.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhc----CCeeEEEeecCCCCCceEEEEecChHHHHHHHHhc
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKY----GPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGR   65 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~----G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l   65 (299)
                      ...|+|.+|. +++.++|+.+|..|    ++. .|....+    .-|-|.|.+.+.|..||..|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~-~IEWIdD----tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPF-RIEWIDD----TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCc-eEEEecC----CcEEEEECCHHHHHHHHHcC
Confidence            4679999984 58889999999998    543 4444322    26899999999999999864

>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=96.86  E-value=0.0089  Score=39.45  Aligned_cols=66  Identities=27%  Similarity=0.496  Sum_probs=41.1

Q ss_pred             eEEEcCCC--CCCCHHHHHHHhhhcC-----CeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            8 TLYVGNLP--GDIREREVEDLFYKYG-----PIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         8 ~l~V~nLp--~~~t~~~l~~~F~~~G-----~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      +||| |+-  ..++..+|..++...+     .|-.|.|.     ..|+||+.... .|..++..|++..+.|+.|.|+.|
T Consensus         2 rl~i-n~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~-----~~~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen    2 RLFI-NVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIF-----DNFSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             EEEE-S-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE------SS-EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             EEEE-EcccccCCCHHHHHHHHHhccCCCHHhEEEEEEe-----eeEEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            5666 553  3589999999998775     45677776     45999999765 888899999999999999999864

; PDB: 2G0C_A 3MOJ_B.

>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=96.80  E-value=0.001  Score=51.94  Aligned_cols=80  Identities=19%  Similarity=0.169  Sum_probs=51.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhh-cCCe---eEEEeecC-----CCCCceEEEEecChHHHHHHHHhcCCCCCCC--
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYK-YGPI---AHIDLKIP-----PRPPGYAFVEFEEARDAEDAIRGRDGYDFDG--   72 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~-~G~v---~~i~~~~~-----~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g--   72 (299)
                      .....|.|.+||+++|++++.+.+.. ++..   ..+.....     .....-|||.|.+.+++......++|..|.+  
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            55679999999999999999997776 6655   33332111     1223579999999999999999999966532  


Q ss_pred             ---ceEEEEEccCC
Q 022301           73 ---HRLRVELAHGG   83 (299)
Q Consensus        73 ---~~i~v~~~~~~   83 (299)
                         ....|++|...
T Consensus        85 g~~~~~~VE~Apyq   98 (176)
T PF03467_consen   85 GNEYPAVVEFAPYQ   98 (176)
T ss_dssp             S-EEEEEEEE-SS-
T ss_pred             CCCcceeEEEcchh
Confidence               24567776543

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.

>KOG2548 consensus SWAP mRNA splicing regulator [RNA processing and modification]

Probab=96.73  E-value=0.0005  Score=60.52  Aligned_cols=7  Identities=14%  Similarity=0.387  Sum_probs=2.8

Q ss_pred             cChhhHH
Q 022301          154 TNYDDMK  160 (299)
Q Consensus       154 ~~~~~a~  160 (299)
                      .+.++|.
T Consensus       235 kdkeea~  241 (653)
T KOG2548|consen  235 KDKEEAK  241 (653)
T ss_pred             hhHHHHH
Confidence            3344443

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.68  E-value=0.0021  Score=51.81  Aligned_cols=73  Identities=30%  Similarity=0.425  Sum_probs=58.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCC----CceEEEEE
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFD----GHRLRVEL   79 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~----g~~i~v~~   79 (299)
                      ..|||.||+.-+..+.|.+.|..||+|..-.+..  .++..+-++|.|...-.|.+|+..+....|.    +.+.-|..
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP  110 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEP  110 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCCh
Confidence            6799999999999999999999999997666543  4677889999999999999999987544333    44444444

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=96.57  E-value=0.013  Score=51.07  Aligned_cols=67  Identities=16%  Similarity=0.288  Sum_probs=58.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcC-CeeEEEeecCCCCC-ceEEEEecChHHHHHHHHhcCCCCCC
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYG-PIAHIDLKIPPRPP-GYAFVEFEEARDAEDAIRGRDGYDFD   71 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G-~v~~i~~~~~~~~~-g~afV~F~~~e~A~~A~~~l~~~~~~   71 (299)
                      +++.|.|-.+|..+|.-||..|...+- .|.+|.+..++.+. =.++|.|.+.++|......+||+.|.
T Consensus        73 ~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn  141 (493)
T KOG0804|consen   73 SSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFN  141 (493)
T ss_pred             CCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCC
Confidence            378999999999999999999888654 68999998777554 46889999999999999999999886

>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=96.35  E-value=0.014  Score=45.79  Aligned_cols=62  Identities=29%  Similarity=0.382  Sum_probs=46.6

Q ss_pred             CHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcC--CCCCCCceEEEEEccCC
Q 022301           19 REREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRD--GYDFDGHRLRVELAHGG   83 (299)
Q Consensus        19 t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~--~~~~~g~~i~v~~~~~~   83 (299)
                      ..+.|.++|..|+.+..+.+.   .+-+-..|.|.+.++|..|...|+  +..+.|..++|.|+...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L---~sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPL---KSFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEE---TTTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEc---CCCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            457899999999998888876   334578999999999999999999  89999999999998543

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=96.31  E-value=0.0024  Score=58.09  Aligned_cols=70  Identities=19%  Similarity=0.248  Sum_probs=63.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      +.-+|||+||...+..+-++.++..||-|..+...     + |||..|.....+..|+..|+...+.|..+.++.-
T Consensus        39 ~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~-----~-fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~d  108 (668)
T KOG2253|consen   39 PRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRD-----K-FGFCEFLKHIGDLRASRLLTELNIDDQKLIENVD  108 (668)
T ss_pred             CCceeEecchhhhhhHHHHHHHHhhCCcchhhhhh-----h-hcccchhhHHHHHHHHHHhcccCCCcchhhccch
Confidence            56789999999999999999999999999888775     2 9999999999999999999999999998888764

>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=96.27  E-value=0.15  Score=42.28  Aligned_cols=161  Identities=11%  Similarity=0.130  Sum_probs=96.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCC----------CCCceEEEEecChHHHHHHHHh----cCC--CC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP----------RPPGYAFVEFEEARDAEDAIRG----RDG--YD   69 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~----------~~~g~afV~F~~~e~A~~A~~~----l~~--~~   69 (299)
                      ++.|.+.||..+++--.+...|-+||+|+.|.+....          .....+.+-|-+.+.|......    |..  +.
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            6778899999999999999999999999999995433          3346789999999998765432    332  44


Q ss_pred             CCCceEEEEEccCCCCCCCC-CCCCCCC-----CCCC-CCCCCCCccEEEEeCCCCCC-CHHHHHHHHHh---cCC----
Q 022301           70 FDGHRLRVELAHGGRGRSSS-DRHSSHS-----SGRG-RGVSRRSEYRVLVTGLPSSA-SWQDLKDHMRR---AGD----  134 (299)
Q Consensus        70 ~~g~~i~v~~~~~~~~~~~~-~~~~~~~-----~~~~-~~~~~~~~~~l~v~nl~~~~-~~~~l~~~f~~---~G~----  134 (299)
                      +.-..|.|.|..-....... .....+-     .... .-........|.|.= ...+ .++-+.+.+..   -+.    
T Consensus        95 L~S~~L~lsFV~l~y~~~~~~~~~~~~~~~~~~~~L~~~i~~~gATRSl~IeF-~~~~~~~dl~~~kL~fL~~~~n~RYV  173 (309)
T PF10567_consen   95 LKSESLTLSFVSLNYQKKTDPNDEEADFSDYLVASLQYNIINRGATRSLAIEF-KDPVDKDDLIEKKLPFLKNSNNKRYV  173 (309)
T ss_pred             cCCcceeEEEEEEeccccccccccccchhhHHhhhhhheeecCCcceEEEEEe-cCccchhHHHHHhhhhhccCCCceEE
Confidence            66777888776532211111 0000000     0111 111222333444432 2333 33333333322   232    


Q ss_pred             eeEEEEEeCCC------CCEEEEEecChhhHHHHHHhcC
Q 022301          135 VCFSQVFRDGS------GTTGIVDYTNYDDMKHAIKKLD  167 (299)
Q Consensus       135 v~~~~~~~~~~------~~~~fv~f~~~~~a~~a~~~l~  167 (299)
                      ++.+.++....      ..||.+.|-+..-|.+.++.|.
T Consensus       174 lEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk  212 (309)
T PF10567_consen  174 LESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLK  212 (309)
T ss_pred             EEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHH
Confidence            34566654432      2399999999999999998876

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.

>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=96.25  E-value=0.022  Score=36.42  Aligned_cols=55  Identities=22%  Similarity=0.456  Sum_probs=44.1

Q ss_pred             CCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEE
Q 022301           17 DIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRV   77 (299)
Q Consensus        17 ~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v   77 (299)
                      .++-++|+..+..|+ ...|...    ..|| ||.|.+.++|..++...+|..+.+-.|.+
T Consensus        11 ~~~v~d~K~~Lr~y~-~~~I~~d----~tGf-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYR-WDRIRDD----RTGF-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCC-cceEEec----CCEE-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            478899999999996 3444443    2566 99999999999999999999888776654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=96.15  E-value=0.0022  Score=53.77  Aligned_cols=75  Identities=31%  Similarity=0.511  Sum_probs=58.9

Q ss_pred             CeEEEcCCCCCCCHHHHH---HHhhhcCCeeEEEeecCC------CCCceEEEEecChHHHHHHHHhcCCCCCCCceEEE
Q 022301            7 RTLYVGNLPGDIREREVE---DLFYKYGPIAHIDLKIPP------RPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRV   77 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~---~~F~~~G~v~~i~~~~~~------~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v   77 (299)
                      +-+||-+|+..+..+.+.   +.|.+||.|..|.+..+.      ....-+||+|...++|..||...+|..++|+.|+.
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            557888898887666554   589999999999995532      11234899999999999999999999999998776


Q ss_pred             EEcc
Q 022301           78 ELAH   81 (299)
Q Consensus        78 ~~~~   81 (299)
                      .+..
T Consensus       158 ~~gt  161 (327)
T KOG2068|consen  158 SLGT  161 (327)
T ss_pred             hhCC
Confidence            5543

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=95.91  E-value=0.0051  Score=55.32  Aligned_cols=67  Identities=13%  Similarity=0.191  Sum_probs=54.4

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcC-CeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeec
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAG-DVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFR  172 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G-~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~  172 (299)
                      .....+.|+|.||--.+|.-+|++++...| .|..++|-.-+  .-|||.|.+.++|.....+|||..|-
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDkIK--ShCyV~yss~eEA~atr~AlhnV~WP  507 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDKIK--SHCYVSYSSVEEAAATREALHNVQWP  507 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHHHHHHhh--cceeEecccHHHHHHHHHHHhccccC
Confidence            445678999999999999999999999654 55555332222  37999999999999999999999874

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=95.89  E-value=0.034  Score=46.04  Aligned_cols=71  Identities=17%  Similarity=0.253  Sum_probs=54.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCce-EEEEEcc
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHR-LRVELAH   81 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~-i~v~~~~   81 (299)
                      ...|.|-++|+... .-|..+|.+||+|+.....   ..-.+-+|.|.+..+|.+||. .||+.|+|.. |-|..+.
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~---~ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpCt  268 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP---SNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPCT  268 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeecC---CCCceEEEEecchhHHHHhhh-hcCeeeccceEEeeeecC
Confidence            45677778877644 4577899999999887765   224588999999999999999 8999998764 4565544

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=95.79  E-value=0.035  Score=46.00  Aligned_cols=64  Identities=16%  Similarity=0.215  Sum_probs=51.0

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCce
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAF  175 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  175 (299)
                      ..=+.|.++|+.. -..|..+|.+||.|+.....  .++.+-+|.|.+..+|++||. .||+.|+|..
T Consensus       197 D~WVTVfGFppg~-~s~vL~~F~~cG~Vvkhv~~--~ngNwMhirYssr~~A~KALs-kng~ii~g~v  260 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQ-VSIVLNLFSRCGEVVKHVTP--SNGNWMHIRYSSRTHAQKALS-KNGTIIDGDV  260 (350)
T ss_pred             cceEEEeccCccc-hhHHHHHHHhhCeeeeeecC--CCCceEEEEecchhHHHHhhh-hcCeeeccce
Confidence            3446677777654 35677899999999887665  455599999999999999999 8899999874

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=95.72  E-value=0.011  Score=49.79  Aligned_cols=69  Identities=13%  Similarity=0.173  Sum_probs=58.6

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcC--CeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCce
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAG--DVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAF  175 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G--~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  175 (299)
                      ..+++||+||-+-+|++||.+.+...|  .+..++++.+...    |||+|...+....++.++.|-.+.|.|..
T Consensus        79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~  153 (498)
T KOG4849|consen   79 RKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQS  153 (498)
T ss_pred             ceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCC
Confidence            457899999999999999999999887  5566666666433    59999999999999999999999999864

>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=95.69  E-value=0.16  Score=36.29  Aligned_cols=65  Identities=11%  Similarity=0.137  Sum_probs=49.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcC-CeeEEEEEeCCCCC--EEEEEecChhhHHHHHHhcCCCeecC
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAG-DVCFSQVFRDGSGT--TGIVDYTNYDDMKHAIKKLDDSEFRN  173 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G-~v~~~~~~~~~~~~--~~fv~f~~~~~a~~a~~~l~g~~~~g  173 (299)
                      ..+.+...|+.++.++|..+...+- .|..+.|+.+....  .+.+.|.+.++|..-...+||+.++.
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            3444455555566677776666654 56678888886554  78899999999999999999999875

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=95.49  E-value=0.01  Score=55.59  Aligned_cols=73  Identities=21%  Similarity=0.196  Sum_probs=59.2

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCC--CCceEEEEEccCCC
Q 022301            9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDF--DGHRLRVELAHGGR   84 (299)
Q Consensus         9 l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~--~g~~i~v~~~~~~~   84 (299)
                      .++.|.+-+.+---|..+|..||.|.+.+...   .-.+|.|+|...+.|..|+..|+|+.+  -|-+.+|.+++.-.
T Consensus       301 ~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr---~~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~  375 (1007)
T KOG4574|consen  301 QSLENNAVNLTSSSLATLCSDYGSVASAWTLR---DLNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLP  375 (1007)
T ss_pred             hhhhcccccchHHHHHHHHHhhcchhhheecc---cccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccccc
Confidence            34445555677788999999999999999863   246899999999999999999999776  48888998886443

>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=95.38  E-value=0.038  Score=43.18  Aligned_cols=79  Identities=15%  Similarity=0.247  Sum_probs=50.6

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHh-cCCe---eEEEEEeCCCC------CEEEEEecChhhHHHHHHhcCCCeecCce-
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRR-AGDV---CFSQVFRDGSG------TTGIVDYTNYDDMKHAIKKLDDSEFRNAF-  175 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~-~G~v---~~~~~~~~~~~------~~~fv~f~~~~~a~~a~~~l~g~~~~g~~-  175 (299)
                      ....|.|.+||+.+|++++.+.+.. ++..   ..+........      .-|||.|.+.+++..-...++|..+.+.. 
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            3468999999999999999997776 6655   23321122111      16999999999999999999998876543 


Q ss_pred             --eeEEEEeccc
Q 022301          176 --SRAYVRVREY  185 (299)
Q Consensus       176 --~~~~~~~~~~  185 (299)
                        ..+.+....+
T Consensus        86 ~~~~~~VE~Apy   97 (176)
T PF03467_consen   86 NEYPAVVEFAPY   97 (176)
T ss_dssp             -EEEEEEEE-SS
T ss_pred             CCcceeEEEcch
Confidence              3344444444

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=95.08  E-value=0.031  Score=37.91  Aligned_cols=72  Identities=24%  Similarity=0.359  Sum_probs=45.8

Q ss_pred             EEEEecChHHHHHHHHhcCC--CCCCCceEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHH
Q 022301           48 AFVEFEEARDAEDAIRGRDG--YDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDL  125 (299)
Q Consensus        48 afV~F~~~e~A~~A~~~l~~--~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l  125 (299)
                      |+|+|.+++-|+..+. +..  ..+.+..+.|............-          .-.......+|.|.|||..+.+++|
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 ALITFEEEGVAQRILK-KKKHPVPLEDCCVRVKVSPVTLGHLQKF----------QVFSGVSKRTVLVSGIPDVLDEEEL   69 (88)
T ss_pred             CEEEeCcHHHHHHHHh-CCEEEEEECCEEEEEEEEeEecCCceEE----------EEEEcccCCEEEEeCCCCCCChhhh
Confidence            7899999999999888 333  34556666665442211100000          0022345678999999999999988


Q ss_pred             HHHHH
Q 022301          126 KDHMR  130 (299)
Q Consensus       126 ~~~f~  130 (299)
                      ++.+.
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 [].

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=94.93  E-value=0.00097  Score=57.33  Aligned_cols=78  Identities=17%  Similarity=0.331  Sum_probs=65.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      ++.|.|.|||+...++-|..|+..||.|+.|....+.......-|+|.+.+.+..|++.|+|..|....++|.|-...
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            567899999999999999999999999999988443322334557899999999999999999999999999886533

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=94.80  E-value=0.15  Score=44.70  Aligned_cols=66  Identities=12%  Similarity=0.232  Sum_probs=58.6

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcC-CeeEEEEEeCCCCC--EEEEEecChhhHHHHHHhcCCCeecC
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAG-DVCFSQVFRDGSGT--TGIVDYTNYDDMKHAIKKLDDSEFRN  173 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G-~v~~~~~~~~~~~~--~~fv~f~~~~~a~~a~~~l~g~~~~g  173 (299)
                      ++.|+|-.+|..++-.||..++..+- .|..+.++++....  ++.|.|.+.++|..-.+.+||..++.
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            68999999999999999999998865 67789998876544  78999999999999999999999886

>KOG2888 consensus Putative RNA binding protein [General function prediction only]

Probab=94.58  E-value=0.022  Score=47.72  Aligned_cols=12  Identities=0%  Similarity=0.221  Sum_probs=5.6

Q ss_pred             HHHHHHHHHhcC
Q 022301          122 WQDLKDHMRRAG  133 (299)
Q Consensus       122 ~~~l~~~f~~~G  133 (299)
                      +.+|.+-|+++-
T Consensus       226 qkqId~~ie~r~  237 (453)
T KOG2888|consen  226 QKQIDEKIEERK  237 (453)
T ss_pred             HHHHHHHHHhcc
Confidence            344555555443

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=94.38  E-value=0.05  Score=41.41  Aligned_cols=113  Identities=17%  Similarity=0.117  Sum_probs=73.5

Q ss_pred             CCCHHHHHHHhhhc-CCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCCCCCCCCCCCCCC
Q 022301           17 DIREREVEDLFYKY-GPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSH   95 (299)
Q Consensus        17 ~~t~~~l~~~F~~~-G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~~~~~~~~~~~~~   95 (299)
                      .++...|.+.+... +....+.+..  ...++..++|.+++++..++. ...-.+.|..+.+....+.......      
T Consensus        28 ~~~~~~l~~~l~~~W~~~~~~~i~~--l~~~~fl~~F~~~~d~~~vl~-~~p~~~~~~~~~l~~W~~~~~~~~~------   98 (153)
T PF14111_consen   28 PISLSALEQELAKIWKLKGGVKIRD--LGDNLFLFQFESEEDRQRVLK-GGPWNFNGHFLILQRWSPDFNPSEV------   98 (153)
T ss_pred             CCCHHHHHHHHHHHhCCCCcEEEEE--eCCCeEEEEEEeccceeEEEe-cccccccccchhhhhhccccccccc------
Confidence            46667777666542 3333444422  125799999999999999998 5556677777777665432211110      


Q ss_pred             CCCCCCCCCCCCccEEEEeCCCCC-CCHHHHHHHHHhcCCeeEEEEEeCCC
Q 022301           96 SSGRGRGVSRRSEYRVLVTGLPSS-ASWQDLKDHMRRAGDVCFSQVFRDGS  145 (299)
Q Consensus        96 ~~~~~~~~~~~~~~~l~v~nl~~~-~~~~~l~~~f~~~G~v~~~~~~~~~~  145 (299)
                             .......=|.|.|||.. .+++.|..+...+|++..++......
T Consensus        99 -------~~~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~i~vD~~t~~~  142 (153)
T PF14111_consen   99 -------KFEHIPVWVRIYGLPLHLWSEEILKAIGSKIGEPIEVDENTLKR  142 (153)
T ss_pred             -------ceeccchhhhhccCCHHHhhhHHHHHHHHhcCCeEEEEcCCCCc
Confidence                   01112234677899998 68899999999999999888765543

>KOG0835 consensus Cyclin L [General function prediction only]

Probab=93.74  E-value=0.13  Score=43.24  Aligned_cols=18  Identities=22%  Similarity=0.180  Sum_probs=10.3

Q ss_pred             ceEEEEecChHHHHHHHH
Q 022301           46 GYAFVEFEEARDAEDAIR   63 (299)
Q Consensus        46 g~afV~F~~~e~A~~A~~   63 (299)
                      .-.||-|.-+.-|..++.
T Consensus       174 T~v~vry~pe~iACaciy  191 (367)
T KOG0835|consen  174 TDVFVRYSPESIACACIY  191 (367)
T ss_pred             cceeeecCHHHHHHHHHH
Confidence            345666665555555554

>KOG4019 consensus Calcineurin-mediated signaling pathway inhibitor DSCR1 [Signal transduction mechanisms; General function prediction only]

Probab=93.60  E-value=0.57  Score=36.12  Aligned_cols=77  Identities=19%  Similarity=0.276  Sum_probs=56.6

Q ss_pred             CCeEEEcCCCCCCC--HH---HHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCc-eEEEEE
Q 022301            6 SRTLYVGNLPGDIR--ER---EVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGH-RLRVEL   79 (299)
Q Consensus         6 ~~~l~V~nLp~~~t--~~---~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~-~i~v~~   79 (299)
                      .++|++.+|+..+-  .+   ....+|.+|.+..-..+.   .+.+..-|.|.+++.|..|...+++..|.|+ .+++.+
T Consensus        10 p~~~~~c~i~~~VF~~~~~k~~~~~lFrq~n~~~~fq~l---rsfrrvRi~f~~p~~a~~a~i~~~~~~f~~~~~~k~yf   86 (193)
T KOG4019|consen   10 PTAIIACDIHEEVFVNREDKALFENLFRQINEDATFQLL---RSFRRVRINFSNPEAAADARIKLHSTSFNGKNELKLYF   86 (193)
T ss_pred             cceeeeecccHHhhccHHHHHHHHhHHhhhCcchHHHHH---HhhceeEEeccChhHHHHHHHHhhhcccCCCceEEEEE
Confidence            35677888877632  22   345677777666555554   3456788999999999999999999999988 888888


Q ss_pred             ccCCCC
Q 022301           80 AHGGRG   85 (299)
Q Consensus        80 ~~~~~~   85 (299)
                      +.....
T Consensus        87 aQ~~~~   92 (193)
T KOG4019|consen   87 AQPGHP   92 (193)
T ss_pred             ccCCCc
Confidence            765543

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=93.52  E-value=0.04  Score=46.51  Aligned_cols=69  Identities=17%  Similarity=0.169  Sum_probs=54.4

Q ss_pred             ccEEEEeCCCCCCCHHHHH---HHHHhcCCeeEEEEEeCCC--C---C--EEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          108 EYRVLVTGLPSSASWQDLK---DHMRRAGDVCFSQVFRDGS--G---T--TGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~---~~f~~~G~v~~~~~~~~~~--~---~--~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..-+||.+|+..+..+.+.   +.|.+||.|..+.+..+..  .   +  -++|+|+..++|..||...+|..++|+.+
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~l  155 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRAL  155 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhh
Confidence            3567788888776544443   4889999999998888662  1   1  68999999999999999999999999763

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=93.48  E-value=0.3  Score=36.09  Aligned_cols=62  Identities=8%  Similarity=0.135  Sum_probs=45.4

Q ss_pred             CCCccEEEEeCCCCCC----CHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCC
Q 022301          105 RRSEYRVLVTGLPSSA----SWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDS  169 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~----~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~  169 (299)
                      .++..+|.|.=|..++    +...+.+.+..||+|..|...-..   .|.|.|.+...|-.|+.+++..
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGrq---savVvF~d~~SAC~Av~Af~s~  148 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGRQ---SAVVVFKDITSACKAVSAFQSR  148 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCCc---eEEEEehhhHHHHHHHHhhcCC
Confidence            3455678886655554    334455566779999988765332   7999999999999999998864

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=93.46  E-value=0.097  Score=48.09  Aligned_cols=68  Identities=13%  Similarity=0.033  Sum_probs=60.0

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      +.++..++||+|+.+.+.++-++.+...+|-|..+....     |||+.|..+.-+..|+..++-..++|..+
T Consensus        36 ~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~-----fgf~~f~~~~~~~ra~r~~t~~~~~~~kl  103 (668)
T KOG2253|consen   36 PLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK-----FGFCEFLKHIGDLRASRLLTELNIDDQKL  103 (668)
T ss_pred             CCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh-----hcccchhhHHHHHHHHHHhcccCCCcchh
Confidence            445678999999999999999999999999998776654     99999999999999999999988888754

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.46  E-value=0.46  Score=43.20  Aligned_cols=78  Identities=22%  Similarity=0.383  Sum_probs=61.6

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHhhhc----CCeeEEEeecC-------------CC---------------------
Q 022301            3 SRASRTLYVGNLPGD-IREREVEDLFYKY----GPIAHIDLKIP-------------PR---------------------   43 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~-~t~~~l~~~F~~~----G~v~~i~~~~~-------------~~---------------------   43 (299)
                      ...++.|-|-||.+. |..++|..+|..|    |.|..|.|.+.             |.                     
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            467899999999997 9999999999866    57889988331             11                     


Q ss_pred             ----------------CCceEEEEecChHHHHHHHHhcCCCCCCC--ceEEEEEc
Q 022301           44 ----------------PPGYAFVEFEEARDAEDAIRGRDGYDFDG--HRLRVELA   80 (299)
Q Consensus        44 ----------------~~g~afV~F~~~e~A~~A~~~l~~~~~~g--~~i~v~~~   80 (299)
                                      .--||.|+|.+.+.|......++|..|..  ..|-+.|.
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFI  305 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFI  305 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeeec
Confidence                            01389999999999999999999999974  45555554

>KOG0835 consensus Cyclin L [General function prediction only]

Probab=93.04  E-value=0.31  Score=41.13  Aligned_cols=10  Identities=0%  Similarity=0.192  Sum_probs=4.5

Q ss_pred             CCHHHHHHHH
Q 022301          120 ASWQDLKDHM  129 (299)
Q Consensus       120 ~~~~~l~~~f  129 (299)
                      +++++|.+++
T Consensus       213 ~~k~eid~ic  222 (367)
T KOG0835|consen  213 TTKREIDEIC  222 (367)
T ss_pred             CcHHHHHHHH
Confidence            3444444443

>KOG2888 consensus Putative RNA binding protein [General function prediction only]

Probab=92.80  E-value=0.072  Score=44.72  Aligned_cols=11  Identities=27%  Similarity=0.033  Sum_probs=4.6

Q ss_pred             HHHHHHHHHhc
Q 022301          122 WQDLKDHMRRA  132 (299)
Q Consensus       122 ~~~l~~~f~~~  132 (299)
                      ..+|...|..|
T Consensus       171 p~dLw~WyEpy  181 (453)
T KOG2888|consen  171 PADLWDWYEPY  181 (453)
T ss_pred             hhHHHHHhhhh
Confidence            34444444443

>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=92.77  E-value=0.63  Score=36.59  Aligned_cols=58  Identities=12%  Similarity=0.112  Sum_probs=44.1

Q ss_pred             CHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcC--CCeecCceeeEEE
Q 022301          121 SWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLD--DSEFRNAFSRAYV  180 (299)
Q Consensus       121 ~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~--g~~~~g~~~~~~~  180 (299)
                      ..+.|.++|..|+.+..+.++..-.  -..|.|.+.+.|..|...|+  +..+.|..+..+.
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sFr--Ri~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf   67 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSFR--RIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYF   67 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTTT--EEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE-
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCCC--EEEEEeCCHHHHHHHHHHhcccccccCCCceEEEE
Confidence            4688999999999988877766533  57899999999999999999  9999998655443

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=90.90  E-value=0.18  Score=44.57  Aligned_cols=65  Identities=17%  Similarity=0.226  Sum_probs=50.6

Q ss_pred             EEEEeCCCCCC-CHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          110 RVLVTGLPSSA-SWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       110 ~l~v~nl~~~~-~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      .|.+.-.|..+ +.++|..+|.+||+|..|++-....  -|.|+|.+..+|-.|.. .++..|+++.+.
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 PLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSSL--HAVVTFKTRAEAGEAYA-SHGAVLNNRFIK  439 (526)
T ss_pred             hhhhhccCCCCchHhhhhhhhhhcCccccccccCchh--hheeeeeccccccchhc-cccceecCceeE
Confidence            34444445553 6799999999999999998876633  68999999999977765 889999998543

>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=88.10  E-value=0.38  Score=34.71  Aligned_cols=56  Identities=23%  Similarity=0.408  Sum_probs=30.3

Q ss_pred             eEEEcCCCCC---------CCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHH-HHHHH
Q 022301            8 TLYVGNLPGD---------IREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA-EDAIR   63 (299)
Q Consensus         8 ~l~V~nLp~~---------~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A-~~A~~   63 (299)
                      ++.|-|++..         ++.++|.+.|..|.++.-..+.......|+++|+|...-.. ..|+.
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            4566688553         46678999999999887555543445678999999865443 34544

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.

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=87.81  E-value=0.27  Score=46.62  Aligned_cols=56  Identities=16%  Similarity=0.200  Sum_probs=48.0

Q ss_pred             CCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeec
Q 022301          115 GLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFR  172 (299)
Q Consensus       115 nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~  172 (299)
                      |.+-..+-.-|..+|..||.|..++...+-+  .|.|+|...+.|..|++.|+|+++-
T Consensus       305 nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N--~alvs~~s~~sai~a~dAl~gkevs  360 (1007)
T KOG4574|consen  305 NNAVNLTSSSLATLCSDYGSVASAWTLRDLN--MALVSFSSVESAILALDALQGKEVS  360 (1007)
T ss_pred             cccccchHHHHHHHHHhhcchhhheeccccc--chhhhhHHHHHHHHhhhhhcCCccc
Confidence            3344556778999999999999999877755  8999999999999999999999864

>KOG4483 consensus Uncharacterized conserved protein [Function unknown]

Probab=86.59  E-value=1.3  Score=38.44  Aligned_cols=59  Identities=15%  Similarity=0.193  Sum_probs=45.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCe-eEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPI-AHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYD   69 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v-~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~   69 (299)
                      ..+|-|.++|.....+||..+|+.|+.- -.|++. +   -..||..|.....|..||. |...+
T Consensus       391 pHVlEIydfp~efkteDll~~f~~yq~kgfdIkWv-D---dthalaVFss~~~AaeaLt-~kh~~  450 (528)
T KOG4483|consen  391 PHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWV-D---DTHALAVFSSVNRAAEALT-LKHDW  450 (528)
T ss_pred             cceeEeccCchhhccHHHHHHHHHhhcCCceeEEe-e---cceeEEeecchHHHHHHhh-ccCce
Confidence            4688999999999999999999999742 222222 1   2389999999999999999 54333

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=86.02  E-value=6.9  Score=35.99  Aligned_cols=72  Identities=14%  Similarity=0.205  Sum_probs=57.9

Q ss_pred             CCCccEEEEeCCCCC-CCHHHHHHHHHhc----CCeeEEEEEeCC-------------C-------------------C-
Q 022301          105 RRSEYRVLVTGLPSS-ASWQDLKDHMRRA----GDVCFSQVFRDG-------------S-------------------G-  146 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~-~~~~~l~~~f~~~----G~v~~~~~~~~~-------------~-------------------~-  146 (299)
                      ......|.|.|+.++ +..++|.-+|..|    |.|..|.|....             +                   . 
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            345678999999997 7899999988876    588888885431             1                   0 


Q ss_pred             ----------------C--EEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          147 ----------------T--TGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       147 ----------------~--~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                                      +  ||.|+|.+.+.|......++|.++.....
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~  298 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSAN  298 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccc
Confidence                            1  79999999999999999999999987544

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=84.82  E-value=1.5  Score=36.30  Aligned_cols=48  Identities=23%  Similarity=0.326  Sum_probs=36.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCe-eEEEeecCCCCCceEEEEecChH
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPI-AHIDLKIPPRPPGYAFVEFEEAR   56 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v-~~i~~~~~~~~~g~afV~F~~~e   56 (299)
                      .+-|+|+||+.++.-.||+..+...|-+ ..|.+.   .+.|-||+.|.+..
T Consensus       330 ~~di~~~nl~rd~rv~dlk~~lr~~~~~pm~iswk---g~~~k~flh~~~~~  378 (396)
T KOG4410|consen  330 KTDIKLTNLSRDIRVKDLKSELRKRECTPMSISWK---GHFGKCFLHFGNRK  378 (396)
T ss_pred             ccceeeccCccccchHHHHHHHHhcCCCceeEeee---cCCcceeEecCCcc
Confidence            3559999999999999999999887643 333333   34678999998754

>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=84.62  E-value=6.4  Score=25.71  Aligned_cols=56  Identities=9%  Similarity=0.172  Sum_probs=33.9

Q ss_pred             CCCCCHHHHHHHHHhcCC-----eeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          117 PSSASWQDLKDHMRRAGD-----VCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       117 ~~~~~~~~l~~~f~~~G~-----v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      -..++..+|..++...+.     |-.+.+..+    |+||+-... .|..++..|++..+.|+.+.
T Consensus        10 ~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~----~S~vev~~~-~a~~v~~~l~~~~~~gk~v~   70 (74)
T PF03880_consen   10 KDGLTPRDIVGAICNEAGIPGRDIGRIDIFDN----FSFVEVPEE-VAEKVLEALNGKKIKGKKVR   70 (74)
T ss_dssp             GGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS-----EEEEE-TT--HHHHHHHHTT--SSS----
T ss_pred             ccCCCHHHHHHHHHhccCCCHHhEEEEEEeee----EEEEEECHH-HHHHHHHHhcCCCCCCeeEE
Confidence            345788899998888754     445666655    888887654 78889999999999998543

; PDB: 2G0C_A 3MOJ_B.

>KOG4008 consensus rRNA processing protein RRP7 [RNA processing and modification]

Probab=84.40  E-value=0.55  Score=37.71  Aligned_cols=36  Identities=14%  Similarity=0.253  Sum_probs=31.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEee
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLK   39 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~   39 (299)
                      ....+||+-|||..+|++.|..+.+++|-++.+.+.
T Consensus        38 ~eKd~lfl~Nvp~~~tee~lkr~vsqlg~vq~~~y~   73 (261)
T KOG4008|consen   38 NEKDCLFLVNVPLLSTEEHLKRFVSQLGHVQELLYN   73 (261)
T ss_pred             ccccceeeecccccccHHHHHHHHHHhhhhhheecc
Confidence            567899999999999999999999999977777664

>TIGR03636 L23_arch archaeal ribosomal protein L23

Probab=83.55  E-value=5.9  Score=26.20  Aligned_cols=57  Identities=16%  Similarity=0.215  Sum_probs=41.1

Q ss_pred             EEEcCCCCCCCHHHHHHHhhh-cC-CeeEEEeecCCCCCceEEEEecChHHHHHHHHhc
Q 022301            9 LYVGNLPGDIREREVEDLFYK-YG-PIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGR   65 (299)
Q Consensus         9 l~V~nLp~~~t~~~l~~~F~~-~G-~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l   65 (299)
                      -|+-.++..++..+|++.++. || +|..|.........--|||.+...+.|...-..+
T Consensus        16 ~y~F~V~~~anK~eIK~avE~lf~VkV~~Vnt~~~~~~~KKA~VtL~~g~~a~~va~k~   74 (77)
T TIGR03636        16 KLTFIVDRKATKGDIKRAVEKLFDVKVEKVNTLITPRGEKKAYVKLAEEYAAEEIASRL   74 (77)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcCCCceEEEEEECCCCcHHHHHHhh
Confidence            344578899999999998886 44 5666666444444568999999888887765433

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.

>KOG1295 consensus Nonsense-mediated decay protein Upf3 [RNA processing and modification]

Probab=83.52  E-value=1.2  Score=38.62  Aligned_cols=67  Identities=21%  Similarity=0.325  Sum_probs=49.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCC-eeEEEeecC-----CCCCceEEEEecChHHHHHHHHhcCCCCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGP-IAHIDLKIP-----PRPPGYAFVEFEEARDAEDAIRGRDGYDF   70 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~-v~~i~~~~~-----~~~~g~afV~F~~~e~A~~A~~~l~~~~~   70 (299)
                      ...+.|.|.+||+.+++++|.+-...|-. |....+...     ..-.+.|||.|..+++.......++|..|
T Consensus         5 ~~~~Kvv~rrlpp~l~~~~~~eqi~p~~~~v~~~~F~~a~~s~~~~~ysrayinFk~~~dv~ef~~~f~g~if   77 (376)
T KOG1295|consen    5 EAKVKVVVRRLPPKLTEEQLLEQINPFPEHVNWEFFAKADESLRNHKYSRAYINFKNPEDVEEFRRRFDGYIF   77 (376)
T ss_pred             ccceeeeeecCCCcccHHHHhhhcCCCccccchheeccccccchhhhhhhhhhccccHHHHHHHHhhCCceEE
Confidence            34578899999999999999988887653 333333211     12347899999999998888888887544

>PRK14548 50S ribosomal protein L23P; Provisional

Probab=82.22  E-value=6.6  Score=26.49  Aligned_cols=56  Identities=14%  Similarity=0.233  Sum_probs=41.5

Q ss_pred             EEcCCCCCCCHHHHHHHhhh-cC-CeeEEEeecCCCCCceEEEEecChHHHHHHHHhc
Q 022301           10 YVGNLPGDIREREVEDLFYK-YG-PIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGR   65 (299)
Q Consensus        10 ~V~nLp~~~t~~~l~~~F~~-~G-~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l   65 (299)
                      |+-.++..++..+|++.++. || +|..|..........-|||.+...+.|......+
T Consensus        24 y~F~V~~~anK~eIK~AvE~lf~VkV~~VnT~~~~~~~KKA~V~L~~g~~A~~va~ki   81 (84)
T PRK14548         24 LTFIVDRRATKPDIKRAVEELFDVKVEKVNTLITPKGEKKAYVKLAEEYDAEEIASRL   81 (84)
T ss_pred             EEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcCCCcEEEEEEeCCCCcHHHHHHhh
Confidence            33367889999999999986 45 6677776544445568999999998888775533

>KOG2295 consensus C2H2 Zn-finger protein [General function prediction only]

Probab=81.43  E-value=0.2  Score=45.09  Aligned_cols=67  Identities=18%  Similarity=0.212  Sum_probs=52.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCC
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFD   71 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~   71 (299)
                      -+|+|||.||+++++-.+|..++..+--+..+.+...   .....++.|.|.-.-....|+.+||+..+.
T Consensus       230 ke~sll~rni~Pnis~aeIe~~ck~i~~~lrfals~~~aek~~~r~lwv~fk~~~ni~~a~~aLn~irl~  299 (648)
T KOG2295|consen  230 KECSLLVRNILPNISVAEIENLCKGIPGFLRFALSTINAEKNFERRLWVTFKRGTNIKEACWALNGIRLR  299 (648)
T ss_pred             HHHHHHHhccCCcccHHHHHHHhccCchheeeeccCchHHHHHHHHhhHhhccccchHHHHHHhhhcccc
Confidence            3689999999999999999999998877777766221   233467889998777777777778886664

>PRK14548 50S ribosomal protein L23P; Provisional

Probab=80.94  E-value=13  Score=25.00  Aligned_cols=56  Identities=16%  Similarity=0.115  Sum_probs=42.5

Q ss_pred             EEEeCCCCCCCHHHHHHHHHh-cC-CeeEEEEEeCCCC-CEEEEEecChhhHHHHHHhc
Q 022301          111 VLVTGLPSSASWQDLKDHMRR-AG-DVCFSQVFRDGSG-TTGIVDYTNYDDMKHAIKKL  166 (299)
Q Consensus       111 l~v~nl~~~~~~~~l~~~f~~-~G-~v~~~~~~~~~~~-~~~fv~f~~~~~a~~a~~~l  166 (299)
                      -|+..++..++..+|++.++. || +|..|.....+.+ .-|||.+...+.|.+....+
T Consensus        23 ~y~F~V~~~anK~eIK~AvE~lf~VkV~~VnT~~~~~~~KKA~V~L~~g~~A~~va~ki   81 (84)
T PRK14548         23 KLTFIVDRRATKPDIKRAVEELFDVKVEKVNTLITPKGEKKAYVKLAEEYDAEEIASRL   81 (84)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcCCCcEEEEEEeCCCCcHHHHHHhh
Confidence            444556778899999999988 56 6777777666544 37999999999998876654

>TIGR02542 B_forsyth_147 Bacteroides forsythus 147-residue repeat

Probab=80.24  E-value=7.2  Score=27.72  Aligned_cols=112  Identities=22%  Similarity=0.306  Sum_probs=58.4

Q ss_pred             CCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCC--CCCCceEEEEEccCCCCCCCCC
Q 022301           13 NLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY--DFDGHRLRVELAHGGRGRSSSD   90 (299)
Q Consensus        13 nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~--~~~g~~i~v~~~~~~~~~~~~~   90 (299)
                      -||+.++.  |-++|+.=|+|.+|....          +|.+    ..|+-.++|.  .++|. |.+--.....    .-
T Consensus        10 VlPPYTnK--LSDYfeSPGKI~svItvt----------qypd----ndal~~~~G~lE~vDg~-i~IGs~q~~~----sV   68 (145)
T TIGR02542        10 VLPPYTNK--LSDYFESPGKIQSVITVT----------QYPD----NDALLYVHGTLEQVDGN-IRIGSGQTPA----SV   68 (145)
T ss_pred             ecCCccch--hhHHhcCCCceEEEEEEe----------ccCC----chhhheeeeehhhccCc-EEEccCCCcc----cE
Confidence            37887664  889999999999886631          1221    1234445553  34444 4442211000    00


Q ss_pred             CCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHh---cCCeeEEEEEeCC--CCC--EEEEEecChh
Q 022301           91 RHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRR---AGDVCFSQVFRDG--SGT--TGIVDYTNYD  157 (299)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~---~G~v~~~~~~~~~--~~~--~~fv~f~~~~  157 (299)
                      ..          ...+.++++.  --|+.+|-.+|+++|.+   |..|..-++..+.  .+.  .||.-|....
T Consensus        69 ~i----------~gTPsgnnv~--F~PYTlT~~e~r~iF~Epm~YQGITReQV~rdGLP~GsYRiCFrL~~~~~  130 (145)
T TIGR02542        69 RI----------QGTPSGNNVI--FPPYTLTYNELRQIFREPMVYQGITREQVQRDGLPEGSYRICFRLFNATQ  130 (145)
T ss_pred             EE----------ecCCCCCcee--cCceeeeHHHHHHHHhhhhhhccccHHHHhhcCCCCCceEEEEEEeccch
Confidence            00          0011112221  23777899999999987   4445444444442  222  6888886653

The longest predicted protein in Bacteroides forsythus ATCC 43037 is over 3000 residues long and lacks homology to other known proteins. Immediately after the signal sequence are four tandem repeats, approximately 147 residues long. This model describes that repeat. This model describes that repeat.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	299
1x4a_A	109	Solution Structure Of Rrm Domain In Splicing Factor		5e-20
3beg_B	115	Crystal Structure Of Sr Protein Kinase 1 Complexed		1e-18
2o3d_A	113	Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (		1e-18
1x4c_A	108	Solution Structure Of Rrm Domain In Splicing Factor		2e-18
1wg4_A	98	Solution Structure Of Rrm Domain In Protein Bab3198		1e-17
2hvz_A	101	Solution Structure Of The Rrm Domain Of Sr Rich Fac		2e-11
2i38_A	150	Solution Structure Of The Rrm Of Srp20 Length = 150		2e-11
2i2y_A	150	Solution Structure Of The Rrm Of Srp20 Bound To The		3e-11
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		3e-08
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		3e-08
2dgt_A	92	Solution Structure Of The Second Rna Binding Domain		5e-08
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		8e-07
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		8e-07
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		9e-07
3lqv_A	115	Branch Recognition By Sf3b14 Length = 115		1e-06
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		1e-06
2dnq_A	90	Solution Structure Of Rna Binding Domain 1 In Rna-B		3e-06
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		3e-06
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		4e-06
2f9d_A	125	2.5 Angstrom Resolution Structure Of The Spliceosom		4e-06
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		5e-06
2fho_B	87	Nmr Solution Structure Of The Human Spliceosomal Pr		7e-06
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		8e-06
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		9e-06
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		1e-05
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		2e-05
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		2e-05
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		2e-05
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		2e-05
4a8x_A	88	Structure Of The Core Asap Complex Length = 88		2e-05
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		2e-05
2jvo_A	108	Segmental Isotope Labeling Of Npl3 Length = 108		2e-05
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		3e-05
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		3e-05
2f9j_A	125	3.0 Angstrom Resolution Structure Of A Y22m Mutant		3e-05
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		3e-05
2osq_A	74	Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein Length		4e-05
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		4e-05
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		4e-05
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		4e-05
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		5e-05
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		5e-05
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		7e-05
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		7e-05
2jvr_A	111	Segmental Isotope Labeling Of Npl3p Length = 111		8e-05
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		9e-05
1wf1_A	110	Solution Structure Of Rrm Domain In Rna-Binding Pro		1e-04
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		1e-04
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		1e-04
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		1e-04
2cpj_A	99	Solution Structure Of The N-Terminal Rna Recognitio		1e-04
1m5k_C	100	Crystal Structure Of A Hairpin Ribozyme In The Cata		1e-04
1aud_A	101	U1a-Utrrna, Nmr, 31 Structures Length = 101		1e-04
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		2e-04
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		2e-04
1fht_A	116	Rna-Binding Domain Of The U1a Spliceosomal Protein		2e-04
1sxl_A	97	Resonance Assignments And Solution Structure Of The		2e-04
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		2e-04
2cqi_A	103	Solution Structure Of The Rna Binding Domain Of Nuc		3e-04
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		4e-04
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		6e-04
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		6e-04
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		6e-04
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		7e-04
1u6b_A	98	Crystal Structure Of A Self-Splicing Group I Intron		7e-04
3k0j_A	96	Crystal Structure Of The E. Coli Thim Riboswitch In		7e-04
1oia_A	95	U1a Rnp Domain 1-95 Length = 95		7e-04
1urn_A	97	U1a MutantRNA COMPLEX + GLYCEROL Length = 97		7e-04
3bo2_A	95	A Relaxed Active Site Following Exon Ligation By A		8e-04
2nz4_A	94	Structural Investigation Of The Glms Ribozyme Bound		8e-04
3iwn_C	91	Co-Crystal Structure Of A Bacterial C-Di-Gmp Ribosw		8e-04
2dnp_A	90	Solution Structure Of Rna Binding Domain 2 In Rna-B		9e-04
2osr_A	87	Nmr Structure Of Rrm-2 Of Yeast Npl3 Protein Length		9e-04

>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2 Length = 109

Iteration: 1
 Score = 94.7 bits (234), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 47/71 (66%), Positives = 57/71 (80%)
Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          +YVGNLP DIR +++ED+FYKYG I  IDLK     P +AFVEFE+ RDAEDA+ GRDGY
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 84
Query: 69 DFDGHRLRVEL 79
          D+DG+RLRVE 
Sbjct: 85 DYDGYRLRVEF 95

>pdb|3BEG|B Chain B, Crystal Structure Of Sr Protein Kinase 1 Complexed To Its Substrate AsfSF2 Length = 115

Iteration: 1
 Score = 90.5 bits (223), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 42/77 (54%), Positives = 60/77 (77%), Gaps = 4/77 (5%)
Query: 108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLD 167
           E RV+V+GLP S SWQDLKDHMR AGDVC++ V+RDG   TG+V++   +DM +A++KLD
Sbjct: 16  ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG---TGVVEFVRKEDMTYAVRKLD 72
Query: 168 DSEFRN-AFSRAYVRVR 183
           +++FR+     AY+RV+
Sbjct: 73  NTKFRSHEGETAYIRVK 89

>pdb|2O3D|A Chain A, Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (RRM2) Length = 113

Iteration: 1
 Score = 90.1 bits (222), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 42/77 (54%), Positives = 60/77 (77%), Gaps = 4/77 (5%)
Query: 108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLD 167
           E RV+V+GLP S SWQDLKDHMR AGDVC++ V+RDG   TG+V++   +DM +A++KLD
Sbjct: 15  ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG---TGVVEFVRKEDMTYAVRKLD 71
Query: 168 DSEFRN-AFSRAYVRVR 183
           +++FR+     AY+RV+
Sbjct: 72  NTKFRSHEGETAYIRVK 88

>pdb|1X4C|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 2 Length = 108

Iteration: 1
 Score = 89.7 bits (221), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 42/77 (54%), Positives = 60/77 (77%), Gaps = 4/77 (5%)
Query: 108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLD 167
           E RV+V+GLP S SWQDLKDHMR AGDVC++ V+RDG   TG+V++   +DM +A++KLD
Sbjct: 15  ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG---TGVVEFVRKEDMTYAVRKLD 71
Query: 168 DSEFRN-AFSRAYVRVR 183
           +++FR+     AY+RV+
Sbjct: 72  NTKFRSHEGETAYIRVK 88

>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986 Length = 98

Iteration: 1
 Score = 86.7 bits (213), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 41/76 (53%), Positives = 59/76 (77%), Gaps = 4/76 (5%)
Query: 108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLD 167
           ++RVLV+GLP S SWQDLKDHMR AGDVC++ V +DG    G+V+Y   +DM++A++KLD
Sbjct: 15  DFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG---MGMVEYLRKEDMEYALRKLD 71
Query: 168 DSEFRN-AFSRAYVRV 182
           D++FR+     +Y+RV
Sbjct: 72  DTKFRSHEGETSYIRV 87

>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8 Length = 101

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 37/72 (51%), Positives = 47/72 (65%), Gaps = 2/72 (2%)
Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          +YVGNL     + E+E  F  YGP+  +   I   PPG+AFVEFE+ RDAEDA+RG DG 
Sbjct: 3  VYVGNLGTGAGKGELERAFSYYGPLRTV--WIARNPPGFAFVEFEDPRDAEDAVRGLDGK 60
Query: 69 DFDGHRLRVELA 80
             G R+RVEL+
Sbjct: 61 VICGSRVRVELS 72

>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20 Length = 150

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/72 (47%), Positives = 46/72 (63%), Gaps = 2/72 (2%)
Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
           +YVGNL  +  + E+E  F  YGP+  +   +   PPG+AFVEFE+ RDA DA+R  DG 
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSV--WVARNPPGFAFVEFEDPRDAADAVRDLDGR 133
Query: 69  DFDGHRLRVELA 80
              G R+RVEL+
Sbjct: 134 TLCGCRVRVELS 145

>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna Cauc Length = 150

Iteration: 1
 Score = 65.9 bits (159), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 34/72 (47%), Positives = 46/72 (63%), Gaps = 2/72 (2%)
Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
           +YVGNL  +  + E+E  F  YGP+  +   +   PPG+AFVEFE+ RDA DA+R  DG 
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSV--WVARNPPGFAFVEFEDPRDAADAVRELDGR 133
Query: 69  DFDGHRLRVELA 80
              G R+RVEL+
Sbjct: 134 TLCGCRVRVELS 145

>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 = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 48/80 (60%), Gaps = 3/80 (3%)
Query: 4  RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAED 60
          R+ R+++VGN+P +  E +++D+F + GP+    L   +   +P GY F E+++   A  
Sbjct: 6  RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65
Query: 61 AIRGRDGYDFDGHRLRVELA 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 = 55.5 bits (132), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 28/75 (37%), Positives = 43/75 (57%), Gaps = 3/75 (4%)
Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
          L+VG L  D  E+ +E +F KYG I+ + +   +   R  G+ FV FE   DA+DA+   
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 66 DGYDFDGHRLRVELA 80
          +G   DG ++RV+ A
Sbjct: 75 NGKSVDGRQIRVDQA 89

>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In Rna- Binding Protein 30 Length = 92

Iteration: 1
 Score = 55.1 bits (131), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 30/77 (38%), Positives = 43/77 (55%), Gaps = 5/77 (6%)
Query: 4  RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIR 63
          +AS  L+VGN+      +E+   F +YGP+   D+        YAFV  E A DA +AIR
Sbjct: 8  KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-----KDYAFVHMERAEDAVEAIR 62
Query: 64 GRDGYDFDGHRLRVELA 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 = 8e-07,   Method: Composition-based stats.
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAI 62
          SR +Y+G++P D  E ++ DL    GP+ ++ +   P   R  GYAF+EF +   +  A+
Sbjct: 4  SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 63
Query: 63 RGRDGYDFDGHRLR 76
          R  +GY      L+
Sbjct: 64 RNLNGYQLGSRFLK 77

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 50.8 bits (120), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAI 62
          SR +Y+G++P D  E ++ DL    GP+ ++ +   P   R  GYAF+EF +   +  A+
Sbjct: 2  SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 63 RGRDGYDFDGHRLR 76
          R  +GY      L+
Sbjct: 62 RNLNGYQLGSRFLK 75

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 50.8 bits (120), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAI 62
          SR +Y+G++P D  E ++ DL    GP+ ++ +   P   R  GYAF+EF +   +  A+
Sbjct: 3  SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 62
Query: 63 RGRDGYDFDGHRLR 76
          R  +GY      L+
Sbjct: 63 RNLNGYQLGSRFLK 76

>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14 Length = 115

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 41/77 (53%)
Query: 1  MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
          +    +R LY+ NLP  I   E+ D+F KYGPI  I +   P   G A+V +E+  DA++
Sbjct: 3  LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKN 62
Query: 61 AIRGRDGYDFDGHRLRV 77
          A+    G++     L V
Sbjct: 63 AVDHLSGFNVSNRYLVV 79

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 3/77 (3%)
Query: 7   RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIR 63
           R L V  +P  + E ++  LF +YGPI  + +       +  GY FV+F+    A+ AI 
Sbjct: 43  RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
Query: 64  GRDGYDFDGHRLRVELA 80
           G +G++    RL+V LA
Sbjct: 103 GLNGFNILNKRLKVALA 119

>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding Protein 30 Length = 90

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 26/70 (37%), Positives = 36/70 (51%), Gaps = 5/70 (7%)
Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          L++GNLP +  E+E+  LF +YG +   D+        Y FV  E+   AEDAIR    Y
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDII-----KNYGFVHIEDKTAAEDAIRNLHHY 65
Query: 69 DFDGHRLRVE 78
             G  + VE
Sbjct: 66 KLHGVNINVE 75

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 2/76 (2%)
Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRG 64
          R LYVGNL   I E  ++  F   GPIA+I + I    +   YAFVE+ ++ DA  A++ 
Sbjct: 1  RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60
Query: 65 RDGYDFDGHRLRVELA 80
           +G   + + +++  A
Sbjct: 61 LNGKQIENNIVKINWA 76

>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 = 48.5 bits (114), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/64 (39%), Positives = 40/64 (62%), Gaps = 3/64 (4%)
Query: 20 EREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLR 76
          ER++ ++F KYGPIA + +   +   R  G+AFV FE   DA++A    +G + DG R+R
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 88
Query: 77 VELA 80
          V+ +
Sbjct: 89 VDFS 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 = 48.5 bits (114), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 40/77 (51%)
Query: 1  MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
          +    +R LY+ NLP  I   E+ D+F KYGPI  I +   P   G A+V +E+  DA++
Sbjct: 13 LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKN 72
Query: 61 AIRGRDGYDFDGHRLRV 77
          A     G++     L V
Sbjct: 73 ACDHLSGFNVCNRYLVV 89

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 48.1 bits (113), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 25/64 (39%), Positives = 40/64 (62%), Gaps = 3/64 (4%)
Query: 20  EREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLR 76
           ER++ ++F KYGPIA + +   +   R  G+AFV FE   DA++A    +G + DG R+R
Sbjct: 60  ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 119
Query: 77  VELA 80
           V+ +
Sbjct: 120 VDFS 123

>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein Complex P14-Sf3b155 Length = 87

Iteration: 1
 Score = 47.8 bits (112), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 25/69 (36%), Positives = 38/69 (55%)
Query: 1  MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
          +    +R LY+ NLP  I   E+ D+F KYGPI  I +   P   G A+V +E+  DA++
Sbjct: 7  LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKN 66
Query: 61 AIRGRDGYD 69
          A     G++
Sbjct: 67 ACDHLSGFN 75

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 47.8 bits (112), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 25/64 (39%), Positives = 40/64 (62%), Gaps = 3/64 (4%)
Query: 20 EREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLR 76
          ER++ ++F KYGPIA + +   +   R  G+AFV FE   DA++A    +G + DG R+R
Sbjct: 26 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 85
Query: 77 VELA 80
          V+ +
Sbjct: 86 VDFS 89

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 47.4 bits (111), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 38/61 (62%), Gaps = 3/61 (4%)
Query: 20 EREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLR 76
          ER++ ++F KYGPIA + +   +   R  G+AFV FE   DA++A    +G + DG R+R
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 88
Query: 77 V 77
          V
Sbjct: 89 V 89

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 43/83 (51%), Gaps = 7/83 (8%)
Query: 3   SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEARD 57
           +   R LYVG L  ++ ++ +   F  +G I   D++IP      +  G+AFVEFE A D
Sbjct: 60  ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDIT--DIQIPLDYETEKHRGFAFVEFELAED 117
Query: 58  AEDAIRGRDGYDFDGHRLRVELA 80
           A  AI   +  +  G  +RV LA
Sbjct: 118 AAAAIDNMNESELFGRTIRVNLA 140

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/78 (37%), Positives = 42/78 (53%), Gaps = 3/78 (3%)
Query: 5   ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDA 61
           A +TL+V  +  D  E ++   F  YGPI  I +   K   +P GYAF+E+E  RD   A
Sbjct: 101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160
Query: 62  IRGRDGYDFDGHRLRVEL 79
            +  DG   DG R+ V++
Sbjct: 161 YKHADGKKIDGRRVLVDV 178

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/83 (36%), Positives = 43/83 (51%), Gaps = 7/83 (8%)
Query: 3  SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEARD 57
          S   R LYVG L  ++ ++ +   F  +G I   D++IP      +  G+AFVEFE A D
Sbjct: 2  STTKRVLYVGGLAEEVDDKVLHAAFIPFGDIT--DIQIPLDYETEKHRGFAFVEFELAED 59
Query: 58 AEDAIRGRDGYDFDGHRLRVELA 80
          A  AI   +  +  G  +RV LA
Sbjct: 60 AAAAIDNMNESELFGRTIRVNLA 82

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDAEDAIRG 64
          TL V NL        +  +F KYG +  + +   P    P G+AFV F + RDA+DA   
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 65 RDGYDFDGHRLRVELA 80
           DG + DG  LRV++A
Sbjct: 75 MDGAELDGRELRVQVA 90

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 39/160 (24%), Positives = 64/160 (40%), Gaps = 27/160 (16%)
Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
           L V  LP ++ + E+  LF   G +    L   K+     GY FV +  A+DAE AI   
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 66  DGYDFDGHRLRVELAXXXXXXXXXXXXXXXXXXXXXXXXXXXEYRVLVTGLPSSASWQDL 125
           +G       ++V  A                           +  + ++GLP + + +D+
Sbjct: 65  NGLRLQSKTIKVSYA-------------------RPSSEVIKDANLYISGLPRTMTQKDV 105
Query: 126 KDHMRRAGDVCFSQVFRDGSGTTGI---VDYTNYDDMKHA 162
           +D   R G +  S+V  D   TTG+   V +  +D    A
Sbjct: 106 EDMFSRFGRIINSRVLVD--QTTGLSRGVAFIRFDKRSEA 143

>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex Length = 88

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 4/71 (5%)
Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKI----PPRPPGYAFVEFEEARDAEDAIRG 64
          +++G L  ++ +  + ++F  YG I  ID+ +    P    GYA+VEFE   +AE A++ 
Sbjct: 7  VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 65 RDGYDFDGHRL 75
           DG   DG  +
Sbjct: 67 MDGGQIDGQEI 77

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 39/160 (24%), Positives = 64/160 (40%), Gaps = 27/160 (16%)
Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
           L V  LP ++ + E+  LF   G +    L   K+     GY FV +  A+DAE AI   
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 66  DGYDFDGHRLRVELAXXXXXXXXXXXXXXXXXXXXXXXXXXXEYRVLVTGLPSSASWQDL 125
           +G       ++V  A                           +  + ++GLP + + +D+
Sbjct: 65  NGLRLQSKTIKVSYA-------------------RPSSEVIKDANLYISGLPRTMTQKDV 105
Query: 126 KDHMRRAGDVCFSQVFRDGSGTTGI---VDYTNYDDMKHA 162
           +D   R G +  S+V  D   TTG+   V +  +D    A
Sbjct: 106 EDMFSRFGRIINSRVLVD--QTTGLSRGVAFIRFDKRSEA 143

>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3 Length = 108

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 36/69 (52%), Gaps = 5/69 (7%)
Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          L+V   P D++E E+ ++F  +GP+  + +       G+AFVEFEEA  A  AI    G 
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL-----NGFAFVEFEEAESAAKAIEEVHGK 88
Query: 69 DFDGHRLRV 77
           F    L V
Sbjct: 89 SFANQPLEV 97

>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 = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 41/78 (52%), Gaps = 3/78 (3%)
Query: 4   RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAED 60
           + S TLYVGNL     E ++ +LF K G I  I +   K+     G+ FVE+    DAE+
Sbjct: 37  KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 96
Query: 61  AIRGRDGYDFDGHRLRVE 78
           A+R  +G   D   +R +
Sbjct: 97  AMRYINGTRLDDRIIRTD 114

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 3/78 (3%)
Query: 3   SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAE 59
           +RA   +YV ++  D+ + +++ +F  +G I    L   P   +  GY F+E+E+A+ ++
Sbjct: 107 ARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQ 166
Query: 60  DAIRGRDGYDFDGHRLRV 77
           DA+   + +D  G  LRV
Sbjct: 167 DAVSSMNLFDLGGQYLRV 184

>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 = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 39/77 (50%)
Query: 1  MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
          +    +R L + NLP  I   E+ D+F KYGPI  I +   P   G A+V +E+  DA++
Sbjct: 13 LPPEVNRILMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKN 72
Query: 61 AIRGRDGYDFDGHRLRV 77
          A     G++     L V
Sbjct: 73 ACDHLSGFNVCNRYLVV 89

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 43/83 (51%), Gaps = 7/83 (8%)
Query: 3  SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEARD 57
          +   R LYVG L  ++ ++ +   F  +G I   D++IP      +  G+AFVEFE A D
Sbjct: 4  ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDIT--DIQIPLDYETEKHRGFAFVEFELAED 61
Query: 58 AEDAIRGRDGYDFDGHRLRVELA 80
          A  AI   +  +  G  +RV LA
Sbjct: 62 AAAAIDNMNESELFGRTIRVNLA 84

>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein Length = 74

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 25/69 (36%), Positives = 36/69 (52%), Gaps = 5/69 (7%)
Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          L+V   P D++E E+ ++F  +GP+  + +       G+AFVEFEEA  A  AI    G 
Sbjct: 7  LFVRPFPLDVQESELNEIFGPFGPMKEVKIL-----NGFAFVEFEEAESAAKAIEEVHGK 61
Query: 69 DFDGHRLRV 77
           F    L V
Sbjct: 62 SFANQPLEV 70

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 31/85 (36%), Positives = 41/85 (48%), Gaps = 7/85 (8%)
Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEA 55
           M      +L V NL        +  +F KYG +   D+ IP         G+AFV F + 
Sbjct: 65  MDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVG--DVYIPRDRYTKESRGFAFVRFHDK 122
Query: 56  RDAEDAIRGRDGYDFDGHRLRVELA 80
           RDAEDA+   DG   DG  LRV++A
Sbjct: 123 RDAEDAMDAMDGAVLDGRELRVQMA 147

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 4/75 (5%)
Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP---GYAFVEFEEARDAEDAIRGR 65
          L++G L  +  E+ ++ +F K+GPI+ + L I  R     G+AF+ FE   DA++A +  
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEV-LLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 66 DGYDFDGHRLRVELA 80
          +G    G  ++VE A
Sbjct: 69 NGKSLHGKAIKVEQA 83

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 43/81 (53%), Gaps = 7/81 (8%)
Query: 5  ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEARDAE 59
          + R LYVG L  ++ ++ +   F  +G I   D++IP      +  G+AFVEFE A DA 
Sbjct: 1  SKRVLYVGGLAEEVDDKVLHAAFIPFGDIT--DIQIPLDYETEKHRGFAFVEFELAEDAA 58
Query: 60 DAIRGRDGYDFDGHRLRVELA 80
           AI   +  +  G  +RV LA
Sbjct: 59 AAIDNMNESELFGRTIRVNLA 79

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 3/78 (3%)
Query: 3   SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAE 59
           +RA   +YV ++  D+ + +++ +F  +G I    L   P   +  GY F+E+E+A+ ++
Sbjct: 106 ARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQ 165
Query: 60  DAIRGRDGYDFDGHRLRV 77
           DA+   + +D  G  LRV
Sbjct: 166 DAVSSXNLFDLGGQYLRV 183

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 3/78 (3%)
Query: 3   SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAE 59
           +RA   +YV ++  D+ + +++ +F  +G I    L   P   +  GY F+E+E+A+ ++
Sbjct: 122 ARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQ 181
Query: 60  DAIRGRDGYDFDGHRLRV 77
           DA+   + +D  G  LRV
Sbjct: 182 DAVSSMNLFDLGGQYLRV 199

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 44.7 bits (104), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 42/79 (53%), Gaps = 7/79 (8%)
Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEARDAEDA 61
          R LYVG L  ++ ++ +   F  +G I   D++IP      +  G+AFVEFE A DA  A
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDIT--DIQIPLDYETEKHRGFAFVEFELAEDAAAA 70
Query: 62 IRGRDGYDFDGHRLRVELA 80
          I   +  +  G  +RV LA
Sbjct: 71 IDNMNESELFGRTIRVNLA 89

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 44.7 bits (104), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIR 63
          R +YVGNL       +V++LF ++G + ++ L   +   +P G+ FVE +E   +E AI 
Sbjct: 2  RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AIA 60
Query: 64 GRDGYDFDGHRLRVELA 80
            D  DF G  +RV  A
Sbjct: 61 KLDNTDFMGRTIRVTEA 77

>pdb|2JVR|A Chain A, Segmental Isotope Labeling Of Npl3p Length = 111

Iteration: 1
 Score = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 25/68 (36%), Positives = 40/68 (58%), Gaps = 3/68 (4%)
Query: 109 YRVLVTGLPSSASWQDLKDHMRRAG-DVCFSQV-FRDGSGTTGIVDYTNYDDMKHAIKKL 166
           YR+ +  LP   SWQDLKD  R    +  FS V  RD  G TG +++ + + +  A+++L
Sbjct: 29  YRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDG-TGALEFPSEEILVEALERL 87
Query: 167 DDSEFRNA 174
           ++ EFR +
Sbjct: 88  NNIEFRGS 95

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 44.3 bits (103), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 27/72 (37%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          L+VGNLP DI E E+  LF KYG    + +    +  G+ F+  E    AE A    D  
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIH---KDKGFGFIRLETRTLAEIAKVELDNM 81
Query: 69 DFDGHRLRVELA 80
             G +LRV  A
Sbjct: 82 PLRGKQLRVRFA 93

>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein Np_057951 Length = 110

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 6/73 (8%)
Query: 9  LYVGNL-PGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG 67
          +++GNL    +++ +VE +F KYG +A   +       GYAFV++   R A  A+ G +G
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSVH-----KGYAFVQYSNERHARAAVLGENG 84
Query: 68 YDFDGHRLRVELA 80
              G  L + +A
Sbjct: 85 RVLAGQTLDINMA 97

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
           LYV NLP  I + +++ +F KYG I   ++   K+  RP G AFV + +  +A++AI   
Sbjct: 92  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 66  DGYDFDG--HRLRVELA 80
           +    +G    L V LA
Sbjct: 152 NNVIPEGGSQPLSVRLA 168

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 29/78 (37%), Positives = 42/78 (53%), Gaps = 3/78 (3%)
Query: 5   ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDA 61
           A +TL+V  +  D  E ++   F  YGPI  I +   K   +P GYAF+E+E  RD   A
Sbjct: 101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160
Query: 62  IRGRDGYDFDGHRLRVEL 79
            +  DG   DG R+ V++
Sbjct: 161 YKHADGKKIDGRRVLVDV 178

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 39/166 (23%), Positives = 68/166 (40%), Gaps = 26/166 (15%)
Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
           L V  LP ++ + E   LF   G I    L   KI  +  GY FV + + +DAE AI   
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 66  DGYDFDGHRLRVELAXXXXXXXXXXXXXXXXXXXXXXXXXXXEYRVLVTGLPSSASWQDL 125
           +G       ++V  A                           +  + V+GLP + + ++L
Sbjct: 65  NGLRLQTKTIKVSYA-------------------RPSSASIRDANLYVSGLPKTMTQKEL 105
Query: 126 KDHMRRAGDVCFSQVFRDG-SGTTGIVDYTNYD---DMKHAIKKLD 167
           +    + G +  S++  D  +G +  V +  +D   + + AIK L+
Sbjct: 106 EQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN 151

>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif Of Nono Length = 99

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 27/72 (37%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          L+VGNLP DI E E+  LF KYG    + +    +  G+ F+  E    AE A    D  
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIH---KDKGFGFIRLETRTLAEIAKVELDNM 74
Query: 69 DFDGHRLRVELA 80
             G +LRV  A
Sbjct: 75 PLRGKQLRVRFA 86

>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The Catalytically-Active Conformation Length = 100

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3  SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
          +R + T+Y+ NL   I++ E++     +F ++G I  I +    +  G AFV F+E   A
Sbjct: 6  TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
           +A+R   G+ F    +R++ A
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA 87

>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures Length = 101

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3  SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
          +R + T+Y+ NL   I++ E++     +F ++G I  I +    +  G AFV F+E   A
Sbjct: 5  TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
           +A+R   G+ F    +R++ A
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA 86

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
           LYV NLP  I + +++ +F KYG I   ++   K+  RP G AFV + +  +A++AI   
Sbjct: 103 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 162
Query: 66  DGYDFDG--HRLRVELA 80
           +    +G    L V LA
Sbjct: 163 NNVIPEGGSQPLSVRLA 179

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 38/166 (22%), Positives = 68/166 (40%), Gaps = 26/166 (15%)
Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
           L V  LP ++ + E + LF   G I    L   KI  +  GY FV + +  DA+ AI   
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 66  DGYDFDGHRLRVELAXXXXXXXXXXXXXXXXXXXXXXXXXXXEYRVLVTGLPSSASWQDL 125
           +G       ++V  A                           +  + V+GLP + S +++
Sbjct: 67  NGLKLQTKTIKVSYA-------------------RPSSASIRDANLYVSGLPKTMSQKEM 107
Query: 126 KDHMRRAGDVCFSQVFRD-GSGTTGIVDYTNYD---DMKHAIKKLD 167
           +    + G +  S++  D  +G +  V +  +D   + + AIK L+
Sbjct: 108 EQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLN 153

>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117, Nmr, 43 Structures Length = 116

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3  SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
          +R + T+Y+ NL   I++ E++     +F ++G I  I +    +  G AFV F+E   A
Sbjct: 5  TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
           +A+R   G+ F    +R++ A
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA 86

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 42/78 (53%), Gaps = 5/78 (6%)
Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRG 64
           LYV NLP  I + +++ +F KYG I   ++   K+  RP G AFV + +  +A++AI  
Sbjct: 15 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 74
Query: 65 RDGYDFDG--HRLRVELA 80
           +    +G    L V LA
Sbjct: 75 LNNVIPEGGSQPLSVRLA 92

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 40/78 (51%), Gaps = 7/78 (8%)
Query: 8   TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEARDAEDAI 62
           +L V NL        +  +F KYG +   D+ IP         G+AFV F + RDAEDA+
Sbjct: 49  SLKVDNLTYRTSPDTLRRVFEKYGRVG--DVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 106
Query: 63  RGRDGYDFDGHRLRVELA 80
              DG   DG  LRV++A
Sbjct: 107 DAMDGAVLDGRELRVQMA 124

>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of Nucleolysin Tiar Length = 103

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRG 64
          RTLYVGNL  D+ E  +  LF + GP     +        P Y FVEF E RDA  A+  
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-YCFVEFYEHRDAAAALAA 74
Query: 65 RDGYDFDGHRLRVELA 80
           +G    G  ++V  A
Sbjct: 75 MNGRKILGKEVKVNWA 90

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 3/81 (3%)
Query: 3  SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRP---PGYAFVEFEEARDAE 59
          S     L+V  +  +  E ++ D F +YG I +I L +  R     GY  VE+E  ++A+
Sbjct: 4  SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 63
Query: 60 DAIRGRDGYDFDGHRLRVELA 80
           A+ G +G D  G  + V+  
Sbjct: 64 AAMEGLNGQDLMGQPISVDWC 84

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRP---PGYAFVEFEEARDAEDAIRGR 65
          L+V  +  +  E ++ D F +YG I +I L +  R     GY  VE+E  ++A+ A+ G 
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 66 DGYDFDGHRLRVE 78
          +G D  G  + V+
Sbjct: 72 NGQDLMGQPISVD 84

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRP---PGYAFVEFEEARDAEDAIRGR 65
          L+V  +  +  E ++ D F +YG I +I L +  R     GY  VE+E  ++A+ A+ G 
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 66 DGYDFDGHRLRVE 78
          +G D  G  + V+
Sbjct: 70 NGQDLMGQPISVD 82

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRP---PGYAFVEFEEARDAEDAIRGR 65
          L+V  +  +  E ++ D F +YG I +I L +  R     GY  VE+E  ++A+ A+ G 
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 66 DGYDFDGHRLRVE 78
          +G D  G  + V+
Sbjct: 70 NGQDLMGQPISVD 82

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 3/81 (3%)
Query: 3  SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRP---PGYAFVEFEEARDAE 59
          S     L+V  +  +  E ++ D F +YG I +I L +  R     GY  VE+E  ++A+
Sbjct: 19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 78
Query: 60 DAIRGRDGYDFDGHRLRVELA 80
           A+ G +G D  G  + V+  
Sbjct: 79 AAMEGLNGQDLMGQPISVDWC 99

>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With Both Exons Length = 98

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3  SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
          +R + T+Y+ NL   I++ E++     +F ++G I  I +    +  G AFV F+E   A
Sbjct: 6  TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
           +A+R   G+ F    +R++ A
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA 87

>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In Complex With Thiamine Pyrophosphate And The U1a Crystallization Module Length = 96

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3  SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
          +R + T+Y+ NL   I++ E++     +F ++G I  I +    +  G AFV F+E   A
Sbjct: 5  TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
           +A+R   G+ F    +R++ A
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA 86

>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95 Length = 95

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3  SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
          +R + T+Y+ NL   I++ E++     +F ++G I  I +    +  G AFV F+E   A
Sbjct: 6  TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
           +A+R   G+ F    +R++ A
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA 87

>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL Length = 97

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3  SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
          +R + T+Y+ NL   I++ E++     +F ++G I  I +    +  G AFV F+E   A
Sbjct: 5  TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
           +A+R   G+ F    +R++ A
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA 86

>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I Intron Length = 95

Iteration: 1
 Score = 41.2 bits (95), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3  SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
          +R + T+Y+ NL   I++ E++     +F ++G I  I +    +  G AFV F+E   A
Sbjct: 3  TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 62
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
           +A+R   G+ F    +R++ A
Sbjct: 63 TNALRSMQGFPFYDKPMRIQYA 84

>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its Catalytic Cofactor Length = 94

Iteration: 1
 Score = 41.2 bits (95), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3  SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
          +R + T+Y+ NL   I++ E++     +F ++G I  I +    +  G AFV F+E   A
Sbjct: 2  TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 61
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
           +A+R   G+ F    +R++ A
Sbjct: 62 TNALRSMQGFPFYDKPMRIQYA 83

>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch Length = 91

Iteration: 1
 Score = 41.2 bits (95), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 3  SRASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
          +R + T+Y+ NL   I++ E++     +F ++G I  I +    +  G AFV F+E   A
Sbjct: 1  TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 60
Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
           +A+R   G+ F    +R++ A
Sbjct: 61 TNALRSMQGFPFYDKPMRIQYA 82

>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding Protein 14 Length = 90

Iteration: 1
 Score = 40.8 bits (94), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 25/79 (31%), Positives = 40/79 (50%), Gaps = 5/79 (6%)
Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
          SS  +  ++VGN+      +E+  LF + G +   D+        YAFV  E+  DA+ A
Sbjct: 5  SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-----KDYAFVHMEKEADAKAA 59
Query: 62 IRGRDGYDFDGHRLRVELA 80
          I   +G +  G R+ VEL+
Sbjct: 60 IAQLNGKEVKGKRINVELS 78

>pdb|2OSR|A Chain A, Nmr Structure Of Rrm-2 Of Yeast Npl3 Protein Length = 87

Iteration: 1
 Score = 40.8 bits (94), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 25/68 (36%), Positives = 40/68 (58%), Gaps = 3/68 (4%)
Query: 109 YRVLVTGLPSSASWQDLKDHMRRAG-DVCFSQV-FRDGSGTTGIVDYTNYDDMKHAIKKL 166
           YR+ +  LP   SWQDLKD  R    +  FS V  RD  G TG +++ + + +  A+++L
Sbjct: 7   YRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDG-TGALEFPSEEILVEALERL 65
Query: 167 DDSEFRNA 174
           ++ EFR +
Sbjct: 66  NNIEFRGS 73

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	299
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-32
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-32
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	7e-32
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	7e-06
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-29
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	6e-29
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-28
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	4e-28
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	4e-27
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	6e-05
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-26
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-24
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	5e-06
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	4e-24
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-23
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	4e-23
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	3e-09
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-23
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-13
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-22
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	9e-06
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-22
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-13
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	5e-22
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	5e-22
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-10
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	8e-22
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-21
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-19
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-21
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-21
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	6e-09
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-21
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-21
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-20
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	9e-14
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-20
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-12
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-20
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	3e-20
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	4e-09
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	4e-20
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-12
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	4e-20
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	3e-08
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	5e-20
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	7e-20
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	7e-20
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-19
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-04
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-19
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-19
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-19
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-13
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-19
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-11
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-19
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	6e-19
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	8e-19
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-18
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	1e-18
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-18
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-18
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	5e-06
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-18
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	5e-18
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	9e-05
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	5e-18
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	4e-04
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-18
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-06
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	7e-18
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-13
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	7e-18
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	9e-18
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-17
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-11
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-17
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	6e-04
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-17
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-17
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-17
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	3e-17
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-17
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-08
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-17
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	3e-17
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-17
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	6e-12
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-17
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	5e-17
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	4e-05
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	7e-17
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-16
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-16
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-16
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-16
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	3e-16
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	4e-16
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	5e-16
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-16
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	5e-16
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	5e-16
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	5e-16
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	5e-04
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-16
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-10
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	6e-16
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	7e-16
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	9e-16
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-15
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-15
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-15
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-15
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	5e-15
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	5e-15
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	4e-04
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	7e-15
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-14
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-14
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-14
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-14
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-14
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-14
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-14
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-14
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	5e-14
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	6e-14
1x4e_A	85	RNA binding motif, single-stranded interacting pro	6e-14
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	9e-14
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	9e-14
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	9e-14
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	9e-14
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-13
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-13
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-13
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	3e-13
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	5e-07
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-13
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-13
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	4e-13
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	5e-13
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	8e-13
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-12
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	1e-12
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-12
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-12
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-08
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-12
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	3e-05
2div_A	99	TRNA selenocysteine associated protein; structural	2e-12
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-12
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-12
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-12
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	5e-12
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	9e-12
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-11
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-11
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-11
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-11
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-11
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	2e-11
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-11
1x5o_A	114	RNA binding motif, single-stranded interacting pro	5e-11
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	5e-11
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-10
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-10
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-10
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	3e-10
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	3e-06
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-10
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	6e-10
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-09
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	1e-09
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-09
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-09
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	3e-09
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-08
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	1e-08
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-08
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-08
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-08
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	3e-08
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	3e-08
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	3e-08
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	6e-08
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	6e-08
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	7e-08
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	1e-07
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	2e-07
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-07
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	3e-07
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	4e-07
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	4e-07
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	8e-07
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-06
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-06
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	3e-06
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	3e-06
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	4e-06
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	4e-06
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	5e-06
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	5e-06
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	7e-06
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	8e-06
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-05
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	3e-05
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	7e-05
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-04
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	1e-04
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	2e-04
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	3e-04
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	5e-04
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	6e-04
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	7e-04
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	8e-04

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score =  115 bits (289), Expect = 2e-32
 Identities = 46/107 (42%), Positives = 57/107 (53%), Gaps = 12/107 (11%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
           +YVGNL     + E+E  F  YGP+  +   I   PPG+AFVEFE+ RDAEDA+RG DG 
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVW--IARNPPGFAFVEFEDPRDAEDAVRGLDGK 60

Query: 69  DFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTG 115
              G R+RVEL+ G   RS             R  +RR    VL  G
Sbjct: 61  VICGSRVRVELSTGMPRRSR----------FDRPPARRKLLEVLFNG 97

>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 =  115 bits (289), Expect = 2e-32
 Identities = 29/91 (31%), Positives = 44/91 (48%)

Query: 1  MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
          +    +R LY+ NLP  I   E+ D+F KYGPI  I +   P   G A+V +E+  DA++
Sbjct: 3  LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKN 62

Query: 61 AIRGRDGYDFDGHRLRVELAHGGRGRSSSDR 91
          A+    G++     L V   +  R     D 
Sbjct: 63 AVDHLSGFNVSNRYLVVLYYNANRAFQKMDT 93

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score =  113 bits (285), Expect = 7e-32
 Identities = 51/90 (56%), Positives = 62/90 (68%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
           +      +YVGNLP DIR +++ED+FYKYG I  IDLK     P +AFVEFE+ RDAEDA
Sbjct: 18  AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDA 77

Query: 62  IRGRDGYDFDGHRLRVELAHGGRGRSSSDR 91
           + GRDGYD+DG+RLRVE    GRG  S   
Sbjct: 78  VYGRDGYDYDGYRLRVEFPRSGRGTGSGPS 107

>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 = 43.1 bits (102), Expect = 7e-06
 Identities = 23/112 (20%), Positives = 41/112 (36%), Gaps = 5/112 (4%)

Query: 88  SSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGT 147
           SS        G  RG +  ++ R+ V  LP     +D++D   + G +    +     G 
Sbjct: 2   SSGSSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGP 61

Query: 148 T-GIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVREYDHRRDGSQSPSRG 198
               V++ +  D + A+   D  ++        +RV      R     PS G
Sbjct: 62  PFAFVEFEDPRDAEDAVYGRDGYDYDG----YRLRVEFPRSGRGTGSGPSSG 109

>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 =  105 bits (265), Expect = 4e-29
 Identities = 29/88 (32%), Positives = 40/88 (45%), Gaps = 5/88 (5%)

Query: 1  MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
            S     L++GNLP +  E+E+  LF +YG +   D+        Y FV  E+   AED
Sbjct: 3  SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-----KNYGFVHIEDKTAAED 57

Query: 61 AIRGRDGYDFDGHRLRVELAHGGRGRSS 88
          AIR    Y   G  + VE +      SS
Sbjct: 58 AIRNLHHYKLHGVNINVEASKNKSKASS 85

>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 =  104 bits (263), Expect = 6e-29
 Identities = 27/91 (29%), Positives = 44/91 (48%), Gaps = 5/91 (5%)

Query: 1  MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
           SS  +  ++VGN+      +E+  LF + G +   D+        YAFV  E+  DA+ 
Sbjct: 4  GSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-----KDYAFVHMEKEADAKA 58

Query: 61 AIRGRDGYDFDGHRLRVELAHGGRGRSSSDR 91
          AI   +G +  G R+ VEL+  G+ +S    
Sbjct: 59 AIAQLNGKEVKGKRINVELSTKGQKKSGPSS 89

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score =  103 bits (259), Expect = 3e-28
 Identities = 32/88 (36%), Positives = 46/88 (52%), Gaps = 5/88 (5%)

Query: 1  MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
           S +AS  L+VGN+      +E+   F +YGP+   D+        YAFV  E A DA +
Sbjct: 5  SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-----KDYAFVHMERAEDAVE 59

Query: 61 AIRGRDGYDFDGHRLRVELAHGGRGRSS 88
          AIRG D  +F G R+ V+L+      +S
Sbjct: 60 AIRGLDNTEFQGKRMHVQLSTSRLRTAS 87

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score =  103 bits (259), Expect = 4e-28
 Identities = 21/96 (21%), Positives = 44/96 (45%), Gaps = 7/96 (7%)

Query: 2  SSRASRTLYVGNLPG-DIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
          +      L++GNLP  ++ + ++  +F  YG I  I++K       + F++F+  +   D
Sbjct: 6  NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-----NAFGFIQFDNPQSVRD 60

Query: 61 AIRGRDGYDFDGHRLRVELAHGG-RGRSSSDRHSSH 95
          AI         G +L +E++    R +     H ++
Sbjct: 61 AIECESQEMNFGKKLILEVSSSNARPQFDHGDHGTN 96

>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 =  102 bits (256), Expect = 4e-27
 Identities = 36/84 (42%), Positives = 50/84 (59%), Gaps = 2/84 (2%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
            S      +YVGNL  +  + E+E  F  YGP+  +   +   PPG+AFVEFE+ RDA D
Sbjct: 68  DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVW--VARNPPGFAFVEFEDPRDAAD 125

Query: 61  AIRGRDGYDFDGHRLRVELAHGGR 84
           A+R  DG    G R+RVEL++G +
Sbjct: 126 AVRELDGRTLCGCRVRVELSNGEK 149

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 41.4 bits (97), Expect = 6e-05
 Identities = 23/121 (19%), Positives = 40/121 (33%), Gaps = 1/121 (0%)

Query: 51  EFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYR 110
              EA DA  A +    Y  D                +    S H        S   + +
Sbjct: 16  TTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCK 75

Query: 111 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSE 170
           V V  L ++ +  +L+      G +    V R+  G    V++ +  D   A+++LD   
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG-FAFVEFEDPRDAADAVRELDGRT 134

Query: 171 F 171
            
Sbjct: 135 L 135

>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 = 98.5 bits (246), Expect = 2e-26
 Identities = 20/84 (23%), Positives = 39/84 (46%), Gaps = 6/84 (7%)

Query: 2  SSRASRTLYVGNLPG-DIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
           S     L++GNLP  ++ + ++  +F  YG I  I++K       + F++F+  +   D
Sbjct: 18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-----NAFGFIQFDNPQSVRD 72

Query: 61 AIRGRDGYDFDGHRLRVELAHGGR 84
          AI         G +L +E++    
Sbjct: 73 AIEXESQEMNFGKKLILEVSSSNA 96

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 94.1 bits (234), Expect = 1e-24
 Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 2/86 (2%)

Query: 1  MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
            +  +  +YVGNLP D R  +++    + G +          P   AF+ + ++  A+ 
Sbjct: 14 EGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLR--LTWQGPRRRAFLHYPDSAAAQQ 71

Query: 61 AIRGRDGYDFDGHRLRVELAHGGRGR 86
          A+    G       LRV LA   R +
Sbjct: 72 AVSCLQGLRLGTDTLRVALARQQRDK 97

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 43.3 bits (102), Expect = 5e-06
 Identities = 17/79 (21%), Positives = 24/79 (30%), Gaps = 1/79 (1%)

Query: 93  SSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVD 152
            S   G   G        V V  LP  A   DLK  +R  G V     ++        + 
Sbjct: 4   GSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRR-RAFLH 62

Query: 153 YTNYDDMKHAIKKLDDSEF 171
           Y +    + A+  L     
Sbjct: 63  YPDSAAAQQAVSCLQGLRL 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 = 93.2 bits (232), Expect = 4e-24
 Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 6/86 (6%)

Query: 4   RASRTLYVGNLPGD-IREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAI 62
             +  +++GNL    +++ +VE +F KYG +A   +       GYAFV++   R A  A+
Sbjct: 25  SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH-----KGYAFVQYSNERHARAAV 79

Query: 63  RGRDGYDFDGHRLRVELAHGGRGRSS 88
            G +G    G  L + +A   +   S
Sbjct: 80  LGENGRVLAGQTLDINMAGEPKPDRS 105

>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 = 90.8 bits (226), Expect = 3e-23
 Identities = 32/97 (32%), Positives = 42/97 (43%), Gaps = 8/97 (8%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
          +      L+VGNLP DI E E+  LF KYG    + +    +  G+ F+  E    AE A
Sbjct: 11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI---HKDKGFGFIRLETRTLAEIA 67

Query: 62 IRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
              D     G +LRV  A       S+   S  SSG
Sbjct: 68 KVELDNMPLRGKQLRVRFA-----CHSASLTSGPSSG 99

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 90.2 bits (224), Expect = 4e-23
 Identities = 13/79 (16%), Positives = 29/79 (36%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
            +  R L + N+P  ++   ++ L  +YG +   +            V +     A  A
Sbjct: 11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQA 70

Query: 62 IRGRDGYDFDGHRLRVELA 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 = 52.5 bits (126), Expect = 3e-09
 Identities = 21/82 (25%), Positives = 34/82 (41%), Gaps = 3/82 (3%)

Query: 93  SSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVC-FSQVFRDGSGTTGIV 151
           SS SSG      R    ++ +  +P    W+ L   + + G V    QV  D       V
Sbjct: 2   SSGSSGSVPKRQRIR--KLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNV 59

Query: 152 DYTNYDDMKHAIKKLDDSEFRN 173
            Y++ D  + A+ KL+  +  N
Sbjct: 60  TYSSKDQARQALDKLNGFQLEN 81

>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 = 92.8 bits (231), Expect = 5e-23
 Identities = 38/179 (21%), Positives = 72/179 (40%), Gaps = 14/179 (7%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP--------RPPGYAFVEFEEARD 57
           +R LYVGN+P  I E  + D F     +  +              +   +AF+EF    +
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63

Query: 58  AEDAIRGRDGYDFDGHRLRVELAHGGRGRSS-SDRHSSHSSGRGRGVSRRSEYRVLVTGL 116
              A+   DG  F G  L++   H  +     S+  S +  G    V   S +++ + GL
Sbjct: 64  TTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGL 122

Query: 117 PSSASWQDLKDHMRRAGDVCFSQVFRD-GSGTT---GIVDYTNYDDMKHAIKKLDDSEF 171
           P+  +   +K+ +   G +    + +D  +G +      +Y + +    AI  L+  + 
Sbjct: 123 PNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 181

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 67.0 bits (164), Expect = 2e-13
 Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 3/78 (3%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAI 62
           +  L++G LP  + + +V++L   +GP+   +L          GYAF E+ +    + AI
Sbjct: 114 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 173

Query: 63  RGRDGYDFDGHRLRVELA 80
            G +G      +L V+ A
Sbjct: 174 AGLNGMQLGDKKLLVQRA 191

>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 = 88.6 bits (220), Expect = 1e-22
 Identities = 30/97 (30%), Positives = 40/97 (41%), Gaps = 11/97 (11%)

Query: 3  SRASRTLYVGNLPGDIREREVEDLFYKYG-PIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
          S  S  + V NLP D   +EV DL   Y     ++D     R    AFV       A++A
Sbjct: 2  SSGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVD-----RNKRTAFVTLLNGEQAQNA 56

Query: 62 IRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
          I+    Y F G  L V+L       + +   S  SSG
Sbjct: 57 IQMFHQYSFRGKDLIVQLQ-----PTDALLCSGPSSG 88

>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 = 42.4 bits (100), Expect = 9e-06
 Identities = 22/97 (22%), Positives = 38/97 (39%), Gaps = 9/97 (9%)

Query: 102 GVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKH 161
           G S  S   +LV  LP  ++ Q++ D ++          + D +  T  V   N +  ++
Sbjct: 1   GSSGSS--GILVKNLPQDSNCQEVHDLLKDYD---LKYCYVDRNKRTAFVTLLNGEQAQN 55

Query: 162 AIKKLDDSEFRNAFSRAYVRVREYDHRRDGSQSPSRG 198
           AI+      FR       V+++  D        PS G
Sbjct: 56  AIQMFHQYSFRG--KDLIVQLQPTDALL--CSGPSSG 88

>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 = 90.7 bits (225), Expect = 4e-22
 Identities = 32/186 (17%), Positives = 65/186 (34%), Gaps = 19/186 (10%)

Query: 5   ASRTLYVGNL-PGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIR 63
            +  L V NL P  +  + +  LF  YG +    +KI       A V+  +   A+ A+ 
Sbjct: 2   GNSVLLVSNLNPERVTPQSLFILFGVYGDV--QRVKILFNKKENALVQMADGNQAQLAMS 59

Query: 64  GRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYR------------- 110
             +G+   G  +R+ L+     +   +        +  G S    ++             
Sbjct: 60  HLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPP 119

Query: 111 ---VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLD 167
              + ++ +P S S +DLK      G V     F        ++   + ++   A+  L 
Sbjct: 120 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLH 179

Query: 168 DSEFRN 173
           + +   
Sbjct: 180 NHDLGE 185

>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 = 66.1 bits (161), Expect = 3e-13
 Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 2/76 (2%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGR 65
           S TL++ N+P  + E +++ LF   G +     K   +    A ++     +A  A+   
Sbjct: 120 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF-KFFQKDRKMALIQMGSVEEAVQALIDL 178

Query: 66  DGYDF-DGHRLRVELA 80
             +D  + H LRV  +
Sbjct: 179 HNHDLGENHHLRVSFS 194

>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 = 86.8 bits (216), Expect = 5e-22
 Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 4/82 (4%)

Query: 3  SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI----PPRPPGYAFVEFEEARDA 58
          S     +++G L  ++ +  + ++F  YG I  ID+ +    P    GYA+VEFE   +A
Sbjct: 1  SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA 60

Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
          E A++  DG   DG  +     
Sbjct: 61 EKALKHMDGGQIDGQEITATAV 82

>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 = 87.5 bits (217), Expect = 5e-22
 Identities = 59/112 (52%), Positives = 78/112 (69%), Gaps = 9/112 (8%)

Query: 96  SSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTN 155
           S   G   SRRSE RV+V+GLP S SWQDLKDHMR AGDVC++ V+RDG   TG+V++  
Sbjct: 3   SGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG---TGVVEFVR 59

Query: 156 YDDMKHAIKKLDDSEFRNAFSR-AYVRVREYDHRRDGSQSPSRGRSYSRGRS 206
            +DM +A++KLD+++FR+     AY+RV     + DG +SPS GRS S G S
Sbjct: 60  KEDMTYAVRKLDNTKFRSHEGETAYIRV-----KVDGPRSPSYGRSRSSGPS 106

>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 = 56.7 bits (137), Expect = 1e-10
 Identities = 24/102 (23%), Positives = 36/102 (35%), Gaps = 5/102 (4%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
           S R+   + V  LP     ++++D   + G + + D+       G   VEF    D   A
Sbjct: 11  SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV----YRDGTGVVEFVRKEDMTYA 66

Query: 62  IRGRDGYDFDGHRLRVELAHGGRGRSSSDRHS-SHSSGRGRG 102
           +R  D   F  H               S  +  S SSG   G
Sbjct: 67  VRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSSGPSSG 108

>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 = 86.5 bits (215), Expect = 8e-22
 Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 5/86 (5%)

Query: 3  SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAI 62
          +  +  L+VG L  +     +   F ++G I  ID     +   +A++++E    A+ A 
Sbjct: 14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDH---VKGDSFAYIQYESLDAAQAAC 70

Query: 63 RGRDGYDFDG--HRLRVELAHGGRGR 86
              G+   G   RLRV+ A  G   
Sbjct: 71 AKMRGFPLGGPDRRLRVDFAKSGPSS 96

>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 = 91.2 bits (227), Expect = 1e-21
 Identities = 35/222 (15%), Positives = 66/222 (29%), Gaps = 34/222 (15%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARD 57
                   L V NLP  + +++ E+L   +G +    L       +  GY F E+ +   
Sbjct: 90  QLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDS 149

Query: 58  AEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLP 117
           A  A     G       L V     G+   +                      + V  LP
Sbjct: 150 AARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSR----------------CLCVDRLP 193

Query: 118 SSAS-WQDLKDHMRRAGDVCFSQVFRDGSGTT---GIVDYTNYDDMKHAIKKLDDSEFRN 173
              +    L   +       F Q+     G      +++Y   +  + A ++ D      
Sbjct: 194 PGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGG 253

Query: 174 AFSRAYVRVREYDHRRDGSQSPSRGRSYSRGRSESRSRSRSR 215
               +++RV               GRS       +++ + +R
Sbjct: 254 ----SHLRVSF-------CAPGPPGRSMLAALIAAQATALNR 284

>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 = 85.8 bits (213), Expect = 1e-19
 Identities = 35/176 (19%), Positives = 54/176 (30%), Gaps = 33/176 (18%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
             R  R + +  LPGD+  +EV DL   Y         +  +  G AFV       AE A
Sbjct: 18  QFRNRRKILIRGLPGDVTNQEVHDLLSDYELK---YCFVD-KYKGTAFVTLLNGEQAEAA 73

Query: 62  IRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSAS 121
           I            L V+L                           ++  + V  LP S +
Sbjct: 74  INAFHQSRLRERELSVQLQ-------------------------PTDALLCVANLPPSLT 108

Query: 122 WQDLKDHMRRAGDVCFSQVFRD-GSGTT---GIVDYTNYDDMKHAIKKLDDSEFRN 173
            Q  ++ +R  G +    +     +G +   G  +Y   D    A   L       
Sbjct: 109 QQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGP 164

>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 = 86.2 bits (214), Expect = 2e-21
 Identities = 29/93 (31%), Positives = 39/93 (41%), Gaps = 8/93 (8%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGR 65
           + LYV NL     E  +E  F    P A   +K   +   YAFV F    DA +A++  
Sbjct: 15 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK---KIRDYAFVHFSNREDAVEAMKAL 71

Query: 66 DGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
          +G   DG  + V LA     +      S  SSG
Sbjct: 72 NGKVLDGSPIEVTLA-----KPVDKDSSGPSSG 99

>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 = 90.1 bits (224), Expect = 2e-21
 Identities = 44/189 (23%), Positives = 65/189 (34%), Gaps = 33/189 (17%)

Query: 8   TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG 67
            L+VGNLP DI E + + LF +YG  + + +    R  G+ F+  E    AE A    DG
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFI---NRDRGFGFIRLESRTLAEIAKAELDG 80

Query: 68  YDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKD 127
                  LR+  A  G                           + V  L    S + L+ 
Sbjct: 81  TILKSRPLRIRFATHGA-------------------------ALTVKNLSPVVSNELLEQ 115

Query: 128 HMRRAGDVCFSQVFRDGSGTT---GIVDYTNYDDMKHAIKKLDDSEF--RNAFSRAYVRV 182
              + G V  + V  D  G     G V++      + A+++  D  F          V  
Sbjct: 116 AFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEP 175

Query: 183 REYDHRRDG 191
            E     DG
Sbjct: 176 MEQFDDEDG 184

>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 = 54.7 bits (132), Expect = 6e-09
 Identities = 17/78 (21%), Positives = 25/78 (32%), Gaps = 6/78 (7%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP----RPPGYAFVEFEEAR 56
             +     L V NL   +    +E  F ++GP+      +      R  G  FVEF    
Sbjct: 91  RFATHGAALTVKNLSPVVSNELLEQAFSQFGPV--EKAVVVVDDRGRATGKGFVEFAAKP 148

Query: 57  DAEDAIRGRDGYDFDGHR 74
            A  A+       F    
Sbjct: 149 PARKALERCGDGAFLLTT 166

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 86.2 bits (214), Expect = 2e-21
 Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 5/81 (6%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGR 65
           +  L+V   P D++E E+ ++F  +GP+  + +       G+AFVEFEEA  A  AI   
Sbjct: 31  NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI-----LNGFAFVEFEEAESAAKAIEEV 85

Query: 66  DGYDFDGHRLRVELAHGGRGR 86
            G  F    L V  +     R
Sbjct: 86  HGKSFANQPLEVVYSKLPAKR 106

>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 = 85.7 bits (213), Expect = 2e-21
 Identities = 32/93 (34%), Positives = 43/93 (46%), Gaps = 3/93 (3%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDA 58
                 TL V NL        +  +F KYG +  + +   P    P G+AFV F + RDA
Sbjct: 9   DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDA 68

Query: 59  EDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDR 91
           +DA    DG + DG  LRV++A  GR   S   
Sbjct: 69  QDAEAAMDGAELDGRELRVQVARYGRRDLSGPS 101

>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 = 85.3 bits (212), Expect = 2e-20
 Identities = 27/176 (15%), Positives = 60/176 (34%), Gaps = 31/176 (17%)

Query: 3   SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP----GYAFVEFEEARDA 58
           S     L++GNL  +    E++    +       DL +          + +V+FE A D 
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAK--NDLAVVDVRTGTNRKFGYVDFESAEDL 67

Query: 59  EDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPS 118
           E A+    G    G+ +++E   G   +                        +L   L  
Sbjct: 68  EKAL-ELTGLKVFGNEIKLEKPKGRDSKKVRAAR-----------------TLLAKNLSF 109

Query: 119 SASWQDLKDHMRRAGDVCFSQVFRDGSGTT---GIVDYTNYDDMKHAIKKLDDSEF 171
           + +  +LK+    A ++          G +     +++ +  D +  +++   +E 
Sbjct: 110 NITEDELKEVFEDALEI----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 = 67.2 bits (165), Expect = 9e-14
 Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 2/80 (2%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
              RA+RTL   NL  +I E E++++F     I  +      +  G A++EF+   DAE 
Sbjct: 94  KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSK--GIAYIEFKSEADAEK 151

Query: 61  AIRGRDGYDFDGHRLRVELA 80
            +  + G + DG  + +   
Sbjct: 152 NLEEKQGAEIDGRSVSLYYT 171

>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 = 85.9 bits (212), Expect = 3e-20
 Identities = 29/201 (14%), Positives = 63/201 (31%), Gaps = 25/201 (12%)

Query: 6   SRTLYVGNL-PGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRG 64
           S  L V  L    +    V ++F  YG +  +  K     PG A VE  +    + AI  
Sbjct: 4   SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKV--KFMKSKPGAAMVEMADGYAVDRAITH 61

Query: 65  RDGYDFDGHRLRVELAH--GGRGRSSSDRHSSHSSGRGRGVSRRSEYR------------ 110
            +     G ++ V ++         S        S +    SR + +             
Sbjct: 62  LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQH 121

Query: 111 ----VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD----GSGTTGIVDYTNYDDMKHA 162
               +     P   + ++  +     G    + V          ++G++++ +  D    
Sbjct: 122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALET 181

Query: 163 IKKLDDSEFRNAFSRAYVRVR 183
           +  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 = 62.8 bits (152), Expect = 5e-12
 Identities = 11/80 (13%), Positives = 25/80 (31%), Gaps = 3/80 (3%)

Query: 3   SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAE 59
              S  L+  N P ++ E    ++  + G      +K+            +E++   DA 
Sbjct: 120 QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDAL 179

Query: 60  DAIRGRDGYDFDGHRLRVEL 79
           + +   + Y           
Sbjct: 180 ETLGFLNHYQMKNPNGPYPY 199

>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 = 82.7 bits (205), Expect = 3e-20
 Identities = 25/94 (26%), Positives = 47/94 (50%), Gaps = 9/94 (9%)

Query: 2  SSRASRTLYVGNLPGDIRE----REVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARD 57
           +R + T+Y+ NL   I++    + +  +F ++G I  I +    +  G AFV F+E   
Sbjct: 4  ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 63

Query: 58 AEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDR 91
          A +A+R   G+ F    +R++ A     ++ SD 
Sbjct: 64 ATNALRSMQGFPFYDKPMRIQYA-----KTDSDI 92

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 83.0 bits (205), Expect = 3e-20
 Identities = 27/114 (23%), Positives = 45/114 (39%), Gaps = 5/114 (4%)

Query: 82  GGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAG-DVCFSQV 140
           G               G          YR+ +  LP   SWQDLKD  R    +  FS V
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSV 61

Query: 141 FRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVREYDHRRDGSQS 194
                  TG +++ + + +  A+++L++ EFR     + + V   D+     +S
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 = 52.5 bits (126), Expect = 4e-09
 Identities = 13/70 (18%), Positives = 26/70 (37%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
           + + NLP     ++++DL  +                G   +EF       +A+   +  
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNI 90

Query: 69  DFDGHRLRVE 78
           +F G  + VE
Sbjct: 91  EFRGSVITVE 100

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 85.8 bits (213), Expect = 4e-20
 Identities = 32/179 (17%), Positives = 66/179 (36%), Gaps = 15/179 (8%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDA 58
           +      +YVG++  ++ E  +   F  +GPI  ID+    +  +  G+AFVE+E    A
Sbjct: 24  ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAA 83

Query: 59  EDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPS 118
           + A+   +     G  ++V                +  +            R+ V  +  
Sbjct: 84  QLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF--------NRIYVASVHQ 135

Query: 119 SASWQDLKDHMRRAGDVCFSQVFRDG-SGTT---GIVDYTNYDDMKHAIKKLDDSEFRN 173
             S  D+K      G +  + + RD  +G     G ++Y      + A+  ++  +   
Sbjct: 136 DLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGG 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 = 63.9 bits (156), Expect = 2e-12
 Identities = 22/84 (26%), Positives = 44/84 (52%), Gaps = 7/84 (8%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEAR 56
            +RA   +YV ++  D+ + +++ +F  +G I      +       +  GY F+E+E+A+
Sbjct: 121 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKI--KSATLARDPTTGKHKGYGFIEYEKAQ 178

Query: 57  DAEDAIRGRDGYDFDGHRLRVELA 80
            ++DA+   + +D  G  LRV  A
Sbjct: 179 SSQDAVSSMNLFDLGGQYLRVGKA 202

>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 = 82.6 bits (204), Expect = 4e-20
 Identities = 62/116 (53%), Positives = 80/116 (68%), Gaps = 5/116 (4%)

Query: 96  SSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTN 155
             GR    SRRSE RV+V+GLP S SWQDLKDHMR AGDVC++ V+RDG   TG+V++  
Sbjct: 4   PRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG---TGVVEFVR 60

Query: 156 YDDMKHAIKKLDDSEFRNAFSR-AYVRVREYDHRRDGSQSPSRGRSYSRGRSESRS 210
            +DM +A++KLD+++FR+     AY+RV+  D  R  S   SR RS SR RS SRS
Sbjct: 61  KEDMTYAVRKLDNTKFRSHEGETAYIRVKV-DGPRSPSYGRSRSRSRSRSRSRSRS 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 = 50.2 bits (120), Expect = 3e-08
 Identities = 27/107 (25%), Positives = 38/107 (35%), Gaps = 7/107 (6%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
           S R+   + V  LP     ++++D   + G + + D+       G   VEF    D   A
Sbjct: 12  SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV----YRDGTGVVEFVRKEDMTYA 67

Query: 62  IRGRDGYDFDGHRLRVELA---HGGRGRSSSDRHSSHSSGRGRGVSR 105
           +R  D   F  H            G    S  R  S S  R R  SR
Sbjct: 68  VRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRSRSRSRSRSR 114

>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 = 82.0 bits (203), Expect = 5e-20
 Identities = 23/90 (25%), Positives = 37/90 (41%), Gaps = 11/90 (12%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----------RPPGYAFV 50
          S   + T++V  L  ++    V D F + G I        P           +  G A V
Sbjct: 9  SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 68

Query: 51 EFEEARDAEDAIRGRDGYDFDGHRLRVELA 80
           F++   A+ AI   DG +F G+ ++V  A
Sbjct: 69 SFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 82.6 bits (204), Expect = 7e-20
 Identities = 15/94 (15%), Positives = 36/94 (38%), Gaps = 9/94 (9%)

Query: 2   SSRASRTLYVGNLPGDIRERE----VEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARD 57
            +  S+ + + N+  ++ + +    +  L    G I  I + +     G A++ F     
Sbjct: 25  HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQES 84

Query: 58  AEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDR 91
           A+  +    GY F G+ L +  +      +   +
Sbjct: 85  AQAFVEAFQGYPFQGNPLVITFS-----ETPQSQ 113

>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 = 81.5 bits (202), Expect = 7e-20
 Identities = 25/98 (25%), Positives = 37/98 (37%), Gaps = 9/98 (9%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
           S     LY+GNL   +   ++  LF          +       GYAFV++ +   A  A
Sbjct: 4  GSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL---LKSGYAFVDYPDQNWAIRA 60

Query: 62 IRGRDG-YDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
          I    G  +  G  + V+ +      S   R S  SSG
Sbjct: 61 IETLSGKVELHGKIMEVDYS-----VSKKLRSSGPSSG 93

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 81.3 bits (201), Expect = 1e-19
 Identities = 18/85 (21%), Positives = 39/85 (45%), Gaps = 3/85 (3%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAI 62
           + +    L  ++RE  ++D+  KYG +  +++ + P   +  G A V F   R A++ +
Sbjct: 6  LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65

Query: 63 RGRDGYDFDGHRLRVELAHGGRGRS 87
          +        G+ +  +L   G+ R 
Sbjct: 66 KNLHLTSVMGNIIHAQLDIKGQQRM 90

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 18/97 (18%), Positives = 33/97 (34%), Gaps = 10/97 (10%)

Query: 110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG----SGTTGIVDYTNYDDMKHAIKK 165
            V    L  +     LKD  R+ G+V   ++              V +T+    K  +K 
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 166 LDDSEFRNAF------SRAYVRVREYDHRRDGSQSPS 196
           L  +             +   R++ Y+   +GS +P 
Sbjct: 68  LHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGSYTPQ 104

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 81.2 bits (201), Expect = 1e-19
 Identities = 20/76 (26%), Positives = 31/76 (40%), Gaps = 3/76 (3%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
          +     T Y+GN+P    E ++  LF  +G I     K  P   G  F++++    A   
Sbjct: 23 APPRVTTAYIGNIPHFATEADLIPLFQNFGFILDF--KHYPEK-GCCFIKYDTHEQAAVC 79

Query: 62 IRGRDGYDFDGHRLRV 77
          I     + F G  LR 
Sbjct: 80 IVALANFPFQGRNLRT 95

>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 = 85.8 bits (213), Expect = 1e-19
 Identities = 25/182 (13%), Positives = 60/182 (32%), Gaps = 24/182 (13%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP----GYAFVEFEEARD 57
           S     TL++ N P    +R + DL      +A + +++P         +A+++     D
Sbjct: 113 SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVA-LSIRLPSLRFNTSRRFAYIDVTSKED 171

Query: 58  AEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLP 117
           A   +   +G   +G+ L  +++         +            +  R      +  L 
Sbjct: 172 ARYCVEKLNGLKIEGYTLVTKVS---------NPLEKSKRTDSATLEGREIM---IRNLS 219

Query: 118 SSAS-WQDLKDHMRRAGDVCFSQVFRDGSGT-----TGIVDYTNYDDMKHAIKKLDDSEF 171
           +       L++     G +    +               + + N D  + A+ +++ S  
Sbjct: 220 TELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLL 278

Query: 172 RN 173
            N
Sbjct: 279 GN 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 = 85.4 bits (212), Expect = 2e-19
 Identities = 32/169 (18%), Positives = 63/169 (37%), Gaps = 32/169 (18%)

Query: 8   TLYVGNLPGDIREREVEDLFYKYGPIAHIDL-KIPPRPPGYAFVEFEEARDAEDAIRGRD 66
           T+ V NLP    + +V   F   GPI H+D+     +   +A +EF     A  AI  + 
Sbjct: 43  TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KT 101

Query: 67  GYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLK 126
                 + + V                             +E  + +T  P S + ++++
Sbjct: 102 HKVVGQNEIIVS--------------------------HLTECTLWMTNFPPSYTQRNIR 135

Query: 127 DHMRRAGDVCFSQVF-RDGSGTT---GIVDYTNYDDMKHAIKKLDDSEF 171
           D ++    V  S         T+     +D T+ +D ++ ++KL+  + 
Sbjct: 136 DLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKI 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 = 66.9 bits (164), Expect = 5e-13
 Identities = 20/87 (22%), Positives = 34/87 (39%), Gaps = 10/87 (11%)

Query: 1   MSSRASRTLYVGNLPGDIR-EREVEDLFYKYGPIAHIDLKIPPRPP------GYAFVEFE 53
            ++   R + + NL  ++  E  + + F  +G I  I   IP            AF+ FE
Sbjct: 205 SATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKI--NIPAGQKEHSFNNCCAFMVFE 262

Query: 54  EARDAEDAIRGRDGYDFDGHRLRVELA 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 = 84.7 bits (209), Expect = 1e-19
 Identities = 32/190 (16%), Positives = 67/190 (35%), Gaps = 19/190 (10%)

Query: 1   MSSRASRTLYVGNL-PGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAE 59
           ++   +  L V NL P  +  + +  LF  YG +    +KI       A V+  +   A+
Sbjct: 29  LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDV--QRVKILFNKKENALVQMADGNQAQ 86

Query: 60  DAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYR--------- 110
            A+   +G+   G  +R+ L+     +   +        +  G S    ++         
Sbjct: 87  LAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQN 146

Query: 111 -------VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAI 163
                  + ++ +P S S +DLK      G V     F        ++   + ++   A+
Sbjct: 147 IFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQAL 206

Query: 164 KKLDDSEFRN 173
             L + +   
Sbjct: 207 IDLHNHDLGE 216

>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 = 61.9 bits (150), Expect = 1e-11
 Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 2/76 (2%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGR 65
           S TL++ N+P  + E +++ LF   G +     K   +    A ++     +A  A+   
Sbjct: 151 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF-KFFQKDRKMALIQMGSVEEAVQALIDL 209

Query: 66  DGYD-FDGHRLRVELA 80
             +D  + H LRV  +
Sbjct: 210 HNHDLGENHHLRVSFS 225

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 80.9 bits (200), Expect = 2e-19
 Identities = 28/112 (25%), Positives = 44/112 (39%), Gaps = 19/112 (16%)

Query: 3   SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----------RPPGYAFVE 51
           +  + T++V  L  ++    V D F + G I        P           +  G A V 
Sbjct: 4   NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63

Query: 52  FEEARDAEDAIRGRDGYDFDGHRLRVELAH--------GGRGRSSSDRHSSH 95
           F++   A+ AI   DG +F G+ ++V  A         GG GR   + H  H
Sbjct: 64  FDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRGGLEHHHHH 115

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 78.7 bits (195), Expect = 6e-19
 Identities = 29/83 (34%), Positives = 43/83 (51%), Gaps = 7/83 (8%)

Query: 3  SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEARD 57
          +   R LYVG L  ++ ++ +   F  +G I   D++IP      +  G+AFVEFE A D
Sbjct: 4  ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDI--TDIQIPLDYETEKHRGFAFVEFELAED 61

Query: 58 AEDAIRGRDGYDFDGHRLRVELA 80
          A  AI   +  +  G  +RV LA
Sbjct: 62 AAAAIDNMNESELFGRTIRVNLA 84

>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 = 78.9 bits (195), Expect = 8e-19
 Identities = 28/97 (28%), Positives = 44/97 (45%), Gaps = 8/97 (8%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
           SS  + T+Y G +   + ++ +   F  +G I  I  ++ P   GY+FV F     A  A
Sbjct: 21  SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEI--RVFPEK-GYSFVRFSTHESAAHA 77

Query: 62  IRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
           I   +G   +GH ++        G+ S D  S  SSG
Sbjct: 78  IVSVNGTTIEGHVVKC-----YWGKESPDMTSGPSSG 109

>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 = 80.3 bits (199), Expect = 1e-18
 Identities = 28/187 (14%), Positives = 69/187 (36%), Gaps = 28/187 (14%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-------PRPPGYAFVEFEEARDA 58
           +  ++VG +P    E+++ +LF +YG +   ++ +        P+  G  FV F   + A
Sbjct: 3   AIKMFVGQVPRTWSEKDLRELFEQYGAV--YEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60

Query: 59  EDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPS 118
            +A            ++   + H  + + +    ++    R          ++ +  +  
Sbjct: 61  LEAQNA-----LHNMKVLPGMHHPIQMKPADSEKNNAVEDR----------KLFIGMISK 105

Query: 119 SASWQDLKDHMRRAGDVCFSQVFRDGSGTT---GIVDYTNYDDMKHAIKKLDDSEFRNAF 175
             +  D++      G +   ++ R   G +     V +T     + AIK +  ++     
Sbjct: 106 KCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGC 165

Query: 176 SRA-YVR 181
           S    V+
Sbjct: 166 SSPMVVK 172

>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 = 78.0 bits (193), Expect = 1e-18
 Identities = 27/93 (29%), Positives = 44/93 (47%), Gaps = 3/93 (3%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAI 62
          SR +Y+G++P D  E ++ DL    GP+ ++ +   P   R  GYAF+EF +   +  A+
Sbjct: 2  SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61

Query: 63 RGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSH 95
          R  +GY      L+   +        S  H  H
Sbjct: 62 RNLNGYQLGSRFLKCGYSSNSDISGVSLEHHHH 94

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 78.1 bits (193), Expect = 2e-18
 Identities = 25/96 (26%), Positives = 41/96 (42%), Gaps = 8/96 (8%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAI 62
           ++ LY+ NL   + ER++  LF ++       ++      R  G AF+ F     A  A+
Sbjct: 25  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84

Query: 63  RGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
              +GY   G  L +E       ++   R S  SSG
Sbjct: 85  HLVNGYKLYGKILVIEFG-----KNKKQRSSGPSSG 115

>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 = 77.8 bits (192), Expect = 2e-18
 Identities = 28/108 (25%), Positives = 43/108 (39%), Gaps = 16/108 (14%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----------RPPGYAFV 50
               +  +YV  L   +   ++ D F + G +        P           +P G A V
Sbjct: 11  EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 70

Query: 51  EFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
            +E+   A+ A+   DG DF G +L+V LA     R     +S  SSG
Sbjct: 71  SYEDPPTAKAAVEWFDGKDFQGSKLKVSLA-----RKKPPMNSGPSSG 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 = 43.6 bits (103), Expect = 5e-06
 Identities = 23/115 (20%), Positives = 41/115 (35%), Gaps = 16/115 (13%)

Query: 96  SSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQ--------VFRDG-SG 146
           S   G          + V GL  S +  DL D  ++ G V  ++        ++ D  +G
Sbjct: 3   SGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETG 62

Query: 147 TT---GIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVREYDHRRDGSQSPSRG 198
                  V Y +    K A++  D  +F+       ++V     +   +  PS G
Sbjct: 63  KPKGDATVSYEDPPTAKAAVEWFDGKDFQG---SK-LKVSLARKKPPMNSGPSSG 113

>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 = 78.8 bits (195), Expect = 4e-18
 Identities = 42/185 (22%), Positives = 69/185 (37%), Gaps = 26/185 (14%)

Query: 5   ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDA 61
           ++  L V  LP D+ +RE+  LF   GPI    +          GYAFV+F    D++ A
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61

Query: 62  IRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSAS 121
           I+  +G      RL+V        R   +                 +  + VT LP + +
Sbjct: 62  IKVLNGITVRNKRLKV-----SYARPGGE--------------SIKDTNLYVTNLPRTIT 102

Query: 122 WQDLKDHMRRAGDVCFSQVFRDG-SGTT---GIVDYTNYDDMKHAIKKLDDSEFRNAFSR 177
              L     + G +    + RD  +G       V Y   ++ + AI  L++         
Sbjct: 103 DDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQP 162

Query: 178 AYVRV 182
             VR+
Sbjct: 163 LSVRL 167

>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 = 77.4 bits (191), Expect = 5e-18
 Identities = 29/114 (25%), Positives = 53/114 (46%), Gaps = 7/114 (6%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP----RPPGYAFVEFEEAR 56
           + +     L++G L  +  E+ ++ +F K+GPI   ++ +      +  G+AF+ FE   
Sbjct: 2   VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPI--SEVLLIKDRTSKSRGFAFITFENPA 59

Query: 57  DAEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYR 110
           DA++A +  +G    G  ++VE A       S  R    +S R R  S   E+ 
Sbjct: 60  DAKNAAKDMNGKSLHGKAIKVEQAK-KPSFQSGGRRRPPASSRNRSPSGSLEHH 112

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 40.4 bits (95), Expect = 9e-05
 Identities = 22/114 (19%), Positives = 43/114 (37%), Gaps = 7/114 (6%)

Query: 103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTT---GIVDYTNYDDM 159
           V      ++ + GL    + + LK    + G +    + +D +  +     + + N  D 
Sbjct: 2   VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADA 61

Query: 160 KHAIKKLDDSEFRNAFSRAYVRVREYDHRRDGSQSPSRGRSYSRGRSESRSRSR 213
           K+A K ++         +A ++V +       S    R  + SR RS S S   
Sbjct: 62  KNAAKDMNGKSL---HGKA-IKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLEH 111

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 77.9 bits (192), Expect = 5e-18
 Identities = 28/82 (34%), Positives = 42/82 (51%), Gaps = 3/82 (3%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDA 58
           S+   R LYVG L  ++ ++ +   F  +G I  I + +     +  G+AFVEFE A DA
Sbjct: 59  SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 118

Query: 59  EDAIRGRDGYDFDGHRLRVELA 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 = 39.0 bits (91), Expect = 4e-04
 Identities = 18/99 (18%), Positives = 34/99 (34%), Gaps = 4/99 (4%)

Query: 77  VELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVC 136
             +A+     +            G G S  ++  + V GL      + L       GD+ 
Sbjct: 32  ESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDIT 91

Query: 137 FSQVFRD-GSGTT---GIVDYTNYDDMKHAIKKLDDSEF 171
             Q+  D  +        V++   +D   AI  +++SE 
Sbjct: 92  DIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL 130

>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 = 76.8 bits (189), Expect = 6e-18
 Identities = 22/79 (27%), Positives = 33/79 (41%), Gaps = 3/79 (3%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
          S R+   +   NLP      E+++ F ++G +  + L   P     A VEF E  +A  A
Sbjct: 6  SGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL---PEGGITAIVEFLEPLEARKA 62

Query: 62 IRGRDGYDFDGHRLRVELA 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 = 45.2 bits (107), Expect = 1e-06
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 2/73 (2%)

Query: 101 RGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMK 160
            G S RS+  +L   LP+     ++++   R G +   +V     G T IV++    + +
Sbjct: 3   SGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSL--GRVLLPEGGITAIVEFLEPLEAR 60

Query: 161 HAIKKLDDSEFRN 173
            A + L  S+F +
Sbjct: 61  KAFRHLAYSKFHH 73

>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 = 78.4 bits (194), Expect = 7e-18
 Identities = 33/179 (18%), Positives = 66/179 (36%), Gaps = 32/179 (17%)

Query: 5   ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP--------PRPPGYAFVEFEEAR 56
           ++R LYVGN+P  I E  + D F     +  +              +   +AF+EF    
Sbjct: 3   SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62

Query: 57  DAEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGL 116
           +   A+   DG  F G  L++        R    +                 +++ + GL
Sbjct: 63  ETTQAM-AFDGIIFQGQSLKI-------RRPHDYQ------------PLPGAHKLFIGGL 102

Query: 117 PSSASWQDLKDHMRRAGDVCFSQVFRD-GSGTT---GIVDYTNYDDMKHAIKKLDDSEF 171
           P+  +   +K+ +   G +    + +D  +G +      +Y + +    AI  L+  + 
Sbjct: 103 PNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 161

>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 = 66.1 bits (162), Expect = 2e-13
 Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
           L++G LP  + + +V++L   +GP+   +L          GYAF E+ +    + AI G 
Sbjct: 97  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156

Query: 66  DGYDFDGHRLRVELA 80
           +G      +L V+ A
Sbjct: 157 NGMQLGDKKLLVQRA 171

>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 = 76.2 bits (188), Expect = 7e-18
 Identities = 24/91 (26%), Positives = 41/91 (45%), Gaps = 1/91 (1%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
            S  S+TL + NL     E  ++++F K   I         +  GYAF+EF    DA++A
Sbjct: 11  WSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQ-NQNGKSKGYAFIEFASFEDAKEA 69

Query: 62  IRGRDGYDFDGHRLRVELAHGGRGRSSSDRH 92
           +   +  + +G  +R+EL       +S    
Sbjct: 70  LNSCNKREIEGRAIRLELQGPRGSPNSGPSS 100

>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 = 76.2 bits (188), Expect = 9e-18
 Identities = 21/95 (22%), Positives = 40/95 (42%), Gaps = 6/95 (6%)

Query: 7   RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRD 66
           + L+V NL   + E  +E  F ++G +  +          YAF+ F+E   A  A+   +
Sbjct: 12  KVLFVRNLANTVTEEILEKAFSQFGKLERVKK-----LKDYAFIHFDERDGAVKAMEEMN 66

Query: 67  GYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGR 101
           G D +G  + +  A     +   +R +   +  G 
Sbjct: 67  GKDLEGENIEIVFAK-PPDQKRKERKAQRQAASGP 100

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 77.6 bits (192), Expect = 1e-17
 Identities = 42/169 (24%), Positives = 74/169 (43%), Gaps = 27/169 (15%)

Query: 7   RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP----RPPGYAFVEFEEARDAEDAI 62
           R LYVGNL   I E  ++  F   GPIA+I  KI      +   YAFVE+ ++ DA  A+
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANI--KIMIDKNNKNVNYAFVEYHQSHDANIAL 58

Query: 63  RGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASW 122
           +  +G   + + +++  A   +  SS D                  + + V  L  +   
Sbjct: 59  QTLNGKQIENNIVKINWAFQSQQSSSDD-----------------TFNLFVGDLNVNVDD 101

Query: 123 QDLKDHMRRAGDVCFSQVFRDG-SGTT---GIVDYTNYDDMKHAIKKLD 167
           + L++  +         V  D  +G++   G V +T+ DD ++A+  + 
Sbjct: 102 ETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQ 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 = 58.3 bits (142), Expect = 9e-11
 Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 7/78 (8%)

Query: 8   TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEARDAEDAI 62
            L+VG+L  ++ +  + + F  +     +   +          GY FV F    DA++A+
Sbjct: 89  NLFVGDLNVNVDDETLRNAFKDFPSY--LSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 146

Query: 63  RGRDGYDFDGHRLRVELA 80
               G D +G  LR+  A
Sbjct: 147 DSMQGQDLNGRPLRINWA 164

>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 = 75.4 bits (186), Expect = 1e-17
 Identities = 24/84 (28%), Positives = 37/84 (44%), Gaps = 6/84 (7%)

Query: 4  RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP----RPPGYAFVEFEEARDAE 59
           A RT++VGNL   +RE  + +LF + GP+    + I      +P  + FV F+      
Sbjct: 14 EADRTVFVGNLEARVREEILYELFLQAGPL--TKVTICKDREGKPKSFGFVCFKHPESVS 71

Query: 60 DAIRGRDGYDFDGHRLRVELAHGG 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 = 37.2 bits (87), Expect = 6e-04
 Identities = 18/82 (21%), Positives = 33/82 (40%), Gaps = 4/82 (4%)

Query: 93  SSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTT---G 149
           SS SSG        ++  V V  L +    + L +   +AG +    + +D  G     G
Sbjct: 2   SSGSSGM-FPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFG 60

Query: 150 IVDYTNYDDMKHAIKKLDDSEF 171
            V + + + + +AI  L+    
Sbjct: 61  FVCFKHPESVSYAIALLNGIRL 82

>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 = 75.6 bits (186), Expect = 1e-17
 Identities = 25/106 (23%), Positives = 40/106 (37%), Gaps = 9/106 (8%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGP-----IAHIDLKIPPRPPGYAFVEFEEAR 56
            S  +  L++G +P   +  E+ +   K        I +       +  G+AFVE+E  R
Sbjct: 4   GSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHR 63

Query: 57  DAEDAIR--GRDGYDFDGHRLRVELAHGGRGR--SSSDRHSSHSSG 98
            A  A R          GH++ V+ A           +  S  SSG
Sbjct: 64  AAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVSGPSSG 109

>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 = 74.9 bits (185), Expect = 2e-17
 Identities = 33/101 (32%), Positives = 49/101 (48%), Gaps = 12/101 (11%)

Query: 3   SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEARD 57
           +   R LYVG L  ++ ++ +   F  +G I   D++IP      +  G+AFVEFE A D
Sbjct: 9   ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDI--TDIQIPLDYETEKHRGFAFVEFELAED 66

Query: 58  AEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
           A  AI   +  +  G  +RV LA     +    + S  SSG
Sbjct: 67  AAAAIDNMNESELFGRTIRVNLA-----KPMRIKESGPSSG 102

>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 = 74.5 bits (184), Expect = 2e-17
 Identities = 29/85 (34%), Positives = 43/85 (50%), Gaps = 3/85 (3%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDA 58
          +   +  L V  L     ER++ ++F KYGPIA + +       R  G+AFV FE   DA
Sbjct: 11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 70

Query: 59 EDAIRGRDGYDFDGHRLRVELAHGG 83
          ++A    +G + DG R+RV     G
Sbjct: 71 KEAKERANGMELDGRRIRVSGPSSG 95

>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 = 74.6 bits (184), Expect = 3e-17
 Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 2/79 (2%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
            RA+RTL   NL  +I E E++++F     I  +      +  G A++EF+   DAE  
Sbjct: 12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSK--GIAYIEFKSEADAEKN 69

Query: 62 IRGRDGYDFDGHRLRVELA 80
          +  + G + DG  + +   
Sbjct: 70 LEEKQGAEIDGRSVSLYYT 88

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 74.1 bits (183), Expect = 3e-17
 Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 1/88 (1%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-RPPGYAFVEFEEARDAED 60
           S  +  ++V NLP D   + ++D F + G + + D+K+   +  G   V+FE    AE 
Sbjct: 4  GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAER 63

Query: 61 AIRGRDGYDFDGHRLRVELAHGGRGRSS 88
          A R  +G    G  + V +     G 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 = 49.9 bits (120), Expect = 2e-08
 Identities = 19/95 (20%), Positives = 37/95 (38%), Gaps = 11/95 (11%)

Query: 104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD--GSGTTGIVDYTNYDDMKH 161
                 ++ V  LP   +W+ LKD     G V ++ +  +   S   G+V + + +  + 
Sbjct: 4   GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAER 63

Query: 162 AIKKLDDSEF--RNAFSRAYVRVREYDHRRDGSQS 194
           A + ++  +   R       + VR  D    G  S
Sbjct: 64  ACRMMNGMKLSGRE------IDVRI-DRNASGPSS 91

>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 = 74.6 bits (184), Expect = 3e-17
 Identities = 29/97 (29%), Positives = 43/97 (44%), Gaps = 10/97 (10%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
          + R   TLYV     D+    +   F  +G I  IDL + P P   AFV +E+   A+ A
Sbjct: 11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNI--IDLSMDP-PRNCAFVTYEKMESADQA 65

Query: 62 IRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
          +   +G   +  +L+V +A     R      S  SSG
Sbjct: 66 VAELNGTQVESVQLKVNIA-----RKQPMLDSGPSSG 97

>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 = 74.2 bits (183), Expect = 3e-17
 Identities = 19/81 (23%), Positives = 38/81 (46%), Gaps = 3/81 (3%)

Query: 3  SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAE 59
          + +  T+YV NLP  +   ++  +F KYG +  + +   K   +  G AF+ F +   A+
Sbjct: 13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72

Query: 60 DAIRGRDGYDFDGHRLRVELA 80
          +  R  +     G  ++  +A
Sbjct: 73 NCTRAINNKQLFGRVIKASIA 93

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 76.5 bits (189), Expect = 3e-17
 Identities = 41/170 (24%), Positives = 70/170 (41%), Gaps = 26/170 (15%)

Query: 5   ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDA 61
           +   L V  LP ++ + E   LF   G I    L   KI  +  GY FV + + +DAE A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 62  IRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSAS 121
           I   +G       ++V  A     R SS                     + V+GLP + +
Sbjct: 61  INTLNGLRLQTKTIKVSYA-----RPSSASIRDA--------------NLYVSGLPKTMT 101

Query: 122 WQDLKDHMRRAGDVCFSQVFRDG-SGTT---GIVDYTNYDDMKHAIKKLD 167
            ++L+    + G +  S++  D  +G +   G + +    + + AIK L+
Sbjct: 102 QKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN 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 = 61.8 bits (151), Expect = 6e-12
 Identities = 29/88 (32%), Positives = 45/88 (51%), Gaps = 11/88 (12%)

Query: 2   SSRASRT--LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEE 54
           SS + R   LYV  LP  + ++E+E LF +YG I  I  +I          G  F+ F++
Sbjct: 82  SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRI--ITSRILVDQVTGVSRGVGFIRFDK 139

Query: 55  ARDAEDAIRGRDGYDFDGHR--LRVELA 80
             +AE+AI+G +G    G    + V+ A
Sbjct: 140 RIEAEEAIKGLNGQKPSGATEPITVKFA 167

>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 = 77.3 bits (191), Expect = 3e-17
 Identities = 42/167 (25%), Positives = 70/167 (41%), Gaps = 22/167 (13%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAI 62
             +LYVG+L  D+ E  + + F   GPI  I +    I  R  GYA+V F++  DAE A+
Sbjct: 15  MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 74

Query: 63  RGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASW 122
              +     G  +R+  +     R  S R S                 + +  L  S   
Sbjct: 75  DTMNFDVIKGKPVRIMWSQ----RDPSLRKSGV-------------GNIFIKNLDKSIDN 117

Query: 123 QDLKDHMRRAGDVCFSQVFRDGSGTTGI--VDYTNYDDMKHAIKKLD 167
           + L D     G++   +V  D +G+ G   V +   +  + AI+K++
Sbjct: 118 KALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 164

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 73.9 bits (182), Expect = 5e-17
 Identities = 21/89 (23%), Positives = 42/89 (47%), Gaps = 6/89 (6%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP----RPPGYAFVEFEEARD 57
          +S     L++  LP    + E+E++   +G +   DL++      +P G A+VE+E    
Sbjct: 13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTV--KDLRLVTNRAGKPKGLAYVEYENESQ 70

Query: 58 AEDAIRGRDGYDFDGHRLRVELAHGGRGR 86
          A  A+   DG     + ++V +++ G   
Sbjct: 71 ASQAVMKMDGMTIKENIIKVAISNSGPSS 99

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 40.7 bits (96), Expect = 4e-05
 Identities = 20/82 (24%), Positives = 40/82 (48%), Gaps = 3/82 (3%)

Query: 93  SSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTT---G 149
           SS SSG  R  +   ++++ ++GLP S + ++L++  +  G V   ++  + +G      
Sbjct: 2   SSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLA 61

Query: 150 IVDYTNYDDMKHAIKKLDDSEF 171
            V+Y N      A+ K+D    
Sbjct: 62  YVEYENESQASQAVMKMDGMTI 83

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 73.6 bits (181), Expect = 7e-17
 Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 8/80 (10%)

Query: 6  SRTLYVGNLPGDIRERE------VEDLFYKYGPIAHIDLKIPP-RPPGYAFVEFEEARDA 58
             + V N+P    +R       +  +F K+G I +        +  GY F+E+     A
Sbjct: 15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHA 74

Query: 59 EDAIRGRDGYDFDG-HRLRV 77
           DA++  DGY  D  H  RV
Sbjct: 75 VDAVKNADGYKLDKQHTFRV 94

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 73.4 bits (181), Expect = 1e-16
 Identities = 26/94 (27%), Positives = 40/94 (42%), Gaps = 3/94 (3%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDA 58
                 T+YVG L   + E  + +LF + GP+ +  +   ++  +  GY FVEF    DA
Sbjct: 11  ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 70

Query: 59  EDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRH 92
           + AI+  D     G  +RV  A       S    
Sbjct: 71  DYAIKIMDMIKLYGKPIRVNKASAHNKNLSGPSS 104

>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 = 73.1 bits (180), Expect = 1e-16
 Identities = 23/95 (24%), Positives = 41/95 (43%), Gaps = 6/95 (6%)

Query: 3  SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP------GYAFVEFEEAR 56
          S  S  L++ NL     E  ++ +F K G I    +             G+ FVE+++  
Sbjct: 2  SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61

Query: 57 DAEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDR 91
           A+ A++   G+  DGH+L V ++      +S   
Sbjct: 62 QAQKALKQLQGHTVDGHKLEVRISERATKPASGPS 96

>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 = 73.1 bits (180), Expect = 1e-16
 Identities = 28/102 (27%), Positives = 54/102 (52%), Gaps = 10/102 (9%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEAR 56
             R+ R+++VGN+P +  E +++D+F + GP+  +  ++       +P GY F E+++  
Sbjct: 4   VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPV--VSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 57  DAEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
            A  A+R  +G +F G  LRV+ A       + +   S  +G
Sbjct: 62  TALSAMRNLNGREFSGRALRVDNA---ASEKNKEELKSLGTG 100

>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 = 71.5 bits (176), Expect = 3e-16
 Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 4/77 (5%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
            +   TLYVG L   I E ++ + FY++G I  I   +  R    AF++F   + AE A
Sbjct: 8  EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTI--TVVQR-QQCAFIQFATRQAAEVA 64

Query: 62 I-RGRDGYDFDGHRLRV 77
            +  +    +G RL V
Sbjct: 65 AEKSFNKLIVNGRRLNV 81

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 71.5 bits (176), Expect = 4e-16
 Identities = 34/96 (35%), Positives = 44/96 (45%), Gaps = 10/96 (10%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP---GYAFVEFEEARDAEDAI 62
            RTLYVGNL  D+ E  +  LF + GP      K+         Y FVEF E RDA  A+
Sbjct: 15  PRTLYVGNLSRDVTEVLILQLFSQIGPCKSC--KMITEHTSNDPYCFVEFYEHRDAAAAL 72

Query: 63  RGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
              +G    G  ++V  A      + S + S  SSG
Sbjct: 73  AAMNGRKILGKEVKVNWA-----TTPSSQKSGPSSG 103

>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 = 71.6 bits (176), Expect = 5e-16
 Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARD 57
             S     L+V ++  + +E E+++ F  YG I +I L +        GYA VE+E  + 
Sbjct: 21  QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQ 80

Query: 58  AEDAIRGRDGYDFDGHRLRVELAH 81
           A  A    +G +  G  ++V+   
Sbjct: 81  ALAAKEALNGAEIMGQTIQVDWCF 104

>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 = 71.1 bits (175), Expect = 5e-16
 Identities = 31/95 (32%), Positives = 41/95 (43%), Gaps = 3/95 (3%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDA 58
           S  S  L+V NL     E ++E LF  YGP++ +   I     +P G+AFV F     A
Sbjct: 4  GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 59 EDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHS 93
            A    DG  F G  L V  +   +  S S   S
Sbjct: 64 VKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSS 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 = 72.5 bits (178), Expect = 5e-16
 Identities = 30/106 (28%), Positives = 45/106 (42%), Gaps = 12/106 (11%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEAR 56
                R L V  +P  + E ++  LF +YGPI    +KI       +  GY FV+F+   
Sbjct: 38  EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPI--ESVKIVCDRETRQSRGYGFVKFQSGS 95

Query: 57  DAEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRG 102
            A+ AI G +G++    RL+V LA      S   R     +     
Sbjct: 96  SAQQAIAGLNGFNILNKRLKVALA-----ASGHQRPGIAGAVGDGN 136

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 71.5 bits (176), Expect = 5e-16
 Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARD 57
             S     L+V  +  +  E ++ D F +YG I +I L +        GY  VE+E  ++
Sbjct: 18  QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 77

Query: 58  AEDAIRGRDGYDFDGHRLRVELAH 81
           A+ A+ G +G D  G  + V+   
Sbjct: 78  AQAAMEGLNGQDLMGQPISVDWCF 101

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 71.2 bits (175), Expect = 5e-16
 Identities = 25/98 (25%), Positives = 45/98 (45%), Gaps = 6/98 (6%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL-KIPPRPPGYAFVEFEEARDAED 60
           S    + L+V N+P   R+ ++  +F ++G I  +++        G+ FV FE + DA+ 
Sbjct: 11  SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADR 70

Query: 61  AIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
           A     G   +G ++ V  A      +    +S  SSG
Sbjct: 71  AREKLHGTVVEGRKIEVNNA-----TARVMTNSGPSSG 103

>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 = 38.0 bits (89), Expect = 5e-04
 Identities = 23/107 (21%), Positives = 40/107 (37%), Gaps = 10/107 (9%)

Query: 96  SSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGI--VDY 153
           S   G   S+ +  R+ V+ +P      DL+    + G +   ++  +  G+ G   V +
Sbjct: 3   SGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTF 62

Query: 154 TNYDDMKHAIKKLDDSEF--RNAFSRAYVRVREYDHRRDGSQSPSRG 198
            N  D   A +KL  +    R       + V     R   +  PS G
Sbjct: 63  ENSADADRAREKLHGTVVEGRK------IEVNNATARVMTNSGPSSG 103

>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 = 75.3 bits (184), Expect = 5e-16
 Identities = 26/96 (27%), Positives = 48/96 (50%), Gaps = 9/96 (9%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFY----KYGPIAHIDLKIPPRPPGYAFVEFEEARD 57
           +R + T+Y+ NL   I++ E++   Y    ++G I  I +    +  G AFV F+E   
Sbjct: 5  ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64

Query: 58 AEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHS 93
          A +A+R   G+ F    +R++ A     ++ SD  +
Sbjct: 65 ATNALRSMQGFPFYDKPMRIQYA-----KTDSDIIA 95

>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 = 58.3 bits (140), Expect = 4e-10
 Identities = 17/74 (22%), Positives = 33/74 (44%), Gaps = 3/74 (4%)

Query: 8   TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG 67
            L++ NLP +  E  +  LF ++      ++++ P     AFVEF+    A  A     G
Sbjct: 209 ILFLTNLPEETNELMLSMLFNQFPGF--KEVRLVPGRHDIAFVEFDNEVQAGAARDALQG 266

Query: 68  YDF-DGHRLRVELA 80
           +     + +++  A
Sbjct: 267 FKITQNNAMKISFA 280

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 70.5 bits (173), Expect = 6e-16
 Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 12/80 (15%)

Query: 8  TLYVGNLP------GDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDA 58
           + V N+P       +  +  +  +F K+G I   +   P    +  GY F+E+     A
Sbjct: 3  VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKI--TNDFYPEEDGKTKGYIFLEYASPAHA 60

Query: 59 EDAIRGRDGYDFDG-HRLRV 77
           DA++  DGY  D  H  RV
Sbjct: 61 VDAVKNADGYKLDKQHTFRV 80

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 70.8 bits (174), Expect = 7e-16
 Identities = 20/89 (22%), Positives = 40/89 (44%), Gaps = 3/89 (3%)

Query: 3  SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAI 62
          S   R+++V   P  +   ++ + F  +GP+A +   +      +A VE  +   A +A+
Sbjct: 5  SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGVFAIVEMGDV-GAREAV 61

Query: 63 RGRDGYDFDGHRLRVELAHGGRGRSSSDR 91
            +  +   GHRLRV        +S + +
Sbjct: 62 LSQSQHSLGGHRLRVRPREQKEFQSPASK 90

>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 = 70.7 bits (174), Expect = 9e-16
 Identities = 30/87 (34%), Positives = 43/87 (49%), Gaps = 3/87 (3%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAI 62
           + T+ V NL  D RE ++++LF  +G I+ I L   K   +  G+AF+ F    DA  AI
Sbjct: 15  NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74

Query: 63  RGRDGYDFDGHRLRVELAHGGRGRSSS 89
            G  G+ +D   L VE A        S
Sbjct: 75  AGVSGFGYDHLILNVEWAKPSTNSGPS 101

>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 = 70.4 bits (173), Expect = 1e-15
 Identities = 21/93 (22%), Positives = 37/93 (39%), Gaps = 5/93 (5%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHI----DLKIPPRPPGYAFVEFEEARD 57
             + +  + V N+P    +RE+ +LF  +G +  +     +       G+ FV+F   +D
Sbjct: 11  KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70

Query: 58  AEDAIRG-RDGYDFDGHRLRVELAHGGRGRSSS 89
           A+ A           G RL +E A       S 
Sbjct: 71  AKKAFNALCHSTHLYGRRLVLEWADSEVTVQSG 103

>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 = 69.5 bits (171), Expect = 2e-15
 Identities = 14/92 (15%), Positives = 30/92 (32%), Gaps = 10/92 (10%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEARDAEDAIR 63
          LY+GNL     + ++ +  +  G    +++K        +  G+A V       ++  + 
Sbjct: 4  LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 64 GRDGYDFDGHRLRVELAHGGRGRSSSDRHSSH 95
               +  G    V  +           H  H
Sbjct: 64 LLPKRELHGQNPVVTPS-----NKLEHHHHHH 90

>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 = 69.4 bits (170), Expect = 2e-15
 Identities = 21/82 (25%), Positives = 34/82 (41%), Gaps = 9/82 (10%)

Query: 4  RASRTLYVGNLPGDIREREVEDLFYKYGPIAH--------IDLKIPPRPPGYAFVEFEEA 55
           ++R LYVGN+P  I E  + D F     +          +      +   +AF+EF   
Sbjct: 4  GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 63

Query: 56 RDAEDAIRGRDGYDFDGHRLRV 77
           +   A+   DG  F G  L++
Sbjct: 64 DETTQAMA-FDGIIFQGQSLKI 84

>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 = 69.1 bits (170), Expect = 3e-15
 Identities = 28/101 (27%), Positives = 44/101 (43%), Gaps = 12/101 (11%)

Query: 3  SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEARD 57
          S  S  LYVG+L  +I E  +  +F  +G I   ++ +       R  GY F+ F ++  
Sbjct: 2  SSGSSGLYVGSLHFNITEDMLRGIFEPFGKI--DNIVLMKDSDTGRSKGYGFITFSDSEC 59

Query: 58 AEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
          A  A+   +G++  G  +RV            D  S  SSG
Sbjct: 60 ARRALEQLNGFELAGRPMRVGHV-----TERLDGGSGPSSG 95

>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 = 68.9 bits (169), Expect = 5e-15
 Identities = 23/82 (28%), Positives = 39/82 (47%), Gaps = 3/82 (3%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDA 58
            S     LYVG+L  +I E  +  +F  +G I  I L +     R  GY F+ F ++  A
Sbjct: 22  GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECA 81

Query: 59  EDAIRGRDGYDFDGHRLRVELA 80
           + A+   +G++  G  ++V   
Sbjct: 82  KKALEQLNGFELAGRPMKVGHV 103

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 70.3 bits (172), Expect = 5e-15
 Identities = 34/94 (36%), Positives = 44/94 (46%), Gaps = 7/94 (7%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEA 55
           M      +L V NL        +  +F KYG +   D+ IP         G+AFV F + 
Sbjct: 65  MDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRV--GDVYIPRDRYTKESRGFAFVRFHDK 122

Query: 56  RDAEDAIRGRDGYDFDGHRLRVELAHGGRGRSSS 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 = 39.1 bits (91), Expect = 4e-04
 Identities = 19/130 (14%), Positives = 37/130 (28%), Gaps = 10/130 (7%)

Query: 46  GYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSR 105
           G    E  +A  AE   +     +        + A      +    H          +  
Sbjct: 14  GETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHH------HHHHMDV 67

Query: 106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD-GSGTT---GIVDYTNYDDMKH 161
                + V  L    S   L+    + G V    + RD  +  +     V + +  D + 
Sbjct: 68  EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 127

Query: 162 AIKKLDDSEF 171
           A+  +D +  
Sbjct: 128 AMDAMDGAVL 137

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 68.2 bits (167), Expect = 7e-15
 Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 4/72 (5%)

Query: 10 YVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAIRGRD 66
           + +    + ++ +  LF K G + +++  I     +  G+ FVE     DA+  I+   
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 67 GYDFDG-HRLRV 77
          G   D  HRL +
Sbjct: 76 GKRLDLKHRLFL 87

>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 = 67.5 bits (166), Expect = 1e-14
 Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 4/78 (5%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAI 62
          +R++YVGN+       E+E  F+  G +  + +   K    P G+A++EF +      ++
Sbjct: 6  ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65

Query: 63 RGRDGYDFDGHRLRVELA 80
             D   F G +++V   
Sbjct: 66 A-LDESLFRGRQIKVIPK 82

>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 = 67.2 bits (165), Expect = 1e-14
 Identities = 27/91 (29%), Positives = 44/91 (48%), Gaps = 8/91 (8%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEARDAEDA 61
          R +YVGNL       +V++LF ++G +   ++K+       +P G+ FVE +E     +A
Sbjct: 2  RNIYVGNLVYSATSEQVKELFSQFGKV--FNVKLIYDRETKKPKGFGFVEMQEE-SVSEA 58

Query: 62 IRGRDGYDFDGHRLRVELAHGGRGRSSSDRH 92
          I   D  DF G  +RV  A+  +       H
Sbjct: 59 IAKLDNTDFMGRTIRVTEANPKKSLEHHHHH 89

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 68.7 bits (168), Expect = 2e-14
 Identities = 33/110 (30%), Positives = 49/110 (44%), Gaps = 6/110 (5%)

Query: 3   SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAE 59
            + S TLYVGNL     E ++ +LF K G I  I +   K+     G+ FVE+    DAE
Sbjct: 36  LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 95

Query: 60  DAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEY 109
           +A+R  +G   D   +R +      G     ++    SG       R +Y
Sbjct: 96  NAMRYINGTRLDDRIIRTDWD---AGFKEGRQYGRGRSGGQVRDEYRQDY 142

>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 = 66.9 bits (164), Expect = 2e-14
 Identities = 19/81 (23%), Positives = 31/81 (38%), Gaps = 3/81 (3%)

Query: 5  ASRTLYVGNLPGDIREREVEDLFYKYGPIA---HIDLKIPPRPPGYAFVEFEEARDAEDA 61
              + V N+P  +   E+ D FY Y  I     +       P G A V FE   +A  A
Sbjct: 14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73

Query: 62 IRGRDGYDFDGHRLRVELAHG 82
          +   +       ++++ L  G
Sbjct: 74 VIDLNDRPIGSRKVKLVLGSG 94

>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 = 68.3 bits (167), Expect = 2e-14
 Identities = 23/102 (22%), Positives = 43/102 (42%), Gaps = 13/102 (12%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIA--------HIDLKIPPRPPGYAFVEFEEARD 57
           +  +YV NL   ++E++++ +F +Y   +         I L    R  G AF+     + 
Sbjct: 45  NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKA 104

Query: 58  AEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGR 99
           A  A++  +GY   G  + V+ A     RS+  +       R
Sbjct: 105 AAKALKEANGYVLFGKPMVVQFA-----RSARPKQDPKEGKR 141

>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 = 66.9 bits (164), Expect = 2e-14
 Identities = 35/98 (35%), Positives = 49/98 (50%), Gaps = 12/98 (12%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEARDAED 60
              L+VG L  D  E+ +E +F KYG I   ++ +       R  G+ FV FE   DA+D
Sbjct: 12  EGKLFVGGLSFDTNEQSLEQVFSKYGQI--SEVVVVKDRETQRSRGFGFVTFENIDDAKD 69

Query: 61  AIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
           A+   +G   DG ++RV+ A       SSD  S  SSG
Sbjct: 70  AMMAMNGKSVDGRQIRVDQA-----GKSSDNRSGPSSG 102

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 67.0 bits (164), Expect = 3e-14
 Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL-KIPPRPPGYAFVEFEEARDAEDAIRG 64
            + L+V N+P   R+ ++  +F ++G I  +++        G+ FV FE + DA+ A   
Sbjct: 29  PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREK 88

Query: 65  RDGYDFDGHRLRVELA 80
             G   +G ++ V  A
Sbjct: 89  LHGTVVEGRKIEVNNA 104

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 65.8 bits (161), Expect = 4e-14
 Identities = 15/91 (16%), Positives = 31/91 (34%), Gaps = 9/91 (9%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEAR 56
                T+ + N+        +      Y  +A  ++++       +  G+AFV+   A 
Sbjct: 5  HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAM 64

Query: 57 DAEDAIRGRDGYD----FDGHRLRVELAHGG 83
          DA   ++           DG  + V+ A   
Sbjct: 65 DASQLLQILQSLHPPLKIDGKTIGVDFAKSA 95

>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 = 66.4 bits (162), Expect = 5e-14
 Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 9/82 (10%)

Query: 8  TLYVGNLPGDIREREV---EDLFYKYGPIAHIDL------KIPPRPPGYAFVEFEEARDA 58
           ++V  L   + + EV    + F K+G I  + +           P   A+V +  + DA
Sbjct: 17 LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76

Query: 59 EDAIRGRDGYDFDGHRLRVELA 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 = 66.2 bits (162), Expect = 6e-14
 Identities = 30/111 (27%), Positives = 46/111 (41%), Gaps = 4/111 (3%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARD 57
             S     L+V  +  +  E ++ D F +YG I +I L +        GY  VE+E  ++
Sbjct: 17  QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 76

Query: 58  AEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSE 108
           A+ A+ G +G D  G  + V+     RG     R       R     RR E
Sbjct: 77  AQAAMEGLNGQDLMGQPISVDWCF-VRGPPKGKRRGGRRRSRSPDRRRRLE 126

>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 = 65.2 bits (160), Expect = 6e-14
 Identities = 17/83 (20%), Positives = 29/83 (34%), Gaps = 7/83 (8%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEARDAED 60
          S  LY+  L     ++++  L   YG I  +  K        +  GY FV+F+    A+ 
Sbjct: 5  SSGLYIRGLQPGTTDQDLVKLCQPYGKI--VSTKAILDKTTNKCKGYGFVDFDSPSAAQK 62

Query: 61 AIRGRDGYDFDGHRLRVELAHGG 83
          A+             +      G
Sbjct: 63 AVTALKASGVQAQMAKQSGPSSG 85

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 65.4 bits (160), Expect = 9e-14
 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP--RPPGYAFVEFEEARDAEDAIR 63
              L V NL   + + ++++LF ++G +    +      R  G A V FE   DA  A++
Sbjct: 29  GGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMK 88

Query: 64  GRDGYDFDGHRLRVELA 80
             +G   DG  + ++L 
Sbjct: 89  QYNGVPLDGRPMNIQLV 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 = 48.4 bits (116), Expect = 1e-07
 Identities = 20/91 (21%), Positives = 35/91 (38%), Gaps = 3/91 (3%)

Query: 84  RGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD 143
           +      +H    SG G G    +  ++LV+ L    S  D+++     G +  + V  D
Sbjct: 5   KQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD 64

Query: 144 GSGT---TGIVDYTNYDDMKHAIKKLDDSEF 171
            SG    T  V +    D   A+K+ +    
Sbjct: 65  RSGRSLGTADVHFERKADALKAMKQYNGVPL 95

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 65.4 bits (160), Expect = 9e-14
 Identities = 21/94 (22%), Positives = 39/94 (41%), Gaps = 4/94 (4%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAH---IDLKIPPRPPGYAFVEFEEARD 57
           +      T ++GNLP D+ E  +++ F      A     +   P R  G+ + EFE+   
Sbjct: 10  LPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDS 69

Query: 58  AEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDR 91
              A+   +       R+RV++A   + + S   
Sbjct: 70  LLSALS-LNEESLGNKRIRVDVADQAQDKDSGPS 102

>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 = 65.4 bits (160), Expect = 9e-14
 Identities = 26/92 (28%), Positives = 41/92 (44%), Gaps = 4/92 (4%)

Query: 3   SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAE 59
            R +RT++   L   IR R++ED F   G +  + +   +   R  G A+VEF E +   
Sbjct: 22  ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP 81

Query: 60  DAIRGRDGYDFDGHRLRVELAHGGRGRSSSDR 91
            AI G  G    G  + V+ +   + R S   
Sbjct: 82  LAI-GLTGQRLLGVPIIVQASQAEKNRLSGPS 112

>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 = 65.0 bits (159), Expect = 9e-14
 Identities = 19/79 (24%), Positives = 31/79 (39%), Gaps = 3/79 (3%)

Query: 5  ASRTLYVGNLPGDIREREVEDLFYKYGPIAH-IDLKIPP--RPPGYAFVEFEEARDAEDA 61
              + V N+P  +   E+ D FY Y  I   + LK      P G A V FE   +A  A
Sbjct: 14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73

Query: 62 IRGRDGYDFDGHRLRVELA 80
          +   +       ++++   
Sbjct: 74 VIDLNDRPIGSRKVKLSGP 92

>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 = 64.8 bits (158), Expect = 1e-13
 Identities = 19/95 (20%), Positives = 36/95 (37%), Gaps = 7/95 (7%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIR-- 63
           S  ++V  L   + E ++ +   K+G I ++ +         A VEFE    A++ +   
Sbjct: 15  SPVVHVRGLCESVVEADLVEALEKFGTICYVMM---MPFKRQALVEFENIDSAKECVTFA 71

Query: 64  GRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
                   G +     +     R +   +S  SSG
Sbjct: 72  ADVPVYIAGQQAFFNYST--SKRITRPGNSGPSSG 104

>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 = 64.7 bits (158), Expect = 3e-13
 Identities = 29/86 (33%), Positives = 45/86 (52%), Gaps = 3/86 (3%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDA 58
           +   +  L V  L     ER++ ++F KYGPIA + +       R  G+AFV FE   DA
Sbjct: 42  NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 101

Query: 59  EDAIRGRDGYDFDGHRLRVELAHGGR 84
           ++A    +G + DG R+RV+ +   R
Sbjct: 102 KEAKERANGMELDGRRIRVDFSITKR 127

>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 = 64.2 bits (157), Expect = 3e-13
 Identities = 21/78 (26%), Positives = 33/78 (42%), Gaps = 5/78 (6%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAI 62
          S  +++ NL   I  + + D F  +G I  +  K+        GY FV FE    AE AI
Sbjct: 5  SGNIFIKNLDKSIDNKALYDTFSAFGNI--LSCKVVCDENGSKGYGFVHFETQEAAERAI 62

Query: 63 RGRDGYDFDGHRLRVELA 80
             +G   +  ++ V   
Sbjct: 63 EKMNGMLLNDRKVFVGRF 80

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 64.3 bits (157), Expect = 3e-13
 Identities = 21/93 (22%), Positives = 36/93 (38%), Gaps = 2/93 (2%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP--RPPGYAFVEFEEARDAE 59
                  L V NL   + + ++++LF ++G +    +      R  G A V FE   DA 
Sbjct: 31  GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADAL 90

Query: 60  DAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRH 92
            A++   G   DG  + ++L            H
Sbjct: 91  KAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHH 123

>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 = 47.0 bits (112), Expect = 5e-07
 Identities = 20/84 (23%), Positives = 33/84 (39%), Gaps = 3/84 (3%)

Query: 91  RHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGT--- 147
           +H    SG G G    +  ++LV+ L    S  D+++     G +  + V  D SG    
Sbjct: 18  QHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLG 77

Query: 148 TGIVDYTNYDDMKHAIKKLDDSEF 171
           T  V +    D   A+K+      
Sbjct: 78  TADVHFERRADALKAMKQYKGVPL 101

>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 = 63.8 bits (156), Expect = 3e-13
 Identities = 20/91 (21%), Positives = 38/91 (41%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
            S+ S+TL+V  L  D  E  +++ F        +  +      G+ FV+F    DA+ A
Sbjct: 11  RSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAA 70

Query: 62  IRGRDGYDFDGHRLRVELAHGGRGRSSSDRH 92
               +  + DG+++ ++ A       S    
Sbjct: 71  KEAMEDGEIDGNKVTLDWAKPKGEGGSGPSS 101

>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 = 65.2 bits (159), Expect = 3e-13
 Identities = 22/92 (23%), Positives = 40/92 (43%), Gaps = 3/92 (3%)

Query: 3   SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAE 59
           S     L+V ++  + +E E+++ F  YG I +I L +        GYA VE+E  + A 
Sbjct: 69  SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 128

Query: 60  DAIRGRDGYDFDGHRLRVELAHGGRGRSSSDR 91
            A    +G +  G  ++V+       +     
Sbjct: 129 AAKEALNGAEIMGQTIQVDWCFVKGPKRVKKS 160

>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 = 63.5 bits (155), Expect = 4e-13
 Identities = 23/102 (22%), Positives = 45/102 (44%), Gaps = 14/102 (13%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAI 62
            +T+++ NL  D  E  + ++  ++G + ++ + + P      G AF +F     A+  +
Sbjct: 15  GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74

Query: 63  RGRD------GYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
                     G   DG +L+V+LA      +  +  S  SSG
Sbjct: 75  AAASLEAEGGGLKLDGRQLKVDLA-----VTRDEAASGPSSG 111

>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 = 63.5 bits (155), Expect = 5e-13
 Identities = 23/95 (24%), Positives = 46/95 (48%), Gaps = 12/95 (12%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEARDAEDAIR 63
           L++ +LP +  ++++  +F  +G +  +  K+           + FV ++    A+ AI+
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNV--VSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 85

Query: 64  GRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
             +G+     RL+V+L      RS +D  S  SSG
Sbjct: 86  SMNGFQIGMKRLKVQLK-----RSKNDSKSGPSSG 115

>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 = 62.6 bits (153), Expect = 8e-13
 Identities = 22/100 (22%), Positives = 39/100 (39%), Gaps = 13/100 (13%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP----RPPGYAFVEFEEARDAEDA 61
             T++VG +   + E E+   F +YG +   ++KI         GY FV F    D +  
Sbjct: 9   PNTVFVGGIDVRMDETEIRSFFARYGSV--KEVKIITDRTGVSKGYGFVSFYNDVDVQKI 66

Query: 62  IRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGR 101
           +      +F G +L++     G      +  + H   R  
Sbjct: 67  V--ESQINFHGKKLKL-----GPAIRKQNLSTYHVQPRPL 99

>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 = 62.8 bits (153), Expect = 1e-12
 Identities = 29/90 (32%), Positives = 43/90 (47%), Gaps = 5/90 (5%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAI 62
            R++YVGN+      +++E  F   G I  I +   K    P GYA++EF E  ++ DA 
Sbjct: 36  KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAER-NSVDAA 94

Query: 63  RGRDGYDFDGHRLRVELAHGGR-GRSSSDR 91
              D   F G  ++V        G SS+DR
Sbjct: 95  VAMDETVFRGRTIKVLPKRTNMPGISSTDR 124

>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 = 62.3 bits (152), Expect = 1e-12
 Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 4/83 (4%)

Query: 1  MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIA---HIDLKIPPRPPGYAFVEFEEARD 57
          +      T ++GNLP D+ E  +++ F      A     +   P R  G+ + EFE+   
Sbjct: 14 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDS 73

Query: 58 AEDAIRGRDGYDFDGHRLRVELA 80
             A+   +       R+RV++A
Sbjct: 74 LLSALS-LNEESLGNRRIRVDVA 95

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 62.8 bits (153), Expect = 2e-12
 Identities = 33/92 (35%), Positives = 43/92 (46%), Gaps = 7/92 (7%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEAR 56
                 +L V NL        +  +F KYG +   D+ IP         G+AFV F + R
Sbjct: 43  DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRV--GDVYIPRDRYTKESRGFAFVRFHDKR 100

Query: 57  DAEDAIRGRDGYDFDGHRLRVELAHGGRGRSS 88
           DAEDA+   DG   DG  LRV++A  GR   S
Sbjct: 101 DAEDAMDAMDGAVLDGRELRVQMARYGRPPDS 132

>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 = 61.9 bits (151), Expect = 2e-12
 Identities = 22/104 (21%), Positives = 43/104 (41%), Gaps = 7/104 (6%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP--RPPGYAFVEFEEARDAE 59
           + R   T++V NL   +  ++++++F   G +   D+      +  G   V FE++ +A 
Sbjct: 11  AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAV 70

Query: 60  DAIRGRDGYDFDGHRLRVELA-----HGGRGRSSSDRHSSHSSG 98
            AI   +G       + V++       G        + S  SSG
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 = 50.0 bits (120), Expect = 3e-08
 Identities = 24/114 (21%), Positives = 37/114 (32%), Gaps = 7/114 (6%)

Query: 96  SSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGT---TGIVD 152
           S   G   + R    V V  L     W+ LK+    AG V  + +  D  G     G V 
Sbjct: 3   SGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVT 62

Query: 153 YTNYDDMKHAIKKLDDSEFRNAFSRA-YVRVREYDHRRDGSQSPSRGRSYSRGR 205
           +    +   AI   +       F R  +V++ E    +     P R +      
Sbjct: 63  FEQSIEAVQAISMFNGQLL---FDRPMHVKMDERALPKGDFFPPERPQQSGPSS 113

>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 = 62.0 bits (151), Expect = 2e-12
 Identities = 17/86 (19%), Positives = 37/86 (43%), Gaps = 6/86 (6%)

Query: 1  MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARD 57
          M    +  L++G +P ++ E++++ LF ++G I  + +   +      G AF+ + E   
Sbjct: 8  MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERES 67

Query: 58 AEDAIRGRDGY---DFDGHRLRVELA 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 = 41.5 bits (98), Expect = 3e-05
 Identities = 22/107 (20%), Positives = 40/107 (37%), Gaps = 6/107 (5%)

Query: 96  SSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD-GSGTT---GIV 151
           SSG   G+      ++ +  +P +   +DLK      G +    V +D  +G       +
Sbjct: 2   SSGSS-GMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFL 60

Query: 152 DYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVREYDHRRDGSQSPSRG 198
            Y   +    A   L + +     +R  ++V+  D    G   PS G
Sbjct: 61  TYCERESALKAQSALHEQKTLPGMNRP-IQVKPADSESRGGSGPSSG 106

>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 = 61.6 bits (150), Expect = 2e-12
 Identities = 19/82 (23%), Positives = 34/82 (41%), Gaps = 4/82 (4%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYG-PIAHIDL---KIPPRPPGYAFVEFEEARD 57
          SS  + +L++G+L   + E  +   F   G  +  + +   ++   P GY FVEF +   
Sbjct: 5  SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLAT 64

Query: 58 AEDAIRGRDGYDFDGHRLRVEL 79
          AE  +   +G    G       
Sbjct: 65 AEKCLHKINGKPLPGATPAKRF 86

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 61.6 bits (150), Expect = 2e-12
 Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 5/76 (6%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPI--AHI--DLKIPPRPPGYAFVEFEEARDAEDAIRG 64
           L++ +LP +  + ++   F  +G +  A +  D K       + FV F+    A+ AI+ 
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFID-KQTSLSKCFGFVSFDNPDSAQVAIKA 101

Query: 65  RDGYDFDGHRLRVELA 80
            +G+     RL+V+L 
Sbjct: 102 MNGFQVGTKRLKVQLK 117

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 60.9 bits (148), Expect = 3e-12
 Identities = 13/76 (17%), Positives = 30/76 (39%), Gaps = 3/76 (3%)

Query: 4  RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP--RPPGYAFVEFEEARDAEDA 61
            +R++Y+   P D    ++++     G + +I ++        G  FV F+    A+  
Sbjct: 9  VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKF 68

Query: 62 IRGRDGYDFDGHRLRV 77
          +    G  +    L +
Sbjct: 69 VE-TPGQKYKETDLLI 83

>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 = 59.8 bits (146), Expect = 5e-12
 Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 7/80 (8%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEARDAED 60
          +  L+VG+L  ++ +  + + F  +     +   +          GY FV F    DA++
Sbjct: 1  TFNLFVGDLNVNVDDETLRNAFKDFPSY--LSGHVMWDMQTGSSRGYGFVSFTSQDDAQN 58

Query: 61 AIRGRDGYDFDGHRLRVELA 80
          A+    G D +G  LR+  A
Sbjct: 59 AMDSMQGQDLNGRPLRINWA 78

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 60.2 bits (146), Expect = 5e-12
 Identities = 17/75 (22%), Positives = 36/75 (48%), Gaps = 5/75 (6%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIR-- 63
          S  +++  L   + E ++ +   ++GPI+++ + +P +    A VEFE+   A +A+   
Sbjct: 21 SPVVHIRGLIDGVVEADLVEALQEFGPISYVVV-MPKK--RQALVEFEDVLGACNAVNYA 77

Query: 64 GRDGYDFDGHRLRVE 78
            +     GH   V 
Sbjct: 78 ADNQIYIAGHPAFVN 92

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 61.1 bits (148), Expect = 9e-12
 Identities = 14/84 (16%), Positives = 28/84 (33%), Gaps = 5/84 (5%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEAR 56
                  +YVG+      ++++  +    G    ++LK        +  GYA V      
Sbjct: 51  LRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASEN 110

Query: 57  DAEDAIRGRDGYDFDGHRLRVELA 80
                +    G   +G ++ V  A
Sbjct: 111 SVHKLLELLPGKVLNGEKVDVRPA 134

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 59.6 bits (145), Expect = 1e-11
 Identities = 22/96 (22%), Positives = 43/96 (44%), Gaps = 9/96 (9%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEA 55
           + +    T YVGNLP +  + +++ +F          +++       +  G+ +VEF+E 
Sbjct: 10  LPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSI---RSVRLVRDKDTDKFKGFCYVEFDEV 66

Query: 56  RDAEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDR 91
              ++A+   DG       LRV++A G +   S   
Sbjct: 67  DSLKEAL-TYDGALLGDRSLRVDIAEGRKQDKSGPS 101

>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 = 59.6 bits (145), Expect = 1e-11
 Identities = 24/91 (26%), Positives = 34/91 (37%), Gaps = 9/91 (9%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP----RPPGYAFVEFEEARDAEDA 61
            R L+VG L     E +V  LF  +G I   +  +         G AFV+F    +A+ A
Sbjct: 15  DRKLFVGMLNKQQSEEDVLRLFQPFGVI--DECTVLRGPDGSSKGCAFVKFSSHTEAQAA 72

Query: 62  IRGRDG---YDFDGHRLRVELAHGGRGRSSS 89
           I    G          L V+ A   +    S
Sbjct: 73  IHALHGSQTMPGASSSLVVKFADTDKESGPS 103

>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 = 59.7 bits (145), Expect = 1e-11
 Identities = 23/96 (23%), Positives = 43/96 (44%), Gaps = 5/96 (5%)

Query: 8   TLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRG 64
            ++VG+L  +I   +++  F  +G I+   +       +  GY FV F    DAE+AI+ 
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76

Query: 65  RDGYDFDGHRLRVELAH--GGRGRSSSDRHSSHSSG 98
             G    G ++R   A       +S+ + ++  S  
Sbjct: 77  MGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGP 112

>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 = 62.0 bits (150), Expect = 1e-11
 Identities = 15/109 (13%), Positives = 34/109 (31%), Gaps = 8/109 (7%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEAR 56
            +     LY+GNL     + ++ +  +  G    +++K        +  G+A V      
Sbjct: 64  YTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEA 123

Query: 57  DAEDAIRGRDGYDFDGHRLRVELA---HGGRGRSSSDRHSSHSSGRGRG 102
            ++  +      +  G    V         +    S + +      G G
Sbjct: 124 SSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEG 172

>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 = 58.8 bits (143), Expect = 2e-11
 Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 3/81 (3%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP--RPPGYAFVEFEEARDAE 59
           S     L++GNL  +    E++    +      + +          + +V+FE A D E
Sbjct: 13 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLE 72

Query: 60 DAIRGRDGYDFDGHRLRVELA 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 = 58.3 bits (142), Expect = 2e-11
 Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 3/75 (4%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGR 65
          ++VG+L  +I    +   F  +G I+   +       +  GY FV F    DAE+AI+  
Sbjct: 9  VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68

Query: 66 DGYDFDGHRLRVELA 80
           G    G ++R   A
Sbjct: 69 GGQWLGGRQIRTNWA 83

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 58.7 bits (142), Expect = 2e-11
 Identities = 18/97 (18%), Positives = 36/97 (37%), Gaps = 9/97 (9%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIR-- 63
           SR +++  LP D+ E EV  L   +G + ++ +    +    AF+E      A   +   
Sbjct: 16  SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLM---LKGKNQAFIEMNTEEAANTMVNYY 72

Query: 64  GRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRG 100
                   G  + ++ ++           SS +  R 
Sbjct: 73  TSVTPVLRGQPIYIQFSN----HKELKTDSSPNQARA 105

>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 = 58.0 bits (141), Expect = 5e-11
 Identities = 17/84 (20%), Positives = 28/84 (33%), Gaps = 6/84 (7%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP----RPPGYAFVEFEEAR 56
              +    LY+ NLP  + E+E+E++   +G +  I  +I         G  F   E   
Sbjct: 20  QQEQDPTNLYISNLPLSMDEQELENMLKPFGQV--ISTRILRDSSGTSRGVGFARMESTE 77

Query: 57  DAEDAIRGRDGYDFDGHRLRVELA 80
             E  I   +G             
Sbjct: 78  KCEAVIGHFNGKFIKTPPGVSAPT 101

>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 = 57.8 bits (140), Expect = 5e-11
 Identities = 19/105 (18%), Positives = 34/105 (32%), Gaps = 5/105 (4%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIA---HIDLKIPPRPPGYAFVEFEEARDA 58
            + A    ++ N+P  I + +V              H+ +    +  G A V+F+   DA
Sbjct: 11  VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 70

Query: 59  EDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHS-SGRGRG 102
             + R       +G    V +      R       +   SG   G
Sbjct: 71  RKSER-LHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSGPSSG 114

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 56.8 bits (137), Expect = 1e-10
 Identities = 16/77 (20%), Positives = 31/77 (40%), Gaps = 5/77 (6%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIR-- 63
          SR L++  LPG++ E EV  L   +G + +I +    +    AF+E      A   +   
Sbjct: 15 SRVLHIRKLPGEVTETEVIALGLPFGKVTNILM---LKGKNQAFLELATEEAAITMVNYY 71

Query: 64 GRDGYDFDGHRLRVELA 80
                     + ++ +
Sbjct: 72 SAVTPHLRNQPIYIQYS 88

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 56.8 bits (138), Expect = 1e-10
 Identities = 27/93 (29%), Positives = 37/93 (39%), Gaps = 10/93 (10%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAIRGR 65
           LYV NL   I +  +   F  +G I     K+     R  G+ FV F    +A  A+   
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTI--TSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEM 75

Query: 66  DGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
           +G       L V LA     +   +R S  SSG
Sbjct: 76  NGRIVATKPLYVALA-----QRKEERQSGPSSG 103

>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 = 56.4 bits (137), Expect = 1e-10
 Identities = 22/90 (24%), Positives = 35/90 (38%), Gaps = 6/90 (6%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEARDAEDAI 62
           +++GNL  +I E+ + D F  +G I     KI          GYAF+ F     ++ AI
Sbjct: 7  GIFIGNLDPEIDEKLLYDTFSAFGVILQ-TPKIMRDPDTGNSKGYAFINFASFDASDAAI 65

Query: 63 RGRDGYDFDGHRLRVELAHGGRGRSSSDRH 92
             +G       + V  A     + S    
Sbjct: 66 EAMNGQYLCNRPITVSYAFKKDSKGSGPSS 95

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 57.6 bits (139), Expect = 3e-10
 Identities = 20/89 (22%), Positives = 35/89 (39%), Gaps = 2/89 (2%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP--RPPGYAFVEFEEARDAE 59
                  L V NL   + + ++++LF ++G +    +      R  G A V FE   DA 
Sbjct: 84  GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADAL 143

Query: 60  DAIRGRDGYDFDGHRLRVELAHGGRGRSS 88
            A++   G   DG  + ++L         
Sbjct: 144 KAMKQYKGVPLDGRPMDIQLVASQIDLEH 172

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 45.6 bits (108), Expect = 3e-06
 Identities = 24/112 (21%), Positives = 38/112 (33%), Gaps = 3/112 (2%)

Query: 63  RGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASW 122
           R        G R R       +      +H    SG G G    +  ++LV+ L    S 
Sbjct: 43  RRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSD 102

Query: 123 QDLKDHMRRAGDVCFSQVFRDGSGT---TGIVDYTNYDDMKHAIKKLDDSEF 171
            D+++     G +  + V  D SG    T  V +    D   A+K+      
Sbjct: 103 ADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPL 154

>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 = 56.1 bits (135), Expect = 3e-10
 Identities = 18/100 (18%), Positives = 37/100 (37%), Gaps = 9/100 (9%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
           +   SR +++  LP D+ E EV  L   +G + ++ +    +    AF+E      A   
Sbjct: 27  AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLM---LKGKNQAFIEMNTEEAANTM 83

Query: 62  IR--GRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGR 99
           +           G  + ++ ++           SS +  R
Sbjct: 84  VNYYTSVTPVLRGQPIYIQFSN----HKELKTDSSPNQAR 119

>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 = 56.0 bits (136), Expect = 6e-10
 Identities = 18/85 (21%), Positives = 40/85 (47%), Gaps = 8/85 (9%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEA 55
                +  ++VG +  D+R +E E+ F ++G I  ID ++       +  G+ FV ++ A
Sbjct: 82  DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTI--IDAQLMLDKDTGQSRGFGFVTYDSA 139

Query: 56  RDAEDAIRGRDGYDFDGHRLRVELA 80
              +   + +   DF   ++ ++ A
Sbjct: 140 DAVDRVCQNK-FIDFKDRKIEIKRA 163

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 55.2 bits (134), Expect = 1e-09
 Identities = 30/169 (17%), Positives = 67/169 (39%), Gaps = 28/169 (16%)

Query: 4   RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAED 60
           + S  +++G L  D  E  + + F KYG +  + +   P   R  G+ F+ FE+    ++
Sbjct: 1   KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60

Query: 61  AIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSA 120
            ++ +  +  DG  +  + A          R     +G           ++ V G+    
Sbjct: 61  VVKTQ--HILDGKVIDPKRA--------IPRDEQDKTG-----------KIFVGGIGPDV 99

Query: 121 SWQDLKDHMRRAGDVCFSQVFRD-GSGTT---GIVDYTNYDDMKHAIKK 165
             ++ ++   + G +  +Q+  D  +G +   G V Y + D +    + 
Sbjct: 100 RPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN 148

>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 = 53.4 bits (129), Expect = 1e-09
 Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 4/78 (5%)

Query: 3  SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAI 62
          S  S  ++VG   GD+ E E+ + F +YG +  +D+ IP     +AFV F + + A+   
Sbjct: 2  SSGSSGVFVGRCTGDMTEDELREFFSQYGDV--MDVFIPKPFRAFAFVTFADDQIAQSLC 59

Query: 63 RGRDGYDFDGHRLRVELA 80
             +     G  + +  A
Sbjct: 60 --GEDLIIKGISVHISNA 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 = 53.8 bits (129), Expect = 1e-09
 Identities = 15/69 (21%), Positives = 30/69 (43%), Gaps = 5/69 (7%)

Query: 2  SSRASRTLYVGN--LPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAE 59
           S A+++L V N  L   +   ++  +  K G +    L +PP    Y+F  +    +++
Sbjct: 21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVD--ALLMPPNK-PYSFARYRTTEESK 77

Query: 60 DAIRGRDGY 68
           A    +G 
Sbjct: 78 RAYVTLNGK 86

>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 = 31/167 (18%), Positives = 66/167 (39%), Gaps = 21/167 (12%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAI 62
            R L++G L  +  +  +   F ++G +    +   P   R  G+ FV +    + + A+
Sbjct: 13  LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 72

Query: 63  RGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASW 122
             R  +  DG  +  + A     R  S R  +H + +          ++ V G+      
Sbjct: 73  NAR-PHKVDGRVVEPKRA---VSREDSQRPGAHLTVK----------KIFVGGIKEDTEE 118

Query: 123 QDLKDHMRRAGDVCFSQVFRD-GSGTT---GIVDYTNYDDMKHAIKK 165
             L+D+  + G +   ++  D GSG       V + ++D +   + +
Sbjct: 119 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 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 = 3e-09
 Identities = 26/103 (25%), Positives = 47/103 (45%), Gaps = 9/103 (8%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDA 58
           +    + ++VG +  D  E  + D F +YG I  I++   +   +  G+AFV F++    
Sbjct: 100 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 159

Query: 59  EDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGR 101
           +  +  +  +  +GH   V  A      S  +  S+ SS RGR
Sbjct: 160 DKIVIQK-YHTVNGHNCEVRKA-----LSKQEMASASSSQRGR 196

>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 = 51.3 bits (123), Expect = 1e-08
 Identities = 19/94 (20%), Positives = 35/94 (37%), Gaps = 2/94 (2%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIA-HIDLKIPPRPPGYAFVEFEEARDAEDAIRG 64
              + V  +P    E +V D F+     A H+      R  G   V+F   +D  +A++ 
Sbjct: 16  DLYVSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALK- 74

Query: 65  RDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
           R+        + V  A   +  ++    +S  S 
Sbjct: 75  RNRMLMIQRYVEVSPATERQWVAAGGHITSGPSS 108

>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 = 51.0 bits (122), Expect = 1e-08
 Identities = 15/65 (23%), Positives = 27/65 (41%), Gaps = 2/65 (3%)

Query: 17  DIREREVEDLFYKYGPIAH--IDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHR 74
           +  E    ++  KYG +    +   +     G  +V+F    DAE A+   +   F+G  
Sbjct: 38  EFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQP 97

Query: 75  LRVEL 79
           +  EL
Sbjct: 98  IHAEL 102

>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 = 49.9 bits (120), Expect = 2e-08
 Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 4/75 (5%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGR 65
             ++VG    D+   E++  F +YG +  +D+ IP     +AFV F + + A+      
Sbjct: 11 GSKVFVGRCTEDMTAEELQQFFCQYGEV--VDVFIPKPFRAFAFVTFADDKVAQSLC--G 66

Query: 66 DGYDFDGHRLRVELA 80
          +     G  + +  A
Sbjct: 67 EDLIIKGISVHISNA 81

>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 = 50.3 bits (121), Expect = 2e-08
 Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 4/78 (5%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAI 62
          S  ++VG +P +  E E+ + F K+G +  + +       RP G+ F+ FE+ +  + A+
Sbjct: 10 SNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69

Query: 63 RGRDGYDFDGHRLRVELA 80
               +D  G ++ V+ A
Sbjct: 70 NMH-FHDIMGKKVEVKRA 86

>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 = 50.0 bits (120), Expect = 2e-08
 Identities = 16/80 (20%), Positives = 30/80 (37%), Gaps = 2/80 (2%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIA-HIDLKIPPRPPGYAFVEFEEARDAED 60
          S     T+ +   P ++ E+ V +      P+A  I         GY FV+F    + + 
Sbjct: 6  SGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQ 65

Query: 61 AIRGRDGYDFDGHRLRVELA 80
          A++  +     G  + V   
Sbjct: 66 ALK-CNREYMGGRYIEVFRE 84

>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 = 50.1 bits (120), Expect = 3e-08
 Identities = 13/83 (15%), Positives = 28/83 (33%), Gaps = 4/83 (4%)

Query: 1  MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIA---HIDLKIPPRPPGYAFVEFEEARD 57
            +     + +  LP    + E+   F     +     + +    R  G AFV+F     
Sbjct: 10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEI 69

Query: 58 AEDAIRGRDGYDFDGHRLRVELA 80
          AE A++ +         + +  +
Sbjct: 70 AEKALK-KHKERIGHRYIEIFKS 91

>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 = 49.0 bits (118), Expect = 3e-08
 Identities = 14/75 (18%), Positives = 36/75 (48%), Gaps = 4/75 (5%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAIRGR 65
          ++VG L  D  E ++ + F  +G +  I+L +     +  G+ F+ F+E    +  +  +
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 66 DGYDFDGHRLRVELA 80
            ++    +  +++A
Sbjct: 62 -YHNVGLSKCEIKVA 75

>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 = 49.6 bits (118), Expect = 3e-08
 Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 4/85 (4%)

Query: 8  TLYVGNLPGDIREREVE----DLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIR 63
           + V N+   +  +E++    + F ++G +  ++L         A V+ E  +DA  A+ 
Sbjct: 11 DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVN 70

Query: 64 GRDGYDFDGHRLRVELAHGGRGRSS 88
              Y     ++ V LA G  G SS
Sbjct: 71 SLHRYKIGSKKILVSLATGASGPSS 95

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 48.9 bits (117), Expect = 6e-08
 Identities = 20/90 (22%), Positives = 34/90 (37%), Gaps = 2/90 (2%)

Query: 3   SRASRTLYVGNLPGDIREREVEDLFYKYGPIA-HIDLKIPPRPPGYAFVEFEEARDAEDA 61
           S     +++  LP    E ++ + F    P+  HI++    R  G A VEF    DA  A
Sbjct: 12  STTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAA 71

Query: 62  IRGRDGYDFDGHRLRVELAHGGRGRSSSDR 91
           +  +D  +     + + L        S   
Sbjct: 72  MA-KDKANMQHRYVELFLNSTAGTSGSGPS 100

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 48.2 bits (116), Expect = 6e-08
 Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 4/75 (5%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAIRGR 65
          ++VG L  +    +V+  F ++G +    L       R  G+ FV FE     E      
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 66 DGYDFDGHRLRVELA 80
            ++ +   +  + A
Sbjct: 62 -FHEINNKMVECKKA 75

>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 = 50.6 bits (120), Expect = 7e-08
 Identities = 13/77 (16%), Positives = 29/77 (37%), Gaps = 3/77 (3%)

Query: 7   RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP--RPPGYAFVEFEEARDAEDAIRG 64
           R++Y+   P D    ++++     G + +I ++        G  FV F+    A+  +  
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE- 168

Query: 65  RDGYDFDGHRLRVELAH 81
             G  +    L +    
Sbjct: 169 TPGQKYKETDLLILFKD 185

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A Length = 105

 Score = 47.9 bits (114), Expect = 1e-07
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 9/88 (10%)

Query: 1  MSSRASRTLYVGNL--PGDIREREVEDLFY---KYGPIAHIDLKIPPRPP----GYAFVE 51
          M    ++ + + N+   G++ E    +      KYG +    +   P  P       F+E
Sbjct: 3  MGKCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLE 62

Query: 52 FEEARDAEDAIRGRDGYDFDGHRLRVEL 79
          FE    A  A+   +G  F G  ++   
Sbjct: 63 FERVESAIKAVVDLNGRYFGGRVVKACF 90

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 112

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 12/92 (13%)

Query: 2   SSRASRTLYVGNL--PGDIRE---------REVEDLFYKYGPIAHIDLKIPPRPPGYAFV 50
             R  R + + N+  P D  +          ++     K+G I  + L     P G A V
Sbjct: 11  RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDRHPDGVASV 69

Query: 51  EFEEARDAEDAIRGRDGYDFDGHRLRVELAHG 82
            F +  +A+  I+  DG  F G ++  +   G
Sbjct: 70  SFRDPEEADYCIQTLDGRWFGGRQITAQAWDG 101

>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 = 47.9 bits (114), Expect = 2e-07
 Identities = 22/105 (20%), Positives = 33/105 (31%), Gaps = 9/105 (8%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIA---HIDLKIPPRPPGYAFVEFEEARDA 58
              A   +Y+  LP +   + V D F K   +    +I      +  G  FVEF    D 
Sbjct: 21  PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADY 80

Query: 59  EDAIRGRDGYDFDGHRLRVELAHGG-----RGRSSSDRHSSHSSG 98
           + A+  R         ++V                    S  SSG
Sbjct: 81  KAALC-RHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQSGPSSG 124

>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 = 47.7 bits (114), Expect = 3e-07
 Identities = 25/105 (23%), Positives = 38/105 (36%), Gaps = 10/105 (9%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAI 62
              ++VG LP    +  +   F  +G I    +       +  GY FV   +   AE A 
Sbjct: 17  FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC 76

Query: 63  RGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRS 107
           +  +    DG +  V LA          +  S  +G   GVS  S
Sbjct: 77  KDPNP-IIDGRKANVNLA------YLGAKPRSLQTGFAIGVSGPS 114

>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 = 47.2 bits (112), Expect = 4e-07
 Identities = 13/78 (16%), Positives = 26/78 (33%), Gaps = 4/78 (5%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIA---HIDLKIPPRPPGYAFVEFEEARDAEDAI 62
              + +  LP    + E+   F     +     + +    +  G AFV+F     AE A+
Sbjct: 42  DGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKAL 101

Query: 63  RGRDGYDFDGHRLRVELA 80
             +         + V  +
Sbjct: 102 G-KHKERIGHRYIEVFKS 118

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 47.3 bits (112), Expect = 4e-07
 Identities = 15/83 (18%), Positives = 31/83 (37%), Gaps = 5/83 (6%)

Query: 2   SSRASRTL--YVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAE 59
            +  S  L   V NL   +    +  +F K+G +    +         A +++ +   A+
Sbjct: 22  MAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLK-IITFTKNNQFQALLQYADPVSAQ 80

Query: 60  DAIRGRDGYDF--DGHRLRVELA 80
            A    DG +       LR++ +
Sbjct: 81  HAKLSLDGQNIYNACCTLRIDFS 103

>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 = 47.4 bits (112), Expect = 8e-07
 Identities = 13/74 (17%), Positives = 29/74 (39%), Gaps = 3/74 (4%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
           + V NL   +    +  +F K+G +    +         A +++ +   A+ A    DG 
Sbjct: 49  IIVENLFYPVTLDVLHQIFSKFGTVLK-IITFTKNNQFQALLQYADPVSAQHAKLSLDGQ 107

Query: 69  DF--DGHRLRVELA 80
           +       LR++ +
Sbjct: 108 NIYNACCTLRIDFS 121

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 45.6 bits (108), Expect = 1e-06
 Identities = 22/104 (21%), Positives = 36/104 (34%), Gaps = 7/104 (6%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIA------HIDLKIPPRPPGYAFVEFEE 54
           +S      + +  LP      EV   F ++ PI               RP G AFV F  
Sbjct: 18  LSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFAC 77

Query: 55  ARDAEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
              A++A+R +         + +  +     +   +R SS S  
Sbjct: 78  EEYAQNALR-KHKDLLGKRYIELFRSTAAEVQQVLNRFSSASGP 120

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 18/80 (22%), Positives = 33/80 (41%), Gaps = 2/80 (2%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPI-AHIDLKIPPRPPGYAFVEFEEARDAED 60
            S     +++  LP    E ++ + F    P+  HI++    R  G A VEF    +A  
Sbjct: 42  QSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEEAVA 101

Query: 61  AIRGRDGYDFDGHRLRVELA 80
           A+  +D  +     + + L 
Sbjct: 102 AMS-KDRANMQHRYIELFLN 120

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 46.7 bits (110), Expect = 3e-06
 Identities = 17/89 (19%), Positives = 30/89 (33%), Gaps = 12/89 (13%)

Query: 3   SRASRTLYVGNLPGDI---------REREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFE 53
            + ++TLYVG + G +          E  +  +F + G I  I  +         FV+F+
Sbjct: 131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRI--RYVESK-NCGFVKFK 187

Query: 54  EARDAEDAIRGRDGYDFDGHRLRVELAHG 82
              +AE A              +      
Sbjct: 188 YQANAEFAKEAMSNQTLLLPSDKEWDDRR 216

>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 = 44.1 bits (104), Expect = 3e-06
 Identities = 13/85 (15%), Positives = 24/85 (28%), Gaps = 6/85 (7%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIA-----HIDLKIPPRPPGYAFVEFEEAR 56
                 +    LP      +V + F            H  L    +  G A +E E  +
Sbjct: 7  EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQ 66

Query: 57 DAEDAIRGRDGYDFDGHRLRVELAH 81
          D + A+  +         + V   +
Sbjct: 67 DVQKALE-KHRMYMGQRYVEVYEIN 90

>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 = 43.3 bits (103), Expect = 4e-06
 Identities = 19/78 (24%), Positives = 40/78 (51%), Gaps = 4/78 (5%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAI 62
          +  ++VG L  D  +++++D F K+G +    +K+ P   R  G+ F+ F++A   E  +
Sbjct: 11 AGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVL 70

Query: 63 RGRDGYDFDGHRLRVELA 80
            ++    DG  +  + A
Sbjct: 71 DQKEHR-LDGRVIDPKKA 87

>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 = 44.1 bits (104), Expect = 4e-06
 Identities = 16/85 (18%), Positives = 27/85 (31%), Gaps = 6/85 (7%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIA-----HIDLKIPPRPPGYAFVEFEEAR 56
                 + +  LP      +V++              H       R  G AFVE E   
Sbjct: 13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESED 72

Query: 57 DAEDAIRGRDGYDFDGHRLRVELAH 81
          D + A++ +D        + V  +H
Sbjct: 73 DVKLALK-KDRESMGHRYIEVFKSH 96

>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 = 43.4 bits (103), Expect = 5e-06
 Identities = 18/90 (20%), Positives = 35/90 (38%), Gaps = 5/90 (5%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAI 62
           +  L V  LP    E+++++ F  +G +  + +K         G+ FV F E       +
Sbjct: 15  TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 74

Query: 63  RGRDGYDFDGHRLRVELAHGGRGRSSSDRH 92
             R  +  DG     +L +  + + S    
Sbjct: 75  SQR--HMIDGRWCDCKLPNSKQSQDSGPSS 102

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} PDB: 3us5_A 2dny_A Length = 118

 Score = 44.0 bits (104), Expect = 5e-06
 Identities = 18/91 (19%), Positives = 37/91 (40%), Gaps = 12/91 (13%)

Query: 1   MSSRASRTLYVGNL--PGDIREREVEDLF---YKYGPIAHIDLKIPPRPP-------GYA 48
           +  + S  + + N+  P DI +    ++     K+G +  + +    +            
Sbjct: 15  LRKQESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKI 74

Query: 49  FVEFEEARDAEDAIRGRDGYDFDGHRLRVEL 79
           FVEF  A +   AI+  +G  F G ++  E+
Sbjct: 75  FVEFSIASETHKAIQALNGRWFAGRKVVAEV 105

>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 = 43.4 bits (102), Expect = 7e-06
 Identities = 25/100 (25%), Positives = 37/100 (37%), Gaps = 11/100 (11%)

Query: 2   SSRASRTLYVGNLPGD-IREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
                R +++ NLP     +  V  L   YG I +  L    R    AF+E E   DA  
Sbjct: 21  KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM---RMKSQAFIEMETREDAMA 77

Query: 61  AIR--GRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
            +    +    F G  ++V+L+            S  SSG
Sbjct: 78  MVDHCLKKALWFQGRCVKVDLSE-----KYKKLVSGPSSG 112

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 42.1 bits (100), Expect = 8e-06
 Identities = 12/75 (16%), Positives = 31/75 (41%), Gaps = 4/75 (5%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAIRGR 65
          +++G L     +  + + F ++G +    +   P   R  G+ FV F +    +  +   
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 66 DGYDFDGHRLRVELA 80
            ++ D   +  ++A
Sbjct: 63 -RHELDSKTIDPKVA 76

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 22/96 (22%), Positives = 39/96 (40%), Gaps = 7/96 (7%)

Query: 8   TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP----GYAFVEFEEARDAEDAIR 63
           +L+VG+L  D+ +  + + F K  P      K+         GY FV+F +  + + A+ 
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCR-GGKVVLDQTGVSKGYGFVKFTDELEQKRALT 69

Query: 64  GRDG-YDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
              G        +R+ +A   +        S  SSG
Sbjct: 70  ECQGAVGLGSKPVRLSVA-IPKASRVKPVESGPSSG 104

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A Length = 114

 Score = 41.6 bits (98), Expect = 3e-05
 Identities = 13/68 (19%), Positives = 25/68 (36%), Gaps = 4/68 (5%)

Query: 13 NLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP-GYAFVEFEEARDAEDAIRGRDGYDFD 71
              +I++ +V +   K+G + HI   +      G  +V+      A  A+    G  F 
Sbjct: 25 GWDTEIKD-DVIEECNKHGGVIHI--YVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFA 81

Query: 72 GHRLRVEL 79
          G  +    
Sbjct: 82 GKMITAAY 89

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 40.8 bits (95), Expect = 7e-05
 Identities = 19/74 (25%), Positives = 27/74 (36%), Gaps = 4/74 (5%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          L + N    I    +  +    G +  I   I  R    A VEFE    A+ A    +G 
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQRI--VIFKRNGIQAMVEFESVLCAQKAKAALNGA 85

Query: 69 DF--DGHRLRVELA 80
          D       L++E A
Sbjct: 86 DIYAGCCTLKIEYA 99

>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 = 40.4 bits (94), Expect = 1e-04
 Identities = 15/85 (17%), Positives = 26/85 (30%), Gaps = 6/85 (7%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIA-----HIDLKIPPRPPGYAFVEFEEAR 56
                  + +  LP      +V++              H       R  G AFVE     
Sbjct: 40  EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSED 99

Query: 57  DAEDAIRGRDGYDFDGHRLRVELAH 81
           D + A++ +D        + V  +H
Sbjct: 100 DVKMALK-KDRESMGHRYIEVFKSH 123

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105

 Score = 39.4 bits (92), Expect = 1e-04
 Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 6/68 (8%)

Query: 17 DIREREVEDLFYKYGPIAHIDL-----KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFD 71
          +I E +V D   KYG +  I++      +     G  FVEF    D + A++G  G  F 
Sbjct: 27 EIVE-DVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFA 85

Query: 72 GHRLRVEL 79
             +  + 
Sbjct: 86 NRVVVTKY 93

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 39.0 bits (90), Expect = 2e-04
 Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 2/53 (3%)

Query: 16 GDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          G   +  +  L  KYG +  ++L +  + PG A VEF   + AE A++   G 
Sbjct: 27 GGYSKDVLLRLLQKYGEV--LNLVLSSKKPGTAVVEFATVKAAELAVQNEVGL 77

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C} Length = 579

 Score = 41.0 bits (96), Expect = 3e-04
 Identities = 16/77 (20%), Positives = 29/77 (37%), Gaps = 3/77 (3%)

Query: 181 RVREYDHRRDGSQSPSRGRSYSRGRSESRSRSRSRG---RSYSRSRSQSKSPKAKSSRRS 237
             +     RD S      +SY        S   ++    RS +R        ++ ++RRS
Sbjct: 502 IGKAMFEIRDYSSRDGNNKSYDYDDDSEISFRGNKNYNNRSQNRDYDDEPFRRSNNNRRS 561

Query: 238 PDRSRSRSASRSRSGSK 254
             RS  ++   SR+ + 
Sbjct: 562 FSRSNDKNNYSSRNSNI 578

>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 = 37.9 bits (88), Expect = 5e-04
 Identities = 10/58 (17%), Positives = 23/58 (39%), Gaps = 4/58 (6%)

Query: 6  SRTLYVGNLPGDI-REREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAI 62
           R +++ +         ++  L   +G I++    +       AF+E     DA+ A+
Sbjct: 15 RRVVHIMDFQRGKNLRYQLLQLVEPFGVISNH---LILNKINEAFIEMATTEDAQAAV 69

>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 = 38.0 bits (89), Expect = 6e-04
 Identities = 16/75 (21%), Positives = 33/75 (44%), Gaps = 4/75 (5%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAIRGR 65
           L++G L  +  E  + + + ++G +    +   P   R  G+ FV F    + + A+  R
Sbjct: 30  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89

Query: 66  DGYDFDGHRLRVELA 80
             +  DG  +  + A
Sbjct: 90  -PHSIDGRVVEPKRA 103

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 37.7 bits (87), Expect = 7e-04
 Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 5/73 (6%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEAR 56
           S  SR ++VG LP DI E E+   F ++GP+               P GYAF+ F+E  
Sbjct: 4  GSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEES 63

Query: 57 DAEDAIRGRDGYD 69
            +  I      D
Sbjct: 64 SVQALIDACLEED 76

>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 = 37.2 bits (87), Expect = 8e-04
 Identities = 12/78 (15%), Positives = 31/78 (39%), Gaps = 4/78 (5%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAI 62
              +++G L     +  + + F ++G +    +   P   R  G+ FV F +    +  +
Sbjct: 25  GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84

Query: 63  RGRDGYDFDGHRLRVELA 80
                ++ D   +  ++A
Sbjct: 85  AQS-RHELDSKTIDPKVA 101

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	299
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	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
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	100.0
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	100.0
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	100.0
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	100.0
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	100.0
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.98
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.98
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.98
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	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
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.97
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.97
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.97
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.92
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.91
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.91
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
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.86
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.85
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.85
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.85
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.85
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.85
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.85
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.84
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.84
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.84
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.84
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.84
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.84
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.83
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.83
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.83
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.83
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.83
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.83
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.83
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.83
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.83
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.83
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	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
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.83
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.83
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.83
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.82
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.82
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.82
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.82
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.82
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.82
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.82
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.82
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.82
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.82
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.82
2div_A	99	TRNA selenocysteine associated protein; structural	99.82
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.82
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.82
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.82
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.82
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.82
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.82
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.82
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.81
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.81
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.81
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.81
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.81
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.81
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.81
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.81
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.81
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.81
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.81
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.81
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.81
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.81
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.8
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.8
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.8
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.8
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.8
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	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
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.8
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.8
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.8
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.8
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.8
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.8
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.8
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.8
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.8
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	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
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.8
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.8
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.79
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.79
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.79
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.79
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.79
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.79
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.79
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.79
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.79
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.79
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.79
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.79
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.78
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.78
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.78
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.78
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.78
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.78
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.78
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.78
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.78
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.78
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.78
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.78
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.78
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.78
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.78
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.78
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.77
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	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
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.77
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.77
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.77
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.77
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	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	99.77
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.76
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.76
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.76
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.76
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.76
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.76
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.76
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.76
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.76
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.76
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.76
1x5p_A	97	Negative elongation factor E; structure genomics,	99.76
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.76
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.76
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.75
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.75
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.75
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.75
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.74
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.74
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.74
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.74
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.73
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.73
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.73
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.73
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.73
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.73
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.73
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.72
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.72
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.56
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.72
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.72
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.72
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.71
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.7
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.69
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.69
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.69
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.68
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.68
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.68
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.68
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.67
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.67
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.67
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.67
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.67
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.66
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.66
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.66
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.66
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.66
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.66
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.66
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.66
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.65
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.65
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.65
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	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
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.65
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.65
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.65
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.65
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.65
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.65
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.64
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.64
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.64
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.64
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.64
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.64
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.63
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.63
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.63
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.63
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.63
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.63
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.63
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.63
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.63
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.63
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.63
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.63
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.63
2div_A	99	TRNA selenocysteine associated protein; structural	99.63
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.63
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.63
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.62
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.62
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.62
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.62
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.62
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.62
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.62
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.62
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.62
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.62
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.61
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.61
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.61
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.61
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.61
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.61
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.61
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.61
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.61
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.61
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.61
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.61
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.61
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.6
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.6
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.6
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.6
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.6
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.6
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.6
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.6
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.6
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.6
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.6
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.6
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.6
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.6
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.59
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.59
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.59
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.59
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.59
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.59
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.59
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.59
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.59
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.59
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.59
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.59
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.58
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.58
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.58
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.58
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.58
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.58
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.58
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.57
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.57
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.57
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.57
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.56
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.56
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.56
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.56
1x5p_A	97	Negative elongation factor E; structure genomics,	99.56
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.56
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.56
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.56
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.56
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.55
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.55
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.55
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.55
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.55
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.55
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.55
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.55
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.54
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.54
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.54
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.54
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.54
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.54
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.54
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.54
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.54
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.54
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.54
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.54
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.53
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.53
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.53
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.53
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.52
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.52
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.52
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.51
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.51
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.51
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.51
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.5
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.5
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.5
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.5
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.5
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.5
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.49
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.49
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.48
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.48
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.48
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.47
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.47
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.46
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.45
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.44
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.44
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.44
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.44
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.44
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.13
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.4
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.4
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.39
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.38
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.36
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.35
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.29
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.27
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.26
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.25
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.23
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.23
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.18
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.15
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.13
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.06
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.02
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.94
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.83
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.77
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.64
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.58
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.48
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.38
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	98.12
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	98.09
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	98.02
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.94
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.89
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.73
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.72
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.69
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.66
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.51
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	97.47
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.4
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.99
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.83
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.42
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.18
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	94.77
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	91.31
4eyt_A	129	Telomerase associated protein P65; RNA, LA protein	90.25
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	89.62
4eyt_A	129	Telomerase associated protein P65; RNA, LA protein	88.63
4e8u_A	172	Putative uncharacterized protein T8P19.180; XS dom	83.87

>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=6.6e-35  Score=236.21  Aligned_cols=157  Identities=24%  Similarity=0.373  Sum_probs=137.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      +.|++||||+|||+++|+++|+++|++||+|.+|.|..   ++.++|||||+|.+.++|..|+..||+..+.|+.|.|.+
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~   91 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW   91 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccc
Confidence            46789999999999999999999999999999999954   467789999999999999999999999999999999998


Q ss_pred             ccCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC--CEEEEEecChh
Q 022301           80 AHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG--TTGIVDYTNYD  157 (299)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~--~~~fv~f~~~~  157 (299)
                      +.....                 .......+|||+|||..+++++|.++|..||.|..+.++.+..+  |||||+|.+.+
T Consensus        92 ~~~~~~-----------------~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~  154 (213)
T 4f02_A           92 SQRDPS-----------------LRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQE  154 (213)
T ss_dssp             CCCCTH-----------------HHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHH
T ss_pred             cccccc-----------------ccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHH
Confidence            754321                 11123468999999999999999999999999999999887643  59999999999


Q ss_pred             hHHHHHHhcCCCeecCcee
Q 022301          158 DMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       158 ~a~~a~~~l~g~~~~g~~~  176 (299)
                      +|+.|++.|||..|+|+.+
T Consensus       155 ~a~~Ai~~lng~~~~g~~i  173 (213)
T 4f02_A          155 AAERAIEKMNGMLLNDRKV  173 (213)
T ss_dssp             HHHHHHHHHTTCEETTEEC
T ss_pred             HHHHHHHHhCCCEECCEEE
Confidence            9999999999999999944

>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=2e-33  Score=225.27  Aligned_cols=172  Identities=16%  Similarity=0.221  Sum_probs=139.4

Q ss_pred             CCCCeEEEcCCC-CCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            4 RASRTLYVGNLP-GDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         4 ~~~~~l~V~nLp-~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      .++++|||+||| ..+|+++|.++|+.||.|..|.|..+  .+|||||+|.+.++|..|+..|||..|.|+.|.|.++..
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            478999999999 79999999999999999999999754  379999999999999999999999999999999999875


Q ss_pred             CCCCCCCC-CC-C------CCCCC--CC--------CCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCe--eEEEEEe
Q 022301           83 GRGRSSSD-RH-S------SHSSG--RG--------RGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDV--CFSQVFR  142 (299)
Q Consensus        83 ~~~~~~~~-~~-~------~~~~~--~~--------~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v--~~~~~~~  142 (299)
                      ....+... .. .      .....  ..        ......+..+|||.|||..+++++|+++|.+||.|  ..+.++.
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 00 0      00000  00        00112456789999999999999999999999999  8888887


Q ss_pred             CCC--CCEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          143 DGS--GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       143 ~~~--~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      +..  .|+|||+|.+.++|..||..|||..|.|....
T Consensus       160 ~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~  196 (205)
T 3tyt_A          160 GKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGP  196 (205)
T ss_dssp             CCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSS
T ss_pred             CCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCC
Confidence            742  36999999999999999999999999997543

>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=3.1e-33  Score=217.55  Aligned_cols=153  Identities=25%  Similarity=0.411  Sum_probs=137.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC--CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCCC
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP--PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGR   84 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~--~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~~   84 (299)
                      ++|||+|||.++|+++|.++|+.||+|..|.+..+  +.++|||||+|.+.++|..|+..|||..+.|+.|.|.++....
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            58999999999999999999999999999999543  5678999999999999999998899999999999999986543


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHH
Q 022301           85 GRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMK  160 (299)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~  160 (299)
                      .                 .......+|+|+|||..+++++|.++|.+||.|..+.+..+...    |||||+|.+.++|.
T Consensus        81 ~-----------------~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~  143 (166)
T 3md3_A           81 Q-----------------SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQ  143 (166)
T ss_dssp             C-----------------CCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHH
T ss_pred             C-----------------CCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHH
Confidence            2                 22345679999999999999999999999999999999988543    49999999999999


Q ss_pred             HHHHhcCCCeecCcee
Q 022301          161 HAIKKLDDSEFRNAFS  176 (299)
Q Consensus       161 ~a~~~l~g~~~~g~~~  176 (299)
                      .|+..|||..++|+.+
T Consensus       144 ~A~~~l~g~~~~g~~i  159 (166)
T 3md3_A          144 NAMDSMQGQDLNGRPL  159 (166)
T ss_dssp             HHHHHHTTCEETTEEC
T ss_pred             HHHHHhCCCccCCcEE
Confidence            9999999999999844

>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=6.4e-33  Score=215.96  Aligned_cols=154  Identities=23%  Similarity=0.402  Sum_probs=138.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ++++|||+|||+++|+++|+++|+.||+|..|.+..   ++.++|||||+|.+.++|..|+..|||..+.|+.|.|.++.
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            478999999999999999999999999999999954   45677999999999999999999999999999999999986


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChh
Q 022301           82 GGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYD  157 (299)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~  157 (299)
                      ....                   .....+|+|.|||..+++++|.++|.+||.|..+.+..+...    |||||+|.+.+
T Consensus        81 ~~~~-------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~  141 (167)
T 1fxl_A           81 PSSA-------------------SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRI  141 (167)
T ss_dssp             CCCG-------------------GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHH
T ss_pred             CCcc-------------------cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHH
Confidence            4321                   234578999999999999999999999999999999988633    59999999999


Q ss_pred             hHHHHHHhcCCCeecCceee
Q 022301          158 DMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       158 ~a~~a~~~l~g~~~~g~~~~  177 (299)
                      +|..|+..|||..+.|+.+.
T Consensus       142 ~A~~A~~~l~g~~~~g~~~~  161 (167)
T 1fxl_A          142 EAEEAIKGLNGQKPSGATEP  161 (167)
T ss_dssp             HHHHHHHHHTTCCCTTCSSC
T ss_pred             HHHHHHHHhcCCccCCCccc
Confidence            99999999999999997543

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

Probab=100.00  E-value=1.3e-32  Score=214.48  Aligned_cols=150  Identities=27%  Similarity=0.430  Sum_probs=136.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ++++|||+|||+++|+++|.++|+.||+|..|.+..   ++.++|||||+|.+.++|..|+..|||..+.|+.|.|.++.
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            689999999999999999999999999999999953   46678999999999999999999999999999999999986


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChh
Q 022301           82 GGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYD  157 (299)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~  157 (299)
                      ....                   .....+|+|.|||..+++++|.++|.+||.|..+.+..+...    |||||+|.+.+
T Consensus        82 ~~~~-------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~  142 (168)
T 1b7f_A           82 PGGE-------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKRE  142 (168)
T ss_dssp             CCSS-------------------TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHH
T ss_pred             CCcc-------------------cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHH
Confidence            4331                   234579999999999999999999999999999999988643    59999999999


Q ss_pred             hHHHHHHhcCCCeecC
Q 022301          158 DMKHAIKKLDDSEFRN  173 (299)
Q Consensus       158 ~a~~a~~~l~g~~~~g  173 (299)
                      +|..|+..|||..+.|
T Consensus       143 ~A~~A~~~l~g~~~~g  158 (168)
T 1b7f_A          143 EAQEAISALNNVIPEG  158 (168)
T ss_dssp             HHHHHHHHHTTCCCTT
T ss_pred             HHHHHHHHhcCCEecC
Confidence            9999999999999988

>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=5.4e-32  Score=228.61  Aligned_cols=173  Identities=20%  Similarity=0.272  Sum_probs=142.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH----HHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVE----DLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVE   78 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~----~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~   78 (299)
                      ..++++|||+|||.++|+++|+    ++|+.||.|..|.|..++..+|||||+|.+.++|..|+..|||..|.|+.|.|.
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             EccCCCCCCCCCCC------------------------------------------------------------------
Q 022301           79 LAHGGRGRSSSDRH------------------------------------------------------------------   92 (299)
Q Consensus        79 ~~~~~~~~~~~~~~------------------------------------------------------------------   92 (299)
                      |+............                                                                  
T Consensus        86 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~  165 (282)
T 3pgw_A           86 YAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMP  165 (282)
T ss_pred             EeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCCCC
Confidence            98654420000000                                                                  


Q ss_pred             --CCC-CCCC-----------------------CCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC
Q 022301           93 --SSH-SSGR-----------------------GRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG  146 (299)
Q Consensus        93 --~~~-~~~~-----------------------~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~  146 (299)
                        ... ....                       ..........+|||+|||..+++++|+++|.+||.|..+.+..+. .
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 0000                       000123356789999999999999999999999999999998765 4


Q ss_pred             CEEEEEecChhhHHHHHHhcCCCeec-Ccee
Q 022301          147 TTGIVDYTNYDDMKHAIKKLDDSEFR-NAFS  176 (299)
Q Consensus       147 ~~~fv~f~~~~~a~~a~~~l~g~~~~-g~~~  176 (299)
                      |||||+|.+.++|..|+..|||..|. |+.+
T Consensus       245 g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l  275 (282)
T 3pgw_A          245 DIAFVEFDNEVQAGAARDALQGFKITQNNAM  275 (282)
T ss_pred             cEEEEEeCCHHHHHHHHHHcCCcEeCCCCEE
Confidence            69999999999999999999999999 8843

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

Probab=100.00  E-value=1.8e-32  Score=219.18  Aligned_cols=158  Identities=14%  Similarity=0.289  Sum_probs=134.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .+.++|||+|||+++|+++|.++|+.||+|..|.|..   ++.++|||||+|.+.++|..|+. +++..|.|+.|.|.++
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            5678999999999999999999999999999999965   35678999999999999999999 5999999999999998


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecCh
Q 022301           81 HGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNY  156 (299)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~  156 (299)
                      ........             ........+|||.|||..+++++|.++|..||.|..+.++.+...    |||||+|.+.
T Consensus        90 ~~~~~~~~-------------~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~  156 (196)
T 1l3k_A           90 VSREDSQR-------------PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH  156 (196)
T ss_dssp             CC------------------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             cCcccccc-------------cccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCH
Confidence            65432111             112334589999999999999999999999999999999988643    5999999999


Q ss_pred             hhHHHHHHhcCCCeecCcee
Q 022301          157 DDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       157 ~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ++|..|+.. +|..|+|+.+
T Consensus       157 ~~A~~A~~~-~~~~~~G~~i  175 (196)
T 1l3k_A          157 DSVDKIVIQ-KYHTVNGHNC  175 (196)
T ss_dssp             HHHHHHHHC-SCCEETTEEC
T ss_pred             HHHHHHHHh-CCcEECCEEE
Confidence            999999986 7999999944

>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=100.00  E-value=8.8e-32  Score=220.25  Aligned_cols=171  Identities=16%  Similarity=0.245  Sum_probs=140.1

Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            3 SRASRTLYVGNLPG-DIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         3 ~~~~~~l~V~nLp~-~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ..++++|||+|||+ ++++++|+++|+.||+|..|.|..+.  +|||||+|.+.++|.+|+..|||..|.|+.|.|.++.
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~--~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  108 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK--KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK  108 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT--SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC--CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEec
Confidence            46789999999999 99999999999999999999997654  7899999999999999999999999999999999987


Q ss_pred             CCCCCCCCCCCCC------C----------CCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcC-CeeEEEEEeCC
Q 022301           82 GGRGRSSSDRHSS------H----------SSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAG-DVCFSQVFRDG  144 (299)
Q Consensus        82 ~~~~~~~~~~~~~------~----------~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G-~v~~~~~~~~~  144 (299)
                      .............      .          ...........+..+|||.|||..+++++|.++|.+|| .|..+.++.. 
T Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-  187 (229)
T 2adc_A          109 HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-  187 (229)
T ss_dssp             CCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-
T ss_pred             CccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-
Confidence            5532211100000      0          00000011234578999999999999999999999999 9999998653 


Q ss_pred             CCCEEEEEecChhhHHHHHHhcCCCeec-Ccee
Q 022301          145 SGTTGIVDYTNYDDMKHAIKKLDDSEFR-NAFS  176 (299)
Q Consensus       145 ~~~~~fv~f~~~~~a~~a~~~l~g~~~~-g~~~  176 (299)
                      ..+||||+|.+.++|..|+..|+|..++ |+.+
T Consensus       188 ~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l  220 (229)
T 2adc_A          188 DRKMALIQMGSVEEAVQALIDLHNHDLGENHHL  220 (229)
T ss_dssp             STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeE
Confidence            3569999999999999999999999999 8844

>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=2.6e-31  Score=212.77  Aligned_cols=176  Identities=22%  Similarity=0.384  Sum_probs=141.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhc----C-------CeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKY----G-------PIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDG   72 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~----G-------~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g   72 (299)
                      ..+++|||+|||+++|+++|.++|+.|    |       .|..+.+.   .++|||||+|.+.++|.+|+ .|||..|.|
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   56899999999999999999 799999999


Q ss_pred             ceEEEEEccCCCCCCCCCCCC-CCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----C
Q 022301           73 HRLRVELAHGGRGRSSSDRHS-SHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----T  147 (299)
Q Consensus        73 ~~i~v~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~  147 (299)
                      +.|.|.++............. ................+|||+|||..+++++|.++|.+||.|..+.+..+...    |
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            999999987654332211111 11111112223456789999999999999999999999999999999988643    5


Q ss_pred             EEEEEecChhhHHHHHHhcCCCeecCceeeEEEEeccccc
Q 022301          148 TGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVREYDH  187 (299)
Q Consensus       148 ~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~~~~~  187 (299)
                      ||||+|.+.++|..|+..|||..|+|+    .+.+....+
T Consensus       158 ~afV~f~~~~~a~~A~~~l~g~~~~g~----~l~v~~a~~  193 (198)
T 2yh0_A          158 YAFCEYVDINVTDQAIAGLNGMQLGDK----KLLVQRASV  193 (198)
T ss_dssp             EEEEEESSSSHHHHHHHHHTTCEETTE----ECEEEESCC
T ss_pred             EEEEEECCHHHHHHHHHHcCCCEECCE----EEEEEECCC
Confidence            999999999999999999999999998    445444433

>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=1.3e-31  Score=217.35  Aligned_cols=164  Identities=20%  Similarity=0.321  Sum_probs=137.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      +.++|||+|||.++|+++|+++|+.||+|..|.|..   ++.++|||||+|.+.++|..|+..||+..|.|+.|.|.++.
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            458999999999999999999999999999999954   46789999999999999999999999999999999998765


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChh
Q 022301           82 GGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYD  157 (299)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~  157 (299)
                      .........        ...........+|||.|||..+++++|.++|.+||.|..+.+..+..    .|||||+|.+.+
T Consensus       107 ~~~~~~~~~--------~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~  178 (216)
T 2qfj_A          107 NIGQAQPII--------DQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQ  178 (216)
T ss_dssp             CCGGGHHHH--------HHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHH
T ss_pred             Cccccchhh--------hhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHH
Confidence            432100000        00000123457999999999999999999999999999999998854    359999999999


Q ss_pred             hHHHHHHhcCCCeecCcee
Q 022301          158 DMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       158 ~a~~a~~~l~g~~~~g~~~  176 (299)
                      +|..|+..|||..|+|+.+
T Consensus       179 ~A~~A~~~l~g~~~~g~~i  197 (216)
T 2qfj_A          179 SSQDAVSSMNLFDLGGQYL  197 (216)
T ss_dssp             HHHHHHHHHTTCBCSSSBC
T ss_pred             HHHHHHHHccCCEeCCcEE
Confidence            9999999999999999954

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

Probab=100.00  E-value=2.4e-31  Score=212.96  Aligned_cols=170  Identities=17%  Similarity=0.261  Sum_probs=139.5

Q ss_pred             CCCeEEEcCCCC-CCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            5 ASRTLYVGNLPG-DIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         5 ~~~~l~V~nLp~-~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      .+++|||+|||+ ++++++|.++|+.||.|..|.|..+.  +|||||+|.+.++|..|+..|||..|.|+.|.|.++...
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            468999999999 99999999999999999999997654  789999999999999999999999999999999998755


Q ss_pred             CCCCCCCCCCC----------------CCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcC-CeeEEEEEeCCCC
Q 022301           84 RGRSSSDRHSS----------------HSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAG-DVCFSQVFRDGSG  146 (299)
Q Consensus        84 ~~~~~~~~~~~----------------~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G-~v~~~~~~~~~~~  146 (299)
                      ...........                ............+..+|||.|||..+++++|.++|..|| .|..+.+..+. .
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            32211100000                000001111234578999999999999999999999999 99999986643 5


Q ss_pred             CEEEEEecChhhHHHHHHhcCCCeec-Cceee
Q 022301          147 TTGIVDYTNYDDMKHAIKKLDDSEFR-NAFSR  177 (299)
Q Consensus       147 ~~~fv~f~~~~~a~~a~~~l~g~~~~-g~~~~  177 (299)
                      |+|||+|.+.++|..|+..|||..++ |+.+.
T Consensus       159 g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~  190 (198)
T 1qm9_A          159 KMALIQMGSVEEAVQALIDLHNHDLGENHHLR  190 (198)
T ss_dssp             SCEEEECSSHHHHHHHHHHHTSSCCSSCCSCC
T ss_pred             cEEEEEeCCHHHHHHHHHHhcCCccCCCCeEE
Confidence            79999999999999999999999999 87553

>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=99.98  E-value=2.3e-31  Score=208.24  Aligned_cols=150  Identities=23%  Similarity=0.439  Sum_probs=133.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhc----C-------CeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKY----G-------PIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDG   72 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~----G-------~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g   72 (299)
                      +++++|||+|||+++|+++|.++|+.|    |       .|..+.+.   ..+|||||+|.+.++|..|+ .|||..|.|
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            467999999999999999999999999    6       77777775   45899999999999999999 799999999


Q ss_pred             ceEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CE
Q 022301           73 HRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TT  148 (299)
Q Consensus        73 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~  148 (299)
                      +.|.|.++.....                   .....+|+|+|||..+++++|.++|.+||.|..+.+..++..    ||
T Consensus        78 ~~i~v~~~~~~~~-------------------~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~  138 (172)
T 2g4b_A           78 QSLKIRRPHDYQP-------------------LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGY  138 (172)
T ss_dssp             EECEEECCSSCCC-------------------CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEE
T ss_pred             ceeeecCCcccCC-------------------CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceE
Confidence            9999998654321                   123579999999999999999999999999999999988643    59


Q ss_pred             EEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          149 GIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       149 ~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      |||+|.+.++|..|+..|||..++|+.+
T Consensus       139 afV~f~~~~~A~~A~~~l~g~~~~g~~l  166 (172)
T 2g4b_A          139 AFCEYVDINVTDQAIAGLNGMQLGDKKL  166 (172)
T ss_dssp             EEEEESSTTHHHHHHHHHTTCEETTEEC
T ss_pred             EEEEeCCHHHHHHHHHHcCCCEECCeEE
Confidence            9999999999999999999999999854

>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=99.98  E-value=2e-31  Score=209.13  Aligned_cols=151  Identities=17%  Similarity=0.340  Sum_probs=132.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCC-----CCCceEEEEecChHHHHHHHHhcCCCCCC---CceEE
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----RPPGYAFVEFEEARDAEDAIRGRDGYDFD---GHRLR   76 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~-----~~~g~afV~F~~~e~A~~A~~~l~~~~~~---g~~i~   76 (299)
                      ++++|||+|||+++|+++|.++|+.||+|..|.|..+.     .++|||||+|.+.++|..|+..|||..+.   +..+.
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            57899999999999999999999999999999995432     56899999999999999999999998776   67788


Q ss_pred             EEEccCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC---CEEEEEe
Q 022301           77 VELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG---TTGIVDY  153 (299)
Q Consensus        77 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv~f  153 (299)
                      +.++.....                  ......+|||+|||..+++++|+++|.+||.|..+.+..+..+   |||||+|
T Consensus        82 ~~~~~~~~~------------------~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f  143 (175)
T 3nmr_A           82 MKPADSEKN------------------NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTF  143 (175)
T ss_dssp             EEECGGGCC------------------SCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEE
T ss_pred             Ecccccccc------------------ccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEE
Confidence            887654331                  2235679999999999999999999999999999999988653   4999999


Q ss_pred             cChhhHHHHHHhcCCCeecC
Q 022301          154 TNYDDMKHAIKKLDDSEFRN  173 (299)
Q Consensus       154 ~~~~~a~~a~~~l~g~~~~g  173 (299)
                      .+.++|..|++.|||..+.+
T Consensus       144 ~~~~~A~~A~~~l~g~~~~~  163 (175)
T 3nmr_A          144 TTRAMAQTAIKAMHQAQTME  163 (175)
T ss_dssp             SSHHHHHHHHHHHTTSCCCT
T ss_pred             CCHHHHHHHHHHhcCCcccC
Confidence            99999999999999988764

>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=99.98  E-value=1.2e-32  Score=216.26  Aligned_cols=160  Identities=17%  Similarity=0.245  Sum_probs=136.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEe--ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL--KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~--~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ..++++|||+|||.++|+++|+++|..||.|..+.+  ..++.++|||||+|.+.++|..|+. |||..|.|+.|.|.++
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            467899999999999999999999999998766333  3456789999999999999999996 9999999999999998


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHH
Q 022301           81 HGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMK  160 (299)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~  160 (299)
                      .....                 .......+|||+|||..+++++|.++|..||.|..+ .......|||||+|.+.++|.
T Consensus        89 ~~~~~-----------------~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-~~~~~~~g~afV~f~~~~~A~  150 (175)
T 1fje_B           89 KGRDS-----------------KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-SQDGKSKGIAYIEFKSEADAE  150 (175)
T ss_dssp             CCSSC-----------------STTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-CSSSSCCSEEEEECSSHHHHH
T ss_pred             CCccc-----------------cccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-cCCCCCceEEEEEECCHHHHH
Confidence            65432                 223356899999999999999999999999999877 333345579999999999999


Q ss_pred             HHHHhcCCCeecCceeeEEEEeccc
Q 022301          161 HAIKKLDDSEFRNAFSRAYVRVREY  185 (299)
Q Consensus       161 ~a~~~l~g~~~~g~~~~~~~~~~~~  185 (299)
                      .|+..|||..|+|+    .+.+..+
T Consensus       151 ~A~~~l~g~~~~g~----~i~v~~a  171 (175)
T 1fje_B          151 KNLEEKQGAEIDGR----SVSLYYT  171 (175)
T ss_dssp             HHHHHHTEEEETTE----EEEEEEC
T ss_pred             HHHHHhCCCEECCe----EEEEEec
Confidence            99999999999998    4555444

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

Probab=99.97  E-value=7.3e-32  Score=210.09  Aligned_cols=151  Identities=18%  Similarity=0.362  Sum_probs=133.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      +++++|||+|||+++|+++|.++|+.||+|..|.|..   ++.++|||||+|.+.++|..|+..  +..+.|+.|.|.++
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            4689999999999999999999999999999999954   467899999999999999999994  56888999999887


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecCh
Q 022301           81 HGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNY  156 (299)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~  156 (299)
                      ....                   ......+|||+|||..+++++|.++|.+||.|..+.+..+..    .|||||+|.+.
T Consensus        79 ~~~~-------------------~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~  139 (167)
T 2cjk_A           79 IPRD-------------------EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSA  139 (167)
T ss_dssp             CCHH-------------------HHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSH
T ss_pred             cchh-------------------hccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCH
Confidence            5321                   112346899999999999999999999999999999988754    35999999999


Q ss_pred             hhHHHHHHhcCCCeecCcee
Q 022301          157 DDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       157 ~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ++|..|++ ++|..++|+.+
T Consensus       140 ~~a~~A~~-~~~~~~~g~~i  158 (167)
T 2cjk_A          140 DAVDRVCQ-NKFIDFKDRKI  158 (167)
T ss_dssp             HHHHHHHH-CSEECSSSSCE
T ss_pred             HHHHHHHh-CCCEEeCCeEE
Confidence            99999998 89999999944

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

Probab=99.97  E-value=4.1e-30  Score=218.16  Aligned_cols=165  Identities=15%  Similarity=0.249  Sum_probs=138.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcC-CeeEEEeecC--CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYG-PIAHIDLKIP--PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G-~v~~i~~~~~--~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      +.++|||+|||+++|+++|.++|..|| +|..|.|..+  +.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.
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 9999999543  5678999999999999999999999999999999999987


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCC-CCHHHHHHHHHhcCCeeEEEEEeCCC-----CCEEEEEecC
Q 022301           82 GGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSS-ASWQDLKDHMRRAGDVCFSQVFRDGS-----GTTGIVDYTN  155 (299)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~-~~~~~l~~~f~~~G~v~~~~~~~~~~-----~~~~fv~f~~  155 (299)
                      +.......            ........+|||.|||.. +++++|.++|..||.|..+.++.+..     .|||||+|.+
T Consensus       196 ~~~~~~~~------------~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~  263 (292)
T 2ghp_A          196 PLEKSKRT------------DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFEN  263 (292)
T ss_dssp             CC---------------------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESS
T ss_pred             CCcccccc------------cccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCC
Confidence            54432111            123345689999999999 99999999999999999999988654     4699999999


Q ss_pred             hhhHHHHHHhcCCCeecCceeeEEEEecccc
Q 022301          156 YDDMKHAIKKLDDSEFRNAFSRAYVRVREYD  186 (299)
Q Consensus       156 ~~~a~~a~~~l~g~~~~g~~~~~~~~~~~~~  186 (299)
                      .++|..|+ .|||..|+|+    .+.+....
T Consensus       264 ~~~A~~A~-~l~g~~~~g~----~i~V~~a~  289 (292)
T 2ghp_A          264 KDSAERAL-QMNRSLLGNR----EISVSLAD  289 (292)
T ss_dssp             HHHHHHHG-GGTTEEETTE----EEEEEECC
T ss_pred             HHHHHHHH-HhcCCEECCc----EEEEEEec
Confidence            99999999 9999999998    45544443

>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=2.3e-29  Score=212.68  Aligned_cols=144  Identities=24%  Similarity=0.326  Sum_probs=132.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      .++++|||+|||.++|+++|.++|+.|| |..|.+   +.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.  
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~---~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~--   93 (284)
T 3smz_A           20 RNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV---DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP--   93 (284)
T ss_dssp             HCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE---ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC--
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE---ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC--
Confidence            3679999999999999999999999999 999998   3668999999999999999999999999999999999853  


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhH
Q 022301           84 RGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDM  159 (299)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a  159 (299)
                                             ...+|||+|||..+++++|.++|..||.|..+.++.+...    |||||+|.+.++|
T Consensus        94 -----------------------~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a  150 (284)
T 3smz_A           94 -----------------------TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSA  150 (284)
T ss_dssp             -----------------------CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHH
T ss_pred             -----------------------CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHH
Confidence                                   2369999999999999999999999999999999987644    4999999999999


Q ss_pred             HHHHHhcCCCeecCcee
Q 022301          160 KHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       160 ~~a~~~l~g~~~~g~~~  176 (299)
                      ..|+..|+|..++|+.+
T Consensus       151 ~~A~~~l~~~~~~g~~i  167 (284)
T 3smz_A          151 ARAKSDLLGKPLGPRTL  167 (284)
T ss_dssp             HHHHHHHTTCEETTEEC
T ss_pred             HHHHHHhCCCEeCCcEE
Confidence            99999999999999844

>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=2e-29  Score=213.09  Aligned_cols=157  Identities=18%  Similarity=0.255  Sum_probs=139.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .+.++|||+|||+++|+++|.++|+.||.|..+.+..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
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            4678999999999999999999999999999999853   4667899999999999999999889999999999999998


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCC-CHHHHHHHHHhcCCeeEEEEEeCCCC---CEEEEEecCh
Q 022301           81 HGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSA-SWQDLKDHMRRAGDVCFSQVFRDGSG---TTGIVDYTNY  156 (299)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~-~~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv~f~~~  156 (299)
                      ......                .......+|||.|||..+ ++++|.++|..||.|..+.++.+..+   |+|||+|.+.
T Consensus       173 ~~~~~~----------------~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~  236 (284)
T 3smz_A          173 DAGQLT----------------PALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETA  236 (284)
T ss_dssp             CGGGCC----------------TTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSH
T ss_pred             CCCCCC----------------cccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCH
Confidence            654321                223456899999999995 99999999999999999999987543   5999999999


Q ss_pred             hhHHHHHHhcCCCeecCcee
Q 022301          157 DDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       157 ~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ++|..|+..|||..|+|+.+
T Consensus       237 ~~A~~A~~~l~g~~~~g~~l  256 (284)
T 3smz_A          237 EMAEEAQQQADGLSLGGSHL  256 (284)
T ss_dssp             HHHHHHHHHHTTCEETTEEC
T ss_pred             HHHHHHHHHhCCCccCCeEE
Confidence            99999999999999999944

>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=1.5e-29  Score=211.02  Aligned_cols=140  Identities=28%  Similarity=0.431  Sum_probs=127.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      .+.++|||+|||+++|+++|.++|+.||.|..|.|.   ..+|||||+|.+.++|..|+..|||..|.|+.|.|.++.. 
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 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN---RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH-   95 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC-
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEe---CCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeeccc-
Confidence            456899999999999999999999999999999996   4479999999999999999999999999999999999852 


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC---CEEEEEecChhhHH
Q 022301           84 RGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG---TTGIVDYTNYDDMK  160 (299)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv~f~~~~~a~  160 (299)
                                              ..+|||+|||..+++++|.++|..||.|..+.++.+..+   |||||+|.+.++|.
T Consensus        96 ------------------------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~  151 (261)
T 3sde_A           96 ------------------------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPAR  151 (261)
T ss_dssp             ------------------------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHH
T ss_pred             ------------------------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHH
Confidence                                    368999999999999999999999999999999988543   59999999999999


Q ss_pred             HHHHhcCCCee
Q 022301          161 HAIKKLDDSEF  171 (299)
Q Consensus       161 ~a~~~l~g~~~  171 (299)
                      .|+..|++..+
T Consensus       152 ~A~~~l~~~~~  162 (261)
T 3sde_A          152 KALERCGDGAF  162 (261)
T ss_dssp             HHHHHHHHSCE
T ss_pred             HHHHHhcCCeE
Confidence            99999955444

>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=1.8e-29  Score=214.22  Aligned_cols=146  Identities=21%  Similarity=0.272  Sum_probs=129.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC-CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~-~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      .++++|||+|||+++|+++|.++|+.||+|..|.|..+ ..++|||||+|.+.++|..|+. |||..|.|+.|.|.++. 
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            56899999999999999999999999999999999654 3357999999999999999996 99999999999999862 


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcC-CeeEEEEEeCC---CCCEEEEEecChhh
Q 022301           83 GRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAG-DVCFSQVFRDG---SGTTGIVDYTNYDD  158 (299)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G-~v~~~~~~~~~---~~~~~fv~f~~~~~  158 (299)
                                               ..+|||+|||..+++++|.++|..|| .|..+.++.+.   ..|||||+|.+.++
T Consensus       117 -------------------------~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~  171 (292)
T 2ghp_A          117 -------------------------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKED  171 (292)
T ss_dssp             -------------------------SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHH
T ss_pred             -------------------------CCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHH
Confidence                                     47999999999999999999999999 99999998765   45799999999999


Q ss_pred             HHHHHHhcCCCeecCcee
Q 022301          159 MKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       159 a~~a~~~l~g~~~~g~~~  176 (299)
                      |..|+..|+|..|.|+.+
T Consensus       172 a~~A~~~l~g~~~~g~~l  189 (292)
T 2ghp_A          172 ARYCVEKLNGLKIEGYTL  189 (292)
T ss_dssp             HHHHHHHHTTCEETTEEC
T ss_pred             HHHHHHHhCCCEeCCcEE
Confidence            999999999999999844

>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=99.92  E-value=4.2e-25  Score=195.67  Aligned_cols=161  Identities=16%  Similarity=0.172  Sum_probs=101.6

Q ss_pred             CCCCCCCHHHHHHHhhhcCCeeEEEe----ecCC-CCCceE-----EEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301           13 NLPGDIREREVEDLFYKYGPIAHIDL----KIPP-RPPGYA-----FVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus        13 nLp~~~t~~~l~~~F~~~G~v~~i~~----~~~~-~~~g~a-----fV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      .||++     |.+||.++|+|..|..    .... ...+|+     |++|....++..++..++...+.+..........
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            46665     7899999999988733    1111 223344     7888776666555543333222211000000000


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhh
Q 022301           83 GRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDD  158 (299)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~  158 (299)
                      ..  ........+...........+..+|||+|||..+++++|.++|.+||.|..|.|+.+..    .|||||+|.+.++
T Consensus        79 ~~--~~~~~~~~~~p~~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~  156 (437)
T 3pgw_S           79 QQ--EVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERD  156 (437)
T ss_pred             HH--HHHHhhhhcCCcccccccCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHH
Confidence            00  00000000000001112234567999999999999999999999999999999987753    4699999999999


Q ss_pred             HHHHHHhcCCCeecCceeeEEE
Q 022301          159 MKHAIKKLDDSEFRNAFSRAYV  180 (299)
Q Consensus       159 a~~a~~~l~g~~~~g~~~~~~~  180 (299)
                      |+.||..|||..|+|..+.+.+
T Consensus       157 A~~Ai~~lng~~i~gr~i~V~~  178 (437)
T 3pgw_S          157 MHSAYKHADGKKIDGRRVLVDV  178 (437)
T ss_pred             HHHHHHHcCCCEECCEEEEEEE
Confidence            9999999999999999654443

>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=99.91  E-value=1.9e-23  Score=185.06  Aligned_cols=81  Identities=36%  Similarity=0.644  Sum_probs=75.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .+.++|||+|||++||+++|.++|.+||+|..|.|+.   ++.++|||||+|.+.++|.+||..|||..|.|+.|.|.|+
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            4668999999999999999999999999999999954   5678999999999999999999999999999999999999


Q ss_pred             cCCC
Q 022301           81 HGGR   84 (299)
Q Consensus        81 ~~~~   84 (299)
                      ....
T Consensus       180 ~~~~  183 (437)
T 3pgw_S          180 RGRT  183 (437)
T ss_pred             CCCC
Confidence            7544

>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=2.6e-24  Score=156.35  Aligned_cols=109  Identities=21%  Similarity=0.352  Sum_probs=72.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC-CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~-~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      .+++|||+|||+++|+++|+++|+.||+|.+|.|..+ +.++|||||+|.+.++|..|+..|||..|.|+.|.|.++...
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            4678999999999999999999999999999999554 446899999999999999999999999999999999998754


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHH
Q 022301           84 RGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQD  124 (299)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~  124 (299)
                      ......           .........+|||+|||+.+|++.
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            321111           111223446799999999998763

>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=1.4e-22  Score=147.39  Aligned_cols=106  Identities=29%  Similarity=0.454  Sum_probs=95.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            2 SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         2 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ...++++|||+|||.++|+++|.++|+.||.|..|.|..++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            45788999999999999999999999999999999998888889999999999999999999999999999999999986


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCC
Q 022301           82 GGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGD  134 (299)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~  134 (299)
                      .....                           .+++...++++|.++|.+||.
T Consensus        84 ~~~~~---------------------------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           84 ANRAF---------------------------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             HHHHT---------------------------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             CChhh---------------------------hhhhHhHhHHHHHHHHHHhCC
Confidence            43211                           456667789999999999984

>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=5.6e-22  Score=139.77  Aligned_cols=78  Identities=28%  Similarity=0.488  Sum_probs=72.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ..++|||+|||+++|+++|+++|++||+|..|.|..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.|++
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            457899999999999999999999999999999954   46788999999999999999999999999999999999986


Q ss_pred             C
Q 022301           82 G   82 (299)
Q Consensus        82 ~   82 (299)
                      +
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            3

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

Probab=99.86  E-value=1.9e-21  Score=138.04  Aligned_cols=100  Identities=43%  Similarity=0.634  Sum_probs=83.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCCCCC
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGRGR   86 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~~~~   86 (299)
                      ++|||+|||+++|+++|+++|++||+|..|.|..+  ++|||||+|.+.++|..|+..|||..|.|+.|.|.++......
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            58999999999999999999999999999999766  6899999999999999999999999999999999999865532


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCccEEEEeCCC
Q 022301           87 SSSDRHSSHSSGRGRGVSRRSEYRVLVTGLP  117 (299)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~  117 (299)
                      .....         .+.......+|||+||+
T Consensus        79 ~~~~~---------~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           79 SRFDR---------PPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             SCCCS---------CCCSCCCCSCCCSCCCC
T ss_pred             ccCCC---------CCccccCCCceecCCCC
Confidence            21111         11122345689999986

>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=2.9e-21  Score=129.54  Aligned_cols=74  Identities=18%  Similarity=0.252  Sum_probs=70.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      -.+..|||+||++.+|+++|+++|.+||+|.++.+..   ++|||||+|.++++|..|+..||+..|.|+.|.|+++
T Consensus         5 ~~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~---~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            5 WGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL---NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET---TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC---CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            4578999999999999999999999999999999974   6999999999999999999999999999999999887

>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=5.8e-21  Score=145.51  Aligned_cols=130  Identities=17%  Similarity=0.156  Sum_probs=105.2

Q ss_pred             CCCCceEEEEecChHHHHHHHHhc-CCCCCCCceEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCC
Q 022301           42 PRPPGYAFVEFEEARDAEDAIRGR-DGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSA  120 (299)
Q Consensus        42 ~~~~g~afV~F~~~e~A~~A~~~l-~~~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~  120 (299)
                      ...+|+++|+|.+.++|++|+..| ||..+.| .|.+.++...........   ...............+|||+|||..+
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~---~~~~~~~~~~~~~~~~l~V~nl~~~~   85 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSH---HHHHHMHRDSCPLDCKVYVGNLGNNG   85 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSS---SCCCCSCSSSSTTSCEEEEESCCSCC
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccc---cccccccccCCCCCCEEEEeCCCCCC
Confidence            356899999999999999999999 9999999 999998754221110000   00011122344567899999999999


Q ss_pred             CHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          121 SWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       121 ~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ++++|.++|.+||.|..+.++.+ ..|||||+|.+.++|..|+..|||..|+|+.+
T Consensus        86 t~~~l~~~F~~~G~i~~v~i~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l  140 (150)
T 2i2y_A           86 NKTELERAFGYYGPLRSVWVARN-PPGFAFVEFEDPRDAADAVRELDGRTLCGCRV  140 (150)
T ss_dssp             SCHHHHHHHHHHSCEEEEEECSS-SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCC
T ss_pred             CHHHHHHHHHhhCCEEEEEEeeC-CCcEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            99999999999999999999887 46799999999999999999999999999954

>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=99.85  E-value=2.1e-20  Score=135.73  Aligned_cols=85  Identities=27%  Similarity=0.509  Sum_probs=78.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEE
Q 022301            1 MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVE   78 (299)
Q Consensus         1 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~   78 (299)
                      |...++++|||+|||.++|+++|.++|+.||.|..|.|..  ++.++|||||+|.+.++|++|+..|||..|.|+.|.|.
T Consensus         2 ~e~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~   81 (116)
T 2fy1_A            2 VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVE   81 (116)
T ss_dssp             CTTCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            4567889999999999999999999999999999999965  56788999999999999999999999999999999999


Q ss_pred             EccCCCC
Q 022301           79 LAHGGRG   85 (299)
Q Consensus        79 ~~~~~~~   85 (299)
                      ++.....
T Consensus        82 ~a~~~~~   88 (116)
T 2fy1_A           82 QAKKPSF   88 (116)
T ss_dssp             ECCCSSC
T ss_pred             ECCCCCC
Confidence            9986554

>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=8e-21  Score=136.69  Aligned_cols=83  Identities=59%  Similarity=1.044  Sum_probs=77.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            2 SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         2 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ...++++|||+|||.++|+++|+++|..||+|..|.|..++.++|||||+|.+.++|+.|+..||+..|.|+.|.|.++.
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   97 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   97 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcc
Confidence            34678999999999999999999999999999999998888889999999999999999999999999999999999997


Q ss_pred             CCC
Q 022301           82 GGR   84 (299)
Q Consensus        82 ~~~   84 (299)
                      ...
T Consensus        98 ~~~  100 (109)
T 1x4a_A           98 SGR  100 (109)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            654

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=3.7e-21  Score=135.30  Aligned_cols=81  Identities=20%  Similarity=0.277  Sum_probs=73.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCC--CCCCCceEEEEE
Q 022301            2 SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG--YDFDGHRLRVEL   79 (299)
Q Consensus         2 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~--~~~~g~~i~v~~   79 (299)
                      +..+.++|||+|||+++|+++|+++|++||+|.+|.|..+   +|||||+|.+.++|..|+..|++  ..|.|+.|.|.+
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~---kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~   88 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG---KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQF   88 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC---CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            4578999999999999999999999999999999999753   79999999999999999998864  789999999999


Q ss_pred             ccCCCC
Q 022301           80 AHGGRG   85 (299)
Q Consensus        80 ~~~~~~   85 (299)
                      +.....
T Consensus        89 A~~~~~   94 (105)
T 1sjq_A           89 SNHKEL   94 (105)
T ss_dssp             CSSSSC
T ss_pred             cCCCCC
Confidence            976554

>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=2.7e-20  Score=143.12  Aligned_cols=136  Identities=15%  Similarity=0.075  Sum_probs=99.1

Q ss_pred             CCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCH
Q 022301           43 RPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASW  122 (299)
Q Consensus        43 ~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~  122 (299)
                      ..+|||||+|.+.++|++|+..+++....+..+.+...........      ...............+|||+|||..+++
T Consensus        11 ~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~l~v~nl~~~~~~   84 (158)
T 2kn4_A           11 TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE------GSHHHHHHMDVEGMTSLKVDNLTYRTSP   84 (158)
T ss_dssp             SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEEC------CCCCSSCCCCCCBCCEEEEESCCTTCCH
T ss_pred             cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccc------cccccccccCCCCCCEEEEeCCCCCCCH
Confidence            5789999999999999999988876433333333322111000000      0000111223355689999999999999


Q ss_pred             HHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEecccccC
Q 022301          123 QDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVREYDHR  188 (299)
Q Consensus       123 ~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~~~~~~  188 (299)
                      ++|.++|..||.|..+.++.+..    .|||||+|.+.++|+.|+..|||..|+|+    .+.+......
T Consensus        85 ~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~----~l~v~~a~~~  150 (158)
T 2kn4_A           85 DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGR----ELRVQMARYG  150 (158)
T ss_dssp             HHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSS----EEEEEEECCS
T ss_pred             HHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCe----EEEEEECCCC
Confidence            99999999999999999988753    36999999999999999999999999999    5555554443

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.84  E-value=2.4e-21  Score=134.45  Aligned_cols=79  Identities=19%  Similarity=0.344  Sum_probs=71.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcC-CeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcC-CCCCCCceEEEEEc
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYG-PIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRD-GYDFDGHRLRVELA   80 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G-~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~-~~~~~g~~i~v~~~   80 (299)
                      +++|||+|||+++|+++|.++|++|| +|.+|.|..   ++.++|||||+|.+.++|..|+..|+ +..|.|+.|.|.++
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 899999954   47889999999999999999999774 56799999999998


Q ss_pred             cCCC
Q 022301           81 HGGR   84 (299)
Q Consensus        81 ~~~~   84 (299)
                      .+..
T Consensus        81 ~~~~   84 (91)
T 2lxi_A           81 DPKP   84 (91)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            7654

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

Probab=99.84  E-value=9.3e-21  Score=131.89  Aligned_cols=78  Identities=22%  Similarity=0.313  Sum_probs=71.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCC--CCCceEEEEEc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYD--FDGHRLRVELA   80 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~--~~g~~i~v~~~   80 (299)
                      ..|+++|||+|||.++|+++|.++|++||+|.+|.|.   ..+|||||+|.+.++|..|+..||+..  |.|+.|.|.|+
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~---~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S   94 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM---PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYS   94 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEE---TTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEE---cCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEec
Confidence            3689999999999999999999999999999999997   357999999999999999999999876  78999999999


Q ss_pred             cCC
Q 022301           81 HGG   83 (299)
Q Consensus        81 ~~~   83 (299)
                      +..
T Consensus        95 ~~k   97 (100)
T 3r27_A           95 TSQ   97 (100)
T ss_dssp             SCS
T ss_pred             ccc
Confidence            754

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

Probab=99.84  E-value=7.4e-21  Score=136.57  Aligned_cols=80  Identities=19%  Similarity=0.338  Sum_probs=74.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..+.++|||+|||+++|+++|.++|++||+|..|.|..   ++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.+
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            46789999999999999999999999999999999954   367889999999999999999999999999999999999


Q ss_pred             ccC
Q 022301           80 AHG   82 (299)
Q Consensus        80 ~~~   82 (299)
                      +..
T Consensus        83 a~~   85 (110)
T 3s8s_A           83 DIK   85 (110)
T ss_dssp             CST
T ss_pred             CCC
Confidence            853

>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=3.1e-20  Score=131.19  Aligned_cols=83  Identities=34%  Similarity=0.509  Sum_probs=76.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..++++|||+|||.++|+++|+++|..||+|..|.|..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.+
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            46789999999999999999999999999999999954   467889999999999999999998999999999999999


Q ss_pred             ccCCCC
Q 022301           80 AHGGRG   85 (299)
Q Consensus        80 ~~~~~~   85 (299)
                      +.....
T Consensus        85 a~~~~~   90 (99)
T 1whw_A           85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             cCCCcc
Confidence            986654

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

Probab=99.84  E-value=4.7e-20  Score=129.25  Aligned_cols=83  Identities=30%  Similarity=0.508  Sum_probs=76.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..++++|||+|||.++|+++|+++|+.||+|..|.|..+   +.++|||||+|.+.++|..|+..|||..|.|+.|.|.+
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            467899999999999999999999999999999999654   67889999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 022301           80 AHGGRG   85 (299)
Q Consensus        80 ~~~~~~   85 (299)
                      +.....
T Consensus        82 a~~~~~   87 (95)
T 2dnz_A           82 VTERLD   87 (95)
T ss_dssp             SSCCCC
T ss_pred             cccccC
Confidence            976543

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

Probab=99.84  E-value=1.9e-20  Score=137.43  Aligned_cols=82  Identities=18%  Similarity=0.395  Sum_probs=75.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH----HHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVE----DLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVE   78 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~----~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~   78 (299)
                      ..++++|||+|||+.+++++|+    ++|++||+|..|.+..++.++|||||+|.+.++|..|+..|||..|.|+.|.|.
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~  105 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVIT  105 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEE
Confidence            3578999999999999999866    799999999999998888899999999999999999999999999999999999


Q ss_pred             EccCCC
Q 022301           79 LAHGGR   84 (299)
Q Consensus        79 ~~~~~~   84 (299)
                      |+....
T Consensus       106 ~a~~~~  111 (127)
T 2a3j_A          106 FSETPQ  111 (127)
T ss_dssp             ECCCCC
T ss_pred             EccCcc
Confidence            987543

>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=2.3e-20  Score=134.64  Aligned_cols=81  Identities=19%  Similarity=0.273  Sum_probs=73.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcC--CCCCCCceEEEEEc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRD--GYDFDGHRLRVELA   80 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~--~~~~~g~~i~v~~~   80 (299)
                      ..++++|||+|||+++|+++|+++|++||.|..|.|..+   +|||||+|.+.++|.+|+..|+  +..|.|+.|.|.++
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            467899999999999999999999999999999999753   7999999999999999999887  46899999999999


Q ss_pred             cCCCCC
Q 022301           81 HGGRGR   86 (299)
Q Consensus        81 ~~~~~~   86 (299)
                      ......
T Consensus       105 ~~k~~~  110 (119)
T 2ad9_A          105 NHKELK  110 (119)
T ss_dssp             SSSSCC
T ss_pred             cCCCCC
Confidence            765543

>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=3.2e-20  Score=132.14  Aligned_cols=82  Identities=37%  Similarity=0.577  Sum_probs=75.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .++++|||+|||.++|+++|+++|..||+|..|.|..+   +.++|||||+|.+.++|+.|+..|||..|.|+.|.|.++
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            57899999999999999999999999999999999653   678899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 022301           81 HGGRG   85 (299)
Q Consensus        81 ~~~~~   85 (299)
                      .....
T Consensus        91 ~~~~~   95 (103)
T 2dnm_A           91 RYGRR   95 (103)
T ss_dssp             SSCCS
T ss_pred             CcCCC
Confidence            76543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.83  E-value=7.3e-21  Score=132.51  Aligned_cols=79  Identities=20%  Similarity=0.345  Sum_probs=70.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCC--eeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCC----CCCce
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGP--IAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYD----FDGHR   74 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~--v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~----~~g~~   74 (299)
                      ..=+||||+|||+++|+++|.++|++||.  |.+|.+..   ++.++|||||+|.+.++|..|+..|||..    |.|+.
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            45689999999999999999999999995  67888854   47889999999999999999999999974    88999


Q ss_pred             EEEEEccC
Q 022301           75 LRVELAHG   82 (299)
Q Consensus        75 i~v~~~~~   82 (299)
                      |.|.|++.
T Consensus        87 i~V~~Aks   94 (95)
T 2lkz_A           87 IGVDFAKS   94 (95)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEccC
Confidence            99999864

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

Probab=99.83  E-value=1.9e-20  Score=132.09  Aligned_cols=83  Identities=27%  Similarity=0.460  Sum_probs=75.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec------CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI------PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLR   76 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~------~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~   76 (299)
                      +.++++|||+|||.++|+++|+++|+.||+|..|.|..      ++.++|||||+|.+.++|..|+..|||..|.|+.|.
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            47899999999999999999999999999999999954      225679999999999999999999999999999999


Q ss_pred             EEEccCCCC
Q 022301           77 VELAHGGRG   85 (299)
Q Consensus        77 v~~~~~~~~   85 (299)
                      |.++.....
T Consensus        82 V~~a~~~~~   90 (98)
T 2cpf_A           82 VRISERATK   90 (98)
T ss_dssp             EECSSCSSC
T ss_pred             EEEccCCCC
Confidence            999976553

>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=2.6e-20  Score=130.78  Aligned_cols=80  Identities=29%  Similarity=0.615  Sum_probs=74.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      |+++|||+|||.++++++|.++|+.||.|..|.|..+   +.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.
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            6899999999999999999999999999999999654   6778999999999999999999999999999999999997


Q ss_pred             CCC
Q 022301           82 GGR   84 (299)
Q Consensus        82 ~~~   84 (299)
                      ...
T Consensus        81 ~~~   83 (96)
T 2x1f_A           81 NSD   83 (96)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            644

>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=6.3e-20  Score=130.57  Aligned_cols=83  Identities=34%  Similarity=0.506  Sum_probs=75.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC-CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~-~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ..+.++|||+|||+++|+++|+++|+.||+|..|.|..+ ..++|||||+|.+.++|..|+..||+..|.|+.|.|.++.
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            467899999999999999999999999999999999664 3468999999999999999999999999999999999997


Q ss_pred             CCCC
Q 022301           82 GGRG   85 (299)
Q Consensus        82 ~~~~   85 (299)
                      ....
T Consensus        92 ~~~~   95 (103)
T 2cqi_A           92 TPSS   95 (103)
T ss_dssp             CTTC
T ss_pred             CCcc
Confidence            6543

>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=8.1e-20  Score=129.02  Aligned_cols=82  Identities=24%  Similarity=0.530  Sum_probs=75.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..++++|||+|||.++|+++|+++|..||+|..|.|..+   +.++|||||+|.+.++|..|+. ||+..|.|+.|.|.+
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            467899999999999999999999999999999999653   6688999999999999999999 999999999999999


Q ss_pred             ccCCCC
Q 022301           80 AHGGRG   85 (299)
Q Consensus        80 ~~~~~~   85 (299)
                      +.....
T Consensus        86 a~~~~~   91 (99)
T 2dgs_A           86 AEPRDS   91 (99)
T ss_dssp             CCCCCC
T ss_pred             CCCCcc
Confidence            976543

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

Probab=99.83  E-value=5.2e-20  Score=130.77  Aligned_cols=83  Identities=34%  Similarity=0.593  Sum_probs=76.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..++++|||+|||+++|+++|+++|+.||+|..|.|..   ++.++|||||+|.+.++|..|+..||+..|.|+.|.|.+
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            36789999999999999999999999999999999965   456789999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 022301           80 AHGGRG   85 (299)
Q Consensus        80 ~~~~~~   85 (299)
                      +.....
T Consensus        89 a~~~~~   94 (102)
T 1x5s_A           89 AGKSSD   94 (102)
T ss_dssp             EECCCC
T ss_pred             CCCCCC
Confidence            976553

>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=99.83  E-value=5.1e-20  Score=129.67  Aligned_cols=80  Identities=20%  Similarity=0.264  Sum_probs=72.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhc--CCCCCCCceEEEEEc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGR--DGYDFDGHRLRVELA   80 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l--~~~~~~g~~i~v~~~   80 (299)
                      ..++++|||+|||+++|+++|.++|++||.|..|.|..+   +|||||+|.+.++|..|+..|  ++..|.|+.|.|.|+
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~---kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a   88 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG---KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYS   88 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC---CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEc
Confidence            468899999999999999999999999999999998743   899999999999999999976  467899999999999


Q ss_pred             cCCCC
Q 022301           81 HGGRG   85 (299)
Q Consensus        81 ~~~~~   85 (299)
                      .....
T Consensus        89 ~~~~~   93 (101)
T 2cq1_A           89 NHKEL   93 (101)
T ss_dssp             SCSSC
T ss_pred             CcccC
Confidence            76554

>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=2.8e-20  Score=132.18  Aligned_cols=83  Identities=34%  Similarity=0.578  Sum_probs=76.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..+.++|||+|||.++|+++|+++|+.||+|..|.|..+   +.++|||||+|.+.++|..|+..|||..|.|+.|.|.+
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            368899999999999999999999999999999999554   67899999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 022301           80 AHGGRG   85 (299)
Q Consensus        80 ~~~~~~   85 (299)
                      +.....
T Consensus        89 a~~~~~   94 (102)
T 2cqb_A           89 AKPMRI   94 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            976553

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

Probab=99.83  E-value=4e-20  Score=131.59  Aligned_cols=84  Identities=25%  Similarity=0.397  Sum_probs=76.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec-CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            2 SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI-PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         2 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~-~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ...+.++|||+|||+++|+++|+++|..||+|..|.|.. ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA   90 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            346889999999999999999999999999999999955 4667899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 022301           81 HGGRG   85 (299)
Q Consensus        81 ~~~~~   85 (299)
                      .....
T Consensus        91 ~~~~~   95 (103)
T 2d9p_A           91 QRKEE   95 (103)
T ss_dssp             SSCCC
T ss_pred             ccccc
Confidence            76553

>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=2.3e-20  Score=128.02  Aligned_cols=79  Identities=34%  Similarity=0.631  Sum_probs=73.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..++++|||+|||+++++++|+++|++||+|..|.+..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.+
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            46889999999999999999999999999999999943   466789999999999999999999999999999999998


Q ss_pred             cc
Q 022301           80 AH   81 (299)
Q Consensus        80 ~~   81 (299)
                      ++
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=3.4e-20  Score=129.16  Aligned_cols=84  Identities=27%  Similarity=0.461  Sum_probs=76.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec-CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            2 SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI-PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         2 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~-~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ...+.++|||+|||.++++++|+++|..||+|..|.|.. ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   83 (92)
T 2dgv_A            4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            357889999999999999999999999999999999964 4667899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 022301           81 HGGRG   85 (299)
Q Consensus        81 ~~~~~   85 (299)
                      .....
T Consensus        84 ~~~~~   88 (92)
T 2dgv_A           84 RNASG   88 (92)
T ss_dssp             SCCSS
T ss_pred             CCCCC
Confidence            76543

>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=3.5e-20  Score=130.06  Aligned_cols=81  Identities=21%  Similarity=0.333  Sum_probs=74.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            4 RASRTLYVGNLPGDIREREVE----DLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~----~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      .+.++|||+|||.++++++|+    ++|++||+|..|.|..+...+|||||+|.+.++|.+|+..|||..|.|+.|.|.+
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    9999999999999976654489999999999999999999999999999999999


Q ss_pred             ccCCC
Q 022301           80 AHGGR   84 (299)
Q Consensus        80 ~~~~~   84 (299)
                      +....
T Consensus        87 a~~~~   91 (96)
T 2dgx_A           87 ATGAS   91 (96)
T ss_dssp             CCCSS
T ss_pred             cCCCC
Confidence            97544

>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=130.72  Aligned_cols=83  Identities=30%  Similarity=0.467  Sum_probs=76.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..++++|||+|||.++|+++|+++|+.||+|..|.|..   ++.++|||||+|.+.++|..|+..||+..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   91 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   91 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            36789999999999999999999999999999999955   467889999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 022301           80 AHGGRG   85 (299)
Q Consensus        80 ~~~~~~   85 (299)
                      +.....
T Consensus        92 a~~~~~   97 (105)
T 1x5u_A           92 ASAHNK   97 (105)
T ss_dssp             TTTTSC
T ss_pred             CCCCCc
Confidence            976543

>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=99.83  E-value=1.8e-20  Score=131.86  Aligned_cols=79  Identities=18%  Similarity=0.176  Sum_probs=71.6

Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCC--CCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPG-DIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY--DFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~-~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~--~~~g~~i~v~~   79 (299)
                      ..++++|||+|||+ ++|+++|.++|++||.|.+|.|..   .+|||||+|.+.++|..|+..||+.  .|.|+.|.|.+
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 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN---KINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHL   88 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECS---SSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEc---CCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEE
Confidence            46889999999999 999999999999999999999974   3689999999999999999998864  48999999999


Q ss_pred             ccCCC
Q 022301           80 AHGGR   84 (299)
Q Consensus        80 ~~~~~   84 (299)
                      +....
T Consensus        89 a~~~~   93 (102)
T 1x4d_A           89 SQKYK   93 (102)
T ss_dssp             ECCCT
T ss_pred             CCCCC
Confidence            97544

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

Probab=99.82  E-value=4.4e-20  Score=129.65  Aligned_cols=83  Identities=25%  Similarity=0.426  Sum_probs=76.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEE-Eeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHI-DLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVE   78 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i-~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~   78 (299)
                      +.++++|||+|||.++|+++|.++|+.||+|..| .|..   ++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.
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            4678999999999999999999999999999999 8854   46788999999999999999999999999999999999


Q ss_pred             EccCCCC
Q 022301           79 LAHGGRG   85 (299)
Q Consensus        79 ~~~~~~~   85 (299)
                      ++.....
T Consensus        82 ~a~~~~~   88 (96)
T 1x5t_A           82 YAFKKDS   88 (96)
T ss_dssp             ESCCCCC
T ss_pred             EecccCC
Confidence            9976543

>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=4.6e-20  Score=129.04  Aligned_cols=78  Identities=23%  Similarity=0.462  Sum_probs=73.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .++++|||+|||.++++++|+++|+.||+|..|.|..+   +.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
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            57899999999999999999999999999999999654   667899999999999999999999999999999999997


Q ss_pred             c
Q 022301           81 H   81 (299)
Q Consensus        81 ~   81 (299)
                      +
T Consensus        94 k   94 (94)
T 2e5h_A           94 I   94 (94)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=1.3e-20  Score=132.67  Aligned_cols=84  Identities=29%  Similarity=0.538  Sum_probs=76.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHH----HHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEE
Q 022301            1 MSSRASRTLYVGNLPGDIREREVE----DLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLR   76 (299)
Q Consensus         1 ~~~~~~~~l~V~nLp~~~t~~~l~----~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~   76 (299)
                      |...++++|||+|||.++++++|.    ++|++||.|..|.+..++.++|||||+|.+.++|..|+..|||..|.|+.|.
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            456889999999999999999999    9999999999999976677789999999999999999999999999999999


Q ss_pred             EEEccCCC
Q 022301           77 VELAHGGR   84 (299)
Q Consensus        77 v~~~~~~~   84 (299)
                      |.++....
T Consensus        83 v~~a~~~~   90 (97)
T 1nu4_A           83 IQYAKTDS   90 (97)
T ss_dssp             EEECSSCC
T ss_pred             EEEccCCC
Confidence            99987543

>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=9e-20  Score=129.20  Aligned_cols=80  Identities=19%  Similarity=0.205  Sum_probs=71.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCC--CCCCCceEEEEEc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG--YDFDGHRLRVELA   80 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~--~~~~g~~i~v~~~   80 (299)
                      ..++++|||+|||+++++++|+++|++||.|..|.|..   .+|||||+|.+.++|..|+..|++  ..|.|+.|.|.|+
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~---~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a   88 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP---FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYS   88 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET---TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEC---CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEc
Confidence            36789999999999999999999999999999999974   379999999999999999998876  4599999999999


Q ss_pred             cCCCC
Q 022301           81 HGGRG   85 (299)
Q Consensus        81 ~~~~~   85 (299)
                      .....
T Consensus        89 ~~~~~   93 (104)
T 1wex_A           89 TSKRI   93 (104)
T ss_dssp             SSSSC
T ss_pred             cCccc
Confidence            76543

>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=1.3e-19  Score=129.97  Aligned_cols=83  Identities=25%  Similarity=0.462  Sum_probs=76.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec----CCCCCceEEEEecChHHHHHHHHhc-CCCCCCCceEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI----PPRPPGYAFVEFEEARDAEDAIRGR-DGYDFDGHRLRV   77 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~----~~~~~g~afV~F~~~e~A~~A~~~l-~~~~~~g~~i~v   77 (299)
                      ..++++|||+|||.++|+++|+++|..||+|..|.|..    ++.++|||||+|.+.++|..|+..| |+..|.|+.|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v   91 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   91 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEE
Confidence            46789999999999999999999999999999999944    4677899999999999999999999 999999999999


Q ss_pred             EEccCCCC
Q 022301           78 ELAHGGRG   85 (299)
Q Consensus        78 ~~~~~~~~   85 (299)
                      .++.....
T Consensus        92 ~~a~~~~~   99 (107)
T 2cph_A           92 EWADSEVT   99 (107)
T ss_dssp             EECCCCCC
T ss_pred             EeCCCCCC
Confidence            99976543

>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=1.3e-19  Score=128.89  Aligned_cols=83  Identities=24%  Similarity=0.458  Sum_probs=75.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC-CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~-~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ..+.++|||+|||+++|+++|+++|..||+|..|.|..+ ..++|||||+|.+.++|..|+..|||..|.|+.|.|.++.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   91 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT   91 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcc
Confidence            467899999999999999999999999999999999654 3468999999999999999999999999999999999997


Q ss_pred             CCCC
Q 022301           82 GGRG   85 (299)
Q Consensus        82 ~~~~   85 (299)
                      ....
T Consensus        92 ~~~~   95 (103)
T 2cq3_A           92 ARVM   95 (103)
T ss_dssp             SSCC
T ss_pred             cCCC
Confidence            6553

>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=129.96  Aligned_cols=82  Identities=24%  Similarity=0.485  Sum_probs=74.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ..+.++|||+|||.++|+++|.++|..||+|..|.|..  ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   93 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS   93 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            35789999999999999999999999999999999954  3566799999999999999999999999999999999998


Q ss_pred             cCCC
Q 022301           81 HGGR   84 (299)
Q Consensus        81 ~~~~   84 (299)
                      .+..
T Consensus        94 ~~~~   97 (100)
T 2do4_A           94 NSGP   97 (100)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            7543

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

Probab=99.82  E-value=1.1e-19  Score=132.01  Aligned_cols=84  Identities=25%  Similarity=0.440  Sum_probs=76.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..+.++|||+|||.++|+++|+++|..||.|..|.|..   ++.++|||||+|.+.++|+.|+..|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   91 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            36789999999999999999999999999999999954   466789999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q 022301           80 AHGGRGR   86 (299)
Q Consensus        80 ~~~~~~~   86 (299)
                      +......
T Consensus        92 a~~~~~~   98 (115)
T 2dgo_A           92 ATRKPPA   98 (115)
T ss_dssp             SSCCCCC
T ss_pred             ccCCCCC
Confidence            9866543

>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=2.9e-20  Score=128.12  Aligned_cols=80  Identities=26%  Similarity=0.447  Sum_probs=71.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..+.++|||+|||.++++++|+++|+.||+|..|.+..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.+
T Consensus         3 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (87)
T 3bs9_A            3 LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   82 (87)
T ss_dssp             ---CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEe
Confidence            35788999999999999999999999999999999954   466789999999999999999999999999999999999


Q ss_pred             ccC
Q 022301           80 AHG   82 (299)
Q Consensus        80 ~~~   82 (299)
                      +..
T Consensus        83 a~~   85 (87)
T 3bs9_A           83 ATR   85 (87)
T ss_dssp             EC-
T ss_pred             cCC
Confidence            864

>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=99.82  E-value=4.7e-20  Score=125.85  Aligned_cols=78  Identities=24%  Similarity=0.454  Sum_probs=72.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      +.+|||+|||.++++++|.++|+.||+|..+.+..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++..
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            47899999999999999999999999999999954   467789999999999999999999999999999999999875


Q ss_pred             C
Q 022301           83 G   83 (299)
Q Consensus        83 ~   83 (299)
                      .
T Consensus        81 ~   81 (83)
T 3md1_A           81 L   81 (83)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=1.3e-19  Score=125.55  Aligned_cols=78  Identities=35%  Similarity=0.622  Sum_probs=73.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      ..+.++|||+|||.++|+++|+++|+.||+|..|.|.     ++||||+|.+.++|..|+..||+..|.|+.|.|.++..
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            4688999999999999999999999999999999998     78999999999999999999999999999999999976


Q ss_pred             CCC
Q 022301           83 GRG   85 (299)
Q Consensus        83 ~~~   85 (299)
                      ...
T Consensus        80 ~~~   82 (90)
T 2dnq_A           80 KSK   82 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            553

>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=4e-20  Score=130.64  Aligned_cols=83  Identities=24%  Similarity=0.418  Sum_probs=75.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhhcCCee-EEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCce---
Q 022301            2 SSRASRTLYVGNLPGDIREREVEDLFYKYGPIA-HIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHR---   74 (299)
Q Consensus         2 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~-~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~---   74 (299)
                      +..++++|||+|||+++++++|+++|..||+|. .|.|..   ++.++|||||+|.+.++|+.|+..|||..|.|+.   
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            457899999999999999999999999999999 999954   4567899999999999999999999999999999   


Q ss_pred             -EEEEEccCCC
Q 022301           75 -LRVELAHGGR   84 (299)
Q Consensus        75 -i~v~~~~~~~   84 (299)
                       |.|.|+....
T Consensus        85 ~l~v~~a~~~~   95 (99)
T 2div_A           85 RFKLNYATYSG   95 (99)
T ss_dssp             ECCEEETTCCS
T ss_pred             eEEEeecCCCC
Confidence             9999987544

>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=99.82  E-value=8.8e-20  Score=130.03  Aligned_cols=82  Identities=24%  Similarity=0.485  Sum_probs=74.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC----CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEE
Q 022301            2 SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP----PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRV   77 (299)
Q Consensus         2 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~----~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v   77 (299)
                      ...+.++|||+|||.++|+++|+++|..|| |..|.|..+    +.++|||||+|.+.++|.+|| .||+..|.|+.|.|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   88 (104)
T 1wi8_A           11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRV   88 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEE
Confidence            346789999999999999999999999999 999999654    667899999999999999999 89999999999999


Q ss_pred             EEccCCCC
Q 022301           78 ELAHGGRG   85 (299)
Q Consensus        78 ~~~~~~~~   85 (299)
                      .++.....
T Consensus        89 ~~a~~~~~   96 (104)
T 1wi8_A           89 DVADQAQD   96 (104)
T ss_dssp             EECCCCCC
T ss_pred             EEccCCCC
Confidence            99976543

>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=99.82  E-value=1.3e-19  Score=129.57  Aligned_cols=83  Identities=19%  Similarity=0.346  Sum_probs=75.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCC---CCceEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDF---DGHRLR   76 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~---~g~~i~   76 (299)
                      ..+.++|||+|||.++|+++|+++|+.||+|..|.|..   ++.++|||||+|.+.++|..|+..||+..+   .|+.|.
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            46789999999999999999999999999999999965   367899999999999999999999999887   899999


Q ss_pred             EEEccCCCC
Q 022301           77 VELAHGGRG   85 (299)
Q Consensus        77 v~~~~~~~~   85 (299)
                      |.++.....
T Consensus        90 v~~a~~~~~   98 (106)
T 2dgp_A           90 VKPADSESR   98 (106)
T ss_dssp             EEECCCCSC
T ss_pred             EEECCcccc
Confidence            999976543

>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=1.7e-19  Score=128.27  Aligned_cols=79  Identities=24%  Similarity=0.496  Sum_probs=73.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      .++++|||+|||+++|+++|+++|..||+|..|.|.     ++||||+|.+.++|.+|+..||+..|.|+.|.|.++...
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            567999999999999999999999999999999997     679999999999999999999999999999999999866


Q ss_pred             CCCC
Q 022301           84 RGRS   87 (299)
Q Consensus        84 ~~~~   87 (299)
                      ....
T Consensus        84 ~~~~   87 (103)
T 2dgu_A           84 DQKR   87 (103)
T ss_dssp             CCCC
T ss_pred             cccc
Confidence            5433

>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=4.1e-20  Score=131.57  Aligned_cols=83  Identities=34%  Similarity=0.572  Sum_probs=75.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..++++|||+|||.++|+++|.++|+.||+|..|.|..   ++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            35789999999999999999999999999999999954   467789999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 022301           80 AHGGRG   85 (299)
Q Consensus        80 ~~~~~~   85 (299)
                      +.....
T Consensus        92 a~~~~~   97 (103)
T 2cq0_A           92 AKPSTN   97 (103)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            976543

>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=6.5e-20  Score=126.60  Aligned_cols=80  Identities=28%  Similarity=0.556  Sum_probs=73.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCC---C-CCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---R-PPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~---~-~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..+++|||+|||.++|+++|.++|+.||+|..|.|..+.   . ++|||||+|.+.++|..|+..|||..|.|+.|.|.+
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            467899999999999999999999999999999995542   2 789999999999999999999999999999999999


Q ss_pred             ccCC
Q 022301           80 AHGG   83 (299)
Q Consensus        80 ~~~~   83 (299)
                      +.+.
T Consensus        82 a~~~   85 (88)
T 4a8x_A           82 VLAP   85 (88)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            8653

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

Probab=99.82  E-value=4.7e-20  Score=131.99  Aligned_cols=80  Identities=28%  Similarity=0.514  Sum_probs=74.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .++++|||+|||.++|+++|.++|+.||+|..|.|..+   +.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
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            56789999999999999999999999999999999644   667899999999999999999999999999999999998


Q ss_pred             cCC
Q 022301           81 HGG   83 (299)
Q Consensus        81 ~~~   83 (299)
                      ...
T Consensus       101 ~~~  103 (106)
T 1p27_B          101 FVR  103 (106)
T ss_dssp             EES
T ss_pred             cCC
Confidence            754

>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=99.82  E-value=9.8e-20  Score=130.07  Aligned_cols=82  Identities=28%  Similarity=0.383  Sum_probs=74.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCC---ceEEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDG---HRLRVE   78 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g---~~i~v~   78 (299)
                      .++++|||+|||.++|+++|.++|+.||+|..|.|..  ++.++|||||+|.+.++|..|+..|||..|.|   +.|.|.
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            5689999999999999999999999999999999954  45668999999999999999999999999998   999999


Q ss_pred             EccCCCC
Q 022301           79 LAHGGRG   85 (299)
Q Consensus        79 ~~~~~~~   85 (299)
                      ++.....
T Consensus        93 ~a~~~~~   99 (105)
T 2dnh_A           93 FADTDKE   99 (105)
T ss_dssp             ESCSSCC
T ss_pred             ECccCcc
Confidence            9976543

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

Probab=99.81  E-value=1.9e-19  Score=130.58  Aligned_cols=83  Identities=20%  Similarity=0.288  Sum_probs=75.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ..++++|||+|||.++|+++|+++|..||+|..|.|..  ++.++|||||+|.+.++|..|+..||+..|.|+.|.|.++
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            36789999999999999999999999999999999954  4566899999999999999999999999999999999998


Q ss_pred             cCCCC
Q 022301           81 HGGRG   85 (299)
Q Consensus        81 ~~~~~   85 (299)
                      .....
T Consensus        92 ~~~~~   96 (114)
T 2do0_A           92 ERALP   96 (114)
T ss_dssp             SCCCC
T ss_pred             ccCCC
Confidence            75443

>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=99.81  E-value=2.1e-19  Score=128.90  Aligned_cols=78  Identities=23%  Similarity=0.305  Sum_probs=72.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCC-----ceEEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDG-----HRLRVE   78 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g-----~~i~v~   78 (299)
                      ...++|||+|||+++|+++|+++|..||+|..|.|..+    |||||+|.+.++|++||..||+..|.|     +.|.|.
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            56899999999999999999999999999999999765    899999999999999999999999999     999999


Q ss_pred             EccCCCC
Q 022301           79 LAHGGRG   85 (299)
Q Consensus        79 ~~~~~~~   85 (299)
                      ++.....
T Consensus        89 ~a~~~~~   95 (108)
T 1x4c_A           89 VDGPRSP   95 (108)
T ss_dssp             ESSCCSC
T ss_pred             eCCCCCC
Confidence            9986543

>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=7.6e-20  Score=132.85  Aligned_cols=82  Identities=20%  Similarity=0.473  Sum_probs=75.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .+.++|||+|||.++++++|+++|..||+|..|.|..   ++.++|||||+|.+.++|.+|+..||+..|.|+.|.|.++
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            4679999999999999999999999999999999954   4567899999999999999999999999999999999998


Q ss_pred             cCCCC
Q 022301           81 HGGRG   85 (299)
Q Consensus        81 ~~~~~   85 (299)
                      .....
T Consensus       103 ~~~~~  107 (115)
T 2cpz_A          103 RSKND  107 (115)
T ss_dssp             CCSCC
T ss_pred             CCCCc
Confidence            76543

>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=99.81  E-value=8.4e-20  Score=130.21  Aligned_cols=80  Identities=26%  Similarity=0.339  Sum_probs=72.1

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcC--CCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGD-IREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRD--GYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~-~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~--~~~~~g~~i~v~~   79 (299)
                      ..++++|||+|||++ +|+++|.++|.+||+|..|.|.   ..+|||||+|.+.++|..|+..||  +..|.|+.|.|.+
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 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM---RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDL   98 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEE---TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEe---cCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            468999999999998 9999999999999999999997   458999999999999999999886  4669999999999


Q ss_pred             ccCCCC
Q 022301           80 AHGGRG   85 (299)
Q Consensus        80 ~~~~~~   85 (299)
                      +.....
T Consensus        99 a~~~~~  104 (112)
T 1x4f_A           99 SEKYKK  104 (112)
T ss_dssp             ECSCSS
T ss_pred             Cccccc
Confidence            975543

>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=1.8e-19  Score=125.45  Aligned_cols=78  Identities=38%  Similarity=0.649  Sum_probs=72.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      ..++++|||+|||.++|+++|+++|+.||+|..|.+.     ++||||+|.+.++|..|+..|||..|.|+.|.|.++..
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            4688999999999999999999999999999999997     56999999999999999999999999999999999976


Q ss_pred             CCC
Q 022301           83 GRG   85 (299)
Q Consensus        83 ~~~   85 (299)
                      ...
T Consensus        82 ~~~   84 (92)
T 2dgt_A           82 RLR   84 (92)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            543

>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=126.81  Aligned_cols=79  Identities=25%  Similarity=0.475  Sum_probs=72.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCC--CceEEEEEc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFD--GHRLRVELA   80 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~--g~~i~v~~~   80 (299)
                      ..++++|||+|||.++|+++|.++|+.||+|..|.+...   +|||||+|.+.++|++|+..||+..|.  |+.|.|.++
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a   90 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG---DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFA   90 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS---SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC---CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEEC
Confidence            357899999999999999999999999999999999743   789999999999999999999999999  999999999


Q ss_pred             cCCC
Q 022301           81 HGGR   84 (299)
Q Consensus        81 ~~~~   84 (299)
                      ....
T Consensus        91 ~~~~   94 (97)
T 1why_A           91 KSGP   94 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7543

>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=2.1e-19  Score=129.66  Aligned_cols=81  Identities=22%  Similarity=0.473  Sum_probs=75.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcC------CCCCCCce
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRD------GYDFDGHR   74 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~------~~~~~g~~   74 (299)
                      .+.++|||+|||+++|+++|+++|..||+|..|.|..+   +.++|||||+|.+.++|..|+..||      +..|.|+.
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            57899999999999999999999999999999999654   6789999999999999999999999      99999999


Q ss_pred             EEEEEccCCC
Q 022301           75 LRVELAHGGR   84 (299)
Q Consensus        75 i~v~~~~~~~   84 (299)
                      |.|.++....
T Consensus        93 l~v~~a~~~~  102 (111)
T 1x4h_A           93 LKVDLAVTRD  102 (111)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEECCCCc
Confidence            9999987654

>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=5.1e-20  Score=129.05  Aligned_cols=80  Identities=35%  Similarity=0.564  Sum_probs=73.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..++++|||+|||+++++++|+++|+.||+|..|.|..+   +.++|||||+|.+.++|.+|+..|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            367899999999999999999999999999999999654   56789999999999999999999999999999999999


Q ss_pred             ccC
Q 022301           80 AHG   82 (299)
Q Consensus        80 ~~~   82 (299)
                      +..
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            863

>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=5.6e-20  Score=128.86  Aligned_cols=80  Identities=28%  Similarity=0.496  Sum_probs=73.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC--CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP--PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~--~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ..+.++|||+|||+++++++|+++|+.||+|..|.|..+  +.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   92 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGP   92 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEc
Confidence            467899999999999999999999999999999999543  566899999999999999999999999999999999998


Q ss_pred             cC
Q 022301           81 HG   82 (299)
Q Consensus        81 ~~   82 (299)
                      ..
T Consensus        93 ~~   94 (95)
T 2ywk_A           93 SS   94 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=7.9e-20  Score=135.13  Aligned_cols=82  Identities=35%  Similarity=0.590  Sum_probs=75.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..++++|||+|||+++|+++|+++|+.||+|..|.|..+   +.++|||||+|.+.++|++|+..|||..|.|+.|.|.+
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~  122 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF  122 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            367899999999999999999999999999999999653   67899999999999999999999999999999999999


Q ss_pred             ccCCC
Q 022301           80 AHGGR   84 (299)
Q Consensus        80 ~~~~~   84 (299)
                      +....
T Consensus       123 a~~~~  127 (129)
T 2kxn_B          123 SITKR  127 (129)
T ss_dssp             CSSSS
T ss_pred             ecCCC
Confidence            87543

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

Probab=99.81  E-value=4e-19  Score=129.23  Aligned_cols=82  Identities=24%  Similarity=0.410  Sum_probs=74.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..+.++|||+|||.++|+++|+++|..||+|..|.|..   ++.++|||||+|.+.++|++|+..||+ .|.|+.|.|.+
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            46789999999999999999999999999999999955   367889999999999999999999998 89999999999


Q ss_pred             ccCCCC
Q 022301           80 AHGGRG   85 (299)
Q Consensus        80 ~~~~~~   85 (299)
                      +.....
T Consensus        93 a~~~~~   98 (116)
T 2cqd_A           93 AYLGAK   98 (116)
T ss_dssp             STTTCC
T ss_pred             cccCCC
Confidence            975543

>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=1.8e-19  Score=124.89  Aligned_cols=77  Identities=32%  Similarity=0.579  Sum_probs=72.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      ..+.++|||+|||.++|+++|+++|+.||+|..|.|.     ++||||+|.+.++|+.|+..|||..|.|+.|.|.++..
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~-----~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   80 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-----KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTK   80 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC-----SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCC
Confidence            4678999999999999999999999999999999997     56999999999999999999999999999999999976


Q ss_pred             CC
Q 022301           83 GR   84 (299)
Q Consensus        83 ~~   84 (299)
                      ..
T Consensus        81 ~~   82 (90)
T 2dnp_A           81 GQ   82 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=9e-20  Score=130.50  Aligned_cols=78  Identities=17%  Similarity=0.219  Sum_probs=71.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcC-CeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYG-PIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G-~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      ...++|||+|||+++|+++|+++|..|| +|..+.|.. ..++|||||+|.+.++|++|+..|||..|.|+.|.|.++..
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 999999853 35789999999999999999999999999999999999864

>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=9.9e-20  Score=128.98  Aligned_cols=78  Identities=17%  Similarity=0.365  Sum_probs=72.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC--CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP--PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~--~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      .+.++|||+|||+++|+++|.++|++||+|..|.|..+  +.++|||||+|.+.++|..|+. +|+..|.|+.|.|.++.
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            46789999999999999999999999999999999653  6789999999999999999999 99999999999999875


Q ss_pred             C
Q 022301           82 G   82 (299)
Q Consensus        82 ~   82 (299)
                      .
T Consensus        88 ~   88 (103)
T 1s79_A           88 D   88 (103)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=129.90  Aligned_cols=81  Identities=28%  Similarity=0.548  Sum_probs=74.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..++++|||+|||.++|+++|.++|+.||+|..|.|..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.+
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            46789999999999999999999999999999999954   466789999999999999999999999999999999999


Q ss_pred             ccCC
Q 022301           80 AHGG   83 (299)
Q Consensus        80 ~~~~   83 (299)
                      +...
T Consensus       103 a~~k  106 (108)
T 2jrs_A          103 VTER  106 (108)
T ss_dssp             SCSS
T ss_pred             cccC
Confidence            8653

>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=3.1e-19  Score=126.01  Aligned_cols=78  Identities=35%  Similarity=0.531  Sum_probs=72.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      .++++|||+|||+++|+++|+++|..||+|..|.|..   .+|||||+|.+.++|.+|+..|||..|.|+.|.|.++...
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 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK---DKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS   89 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEET---TTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEec---CCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCC
Confidence            5778999999999999999999999999999999973   4799999999999999999999999999999999999764


Q ss_pred             C
Q 022301           84 R   84 (299)
Q Consensus        84 ~   84 (299)
                      .
T Consensus        90 ~   90 (99)
T 2cpj_A           90 A   90 (99)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.80  E-value=1.4e-19  Score=130.28  Aligned_cols=78  Identities=27%  Similarity=0.341  Sum_probs=72.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      ...++|||+|||+++|+++|+++|.+||.|..|.|.   ..+|||||+|.+.++|..|+..|||..|.|+.|.|.|+...
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 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP---EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC---SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEe---CCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            456899999999999999999999999999999986   35789999999999999999999999999999999999764


Q ss_pred             C
Q 022301           84 R   84 (299)
Q Consensus        84 ~   84 (299)
                      .
T Consensus        85 ~   85 (111)
T 1whx_A           85 V   85 (111)
T ss_dssp             T
T ss_pred             c
Confidence            4

>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=1.3e-19  Score=129.91  Aligned_cols=78  Identities=26%  Similarity=0.472  Sum_probs=72.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      .++++|||+|||+++|+++|+++|..||+|..|.|..  ++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++.
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            5689999999999999999999999999999999954  46678999999999999999999999999999999999974

>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=133.33  Aligned_cols=82  Identities=27%  Similarity=0.494  Sum_probs=75.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .++++|||+|||+++|+++|+++|..||.|..|.|..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
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            5678999999999999999999999999999999954   4677899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 022301           81 HGGRG   85 (299)
Q Consensus        81 ~~~~~   85 (299)
                      .....
T Consensus       100 ~~~~~  104 (126)
T 3ex7_B          100 FVRGP  104 (126)
T ss_dssp             EESSS
T ss_pred             cCCCC
Confidence            76543

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

Probab=99.80  E-value=2.3e-19  Score=127.93  Aligned_cols=82  Identities=22%  Similarity=0.388  Sum_probs=75.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhh-cCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCC-CCCceEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYK-YGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYD-FDGHRLRVE   78 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~-~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~-~~g~~i~v~   78 (299)
                      ..++++|||+|||+++|+++|.++|.. ||.|..|.|..  ++.++|||||+|.+.++|..|+..||+.. |.|+.|.|.
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            467899999999999999999999999 99999999954  46678999999999999999999999999 999999999


Q ss_pred             EccCCC
Q 022301           79 LAHGGR   84 (299)
Q Consensus        79 ~~~~~~   84 (299)
                      ++....
T Consensus        86 ~a~~~~   91 (104)
T 2dhg_A           86 VAIPKA   91 (104)
T ss_dssp             BCCCCC
T ss_pred             EccCCC
Confidence            986554

>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=1.5e-19  Score=127.58  Aligned_cols=79  Identities=29%  Similarity=0.452  Sum_probs=72.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeE--------EEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCC
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAH--------IDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFD   71 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~--------i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~   71 (299)
                      ..+.++|||+|||.++|+++|+++|+.||.|..        |.|..   ++.++|||||+|.+.++|..|+..|||..|.
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~   89 (99)
T 2la6_A           10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   89 (99)
T ss_dssp             CCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeC
Confidence            467899999999999999999999999999999        88854   4677899999999999999999999999999


Q ss_pred             CceEEEEEcc
Q 022301           72 GHRLRVELAH   81 (299)
Q Consensus        72 g~~i~v~~~~   81 (299)
                      |+.|.|.+++
T Consensus        90 g~~l~V~~A~   99 (99)
T 2la6_A           90 GNPIKVSFAT   99 (99)
T ss_dssp             SSBCEEEECC
T ss_pred             CcEEEEEecC
Confidence            9999999873

>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=3.1e-19  Score=128.29  Aligned_cols=80  Identities=24%  Similarity=0.449  Sum_probs=74.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      ..+.++|||+|||.++|+++|+++|..||.|..|.|..+   +|||||+|.+.++|..|+..|||..|.|+.|.|.|+..
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~---~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   98 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE---KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE   98 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT---TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC---CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCC
Confidence            356889999999999999999999999999999999754   79999999999999999999999999999999999976


Q ss_pred             CCC
Q 022301           83 GRG   85 (299)
Q Consensus        83 ~~~   85 (299)
                      ...
T Consensus        99 ~~~  101 (109)
T 1x4g_A           99 SPD  101 (109)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            543

>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=99.80  E-value=1.3e-19  Score=130.57  Aligned_cols=81  Identities=26%  Similarity=0.466  Sum_probs=74.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .++++|||+|||.++|+++|.++|+.||+|..|.|..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
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            5678999999999999999999999999999999954   4677899999999999999999999999999999999998


Q ss_pred             cCCC
Q 022301           81 HGGR   84 (299)
Q Consensus        81 ~~~~   84 (299)
                      ....
T Consensus       104 ~~~~  107 (110)
T 1oo0_B          104 FVKG  107 (110)
T ss_dssp             EESS
T ss_pred             ccCC
Confidence            6543

>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=99.80  E-value=2.5e-20  Score=129.19  Aligned_cols=78  Identities=17%  Similarity=0.223  Sum_probs=67.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcC--CeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYG--PIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G--~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      .+|||+|||.++|+++|+++|+.||  .|..|.|..   ++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++.
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            5899999999999999999999999  999999854   56788999999999999999999999999999999999987


Q ss_pred             CCC
Q 022301           82 GGR   84 (299)
Q Consensus        82 ~~~   84 (299)
                      +..
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            544

>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=1.6e-19  Score=129.64  Aligned_cols=81  Identities=25%  Similarity=0.488  Sum_probs=74.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC-CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~-~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ..+.++|||+|||.++|+++|+++|+.||+|..|.|..+ +.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++.
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  105 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT  105 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            367899999999999999999999999999999999544 4578999999999999999999999999999999999986


Q ss_pred             CC
Q 022301           82 GG   83 (299)
Q Consensus        82 ~~   83 (299)
                      ..
T Consensus       106 ~~  107 (109)
T 2err_A          106 AR  107 (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=2.4e-19  Score=127.51  Aligned_cols=82  Identities=28%  Similarity=0.524  Sum_probs=74.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEE
Q 022301            2 SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVE   78 (299)
Q Consensus         2 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~   78 (299)
                      ...+.++|||+|||.++|+++|+++|..|| |..|.|..+   +.++|||||+|.+.++|..|+ .|||..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   88 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVD   88 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEE
Confidence            357889999999999999999999999997 999999643   567899999999999999999 799999999999999


Q ss_pred             EccCCCC
Q 022301           79 LAHGGRG   85 (299)
Q Consensus        79 ~~~~~~~   85 (299)
                      ++.....
T Consensus        89 ~a~~~~~   95 (103)
T 2dng_A           89 IAEGRKQ   95 (103)
T ss_dssp             ECCCCCC
T ss_pred             EecCCCC
Confidence            9976543

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

Probab=99.80  E-value=1.3e-19  Score=132.27  Aligned_cols=79  Identities=22%  Similarity=0.495  Sum_probs=72.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..+.++|||+|||.++++++|+++|+.||+|..|.|..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.+
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            45679999999999999999999999999999999964   367899999999999999999999999999999999998


Q ss_pred             cc
Q 022301           80 AH   81 (299)
Q Consensus        80 ~~   81 (299)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            73

>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=2.6e-19  Score=129.63  Aligned_cols=83  Identities=28%  Similarity=0.489  Sum_probs=75.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCee--------EEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCC
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIA--------HIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFD   71 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~--------~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~   71 (299)
                      ..++++|||+|||.++|+++|+++|..||.|.        .|.|..   ++.++|||||+|.+.++|..|+..|||..|.
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            35789999999999999999999999999998        688854   4677899999999999999999999999999


Q ss_pred             CceEEEEEccCCCC
Q 022301           72 GHRLRVELAHGGRG   85 (299)
Q Consensus        72 g~~i~v~~~~~~~~   85 (299)
                      |+.|.|.++.....
T Consensus        92 g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           92 GSKLKVSLARKKPP  105 (113)
T ss_dssp             TEECEEECSSCCCC
T ss_pred             CCEEEEEECCCCCC
Confidence            99999999876543

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

Probab=99.80  E-value=5.8e-20  Score=129.84  Aligned_cols=78  Identities=24%  Similarity=0.420  Sum_probs=72.5

Q ss_pred             CCCCeEEEcCCCC------CCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCC-c
Q 022301            4 RASRTLYVGNLPG------DIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDG-H   73 (299)
Q Consensus         4 ~~~~~l~V~nLp~------~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g-~   73 (299)
                      ..+++|||+|||.      ++++++|.++|++||+|..|.|..   ++.++|||||+|.+.++|.+|+..|||..|.| +
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            3578999999999      999999999999999999999954   36789999999999999999999999999999 9


Q ss_pred             eEEEEEcc
Q 022301           74 RLRVELAH   81 (299)
Q Consensus        74 ~i~v~~~~   81 (299)
                      .|.|.++.
T Consensus        84 ~l~V~~a~   91 (100)
T 3ns6_A           84 RLFLYTMK   91 (100)
T ss_dssp             BCEEEESH
T ss_pred             EEEEEECc
Confidence            99999985

>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=2.9e-19  Score=129.76  Aligned_cols=81  Identities=25%  Similarity=0.437  Sum_probs=73.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCe----eEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPI----AHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v----~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      .++++|||+|||.++|+++|.++|..||.|    ..+.+. ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.+
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 022301           80 AHGGRG   85 (299)
Q Consensus        80 ~~~~~~   85 (299)
                      +.....
T Consensus       102 a~~~~~  107 (115)
T 2cpx_A          102 GKNKKQ  107 (115)
T ss_dssp             CCCCSC
T ss_pred             ccCCCC
Confidence            976553

>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=9e-20  Score=131.48  Aligned_cols=81  Identities=23%  Similarity=0.360  Sum_probs=73.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH---HHhhhcCCeeEEEeecCC------CCCceEEEEecChHHHHHHHHhcCCCCCCCce
Q 022301            4 RASRTLYVGNLPGDIREREVE---DLFYKYGPIAHIDLKIPP------RPPGYAFVEFEEARDAEDAIRGRDGYDFDGHR   74 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~---~~F~~~G~v~~i~~~~~~------~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~   74 (299)
                      ...++|||+|||+++++++|.   ++|.+||+|..|.|..+.      .++|||||+|.+.++|++|+..|||..|.|+.
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   999999999999996542      45689999999999999999999999999999


Q ss_pred             EEEEEccCCC
Q 022301           75 LRVELAHGGR   84 (299)
Q Consensus        75 i~v~~~~~~~   84 (299)
                      |.|.++....
T Consensus        93 l~V~~a~~k~  102 (111)
T 2cpi_A           93 LKASLGTTKY  102 (111)
T ss_dssp             EEEESCCCCS
T ss_pred             EEEEeccccc
Confidence            9999987654

>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=99.80  E-value=3.1e-19  Score=123.42  Aligned_cols=78  Identities=23%  Similarity=0.485  Sum_probs=72.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      +.++|||+|||.++|+++|.++|+.||+|..|.+..   ++.++|||||+|.+.++|..|+ .|||..|.|+.|.|.++.
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 799999999999999987


Q ss_pred             CC
Q 022301           82 GG   83 (299)
Q Consensus        82 ~~   83 (299)
                      ..
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            53

>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=3.6e-19  Score=124.95  Aligned_cols=75  Identities=27%  Similarity=0.550  Sum_probs=71.1

Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            3 SRASRTLYVGNLPG-DIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         3 ~~~~~~l~V~nLp~-~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ..++++|||+|||. ++++++|.++|+.||.|..|.|.     +|||||+|.+.++|..|+..|||..|.|+.|.|.++.
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~-----~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   93 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-----NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSS   93 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC-----SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-----CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            46789999999998 99999999999999999999995     7999999999999999999999999999999999986


Q ss_pred             C
Q 022301           82 G   82 (299)
Q Consensus        82 ~   82 (299)
                      .
T Consensus        94 ~   94 (97)
T 2xnq_A           94 S   94 (97)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=2.7e-19  Score=127.64  Aligned_cols=80  Identities=16%  Similarity=0.280  Sum_probs=71.9

Q ss_pred             CCCCCCeEEE--cCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCC-----CCce
Q 022301            2 SSRASRTLYV--GNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDF-----DGHR   74 (299)
Q Consensus         2 ~~~~~~~l~V--~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~-----~g~~   74 (299)
                      +..++++|||  +||+.++|+++|+++|++||+|..|.|..   .+|||||+|.+.++|++|+..|||..|     .|.+
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            4678999999  77999999999999999999999998863   378999999999999999999999977     6889


Q ss_pred             EEEEEccCCC
Q 022301           75 LRVELAHGGR   84 (299)
Q Consensus        75 i~v~~~~~~~   84 (299)
                      |.|.|+....
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            9999987544

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

Probab=99.80  E-value=2.2e-19  Score=126.00  Aligned_cols=78  Identities=24%  Similarity=0.500  Sum_probs=71.9

Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            3 SRASRTLYVGNLPG-DIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         3 ~~~~~~l~V~nLp~-~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ..++++|||+|||+ ++|+++|.++|+.||+|..|.|.     +|||||+|.+.++|..|+..|||..|.|+.|.|.++.
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            36889999999998 99999999999999999999996     7899999999999999999999999999999999997


Q ss_pred             CCCC
Q 022301           82 GGRG   85 (299)
Q Consensus        82 ~~~~   85 (299)
                      ....
T Consensus        82 ~~~~   85 (96)
T 2kvi_A           82 SNAR   85 (96)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            6543

>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=7.8e-19  Score=126.23  Aligned_cols=83  Identities=24%  Similarity=0.333  Sum_probs=74.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCC-eeEEEee-c---CCCCCceEEEEecChHHHHHHHHhcC--CCCCCCceE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGP-IAHIDLK-I---PPRPPGYAFVEFEEARDAEDAIRGRD--GYDFDGHRL   75 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~-v~~i~~~-~---~~~~~g~afV~F~~~e~A~~A~~~l~--~~~~~g~~i   75 (299)
                      +.++++|||+|||.++|+++|.++|..||. |..|.|. .   ++.++|||||+|.+.++|..|+..||  +..|.|+.|
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   34678999999999999999999996  589999999


Q ss_pred             EEEEccCCCC
Q 022301           76 RVELAHGGRG   85 (299)
Q Consensus        76 ~v~~~~~~~~   85 (299)
                      .|.++.....
T Consensus        85 ~V~~a~~~~~   94 (109)
T 2dis_A           85 AVDWAEPEID   94 (109)
T ss_dssp             EEEESCSSCS
T ss_pred             EEEEcCCCCC
Confidence            9999976554

>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=2.1e-19  Score=123.18  Aligned_cols=76  Identities=30%  Similarity=0.518  Sum_probs=70.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhc-CCCCCCCceEEEEEcc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGR-DGYDFDGHRLRVELAH   81 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l-~~~~~~g~~i~v~~~~   81 (299)
                      ..++++|||+|||.++++++|+++|++||+|..|.+..   .+|||||+|.+.++|..|+..| ||..+.|+.|.|.|++
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~---~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ---RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG---GGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC---CCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            36789999999999999999999999999999999974   4789999999999999999998 9999999999999874

>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=129.53  Aligned_cols=82  Identities=24%  Similarity=0.426  Sum_probs=75.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      .++++|||+|||.++++++|+++|+.||+|..|.|..  ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.
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            5678999999999999999999999999999999954  46788999999999999999999999999999999999997


Q ss_pred             CCCC
Q 022301           82 GGRG   85 (299)
Q Consensus        82 ~~~~   85 (299)
                      ....
T Consensus       113 ~~~~  116 (124)
T 2kt5_A          113 SQID  116 (124)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            6543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.79  E-value=1.2e-19  Score=123.18  Aligned_cols=72  Identities=28%  Similarity=0.505  Sum_probs=66.7

Q ss_pred             CCeEEEcCCCCCC------CHHHHHHHhhhcCCeeEEEee-cCCCCCceEEEEecChHHHHHHHHhcCCCCCCCc-eEEE
Q 022301            6 SRTLYVGNLPGDI------REREVEDLFYKYGPIAHIDLK-IPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGH-RLRV   77 (299)
Q Consensus         6 ~~~l~V~nLp~~~------t~~~l~~~F~~~G~v~~i~~~-~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~-~i~v   77 (299)
                      +++|||+|||..+      |+++|.++|++||+|..|.|. .++.++|||||+|.+.++|..|+..|||..|.|+ .|.|
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      779999999999999999995 4577899999999999999999999999999999 8876

>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=3e-19  Score=126.57  Aligned_cols=81  Identities=28%  Similarity=0.443  Sum_probs=71.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      ..++++|||+|||.++|+++|+++|..||.|. +....++..+|||||+|.+.++|++|+..||+..|.|+.|.|.++..
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~-~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   90 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFIK-VPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGP   90 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEEE-CCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEEE-EEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCC
Confidence            35789999999999999999999999999883 22234677899999999999999999999999999999999999976


Q ss_pred             CC
Q 022301           83 GR   84 (299)
Q Consensus        83 ~~   84 (299)
                      ..
T Consensus        91 ~~   92 (101)
T 2fc9_A           91 RG   92 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

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

Probab=99.79  E-value=2.8e-19  Score=127.52  Aligned_cols=79  Identities=27%  Similarity=0.463  Sum_probs=72.7

Q ss_pred             CCCCeEEEcCCCCCC------CHHHHHHHhhhcCCeeEEEee-cCCCCCceEEEEecChHHHHHHHHhcCCCCCCCc-eE
Q 022301            4 RASRTLYVGNLPGDI------REREVEDLFYKYGPIAHIDLK-IPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGH-RL   75 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~------t~~~l~~~F~~~G~v~~i~~~-~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~-~i   75 (299)
                      ...++|||+|||..+      |+++|.++|++||+|..|.|. .++.++|||||+|.+.++|..|+..|||..|.|+ .|
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            446899999999999      789999999999999999995 3567899999999999999999999999999999 99


Q ss_pred             EEEEccC
Q 022301           76 RVELAHG   82 (299)
Q Consensus        76 ~v~~~~~   82 (299)
                      .|.++..
T Consensus        93 ~V~~a~~   99 (105)
T 2nlw_A           93 RVNLFTD   99 (105)
T ss_dssp             EEECSCC
T ss_pred             EEEEcch
Confidence            9999864

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

Probab=99.79  E-value=3.1e-19  Score=127.79  Aligned_cols=77  Identities=32%  Similarity=0.580  Sum_probs=72.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      ..++++|||+|||.++|+++|.++|+.||+|..|.|.     +|||||+|.+.++|..|+..|||..|.|+.|.|.++..
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            3678999999999999999999999999999999998     79999999999999999999999999999999999875


Q ss_pred             CC
Q 022301           83 GR   84 (299)
Q Consensus        83 ~~   84 (299)
                      ..
T Consensus       103 ~~  104 (108)
T 2jvo_A          103 PA  104 (108)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.79  E-value=3e-19  Score=122.94  Aligned_cols=77  Identities=23%  Similarity=0.533  Sum_probs=70.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..+.++|||+|||+++|+++|.++|++||+|..|.|..   ++.++|||||+|.+.++|..|+. +++..|.|+.|.|.+
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            46789999999999999999999999999999999954   36778999999999999999997 688889999999987


Q ss_pred             c
Q 022301           80 A   80 (299)
Q Consensus        80 ~   80 (299)
                      +
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=6.8e-19  Score=132.26  Aligned_cols=82  Identities=33%  Similarity=0.654  Sum_probs=75.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .+.++|||+|||.++|+++|+++|+.||+|..|.|..   ++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++
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            5678999999999999999999999999999999954   3567899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 022301           81 HGGRG   85 (299)
Q Consensus        81 ~~~~~   85 (299)
                      .....
T Consensus       120 ~~~~~  124 (139)
T 1u6f_A          120 ASGHQ  124 (139)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            86654

>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=9.8e-19  Score=123.40  Aligned_cols=76  Identities=30%  Similarity=0.462  Sum_probs=71.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhc--CCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKY--GPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~--G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      .++++|||+|||+++|+++|+++|..|  |.|..|.+.     +|||||+|.+.++|..|+..|||..|.|+.|.|.++.
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            578999999999999999999999999  999999886     7899999999999999999999999999999999997


Q ss_pred             CCC
Q 022301           82 GGR   84 (299)
Q Consensus        82 ~~~   84 (299)
                      ...
T Consensus        88 ~~~   90 (99)
T 2cpd_A           88 PVD   90 (99)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=4.3e-19  Score=124.76  Aligned_cols=79  Identities=28%  Similarity=0.498  Sum_probs=70.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      ..+++|||+|||+++|+++|+++|..||.|. +.+.. +.++|||||+|.+.++|..|+..|||..|.|+.|.|.++...
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-LRLTW-QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ   94 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE-ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc-CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCC
Confidence            4589999999999999999999999999996 55532 467899999999999999999999999999999999998754


Q ss_pred             C
Q 022301           84 R   84 (299)
Q Consensus        84 ~   84 (299)
                      .
T Consensus        95 ~   95 (97)
T 2e5j_A           95 R   95 (97)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=6.5e-19  Score=126.42  Aligned_cols=81  Identities=15%  Similarity=0.363  Sum_probs=70.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..+.++|||+|||.++|+++|.++|+.||+|..|.|..+   +.++|||||+|.+.++|..|+..+ +..|.|+.|.|.+
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~  100 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKV  100 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEE
Confidence            357899999999999999999999999999999999653   678999999999999999999965 5899999999999


Q ss_pred             ccCCC
Q 022301           80 AHGGR   84 (299)
Q Consensus        80 ~~~~~   84 (299)
                      +....
T Consensus       101 a~~~~  105 (109)
T 2rs2_A          101 AFPRR  105 (109)
T ss_dssp             CCCCC
T ss_pred             ccCCC
Confidence            87544

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

Probab=99.79  E-value=6.5e-20  Score=125.75  Aligned_cols=78  Identities=21%  Similarity=0.364  Sum_probs=71.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..++++|||+|||+++++++|+++|+.||+|..|.|..   ++.++|||||+|.+.++|..|+..|||..|.|+.|+|.+
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            46889999999999999999999999999999999954   367789999999999999999999999999999988765


Q ss_pred             c
Q 022301           80 A   80 (299)
Q Consensus        80 ~   80 (299)
                      +
T Consensus        82 ~   82 (85)
T 1x4e_A           82 P   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=3.6e-19  Score=124.16  Aligned_cols=79  Identities=27%  Similarity=0.433  Sum_probs=71.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhhcCC-eeEEEeecCCCCCceEEEEecChHHHHHHHHhcCC-CCCCCceEEEEE
Q 022301            2 SSRASRTLYVGNLPGDIREREVEDLFYKYGP-IAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG-YDFDGHRLRVEL   79 (299)
Q Consensus         2 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~-v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~-~~~~g~~i~v~~   79 (299)
                      ...+.++|||+|||.++|+++|+++|.+||. |..+.+.    .+|||||+|.+.++|..|+..||| ..|.|+.|.|.+
T Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~   79 (93)
T 2cqh_A            4 GSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL----KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDY   79 (93)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE----ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc----CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEE
Confidence            3467899999999999999999999999999 6666663    478999999999999999999999 999999999999


Q ss_pred             ccCCC
Q 022301           80 AHGGR   84 (299)
Q Consensus        80 ~~~~~   84 (299)
                      +....
T Consensus        80 a~~~~   84 (93)
T 2cqh_A           80 SVSKK   84 (93)
T ss_dssp             CCCCC
T ss_pred             ccCcc
Confidence            97654

>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=132.85  Aligned_cols=82  Identities=35%  Similarity=0.571  Sum_probs=75.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .++++|||+|||.++|+++|+++|+.||+|..|.|..   ++.++|||||+|.+.++|+.|+..|||..|.|+.|.|.++
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            4678999999999999999999999999999999954   4678999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 022301           81 HGGRG   85 (299)
Q Consensus        81 ~~~~~   85 (299)
                      .....
T Consensus       125 ~~~~~  129 (135)
T 2lea_A          125 RYGRP  129 (135)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76554

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=3e-19  Score=127.47  Aligned_cols=82  Identities=16%  Similarity=0.318  Sum_probs=74.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..+.++|||+|||+++|+++|+++|..||+|..|.|..   ++.++|||||+|.+.++|.+|+.. |+..|.|+.|.|.+
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            46789999999999999999999999999999999955   356789999999999999999997 99999999999999


Q ss_pred             ccCCCC
Q 022301           80 AHGGRG   85 (299)
Q Consensus        80 ~~~~~~   85 (299)
                      +.....
T Consensus        92 a~~~~~   97 (105)
T 2dh8_A           92 CTPRGM   97 (105)
T ss_dssp             SCCSSC
T ss_pred             ccCCCC
Confidence            875543

>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=3.2e-19  Score=126.42  Aligned_cols=76  Identities=24%  Similarity=0.431  Sum_probs=71.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      ..+++|||+|||.++++++|.++|+.||.|..|.+.   ..+|||||+|.+.++|..|+..|||..|.|+.|.|.|+..
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            357899999999999999999999999999999997   5689999999999999999999999999999999998864

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

Probab=99.78  E-value=1.4e-18  Score=117.55  Aligned_cols=75  Identities=27%  Similarity=0.349  Sum_probs=67.3

Q ss_pred             CCCCe-EEEcCCCCCCCHHH----HHHHhhhc-CCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEE
Q 022301            4 RASRT-LYVGNLPGDIRERE----VEDLFYKY-GPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRV   77 (299)
Q Consensus         4 ~~~~~-l~V~nLp~~~t~~~----l~~~F~~~-G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v   77 (299)
                      .|+.| |||+|||..+++++    |.++|++| |+|.+|    ++   |+|||+|.+.++|..|++.|||..|.|++|.|
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V----tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v   78 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI----TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIV   78 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC----CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE----ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEE
Confidence            46777 99999999999998    55899999 599999    22   99999999999999999999999999999999


Q ss_pred             EEccCCCC
Q 022301           78 ELAHGGRG   85 (299)
Q Consensus        78 ~~~~~~~~   85 (299)
                      .+++....
T Consensus        79 ~~A~~~sd   86 (96)
T 2diu_A           79 SFTPKNRE   86 (96)
T ss_dssp             ESSCCSCC
T ss_pred             EecCCCcc
Confidence            99986654

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

Probab=99.78  E-value=3.5e-19  Score=118.98  Aligned_cols=72  Identities=21%  Similarity=0.377  Sum_probs=67.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         8 ~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      +|||+|||+++|+++|.++|++||+|..|.+..   ++.++|||||+|.+.++|+.|+. ||+..|.|+.|.|.++
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            599999999999999999999999999999954   46788999999999999999998 9999999999999875

>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=99.78  E-value=3.7e-19  Score=126.79  Aligned_cols=81  Identities=33%  Similarity=0.701  Sum_probs=74.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .+.++|||+|||.++++++|+++|+.||.|..|.|..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            4568999999999999999999999999999999954   4567899999999999999999999999999999999998


Q ss_pred             cCCC
Q 022301           81 HGGR   84 (299)
Q Consensus        81 ~~~~   84 (299)
                      ....
T Consensus        86 ~~~~   89 (104)
T 1p1t_A           86 ASEK   89 (104)
T ss_dssp             TCTT
T ss_pred             CCcc
Confidence            7543

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

Probab=99.78  E-value=4.1e-19  Score=135.48  Aligned_cols=77  Identities=16%  Similarity=0.264  Sum_probs=71.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcC--CeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYG--PIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G--~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..++|||+|||+++|+++|.++|+.||  .|..|.|..   ++.++|||||+|.+.++|..||..|||..|.|+.|.|.+
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            568999999999999999999999999  999999954   577889999999999999999999999999999999999


Q ss_pred             cc
Q 022301           80 AH   81 (299)
Q Consensus        80 ~~   81 (299)
                      +.
T Consensus       134 a~  135 (156)
T 3n9u_C          134 AT  135 (156)
T ss_dssp             CC
T ss_pred             cC
Confidence            85

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

Probab=99.78  E-value=5.1e-19  Score=131.42  Aligned_cols=81  Identities=19%  Similarity=0.347  Sum_probs=73.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeE--EEeec---CCCCCceEEEEecChHHHHHHHHhcCCC----CCCCc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAH--IDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGY----DFDGH   73 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~--i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~----~~~g~   73 (299)
                      +.++++|||+|||+++|+++|+++|..||.|..  |.|..   ++.++|||||+|.+. +|..|+..|||.    .|.|+
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            467899999999999999999999999999966  88844   567899999999999 999999999999    99999


Q ss_pred             eEEEEEccCCC
Q 022301           74 RLRVELAHGGR   84 (299)
Q Consensus        74 ~i~v~~~~~~~   84 (299)
                      .|.|.++....
T Consensus        99 ~l~V~~a~~~~  109 (131)
T 2m2b_A           99 TINVEFAKGSK  109 (131)
T ss_dssp             CCCCEECCCSC
T ss_pred             EEEEEECCCCC
Confidence            99999997654

>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=99.78  E-value=1.8e-19  Score=126.95  Aligned_cols=79  Identities=24%  Similarity=0.364  Sum_probs=71.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEe---ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~---~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ...++|||+|||+++++++|+++|..||.|..+.+   ..++.++|||||+|.+.++|++|+..|||..|.|+.|.|.++
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            45789999999999999999999999999976655   335677899999999999999999999999999999999998


Q ss_pred             cC
Q 022301           81 HG   82 (299)
Q Consensus        81 ~~   82 (299)
                      ..
T Consensus        93 ~~   94 (98)
T 2cqp_A           93 SG   94 (98)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>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=99.78  E-value=7.3e-19  Score=134.72  Aligned_cols=82  Identities=34%  Similarity=0.500  Sum_probs=75.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .++++|||+|||.++|+++|+++|+.||+|..|.|..+   +.++|||||+|.+.++|++||..||+..|.|+.|.|.|+
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            47899999999999999999999999999999999554   567899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 022301           81 HGGRG   85 (299)
Q Consensus        81 ~~~~~   85 (299)
                      .....
T Consensus       117 ~~~~~  121 (156)
T 1h2v_Z          117 AGFKE  121 (156)
T ss_dssp             SCCCT
T ss_pred             CCCCC
Confidence            76443

>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=1.3e-19  Score=126.93  Aligned_cols=78  Identities=22%  Similarity=0.303  Sum_probs=69.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEee---cCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLK---IPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~---~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .++++|||+|||+++|+++|+++|..||.|..+.+.   .++.++|||||+|.+.++|++|+..||+..|.|+.|.|.++
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            457899999999999999999999999999876663   34667899999999999999999999999999999999987


Q ss_pred             c
Q 022301           81 H   81 (299)
Q Consensus        81 ~   81 (299)
                      .
T Consensus        93 ~   93 (95)
T 2ek1_A           93 S   93 (95)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=3.9e-19  Score=125.66  Aligned_cols=78  Identities=27%  Similarity=0.535  Sum_probs=69.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec----CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI----PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~----~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      .+.++|||+|||.++++++|.++|+.|| |..|.|..    ++.++|||||+|.+.++|..|+ .|||..|.|+.|.|.+
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            5689999999999999999999999999 99999954    4678999999999999999999 7999999999999999


Q ss_pred             ccCC
Q 022301           80 AHGG   83 (299)
Q Consensus        80 ~~~~   83 (299)
                      +...
T Consensus        95 a~~~   98 (100)
T 2j76_E           95 ADQA   98 (100)
T ss_dssp             CCCS
T ss_pred             ccCC
Confidence            8653

>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=6.5e-19  Score=127.69  Aligned_cols=77  Identities=30%  Similarity=0.479  Sum_probs=71.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      +.++|||+|||.++|+++|+++|..||.|..|.|..+   +.++|||||+|.+.++|.+|+ .|||..|.|+.|.|.++.
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            4579999999999999999999999999999999643   677899999999999999999 799999999999999986


Q ss_pred             C
Q 022301           82 G   82 (299)
Q Consensus        82 ~   82 (299)
                      .
T Consensus       103 ~  103 (114)
T 2cq4_A          103 A  103 (114)
T ss_dssp             H
T ss_pred             C
Confidence            4

>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=1e-18  Score=125.76  Aligned_cols=75  Identities=31%  Similarity=0.651  Sum_probs=70.2

Q ss_pred             CCCeEEEcCCCCC-CCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            5 ASRTLYVGNLPGD-IREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         5 ~~~~l~V~nLp~~-~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      ++++|||+|||++ +|+++|+++|++||+|..|.|.     +|||||+|.+.++|+.|+..|||..|.|+.|.|.++...
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 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH-----KGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEP  100 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEEE-----TTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEe-----CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            4589999999999 9999999999999999999993     899999999999999999999999999999999999754


Q ss_pred             C
Q 022301           84 R   84 (299)
Q Consensus        84 ~   84 (299)
                      .
T Consensus       101 ~  101 (110)
T 1wf1_A          101 K  101 (110)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.78  E-value=2e-18  Score=122.90  Aligned_cols=80  Identities=18%  Similarity=0.255  Sum_probs=72.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeE-EEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAH-IDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .+.++|||+|||+++|+++|+++|..||.|.. |.|..  ++.++|||||+|.+.++|.+||.. |+..|.|+.|.|.++
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            56799999999999999999999999999987 77744  567889999999999999999995 999999999999988


Q ss_pred             cCCC
Q 022301           81 HGGR   84 (299)
Q Consensus        81 ~~~~   84 (299)
                      ....
T Consensus        92 ~~~~   95 (104)
T 1wg5_A           92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            6433

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

Probab=99.77  E-value=4e-19  Score=119.37  Aligned_cols=73  Identities=15%  Similarity=0.393  Sum_probs=68.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ++|||+|||+++++++|+++|++||+|..|.+..   ++.++|||||+|.+.++|..|+..|+ ..+.|+.|.|.++
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            5899999999999999999999999999999954   36778999999999999999999888 9999999999986

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.77  E-value=2.5e-19  Score=125.78  Aligned_cols=79  Identities=28%  Similarity=0.440  Sum_probs=72.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      .+.++|||+|||.++|+++|+++|..||.|..+  ..++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++...
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            567999999999999999999999999999887  566778899999999999999999999999999999999998654


Q ss_pred             C
Q 022301           84 R   84 (299)
Q Consensus        84 ~   84 (299)
                      .
T Consensus        92 ~   92 (96)
T 1fjc_A           92 G   92 (96)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=8.5e-19  Score=124.45  Aligned_cols=82  Identities=23%  Similarity=0.377  Sum_probs=72.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      ..++++|||+|||.++|+++|+++|..|+.|.-+....++.++|||||+|.+.++|++|+..||+..|.|+.|.|.++..
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   91 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKP   91 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecC
Confidence            46789999999999999999999999886555444445677889999999999999999999999999999999999976


Q ss_pred             CC
Q 022301           83 GR   84 (299)
Q Consensus        83 ~~   84 (299)
                      ..
T Consensus        92 ~~   93 (102)
T 2fc8_A           92 KG   93 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=2e-19  Score=124.63  Aligned_cols=77  Identities=34%  Similarity=0.618  Sum_probs=69.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      ++|||+|||.++++++|.++|+.||+|..|.+..+   +.++|||||+|.+.+ |..|+..|||..|.|+.|.|.++...
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            68999999999999999999999999999999653   678999999999999 99999999999999999999998754


Q ss_pred             C
Q 022301           84 R   84 (299)
Q Consensus        84 ~   84 (299)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            4

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.3e-18  Score=120.79  Aligned_cols=79  Identities=18%  Similarity=0.322  Sum_probs=72.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ..+.++|||+|||.++|+++|+++|..| .|..|.|..  ++.++|||||+|.+.++|..|+. |||..|.|+.|.|.++
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a   84 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFRE   84 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEEC
Confidence            3578999999999999999999999999 999999965  46678999999999999999999 9999999999999998


Q ss_pred             cCC
Q 022301           81 HGG   83 (299)
Q Consensus        81 ~~~   83 (299)
                      ...
T Consensus        85 ~~~   87 (91)
T 2dgw_A           85 KSG   87 (91)
T ss_dssp             SSC
T ss_pred             CcC
Confidence            754

>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=99.77  E-value=2e-18  Score=132.60  Aligned_cols=82  Identities=35%  Similarity=0.571  Sum_probs=75.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .+.++|||+|||+++|+++|.++|+.||+|..|.|..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
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            4578999999999999999999999999999999955   5778999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 022301           81 HGGRG   85 (299)
Q Consensus        81 ~~~~~   85 (299)
                      .....
T Consensus       148 ~~~~~  152 (158)
T 2kn4_A          148 RYGRP  152 (158)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            76543

>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=2e-18  Score=122.80  Aligned_cols=81  Identities=20%  Similarity=0.378  Sum_probs=72.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..+.++|||+|||.++++++|+++|..||+|..|.|..+   +.++|||||+|.+.++|..|+.  ++..|.|+.|.|.+
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            467899999999999999999999999999999999553   6778999999999999999999  46789999999999


Q ss_pred             ccCCCC
Q 022301           80 AHGGRG   85 (299)
Q Consensus        80 ~~~~~~   85 (299)
                      +.....
T Consensus        90 a~~~~~   95 (103)
T 2cqg_A           90 PNSKQS   95 (103)
T ss_dssp             CCTTCC
T ss_pred             cCCCCc
Confidence            976543

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

Probab=99.77  E-value=1.3e-18  Score=130.89  Aligned_cols=78  Identities=35%  Similarity=0.633  Sum_probs=72.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..+.++|||+|||.++|+++|+++|+.||+|..|.|..+   +.++|||||+|.+.++|.+|+..|||..|.|+.|.|.+
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  139 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL  139 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            357899999999999999999999999999999999543   67899999999999999999999999999999999987


Q ss_pred             c
Q 022301           80 A   80 (299)
Q Consensus        80 ~   80 (299)
                      +
T Consensus       140 A  140 (140)
T 2ku7_A          140 A  140 (140)
T ss_dssp             -
T ss_pred             C
Confidence            5

>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=7.2e-19  Score=135.94  Aligned_cols=81  Identities=26%  Similarity=0.466  Sum_probs=73.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .++++|||+|||+++|+++|.++|..||+|..|.|..   ++.++|||||+|.+.++|..||..|||..|.|+.|.|.|+
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            5678899999999999999999999999999999964   4667899999999999999999999999999999999998


Q ss_pred             cCCC
Q 022301           81 HGGR   84 (299)
Q Consensus        81 ~~~~   84 (299)
                      ....
T Consensus       150 ~~~~  153 (165)
T 1rk8_A          150 FVKG  153 (165)
T ss_dssp             EECC
T ss_pred             cCCC
Confidence            7544

>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=8.2e-19  Score=127.17  Aligned_cols=75  Identities=25%  Similarity=0.369  Sum_probs=66.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCce-----EEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHR-----LRVE   78 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~-----i~v~   78 (299)
                      ...++|||+|||+++|+++|+++|.+||+|..|.|..+    |||||+|.+.++|++||..|||..|.|+.     |.|.
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            45789999999999999999999999999999999754    89999999999999999999999999988     6666


Q ss_pred             EccC
Q 022301           79 LAHG   82 (299)
Q Consensus        79 ~~~~   82 (299)
                      .+..
T Consensus        90 ~~~~   93 (115)
T 3beg_B           90 VDGP   93 (115)
T ss_dssp             ECC-
T ss_pred             cCCC
Confidence            6543

>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=99.77  E-value=1.5e-18  Score=125.70  Aligned_cols=79  Identities=20%  Similarity=0.360  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCC--------CCc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDF--------DGH   73 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~--------~g~   73 (299)
                      .+.++|||+|||.++|+++|.++|..||+|..|.|..  ++.++|||||+|.+.++|..|+..|||..|        .++
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            5789999999999999999999999999999999955  466789999999999999999999999999        578


Q ss_pred             eEEEEEccC
Q 022301           74 RLRVELAHG   82 (299)
Q Consensus        74 ~i~v~~~~~   82 (299)
                      +|.|.|+.+
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            899999864

>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=99.76  E-value=7.8e-19  Score=127.17  Aligned_cols=79  Identities=18%  Similarity=0.192  Sum_probs=71.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCe-eEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPI-AHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v-~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..+.++|||+|||+++|+++|+++|..||.| ..|.|..  ++.++|||||+|.+.++|.+||.. |+..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHV   90 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEE
Confidence            3578999999999999999999999999999 7888844  567899999999999999999995 99999999999999


Q ss_pred             ccC
Q 022301           80 AHG   82 (299)
Q Consensus        80 ~~~   82 (299)
                      +..
T Consensus        91 a~~   93 (114)
T 2cpy_A           91 VTL   93 (114)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            864

>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=99.76  E-value=5.5e-19  Score=133.39  Aligned_cols=82  Identities=26%  Similarity=0.474  Sum_probs=74.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeE--------EEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCce
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAH--------IDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHR   74 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~--------i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~   74 (299)
                      ..++++|||+|||+++|+++|.++|+.||.|..        +.+..++.++|||||+|.+.++|..|+..|||..|.|+.
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            367899999999999999999999999999876        555667888999999999999999999999999999999


Q ss_pred             EEEEEccCCC
Q 022301           75 LRVELAHGGR   84 (299)
Q Consensus        75 i~v~~~~~~~   84 (299)
                      |.|.++....
T Consensus       122 l~V~~a~~~~  131 (143)
T 3egn_A          122 MVVQFARSAR  131 (143)
T ss_dssp             CEEEECCCSC
T ss_pred             EEEEECCCCC
Confidence            9999997544

>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=99.76  E-value=9e-19  Score=120.74  Aligned_cols=78  Identities=32%  Similarity=0.421  Sum_probs=72.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      +.+.++|||+|||+++++++|+++|.+| +|..+.+.   .++|||||+|.+.++|..|+..|||..+.|+.|.|.++..
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            4678999999999999999999999999 99999985   6689999999999999999999999999999999999865


Q ss_pred             CC
Q 022301           83 GR   84 (299)
Q Consensus        83 ~~   84 (299)
                      ..
T Consensus        78 ~~   79 (88)
T 1wg1_A           78 DA   79 (88)
T ss_dssp             CC
T ss_pred             Cc
Confidence            43

>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=99.76  E-value=5.1e-19  Score=128.25  Aligned_cols=79  Identities=56%  Similarity=1.000  Sum_probs=66.1

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee-eEEEEec
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS-RAYVRVR  183 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~-~~~~~~~  183 (299)
                      ....++|||+|||..+++++|+++|.+||+|..+.|+.+   +||||+|.+.++|++||+.|||..|+|+.+ ..++.+.
T Consensus        13 ~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           13 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   89 (115)
T ss_dssp             ----CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT---SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC---CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEec
Confidence            346789999999999999999999999999999999877   799999999999999999999999999752 2234554


Q ss_pred             ccc
Q 022301          184 EYD  186 (299)
Q Consensus       184 ~~~  186 (299)
                      ...
T Consensus        90 ~~~   92 (115)
T 3beg_B           90 VDG   92 (115)
T ss_dssp             ECC
T ss_pred             cCC
Confidence            443

>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=3.1e-18  Score=120.12  Aligned_cols=79  Identities=16%  Similarity=0.370  Sum_probs=70.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEE-eecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHID-LKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~-~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      ..+++|||+|||+++|+++|+++|..||+|..|. |..+. ..+.|||+|.+.++|..|+..|||..|.|+.|.|.++.+
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            4578999999999999999999999999999994 65443 245599999999999999999999999999999999976


Q ss_pred             C
Q 022301           83 G   83 (299)
Q Consensus        83 ~   83 (299)
                      .
T Consensus        92 ~   92 (96)
T 2e44_A           92 E   92 (96)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=2.1e-18  Score=131.33  Aligned_cols=78  Identities=45%  Similarity=0.745  Sum_probs=73.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      .+.++|||+|||+++|+++|.++|+.||.|..|.|..+  ++|||||+|.+.++|..|+..|||..|.|+.|.|.++...
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            56799999999999999999999999999999999765  5899999999999999999999999999999999998653

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

Probab=99.76  E-value=2.7e-18  Score=124.78  Aligned_cols=80  Identities=19%  Similarity=0.377  Sum_probs=72.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      +.++|||+|||.++|+++|+++|..||+|..|.|..+   +.++|||||+|.+.++|..||.. |+..|.|+.|.|.++.
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            4589999999999999999999999999999999654   67889999999999999999996 9999999999999987


Q ss_pred             CCCC
Q 022301           82 GGRG   85 (299)
Q Consensus        82 ~~~~   85 (299)
                      ....
T Consensus       105 ~~~~  108 (116)
T 1x4b_A          105 AREE  108 (116)
T ss_dssp             SCCC
T ss_pred             CCcc
Confidence            6543

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

Probab=99.76  E-value=2.5e-18  Score=133.97  Aligned_cols=80  Identities=25%  Similarity=0.446  Sum_probs=74.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      .++++|||+|||+++++++|+++|+.||+|..|.|..  ++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++.
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            4678999999999999999999999999999999955  46788999999999999999999999999999999999986


Q ss_pred             CC
Q 022301           82 GG   83 (299)
Q Consensus        82 ~~   83 (299)
                      ..
T Consensus       166 ~~  167 (177)
T 2f3j_A          166 SQ  167 (177)
T ss_dssp             SG
T ss_pred             CC
Confidence            53

>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=1.6e-18  Score=122.70  Aligned_cols=80  Identities=23%  Similarity=0.342  Sum_probs=70.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ..+.++|||+|||+++|+++|+++|..||.| .|.|..  ++.++|||||+|.+.++|++||. +|+..|.|+.|.|.++
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            3567899999999999999999999999954 888843  56778999999999999999996 8999999999999988


Q ss_pred             cCCC
Q 022301           81 HGGR   84 (299)
Q Consensus        81 ~~~~   84 (299)
                      ....
T Consensus        90 ~~~~   93 (102)
T 1wez_A           90 STAG   93 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
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=99.76  E-value=2.2e-18  Score=126.79  Aligned_cols=79  Identities=28%  Similarity=0.501  Sum_probs=72.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      +.++|||+|||.++|+++|.++|+.||+|..|.|..   ++.++|||||+|.+.++|..|+ .|||..|.|+.|.|.++.
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            358999999999999999999999999999999953   5778999999999999999999 699999999999999987


Q ss_pred             CCC
Q 022301           82 GGR   84 (299)
Q Consensus        82 ~~~   84 (299)
                      ...
T Consensus       114 ~~~  116 (124)
T 2jwn_A          114 TNM  116 (124)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=9.4e-19  Score=116.90  Aligned_cols=72  Identities=19%  Similarity=0.493  Sum_probs=66.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         8 ~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      +|||+|||+++|+++|+++|+.||+|..|.+..+   +.++|||||+|.+.++|..|+. +++..|.|+.|.|.++
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            6999999999999999999999999999999543   6788999999999999999999 6999999999999874

>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=6.9e-18  Score=118.52  Aligned_cols=76  Identities=26%  Similarity=0.471  Sum_probs=70.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      .++++|||+||  ++|+++|+++|.+||+|..|.|.   ..+|||||+|.+.++|.+|+..|||..|.|+.|.|.++...
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            57799999996  99999999999999999999995   56899999999999999999999999999999999998765


Q ss_pred             C
Q 022301           84 R   84 (299)
Q Consensus        84 ~   84 (299)
                      .
T Consensus        88 ~   88 (97)
T 1x5p_A           88 P   88 (97)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=126.08  Aligned_cols=80  Identities=20%  Similarity=0.328  Sum_probs=70.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEe--ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL--KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~--~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      .+.++|||+|||.++|+++|+++|..||.|..+.+  ..++.++|||||+|.+.++|.+|+. |||..|.|+.|.|.++.
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            47889999999999999999999999999877222  2346789999999999999999999 99999999999999987


Q ss_pred             CCC
Q 022301           82 GGR   84 (299)
Q Consensus        82 ~~~   84 (299)
                      ...
T Consensus        94 ~~~   96 (101)
T 1fj7_A           94 GRD   96 (101)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            544

>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=99.76  E-value=2.1e-17  Score=118.40  Aligned_cols=82  Identities=55%  Similarity=0.960  Sum_probs=70.0

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCce-eeEEEE
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAF-SRAYVR  181 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~-~~~~~~  181 (299)
                      +.....++|||+|||..+++++|+++|.+||.|..+.++.+   +||||+|.+.++|++||+.|||..|.|+. ....|.
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            44556789999999999999999999999999999999887   79999999999999999999999999921 111566


Q ss_pred             eccccc
Q 022301          182 VREYDH  187 (299)
Q Consensus       182 ~~~~~~  187 (299)
                      |..+.+
T Consensus        87 V~~a~~   92 (108)
T 1x4c_A           87 VKVDGP   92 (108)
T ss_dssp             EEESSC
T ss_pred             EEeCCC
Confidence            665544

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.75  E-value=9.6e-19  Score=127.37  Aligned_cols=77  Identities=21%  Similarity=0.295  Sum_probs=70.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCC---eeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGP---IAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVE   78 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~---v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~   78 (299)
                      .+.++|||+|||+++|+++|+++|..||.   |..|.|..  ++.++|||||+|.+.++|.+||. ||+..|.|+.|.|.
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            56789999999999999999999999999   88888854  36778999999999999999999 99999999999999


Q ss_pred             Ecc
Q 022301           79 LAH   81 (299)
Q Consensus        79 ~~~   81 (299)
                      ++.
T Consensus        94 ~a~   96 (118)
T 2db1_A           94 KSH   96 (118)
T ss_dssp             EEC
T ss_pred             ECC
Confidence            874

>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=2e-18  Score=128.16  Aligned_cols=77  Identities=19%  Similarity=0.261  Sum_probs=70.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCC---eeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGP---IAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVE   78 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~---v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~   78 (299)
                      .+.++|||+|||+++|+++|+++|+.||.   |..|.|..  ++.++|||||+|.+.++|.+||. ||+..|.|+.|.|.
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   88888854  36778999999999999999999 99999999999998


Q ss_pred             Ecc
Q 022301           79 LAH   81 (299)
Q Consensus        79 ~~~   81 (299)
                      ++.
T Consensus       121 ~a~  123 (136)
T 2hgl_A          121 KSH  123 (136)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            873

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=3.9e-18  Score=119.09  Aligned_cols=78  Identities=22%  Similarity=0.490  Sum_probs=67.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      ...++|||+|||.++|+++|.++|..||+|..|.+... ... ||||+|.+.++|.+|+. |||..|.|+.|.|.++...
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 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD-KGV-FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQK   82 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSS-SCC-EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCC-CCc-EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcC
Confidence            56789999999999999999999999999999833221 223 99999999999999999 9999999999999987644


Q ss_pred             C
Q 022301           84 R   84 (299)
Q Consensus        84 ~   84 (299)
                      .
T Consensus        83 ~   83 (94)
T 2e5g_A           83 E   83 (94)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=1.9e-18  Score=127.09  Aligned_cols=77  Identities=22%  Similarity=0.308  Sum_probs=69.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEE-Ee--ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHI-DL--KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i-~~--~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .+.++|||+|||+++|+++|.++|..||.|..+ .+  ..++.++|||||+|.+.++|.+||. ||+..|.|+.|.|.++
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            467899999999999999999999999999763 33  3467789999999999999999999 9999999999999987


Q ss_pred             c
Q 022301           81 H   81 (299)
Q Consensus        81 ~   81 (299)
                      .
T Consensus       102 ~  102 (124)
T 1wel_A          102 T  102 (124)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.74  E-value=1.4e-17  Score=126.11  Aligned_cols=77  Identities=18%  Similarity=0.224  Sum_probs=69.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCC--ceEEEEEccCCC
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDG--HRLRVELAHGGR   84 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g--~~i~v~~~~~~~   84 (299)
                      .+|||+||++.+|+++|.++|++||+|..|.|.. ...+|||||+|.+.++|..|+..|||..|.|  +.|.|+|++...
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            4578999999999999999999999999999953 2357899999999999999999999999966  999999998654

>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=1.9e-18  Score=123.68  Aligned_cols=78  Identities=15%  Similarity=0.182  Sum_probs=71.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCC---eeEEEeecC--CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGP---IAHIDLKIP--PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRV   77 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~---v~~i~~~~~--~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v   77 (299)
                      ....++|||+|||+++|+++|+++|..||.   |..|.|..+  +.++|||||+|.+.++|.+||. ||+..|.|+.|.|
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            357889999999999999999999999998   899999543  6789999999999999999999 9999999999999


Q ss_pred             EEcc
Q 022301           78 ELAH   81 (299)
Q Consensus        78 ~~~~   81 (299)
                      .++.
T Consensus        87 ~~a~   90 (107)
T 2lmi_A           87 YEIN   90 (107)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            9874

>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=99.74  E-value=3e-18  Score=139.13  Aligned_cols=77  Identities=17%  Similarity=0.241  Sum_probs=70.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcC--CeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYG--PIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G--~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..++|||+|||+++|+++|+++|..||  +|..|.|..   ++.++|||||+|.+.++|.+||..||+..|.|+.|.|.+
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  999999954   467889999999999999999999999999999999999


Q ss_pred             cc
Q 022301           80 AH   81 (299)
Q Consensus        80 ~~   81 (299)
                      +.
T Consensus       147 a~  148 (229)
T 3q2s_C          147 VN  148 (229)
T ss_dssp             CC
T ss_pred             CC
Confidence            85

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

Probab=99.74  E-value=6.1e-18  Score=120.71  Aligned_cols=74  Identities=22%  Similarity=0.272  Sum_probs=68.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      .++|||+|||+++|+++|+++|+.| .|..|.|..  ++.++|||||+|.+.++|.+||. ||+..|.|+.|.|..+.
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALK-RNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHHH-TTTEEETTEEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEEECC
Confidence            4699999999999999999999999 899999954  46789999999999999999995 99999999999998874

>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=99.73  E-value=7e-18  Score=116.03  Aligned_cols=73  Identities=32%  Similarity=0.622  Sum_probs=67.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhc----C-------CeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCC
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKY----G-------PIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFD   71 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G-------~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~   71 (299)
                      +.+.++|||+|||+++|+++|+++|.+|    |       +|..+.+..   .+|||||+|.+.++|.+|+ .|||..|.
T Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~---~kg~afV~f~~~~~a~~A~-~l~g~~~~   78 (87)
T 2hzc_A            3 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ---DKNFAFLEFRSVDETTQAM-AFDGIIFQ   78 (87)
T ss_dssp             SGGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECS---SSSEEEEEESSHHHHHHHG-GGTTCEET
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecC---CCcEEEEEcCCHHHHHHHH-hcCCCEEC
Confidence            4678999999999999999999999999    8       999999974   3799999999999999999 89999999


Q ss_pred             CceEEEEE
Q 022301           72 GHRLRVEL   79 (299)
Q Consensus        72 g~~i~v~~   79 (299)
                      |+.|.|..
T Consensus        79 g~~l~V~r   86 (87)
T 2hzc_A           79 GQSLKIRR   86 (87)
T ss_dssp             TEECEEEC
T ss_pred             CeEEEEeC
Confidence            99999864

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.73  E-value=1.8e-17  Score=120.48  Aligned_cols=77  Identities=25%  Similarity=0.251  Sum_probs=68.1

Q ss_pred             CCCe--EEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCce-EEEEecChHHHHHHHHhcCCCCCCC--ceEEEEE
Q 022301            5 ASRT--LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGY-AFVEFEEARDAEDAIRGRDGYDFDG--HRLRVEL   79 (299)
Q Consensus         5 ~~~~--l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~-afV~F~~~e~A~~A~~~l~~~~~~g--~~i~v~~   79 (299)
                      ++++  |||+||++.+|+++|.++|++||+|..|.|...   .|| |||+|.+.++|..|+..|||..|.|  +.|.|.+
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            4555  468999999999999999999999999999542   386 9999999999999999999999987  5899999


Q ss_pred             ccCCC
Q 022301           80 AHGGR   84 (299)
Q Consensus        80 ~~~~~   84 (299)
                      ++...
T Consensus        99 Ak~~~  103 (124)
T 2e5i_A           99 ARPTR  103 (124)
T ss_dssp             CSCSC
T ss_pred             ecCCc
Confidence            97654

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

Probab=99.73  E-value=1.9e-17  Score=127.89  Aligned_cols=127  Identities=13%  Similarity=0.119  Sum_probs=66.9

Q ss_pred             EEecChHHHHHHHHhcCCCCCC--CceEEEEEccCCCCCCCCCCCC-CCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHH
Q 022301           50 VEFEEARDAEDAIRGRDGYDFD--GHRLRVELAHGGRGRSSSDRHS-SHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLK  126 (299)
Q Consensus        50 V~F~~~e~A~~A~~~l~~~~~~--g~~i~v~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~  126 (299)
                      .+|.+.++|..|+..|++....  |+.+.+.+.............. ........+......++|||+|||..+++++|.
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~   90 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQ   90 (165)
T ss_dssp             -------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHH
Confidence            7899999999999999987665  6666655532211110000000 000011222344567899999999999999999


Q ss_pred             HHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          127 DHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       127 ~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ++|.+||.|..|.|+.+..+    |||||+|.+.++|+.||..|||..|.|+.+
T Consensus        91 ~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l  144 (165)
T 1rk8_A           91 EKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTI  144 (165)
T ss_dssp             HHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             HHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            99999999999999988644    599999999999999999999999999844

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.73  E-value=1.1e-17  Score=122.08  Aligned_cols=75  Identities=19%  Similarity=0.284  Sum_probs=67.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCce-EEEEecChHHHHHHHHhcCCCCCCC--ceEEEEEccCCC
Q 022301            8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGY-AFVEFEEARDAEDAIRGRDGYDFDG--HRLRVELAHGGR   84 (299)
Q Consensus         8 ~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~-afV~F~~~e~A~~A~~~l~~~~~~g--~~i~v~~~~~~~   84 (299)
                      .|||+||++.+|+++|.++|++||+|..|.|...  .+|+ |||+|.+.++|..|+..|||..|.|  +.|.|+|++...
T Consensus        30 ~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~--~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~  107 (130)
T 3zzy_A           30 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK--NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS  107 (130)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE--TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSS
T ss_pred             EEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC--CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCc
Confidence            4569999999999999999999999999988642  3677 9999999999999999999999988  899999997654

>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=2.8e-18  Score=127.76  Aligned_cols=79  Identities=19%  Similarity=0.281  Sum_probs=70.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      .+.++|||+|||+++|+++|+++|++|| |+.|.|..  ++.++|||||+|.+.++|++|| .||+..|.|+.|.|.++.
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            4678999999999999999999999999 77998854  4678999999999999999999 599999999999999886


Q ss_pred             CCC
Q 022301           82 GGR   84 (299)
Q Consensus        82 ~~~   84 (299)
                      ...
T Consensus       122 ~~~  124 (139)
T 2hgn_A          122 TTG  124 (139)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            543

>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=1.9e-18  Score=125.90  Aligned_cols=78  Identities=23%  Similarity=0.241  Sum_probs=69.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCe----eEEEee--cCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPI----AHIDLK--IPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLR   76 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v----~~i~~~--~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~   76 (299)
                      ..+.++|||+|||+++|+++|+++|+.||+|    ..|.|.  .++.++|||||+|.+.++|++||. +|+..|.|+.|.
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~-~~~~~l~gR~i~   98 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALR-KHKDLLGKRYIE   98 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHT-TTTEESSSCEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeeCCeEEE
Confidence            4577999999999999999999999999975    577774  357788999999999999999999 599999999999


Q ss_pred             EEEcc
Q 022301           77 VELAH   81 (299)
Q Consensus        77 v~~~~   81 (299)
                      |..+.
T Consensus        99 V~~a~  103 (123)
T 2dha_A           99 LFRST  103 (123)
T ss_dssp             CEEEC
T ss_pred             EEECC
Confidence            98763

>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=1.6e-17  Score=114.46  Aligned_cols=75  Identities=23%  Similarity=0.460  Sum_probs=62.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCC--CCCceEEEEEc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYD--FDGHRLRVELA   80 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~--~~g~~i~v~~~   80 (299)
                      ..+.++|||+|||+++|+++|+++|++||+|.+|.|..+  ++|||||+|.+.++|.+    |++..  +.|+.|.|.++
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~--srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a   81 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP--FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNA   81 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS--CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC--CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEc
Confidence            367899999999999999999999999999999999764  78999999999999883    55554  45899999998


Q ss_pred             cCC
Q 022301           81 HGG   83 (299)
Q Consensus        81 ~~~   83 (299)
                      .+.
T Consensus        82 ~~k   84 (89)
T 3d2w_A           82 EPK   84 (89)
T ss_dssp             C--
T ss_pred             CCC
Confidence            643

>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=99.72  E-value=9.2e-18  Score=115.67  Aligned_cols=78  Identities=24%  Similarity=0.439  Sum_probs=66.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      +.++++|||+|||.++|+++|+++|+.||+|..|.|..+  ++|||||+|.+.++|++|+..  +..+.|..|.|.++..
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--FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAEP   77 (88)
T ss_dssp             CSCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS--CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC--CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecCC
Confidence            467899999999999999999999999999999999754  689999999999999754331  3445899999998875


Q ss_pred             CC
Q 022301           83 GR   84 (299)
Q Consensus        83 ~~   84 (299)
                      ..
T Consensus        78 ~~   79 (88)
T 1wf0_A           78 KH   79 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=1.2e-17  Score=122.03  Aligned_cols=76  Identities=21%  Similarity=0.258  Sum_probs=68.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCee--EEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIA--HIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~--~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      .+.++|||+|||+++|+++|+++|+.| .|.  .|.|..  ++.++|||||+|.++++|.+||. +++..|.|+.|.|.+
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  888854  36789999999999999999999 688999999999988


Q ss_pred             cc
Q 022301           80 AH   81 (299)
Q Consensus        80 ~~   81 (299)
                      +.
T Consensus       118 a~  119 (126)
T 2hgm_A          118 SS  119 (126)
T ss_dssp             EC
T ss_pred             CC
Confidence            74

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.56  E-value=3.9e-19  Score=129.26  Aligned_cols=82  Identities=28%  Similarity=0.430  Sum_probs=74.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeE--------EEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCC
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAH--------IDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFD   71 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~--------i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~   71 (299)
                      ..++++|||+|||.++++++|+++|+.||.|..        |.|..   ++.++|||||+|.+.++|..|+..|||..|.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            467899999999999999999999999999998        77754   3678899999999999999999999999999


Q ss_pred             CceEEEEEccCCC
Q 022301           72 GHRLRVELAHGGR   84 (299)
Q Consensus        72 g~~i~v~~~~~~~   84 (299)
                      |+.|.|.++....
T Consensus        84 g~~l~V~~a~~~~   96 (116)
T 2lcw_A           84 GNPIKVSFATRRA   96 (116)
Confidence            9999999987554

>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=99.72  E-value=5.4e-17  Score=114.10  Aligned_cols=70  Identities=21%  Similarity=0.368  Sum_probs=64.9

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .+++|||+|||..+++++|.++|.+||.|..+.++.++.+    |||||+|.+.++|+.|++.|||..|+|+.+
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l   91 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI   91 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            4579999999999999999999999999999999988654    499999999999999999999999999843

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

Probab=99.72  E-value=2.7e-17  Score=116.61  Aligned_cols=81  Identities=20%  Similarity=0.254  Sum_probs=71.6

Q ss_pred             CCCCCCeEEEcCCCC-----CCCHHHHHHHhhhcCCeeEEEeecC----CCCCceEEEEecChHHHHHHHHhcCCCCCCC
Q 022301            2 SSRASRTLYVGNLPG-----DIREREVEDLFYKYGPIAHIDLKIP----PRPPGYAFVEFEEARDAEDAIRGRDGYDFDG   72 (299)
Q Consensus         2 ~~~~~~~l~V~nLp~-----~~t~~~l~~~F~~~G~v~~i~~~~~----~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g   72 (299)
                      ...++++|+|.||..     +-++++|+++|++||+|..|.|..+    +.++|||||+|.+.++|.+|+..|||..|.|
T Consensus         4 ~~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~G   83 (105)
T 2pe8_A            4 GKCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGG   83 (105)
T ss_dssp             GGSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            457899999999963     2478999999999999999999653    4678999999999999999999999999999


Q ss_pred             ceEEEEEccC
Q 022301           73 HRLRVELAHG   82 (299)
Q Consensus        73 ~~i~v~~~~~   82 (299)
                      +.|.|.++..
T Consensus        84 r~i~v~~a~~   93 (105)
T 2pe8_A           84 RVVKACFYNL   93 (105)
T ss_dssp             EECEEEECCH
T ss_pred             cEEEEEEcCH
Confidence            9999999853

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

Probab=99.71  E-value=3.1e-17  Score=118.66  Aligned_cols=74  Identities=34%  Similarity=0.547  Sum_probs=62.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC------CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP------PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLR   76 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~------~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~   76 (299)
                      ..++++|||+|||+++|+++|+++|++||+|. +.+..+      +.++|||||+|.+.++|++|+..|++  +.|+.|.
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~--~~G~~~~   81 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLE--EDGKLYL   81 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEE--ETTEEEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhh--cCCcEEE
Confidence            36789999999999999999999999999999 766433      57799999999999999999998843  5566555


Q ss_pred             EEE
Q 022301           77 VEL   79 (299)
Q Consensus        77 v~~   79 (299)
                      +..
T Consensus        82 ~~~   84 (114)
T 2dnl_A           82 CVS   84 (114)
T ss_dssp             EEC
T ss_pred             ecc
Confidence            544

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.70  E-value=1e-17  Score=118.76  Aligned_cols=78  Identities=23%  Similarity=0.498  Sum_probs=70.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      .++++|||+|||.++++++|.++|+.||.|..|.|..  ++.++|||||+|.+.++|..|+.  ++..|.|+.|.|.++.
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            4578999999999999999999999999999999955  46678999999999999999999  8999999999999886


Q ss_pred             CC
Q 022301           82 GG   83 (299)
Q Consensus        82 ~~   83 (299)
                      ..
T Consensus        85 ~~   86 (102)
T 2xs2_A           85 RK   86 (102)
T ss_dssp             EC
T ss_pred             cC
Confidence            43

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.69  E-value=7e-17  Score=115.43  Aligned_cols=77  Identities=31%  Similarity=0.572  Sum_probs=68.6

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcC-CeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEecc
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAG-DVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVRE  184 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G-~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~~  184 (299)
                      ...++|||+|||..+++++|+++|.+|| .|..+.+......|||||+|.+.++|++|++.|||..|+|+    .|.|..
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr----~i~V~~  101 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGS----VITVER  101 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTE----EEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCe----EEEEEE
Confidence            3568999999999999999999999999 89999987666778999999999999999999999999999    555554


Q ss_pred             cc
Q 022301          185 YD  186 (299)
Q Consensus       185 ~~  186 (299)
                      ..
T Consensus       102 a~  103 (111)
T 2jvr_A          102 DD  103 (111)
T ss_dssp             SC
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=99.69  E-value=3.4e-17  Score=121.95  Aligned_cols=111  Identities=13%  Similarity=0.043  Sum_probs=67.2

Q ss_pred             ceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHH
Q 022301           46 GYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDL  125 (299)
Q Consensus        46 g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l  125 (299)
                      -++|++|.+...|..|+..|+|....|... +.+                   ...++......+|||+|||..+++++|
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~g~~~-~~~-------------------~~~~~~~~~~~~l~V~nLp~~~te~~L   64 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQMGRGS-MSY-------------------GRPPPDVEGMTSLKVDNLTYRTSPDTL   64 (135)
T ss_dssp             -------------------------------CCS-------------------CCSCSSGGGCCCEEEECCCSSCHHHHH
T ss_pred             ccccccccCCCchhhhhhhccCCCCCCCCC-CCc-------------------CCCCCCCCCCCEEEEeCCCCCCCHHHH
Confidence            477888888888888998888866554421 100                   111233445689999999999999999


Q ss_pred             HHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          126 KDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       126 ~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .++|.+||.|..+.++.+..    .|||||+|.+.++|+.|+..|||..|.|+.+
T Consensus        65 ~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l  119 (135)
T 2lea_A           65 RRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGREL  119 (135)
T ss_dssp             HHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCC
T ss_pred             HHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            99999999999999987753    4599999999999999999999999999944

>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=1.1e-16  Score=129.31  Aligned_cols=81  Identities=28%  Similarity=0.548  Sum_probs=74.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .+.++|||+|||.++|+++|+++|+.||.|..|.|..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
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            4668999999999999999999999999999999954   4567899999999999999999999999999999999999


Q ss_pred             cCCC
Q 022301           81 HGGR   84 (299)
Q Consensus        81 ~~~~   84 (299)
                      ....
T Consensus       203 ~~~~  206 (216)
T 2qfj_A          203 VTPP  206 (216)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            7654

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

Probab=99.68  E-value=8.8e-17  Score=124.17  Aligned_cols=79  Identities=25%  Similarity=0.479  Sum_probs=73.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..++++|||+|||.++|+++|.++|+.||.|..+.+..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.|
T Consensus        84 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  163 (166)
T 3md3_A           84 SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINW  163 (166)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Confidence            35678999999999999999999999999999999954   467789999999999999999999999999999999999


Q ss_pred             cc
Q 022301           80 AH   81 (299)
Q Consensus        80 ~~   81 (299)
                      +.
T Consensus       164 a~  165 (166)
T 3md3_A          164 AA  165 (166)
T ss_dssp             SC
T ss_pred             cC
Confidence            85

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.68  E-value=4.9e-17  Score=131.35  Aligned_cols=78  Identities=27%  Similarity=0.419  Sum_probs=70.6

Q ss_pred             CCCCeEEEcCCCCCC---------CHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCC----
Q 022301            4 RASRTLYVGNLPGDI---------REREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDF----   70 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~---------t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~----   70 (299)
                      ..+++|||+||+..+         ++++|.++|++||+|..|.|..   .+|||||+|.+.++|+.|+..|+|..|    
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            578999999999998         7999999999999999999973   489999999999999999999999999    


Q ss_pred             --------CCceEEEEEccCCC
Q 022301           71 --------DGHRLRVELAHGGR   84 (299)
Q Consensus        71 --------~g~~i~v~~~~~~~   84 (299)
                              .|+.|.|.|+....
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                    89999999997544

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

Probab=99.68  E-value=6.6e-17  Score=130.31  Aligned_cols=78  Identities=24%  Similarity=0.405  Sum_probs=71.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC-CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~-~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      +.++|||+|||+++|+++|+++|+.||.|..|.|..+ +.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++..
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS  180 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            4678999999999999999999999999999999543 45689999999999999999999999999999999999864

>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=99.68  E-value=1.3e-15  Score=109.25  Aligned_cols=82  Identities=16%  Similarity=0.226  Sum_probs=70.9

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC-CCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEE
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS-GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVR  181 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~  181 (299)
                      .......+|||+|||..+++++|+++|.+||.|..+.+..+.. .+||||+|.+.++|+.|++.|||..|+|+    .+.
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 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGY----RLR   92 (109)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTE----ECE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCe----EEE
Confidence            4455678999999999999999999999999999999977654 57999999999999999999999999998    555


Q ss_pred             ecccccC
Q 022301          182 VREYDHR  188 (299)
Q Consensus       182 ~~~~~~~  188 (299)
                      |......
T Consensus        93 V~~a~~~   99 (109)
T 1x4a_A           93 VEFPRSG   99 (109)
T ss_dssp             EECCCCC
T ss_pred             EEEcccC
Confidence            5555443

>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=7e-16  Score=111.77  Aligned_cols=71  Identities=17%  Similarity=0.253  Sum_probs=65.2

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC---CCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG---SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~---~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ....+|||+|||..+++++|.++|.+||.|..+.+..+.   ..|||||+|.+.++|+.|++.|||..|+|+.+
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l   78 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAI   78 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            345799999999999999999999999999999999876   23699999999999999999999999999954

>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=3.2e-16  Score=112.94  Aligned_cols=81  Identities=23%  Similarity=0.379  Sum_probs=70.6

Q ss_pred             CCCCCeEEEcCCCCCCC-----------HHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCC
Q 022301            3 SRASRTLYVGNLPGDIR-----------EREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFD   71 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t-----------~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~   71 (299)
                      ..++++|+|.||.....           +++|+++|++||+|..|.| .+..++|||||+|.+.++|..|+..|||..|.
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~   90 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDRHPDGVASVSFRDPEEADYCIQTLDGRWFG   90 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETTCTTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecCCCCEEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            36789999999944432           5899999999999999977 45568999999999999999999999999999


Q ss_pred             CceEEEEEccCCC
Q 022301           72 GHRLRVELAHGGR   84 (299)
Q Consensus        72 g~~i~v~~~~~~~   84 (299)
                      |+.|.|.++.+..
T Consensus        91 gr~l~v~~a~~~~  103 (112)
T 2dit_A           91 GRQITAQAWDGTT  103 (112)
T ss_dssp             TEECEEEECCSCC
T ss_pred             CcEEEEEEeCCCC
Confidence            9999999986543

>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=99.67  E-value=1.9e-15  Score=107.18  Aligned_cols=82  Identities=10%  Similarity=0.091  Sum_probs=71.0

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC--CEEEEEecChhhHHHHHHhcCCCeecCceeeEEE
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG--TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYV  180 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~--~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~  180 (299)
                      .......+|||+|||..+++++|.++|.+||.|..|.++.+...  +||||+|.+.++|+.|+..|||..|.|+    .+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~----~l   85 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGK----EV   85 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTE----EE
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCC----eE
Confidence            34456789999999999999999999999999999999987543  6999999999999999999999999998    55


Q ss_pred             EecccccC
Q 022301          181 RVREYDHR  188 (299)
Q Consensus       181 ~~~~~~~~  188 (299)
                      .|......
T Consensus        86 ~V~~a~~~   93 (103)
T 2cqi_A           86 KVNWATTP   93 (103)
T ss_dssp             EEEECCCT
T ss_pred             EEEECCCC
Confidence            55554443

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

Probab=99.67  E-value=5.8e-16  Score=110.90  Aligned_cols=72  Identities=18%  Similarity=0.119  Sum_probs=66.2

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      .+..+|||+|||..+++++|.++|.+||.|..+.|+.++.+    |||||+|.+.++|++|++.|||..|+|+.+.
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~   79 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIH   79 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            34579999999999999999999999999999999998764    5999999999999999999999999999553

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

Probab=99.67  E-value=5.7e-16  Score=103.82  Aligned_cols=73  Identities=12%  Similarity=0.172  Sum_probs=65.5

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEeccc
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVREY  185 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~~~  185 (299)
                      ...-|+|+||++.+++++|.++|.+||+|..+++..  ..|||||+|.+.++|.+|++.|||..+.|+    .|.|..+
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~--~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr----~I~V~~A   78 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL--NQGIALCKYTTREEANKAQMALNNCVLANT----TIFAESP   78 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET--TTTEEEEEESSHHHHHHHHHHHTTEEETTE----EEEEECC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC--CCcEEEEEECCHHHHHHHHHHhcCCEECCc----EEEEEEC
Confidence            346899999999999999999999999999999876  568999999999999999999999999999    5555443

>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=99.66  E-value=2e-15  Score=107.14  Aligned_cols=82  Identities=20%  Similarity=0.261  Sum_probs=70.9

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC--CCEEEEEecChhhHHHHHHhcCCCeecCceeeEEE
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS--GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYV  180 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~--~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~  180 (299)
                      .......+|||+|||..+++++|+++|.+||.|..+.++.+..  .+||||+|.+.++|+.|+..|||..|+|+    .+
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 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGR----KI   85 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTE----EC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCE----EE
Confidence            4455678999999999999999999999999999999998754  46999999999999999999999999998    44


Q ss_pred             EecccccC
Q 022301          181 RVREYDHR  188 (299)
Q Consensus       181 ~~~~~~~~  188 (299)
                      .+......
T Consensus        86 ~v~~a~~~   93 (103)
T 2cq3_A           86 EVNNATAR   93 (103)
T ss_dssp             EEEECCSS
T ss_pred             EEEEcccC
Confidence            44444433

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=6e-16  Score=108.69  Aligned_cols=77  Identities=8%  Similarity=0.105  Sum_probs=66.7

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcC--CCeecCceeeEEEEe
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLD--DSEFRNAFSRAYVRV  182 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~--g~~~~g~~~~~~~~~  182 (299)
                      ..+..+|||+|||+.+++++|+++|.+||.|..+.++.+  .|||||+|.+.++|..|++.|+  +..|.|+    .+.|
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~--kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr----~l~V   86 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG--KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQ----PIYI   86 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT--TTEEEEEESSHHHHHHHHHHHTTSCCEETTE----ECCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCEEEEEECCHHHHHHHHHHhccCCceECCE----EEEE
Confidence            345689999999999999999999999999999999876  5799999999999999999886  4789998    5555


Q ss_pred             ccccc
Q 022301          183 REYDH  187 (299)
Q Consensus       183 ~~~~~  187 (299)
                      .....
T Consensus        87 ~~A~~   91 (105)
T 1sjq_A           87 QFSNH   91 (105)
T ss_dssp             CCCSS
T ss_pred             EEcCC
Confidence            55443

>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=3.4e-16  Score=115.39  Aligned_cols=73  Identities=18%  Similarity=0.312  Sum_probs=66.3

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ......+|||+|||..+++++|.++|.+||.|..|.++.+..    .+||||+|.+.++|+.|++.|||..|+|+.+
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   94 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPI   94 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEE
Confidence            445678999999999999999999999999999999987753    4599999999999999999999999999955

>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=99.66  E-value=1.3e-16  Score=124.48  Aligned_cols=77  Identities=29%  Similarity=0.461  Sum_probs=72.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      .+.++|||+|||.++|+++|+++|+.||.|..+  ..++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.|+.+
T Consensus        97 ~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~--~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  173 (175)
T 1fje_B           97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE  173 (175)
T ss_dssp             GGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE--CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSS
T ss_pred             ccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe--cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCC
Confidence            356899999999999999999999999999888  66778899999999999999999999999999999999999864

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.66  E-value=1.2e-16  Score=114.40  Aligned_cols=75  Identities=23%  Similarity=0.355  Sum_probs=66.3

Q ss_pred             CeEEEcCC----CCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecC----hHH----HHHHHH--hcCCCC
Q 022301            7 RTLYVGNL----PGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEE----ARD----AEDAIR--GRDGYD   69 (299)
Q Consensus         7 ~~l~V~nL----p~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~----~e~----A~~A~~--~l~~~~   69 (299)
                      +.|||+||    |+.+++++|+++|+.||+|.+|.+..   ++.++|||||+|.+    +++    |..|+.  .|||..
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    99999999999999999999999955   46779999999996    333    788888  789999


Q ss_pred             CCCceEEEEEcc
Q 022301           70 FDGHRLRVELAH   81 (299)
Q Consensus        70 ~~g~~i~v~~~~   81 (299)
                      |.|+.|.|.+-.
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999999864

>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=99.66  E-value=1.5e-16  Score=123.65  Aligned_cols=77  Identities=27%  Similarity=0.586  Sum_probs=71.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .+.++|||+|||.++|+++|.++|++||+|..+.+..   ++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++
T Consensus        92 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            3468999999999999999999999999999999954   4567899999999999999999999999999999999987

>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=99.66  E-value=2e-16  Score=122.42  Aligned_cols=77  Identities=22%  Similarity=0.534  Sum_probs=71.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ++++|||+|||.++|+++|.++|+.||.|..+.+..   ++.++|||||+|.+.++|.+|+. |+|..|.|+.|.|.++.
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            467999999999999999999999999999999954   46788999999999999999999 99999999999999986


Q ss_pred             C
Q 022301           82 G   82 (299)
Q Consensus        82 ~   82 (299)
                      +
T Consensus       165 p  165 (167)
T 2cjk_A          165 P  165 (167)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.66  E-value=2.7e-16  Score=125.12  Aligned_cols=81  Identities=27%  Similarity=0.573  Sum_probs=74.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .+.++|||+|||.++++++|+++|+.||.|..|.+..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
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            5679999999999999999999999999999999954   4567899999999999999999999999999999999999


Q ss_pred             cCCC
Q 022301           81 HGGR   84 (299)
Q Consensus        81 ~~~~   84 (299)
                      .+..
T Consensus       192 ~~~~  195 (198)
T 2yh0_A          192 SVGA  195 (198)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7543

>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=99.65  E-value=5.9e-16  Score=112.05  Aligned_cols=75  Identities=20%  Similarity=0.324  Sum_probs=66.8

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC--CEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEeccc
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG--TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVREY  185 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~--~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~~~  185 (299)
                      ..+|||+|||..+++++|.++|.+||.|..|.|+.+..+  |||||+|.+.++|+.|++.|+|..|+|+    .+.|...
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~----~i~V~~a   80 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR----KVFVGRF   80 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTE----ECEEEES
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCE----EEEEEEC
Confidence            468999999999999999999999999999999988653  5999999999999999999999999998    4444444


Q ss_pred             c
Q 022301          186 D  186 (299)
Q Consensus       186 ~  186 (299)
                      .
T Consensus        81 ~   81 (115)
T 4f25_A           81 K   81 (115)
T ss_dssp             S
T ss_pred             C
Confidence            3

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

Probab=99.65  E-value=8.8e-16  Score=108.95  Aligned_cols=74  Identities=14%  Similarity=0.216  Sum_probs=66.5

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeC--CCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD--GSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~--~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .......+|||+|||..+++++|.++|.+||.|..+.+..+  ...+||||+|.+.++|+.|++.|||..|.|+.+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   85 (103)
T 2d9p_A           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPL   85 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBC
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEE
Confidence            34456789999999999999999999999999999999987  223599999999999999999999999999944

>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=3.8e-16  Score=120.89  Aligned_cols=77  Identities=34%  Similarity=0.578  Sum_probs=71.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCC--ceEEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDG--HRLRVE   78 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g--~~i~v~   78 (299)
                      .+.++|||+|||.++++++|.++|+.||.|..+.+..   ++.++|||||+|.+.++|..|+..|||..|.|  ++|.|.
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            5678999999999999999999999999999999954   45667999999999999999999999999988  999998


Q ss_pred             Ec
Q 022301           79 LA   80 (299)
Q Consensus        79 ~~   80 (299)
                      ||
T Consensus       167 ~A  168 (168)
T 1b7f_A          167 LA  168 (168)
T ss_dssp             EC
T ss_pred             eC
Confidence            85

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

Probab=99.65  E-value=1.8e-15  Score=104.50  Aligned_cols=76  Identities=16%  Similarity=0.318  Sum_probs=67.1

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEecc
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVRE  184 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~~  184 (299)
                      ..+..+|||+|||..+++++|+++|.+||.|..+.+.    .+||||+|.+.++|+.|++.|||..|+|+    .+.+..
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----KNYGFVHIEDKTAAEDAIRNLHHYKLHGV----NINVEA   76 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE----TTEEEEEESSHHHHHHHHHHHTTCBCSSC----BCEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE----CCEEEEEECCHHHHHHHHHHhcCCccCCc----EEEEEE
Confidence            4466899999999999999999999999999999998    46999999999999999999999999999    455555


Q ss_pred             cccC
Q 022301          185 YDHR  188 (299)
Q Consensus       185 ~~~~  188 (299)
                      ....
T Consensus        77 a~~~   80 (90)
T 2dnq_A           77 SKNK   80 (90)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            4444

>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=1.1e-15  Score=108.50  Aligned_cols=74  Identities=16%  Similarity=0.131  Sum_probs=67.0

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      +......+|||+|||..+++++|.++|.+||.|..+.++.+..    .+||||+|.+.++|+.|++.|||..|+|+.+
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   85 (103)
T 2dnm_A            8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGREL   85 (103)
T ss_dssp             SCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCC
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEE
Confidence            3445678999999999999999999999999999999988754    3699999999999999999999999999944

>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=3.4e-16  Score=121.99  Aligned_cols=76  Identities=22%  Similarity=0.359  Sum_probs=69.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCC---CceEEEEE
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFD---GHRLRVEL   79 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~---g~~i~v~~   79 (299)
                      +.++|||+|||.++|+++|+++|+.||.|..|.+..  ++.++|||||+|.+.++|..|+..|||..+.   |++|.|.|
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            678999999999999999999999999999999954  4567899999999999999999999998776   48999998


Q ss_pred             c
Q 022301           80 A   80 (299)
Q Consensus        80 ~   80 (299)
                      +
T Consensus       174 a  174 (175)
T 3nmr_A          174 A  174 (175)
T ss_dssp             C
T ss_pred             c
Confidence            7

>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=2.5e-15  Score=105.79  Aligned_cols=79  Identities=16%  Similarity=0.166  Sum_probs=69.3

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC----CCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEE
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG----SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVR  181 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~  181 (299)
                      ....+|||+|||..+++++|.++|.+||.|..+.++.+.    ..+||||+|.+.++|+.|++.|||..|.|+    .+.
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 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGR----MLH   81 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSC----EEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCc----EEE
Confidence            456899999999999999999999999999999998876    336999999999999999999999999999    555


Q ss_pred             ecccccC
Q 022301          182 VREYDHR  188 (299)
Q Consensus       182 ~~~~~~~  188 (299)
                      |......
T Consensus        82 V~~a~~~   88 (99)
T 1whw_A           82 VLPSTIK   88 (99)
T ss_dssp             EEECCCC
T ss_pred             EEEcCCC
Confidence            5555444

>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=99.65  E-value=1.7e-15  Score=105.99  Aligned_cols=80  Identities=16%  Similarity=0.164  Sum_probs=69.9

Q ss_pred             CCCccEEEEeCCCCCCCHHHHH----HHHHhcCCeeEEEEEeCCC-CCEEEEEecChhhHHHHHHhcCCCeecCceeeEE
Q 022301          105 RRSEYRVLVTGLPSSASWQDLK----DHMRRAGDVCFSQVFRDGS-GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY  179 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~----~~f~~~G~v~~~~~~~~~~-~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  179 (299)
                      ....++|||+|||..+++++|+    ++|.+||.|..+.++.+.. .+||||+|.+.++|+.|++.|||..|+|+    .
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr----~   81 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSK----K   81 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTE----E
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCe----E
Confidence            3456899999999999999999    9999999999999987754 47999999999999999999999999999    5


Q ss_pred             EEecccccC
Q 022301          180 VRVREYDHR  188 (299)
Q Consensus       180 ~~~~~~~~~  188 (299)
                      +.|....+.
T Consensus        82 l~V~~a~~~   90 (96)
T 2dgx_A           82 ILVSLATGA   90 (96)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEEcCCC
Confidence            555555443

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

Probab=99.65  E-value=1.9e-15  Score=107.17  Aligned_cols=81  Identities=15%  Similarity=0.202  Sum_probs=70.6

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceeeEE
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY  179 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  179 (299)
                      ......+|||+|||..+++++|.++|.+||.|..|.++.++..    +||||+|.+.++|+.|+..|||..|.|+    .
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~----~   86 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHL----I   86 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTE----E
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCc----E
Confidence            4456789999999999999999999999999999999988643    4999999999999999999999999998    5


Q ss_pred             EEecccccC
Q 022301          180 VRVREYDHR  188 (299)
Q Consensus       180 ~~~~~~~~~  188 (299)
                      +.|......
T Consensus        87 l~v~~a~~~   95 (103)
T 2cq0_A           87 LNVEWAKPS   95 (103)
T ss_dssp             CEEEESSCC
T ss_pred             EEEEECCCC
Confidence            555544443

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

Probab=99.65  E-value=1.6e-15  Score=105.90  Aligned_cols=78  Identities=15%  Similarity=0.237  Sum_probs=68.5

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEe
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRV  182 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~  182 (299)
                      +..+|||+|||..+++++|+++|.+||.|..+.++.++.    .+||||+|.+.++|+.|++.|||..|.|+    .+.+
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 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGR----PMRV   79 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSS----CCEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCc----EEEE
Confidence            458999999999999999999999999999999998754    46999999999999999999999999999    4444


Q ss_pred             cccccC
Q 022301          183 REYDHR  188 (299)
Q Consensus       183 ~~~~~~  188 (299)
                      .....+
T Consensus        80 ~~a~~~   85 (95)
T 2dnz_A           80 GHVTER   85 (95)
T ss_dssp             EESSCC
T ss_pred             EEcccc
Confidence            444443

>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=99.65  E-value=9.4e-16  Score=105.50  Aligned_cols=71  Identities=14%  Similarity=0.216  Sum_probs=65.1

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC-----CCCEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG-----SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~-----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      ...+|||+|||..+++++|.++|.+||.|..+.+..+.     ..|||||+|.+.++|+.|+..|||..++|+.+.
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   78 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEIT   78 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEE
Confidence            34799999999999999999999999999999998876     457999999999999999999999999999543

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

Probab=99.65  E-value=4.6e-15  Score=107.41  Aligned_cols=81  Identities=21%  Similarity=0.256  Sum_probs=70.6

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceeeEE
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY  179 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  179 (299)
                      ......+|||+|||..+++++|+++|..||.|..+.++.+...    +||||+|.+.++|+.|++.|||..|+|+    .
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~----~   96 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMK----R   96 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTE----E
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCE----E
Confidence            3445689999999999999999999999999999999988744    4999999999999999999999999998    5


Q ss_pred             EEecccccC
Q 022301          180 VRVREYDHR  188 (299)
Q Consensus       180 ~~~~~~~~~  188 (299)
                      +.|......
T Consensus        97 l~V~~a~~~  105 (115)
T 2cpz_A           97 LKVQLKRSK  105 (115)
T ss_dssp             CEEECCCCS
T ss_pred             EEEEEcCCC
Confidence            555555444

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

Probab=99.64  E-value=2.9e-15  Score=103.96  Aligned_cols=77  Identities=22%  Similarity=0.368  Sum_probs=68.2

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEec
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVR  183 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~  183 (299)
                      ......+|||+|||..+++++|+++|.+||.|..+.+..+    ||||+|.+.++|+.|+..|||..|.|+    .+.+.
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~----~afV~f~~~~~a~~A~~~l~g~~~~g~----~l~V~   77 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD----YAFVHMERAEDAVEAIRGLDNTEFQGK----RMHVQ   77 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS----EEEEEESCHHHHHHHHHHHTTEEETTE----EEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC----EEEEEECCHHHHHHHHHHhCCCeeCCc----EEEEE
Confidence            4456789999999999999999999999999999999855    999999999999999999999999998    55555


Q ss_pred             ccccC
Q 022301          184 EYDHR  188 (299)
Q Consensus       184 ~~~~~  188 (299)
                      .....
T Consensus        78 ~a~~~   82 (92)
T 2dgt_A           78 LSTSR   82 (92)
T ss_dssp             ESSCC
T ss_pred             EccCC
Confidence            55444

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

Probab=99.64  E-value=8.8e-15  Score=105.92  Aligned_cols=82  Identities=18%  Similarity=0.270  Sum_probs=70.9

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceeeE
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA  178 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  178 (299)
                      .......+|||+|||..+++++|+++|..||.|..|.++.+...    +||||+|.+.++|+.|++.|+|..|+|+    
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~----   85 (115)
T 2dgo_A           10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGR----   85 (115)
T ss_dssp             CCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTE----
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCE----
Confidence            34556789999999999999999999999999999999988643    5999999999999999999999999998    


Q ss_pred             EEEecccccC
Q 022301          179 YVRVREYDHR  188 (299)
Q Consensus       179 ~~~~~~~~~~  188 (299)
                      .|.|......
T Consensus        86 ~l~V~~a~~~   95 (115)
T 2dgo_A           86 QIRTNWATRK   95 (115)
T ss_dssp             ECEEEESSCC
T ss_pred             EEEEEEccCC
Confidence            4455444433

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=1.8e-15  Score=106.07  Aligned_cols=73  Identities=21%  Similarity=0.254  Sum_probs=65.8

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .......+|||+|||..+++++|+++|.+||.|. +.++.+...+||||+|.+.++|+.|++.|||..|+|+.+
T Consensus        14 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   86 (97)
T 2e5j_A           14 EGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTL   86 (97)
T ss_dssp             SSSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CCCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEE
Confidence            3445568999999999999999999999999997 677777778899999999999999999999999999944

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

Probab=99.64  E-value=2e-15  Score=106.11  Aligned_cols=78  Identities=17%  Similarity=0.265  Sum_probs=68.4

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC-------CCEEEEEecChhhHHHHHHhcCCCeecCceeeEE
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS-------GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY  179 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-------~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  179 (299)
                      +..+|||+|||..+++++|+++|.+||.|..+.+..+..       .+||||+|.+.++|+.|+..|||..|+|+    .
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 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGH----K   79 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTE----E
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCe----E
Confidence            457999999999999999999999999999999987654       25999999999999999999999999998    5


Q ss_pred             EEecccccC
Q 022301          180 VRVREYDHR  188 (299)
Q Consensus       180 ~~~~~~~~~  188 (299)
                      +.|......
T Consensus        80 l~V~~a~~~   88 (98)
T 2cpf_A           80 LEVRISERA   88 (98)
T ss_dssp             CEEECSSCS
T ss_pred             EEEEEccCC
Confidence            555555443

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

Probab=99.64  E-value=1.9e-15  Score=107.05  Aligned_cols=76  Identities=22%  Similarity=0.304  Sum_probs=67.6

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCceeeEE
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY  179 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  179 (299)
                      ......+|||+|||..+++++|.++|.+||.|..+.++.++.    .+||||+|.+.++|+.|++.|||..|.|+.+.+.
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   87 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD   87 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            344668999999999999999999999999999999988753    4599999999999999999999999999955433

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.64  E-value=6.1e-16  Score=122.26  Aligned_cols=77  Identities=17%  Similarity=0.353  Sum_probs=69.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      .++|||+|||+++|+++|.++|++||+|..|.|..  ++.++|||||+|.+.++|..|+..+ +..|.|+.|.|.+....
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            48999999999999999999999999999999954  4667899999999999999999854 56899999999997654

>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=2.7e-15  Score=105.64  Aligned_cols=72  Identities=14%  Similarity=0.295  Sum_probs=65.3

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ......+|||+|||..+++++|+++|.+||.|..+.++.++.    .+||||+|.+.++|+.|++ |+|..|+|+.+
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l   81 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKV   81 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEE
Confidence            345668999999999999999999999999999999988753    4699999999999999999 99999999944

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

Probab=99.63  E-value=5.9e-16  Score=122.97  Aligned_cols=81  Identities=23%  Similarity=0.480  Sum_probs=70.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .+.++|||+|||.++|+++|.++|+.||.|..|.|..   ++.++|||||+|.+.++|.+|+. ++|..|.|+.|.|.++
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~-~~~~~~~G~~i~v~~a  180 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA  180 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHH-hCCcEECCEEEEEEec
Confidence            3568999999999999999999999999999999964   46678999999999999999999 5899999999999998


Q ss_pred             cCCCC
Q 022301           81 HGGRG   85 (299)
Q Consensus        81 ~~~~~   85 (299)
                      .....
T Consensus       181 ~~k~~  185 (196)
T 1l3k_A          181 LSKQE  185 (196)
T ss_dssp             C----
T ss_pred             CChhH
Confidence            76543

>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=1.7e-15  Score=107.28  Aligned_cols=80  Identities=20%  Similarity=0.194  Sum_probs=69.6

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCceeeEEE
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYV  180 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~  180 (299)
                      .....+|||+|||..+++++|+++|.+||.|..+.++.+..    .+||||+|.+.++|+.|++.|||..|+|+    .+
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 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGR----TI   84 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTE----EE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCc----EE
Confidence            34568999999999999999999999999999999987743    46999999999999999999999999999    55


Q ss_pred             EecccccC
Q 022301          181 RVREYDHR  188 (299)
Q Consensus       181 ~~~~~~~~  188 (299)
                      .+....+.
T Consensus        85 ~V~~a~~~   92 (102)
T 2cqb_A           85 RVNLAKPM   92 (102)
T ss_dssp             EEEECCCC
T ss_pred             EEEeCCCC
Confidence            55555444

>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=99.63  E-value=3.7e-15  Score=106.07  Aligned_cols=74  Identities=24%  Similarity=0.244  Sum_probs=66.9

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .......+|||+|||..+++++|.++|.+||.|..+.++.+..    .|||||+|.+.++|+.|+..|||..|+|+.+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   87 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPI   87 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEE
Confidence            3445678999999999999999999999999999999988763    3599999999999999999999999999844

>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=8e-16  Score=118.88  Aligned_cols=77  Identities=31%  Similarity=0.589  Sum_probs=69.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCce--EEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHR--LRVE   78 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~--i~v~   78 (299)
                      .+.++|||+|||.++++++|.++|+.||.|..+.+..   ++.++|||||+|.+.++|..|+..|||..|.|+.  |.|.
T Consensus        86 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~  165 (167)
T 1fxl_A           86 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK  165 (167)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEE
Confidence            3568999999999999999999999999999999954   4566899999999999999999999999999964  8887


Q ss_pred             Ec
Q 022301           79 LA   80 (299)
Q Consensus        79 ~~   80 (299)
                      ||
T Consensus       166 ~A  167 (167)
T 1fxl_A          166 FA  167 (167)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>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=5.5e-15  Score=103.17  Aligned_cols=74  Identities=19%  Similarity=0.227  Sum_probs=67.2

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ....+..+|||+|||..+++++|.++|.+||.|..+.++.++.+    +||||+|.+.++|+.|+..|||..|+|+.+
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   87 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI   87 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            44566789999999999999999999999999999999988654    599999999999999999999999999843

>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=99.63  E-value=2.4e-15  Score=103.17  Aligned_cols=71  Identities=18%  Similarity=0.236  Sum_probs=64.3

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .+..+|||+|||..+++++|+++|.+||.|..+.+..+...    |||||+|.+.++|+.|++.|||..++|+.+
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   78 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI   78 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            34679999999999999999999999999999999988643    599999999999999999999999999854

>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=7.2e-15  Score=104.17  Aligned_cols=75  Identities=9%  Similarity=0.194  Sum_probs=66.0

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEeccc
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVREY  185 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~~~  185 (299)
                      .+..+|||+|||..+++++|+++|.+||.|..+.++.+    ||||+|.+.++|+.|++.|||..|.|+    .+.+...
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~----~afV~f~~~~~a~~A~~~l~g~~~~g~----~l~v~~a   80 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD----YAFIHFDERDGAVKAMEEMNGKDLEGE----NIEIVFA   80 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECSS----CEEEEESSHHHHHHHHHHHTTEEETTE----EEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC----EEEEEeCCHHHHHHHHHHHCCCccCCC----EEEEEEc
Confidence            45689999999999999999999999999999998744    999999999999999999999999998    5555544


Q ss_pred             ccC
Q 022301          186 DHR  188 (299)
Q Consensus       186 ~~~  188 (299)
                      ...
T Consensus        81 ~~~   83 (103)
T 2dgu_A           81 KPP   83 (103)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            443

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

Probab=99.63  E-value=2.2e-15  Score=105.48  Aligned_cols=77  Identities=14%  Similarity=0.217  Sum_probs=67.3

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEE-EEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEE
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFS-QVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVR  181 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~-~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~  181 (299)
                      +..+|||+|||..+++++|.++|.+||.|..+ .++.++.    .+||||+|.+.++|+.|++.|||..|+|+    .+.
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 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNR----PIT   79 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTE----ECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCE----EEE
Confidence            46899999999999999999999999999999 8888743    36999999999999999999999999998    444


Q ss_pred             eccccc
Q 022301          182 VREYDH  187 (299)
Q Consensus       182 ~~~~~~  187 (299)
                      +.....
T Consensus        80 v~~a~~   85 (96)
T 1x5t_A           80 VSYAFK   85 (96)
T ss_dssp             EEESCC
T ss_pred             EEEecc
Confidence            444433

>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=99.63  E-value=6.2e-15  Score=106.01  Aligned_cols=83  Identities=10%  Similarity=0.157  Sum_probs=71.7

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcC------CCeec
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLD------DSEFR  172 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~------g~~~~  172 (299)
                      .......+|||+|||..+++++|.++|.+||.|..|.++.+..    .+||||+|.+.++|..|++.||      |..|+
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~   89 (111)
T 1x4h_A           10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   89 (111)
T ss_dssp             CCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             CcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEc
Confidence            3445678999999999999999999999999999999998754    4699999999999999999999      99999


Q ss_pred             CceeeEEEEecccccCC
Q 022301          173 NAFSRAYVRVREYDHRR  189 (299)
Q Consensus       173 g~~~~~~~~~~~~~~~~  189 (299)
                      |+    .+.|.....+.
T Consensus        90 g~----~l~v~~a~~~~  102 (111)
T 1x4h_A           90 GR----QLKVDLAVTRD  102 (111)
T ss_dssp             SC----EEEEECCCCCC
T ss_pred             CE----EEEEEECCCCc
Confidence            99    56665554443

>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=99.63  E-value=8.4e-16  Score=108.93  Aligned_cols=79  Identities=25%  Similarity=0.436  Sum_probs=69.5

Q ss_pred             CCCCCeEEEcCC--CCCCC--------HHHHHHHhhhcCCeeEEEeecC-----CCCCceEEEEecChHHHHHHHHhcCC
Q 022301            3 SRASRTLYVGNL--PGDIR--------EREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEARDAEDAIRGRDG   67 (299)
Q Consensus         3 ~~~~~~l~V~nL--p~~~t--------~~~l~~~F~~~G~v~~i~~~~~-----~~~~g~afV~F~~~e~A~~A~~~l~~   67 (299)
                      ..|+++|.|.|+  |..+.        +++|+++|++||+|..|.|..+     +.++|+|||+|.+.++|.+|+..|||
T Consensus         2 g~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG   81 (105)
T 3v4m_A            2 GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG   81 (105)
T ss_dssp             CSCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCC
Confidence            478999999999  44443        3689999999999999999654     25689999999999999999999999


Q ss_pred             CCCCCceEEEEEcc
Q 022301           68 YDFDGHRLRVELAH   81 (299)
Q Consensus        68 ~~~~g~~i~v~~~~   81 (299)
                      ..|.|+.|.|.++.
T Consensus        82 ~~f~GR~i~v~~~~   95 (105)
T 3v4m_A           82 RKFANRVVVTKYCD   95 (105)
T ss_dssp             CEETTEECEEEEEC
T ss_pred             CEeCCCEEEEEEeC
Confidence            99999999999874

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

Probab=99.63  E-value=3e-15  Score=103.40  Aligned_cols=76  Identities=21%  Similarity=0.346  Sum_probs=66.7

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEecc
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVRE  184 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~~  184 (299)
                      .....+|||+|||..+++++|.++|.+||.|..+.+..+    ||||+|.+.++|+.|++.|||..|+|+    .+.+..
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~----~afV~f~~~~~a~~A~~~l~g~~~~g~----~l~v~~   77 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD----YAFVHMEKEADAKAAIAQLNGKEVKGK----RINVEL   77 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS----CEEEEESCHHHHHHHHHHHTTCEETTE----ECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC----EEEEEECCHHHHHHHHHHhCCCEECCc----EEEEEE
Confidence            345689999999999999999999999999999999855    999999999999999999999999998    444444


Q ss_pred             cccC
Q 022301          185 YDHR  188 (299)
Q Consensus       185 ~~~~  188 (299)
                      ....
T Consensus        78 a~~~   81 (90)
T 2dnp_A           78 STKG   81 (90)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            4433

>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=99.63  E-value=4.1e-15  Score=106.58  Aligned_cols=77  Identities=16%  Similarity=0.219  Sum_probs=68.2

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEeccc
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVREY  185 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~~~  185 (299)
                      ....+|||+|||..+++++|+++|.+||.|..+.++.+  .+||||+|.+.++|+.|+..|+|..|+|+    .+.|...
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--KGYSFVRFSTHESAAHAIVSVNGTTIEGH----VVKCYWG   96 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT--TTEEEEEESSHHHHHHHHHHHTTCEETTE----ECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC--CCEEEEEECCHHHHHHHHHHcCCCEECCc----EEEEEec
Confidence            45689999999999999999999999999999999887  56999999999999999999999999998    4555544


Q ss_pred             ccC
Q 022301          186 DHR  188 (299)
Q Consensus       186 ~~~  188 (299)
                      ...
T Consensus        97 ~~~   99 (109)
T 1x4g_A           97 KES   99 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            443

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

Probab=99.63  E-value=3.9e-15  Score=104.76  Aligned_cols=83  Identities=7%  Similarity=0.106  Sum_probs=71.2

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCee-EEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceeeEE
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVC-FSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY  179 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~-~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  179 (299)
                      .....+|||+|||..+++++|.++|.+||.|. .+.++.++..    +||||+|.+.++|+.|++.|||..|.|+.....
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            34568999999999999999999999999999 9999988644    599999999999999999999999999964333


Q ss_pred             EEeccccc
Q 022301          180 VRVREYDH  187 (299)
Q Consensus       180 ~~~~~~~~  187 (299)
                      +.+.....
T Consensus        86 l~v~~a~~   93 (99)
T 2div_A           86 FKLNYATY   93 (99)
T ss_dssp             CCEEETTC
T ss_pred             EEEeecCC
Confidence            55555443

>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=3.8e-15  Score=105.81  Aligned_cols=80  Identities=19%  Similarity=0.385  Sum_probs=68.6

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC-----CCEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS-----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      .+..+..+|||+|||..+++++|+++|..|| |..|.++.+..     .|||||+|.+.++|+.|+ .|||..|.|+   
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~---   84 (104)
T 1wi8_A           10 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNK---   84 (104)
T ss_dssp             CCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTE---
T ss_pred             CCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCc---
Confidence            3445678999999999999999999999999 99999988764     369999999999999999 9999999999   


Q ss_pred             EEEEecccccC
Q 022301          178 AYVRVREYDHR  188 (299)
Q Consensus       178 ~~~~~~~~~~~  188 (299)
                       .+.|.....+
T Consensus        85 -~l~V~~a~~~   94 (104)
T 1wi8_A           85 -RIRVDVADQA   94 (104)
T ss_dssp             -ECEEEECCCC
T ss_pred             -EEEEEEccCC
Confidence             4455444443

>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=99.63  E-value=1.3e-15  Score=128.10  Aligned_cols=76  Identities=22%  Similarity=0.404  Sum_probs=70.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCC-CceEEEEEcc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFD-GHRLRVELAH   81 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~-g~~i~v~~~~   81 (299)
                      .++++|||+|||.++|+++|+++|+.||.|..|.|..+.  +|||||+|.+.++|..|+..|||..|. |+.|.|.|++
T Consensus       205 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          205 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR--HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC--CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            367899999999999999999999999999999997433  589999999999999999999999999 9999999985

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=5.9e-15  Score=103.65  Aligned_cols=72  Identities=8%  Similarity=0.079  Sum_probs=63.5

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhc--CCCeecCcee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKL--DDSEFRNAFS  176 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l--~g~~~~g~~~  176 (299)
                      ....+..+|||+|||..+++++|.++|.+||.|..+.++.+  .|||||+|.+.++|..|++.|  ++..|.|+.+
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~--kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   83 (101)
T 2cq1_A           10 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG--KNQAFLELATEEAAITMVNYYSAVTPHLRNQPI   83 (101)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT--TTEEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC--CCEEEEEECCHHHHHHHHHHhccCCceECCcEE
Confidence            33456789999999999999999999999999999988865  579999999999999999987  5678999844

>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=99.62  E-value=1.4e-15  Score=106.83  Aligned_cols=69  Identities=7%  Similarity=0.057  Sum_probs=62.3

Q ss_pred             CCccEEEEeCCCC-CCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCC--eecCcee
Q 022301          106 RSEYRVLVTGLPS-SASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDS--EFRNAFS  176 (299)
Q Consensus       106 ~~~~~l~v~nl~~-~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~--~~~g~~~  176 (299)
                      .+..+|||+|||. .+++++|.++|.+||.|..+.++.++  +||||+|++.++|..|++.|++.  .|.|+.+
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~k--g~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   84 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI--NEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   84 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS--SCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCC--CEEEEEECCHHHHHHHHHHHcCCCceECCcEE
Confidence            3568999999999 99999999999999999999998764  69999999999999999999865  5999944

>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=99.62  E-value=4.9e-15  Score=105.45  Aligned_cols=68  Identities=19%  Similarity=0.234  Sum_probs=63.4

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC---CEEEEEecChhhHHHHHHhcCCCeecC
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG---TTGIVDYTNYDDMKHAIKKLDDSEFRN  173 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g  173 (299)
                      ....+|||+|||..+++++|.++|.+||.|..+.++.+..+   +||||+|.+.++|+.|++.|||..+.|
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   83 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMP   83 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCC
Confidence            45689999999999999999999999999999999988643   599999999999999999999999988

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

Probab=99.62  E-value=1.2e-15  Score=121.40  Aligned_cols=77  Identities=22%  Similarity=0.362  Sum_probs=71.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcC-CeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCC-CceEEEEEcc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYG-PIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFD-GHRLRVELAH   81 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G-~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~-g~~i~v~~~~   81 (299)
                      .++++|||+|||..+++++|.++|+.|| .|..|.+..+  .+|||||+|.+.++|..|+..|||..|. |+.|.|.|+.
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            4589999999999999999999999999 9999999653  3789999999999999999999999999 9999999986


Q ss_pred             C
Q 022301           82 G   82 (299)
Q Consensus        82 ~   82 (299)
                      .
T Consensus       196 ~  196 (198)
T 1qm9_A          196 S  196 (198)
T ss_dssp             C
T ss_pred             c
Confidence            4

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

Probab=99.62  E-value=8e-15  Score=103.93  Aligned_cols=80  Identities=19%  Similarity=0.300  Sum_probs=68.6

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceeeE
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA  178 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  178 (299)
                      .+..+..+|||+|||..+++++|+++|.+|| |..+.++.+..+    |||||+|.+.++|+.|+ .|||..|.|+    
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-TYDGALLGDR----   83 (103)
T ss_dssp             CCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTE----
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCe----
Confidence            4455678999999999999999999999997 999999988753    59999999999999999 8999999999    


Q ss_pred             EEEecccccC
Q 022301          179 YVRVREYDHR  188 (299)
Q Consensus       179 ~~~~~~~~~~  188 (299)
                      .+.|......
T Consensus        84 ~l~V~~a~~~   93 (103)
T 2dng_A           84 SLRVDIAEGR   93 (103)
T ss_dssp             ECEEEECCCC
T ss_pred             EEEEEEecCC
Confidence            4455444433

>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=99.62  E-value=4.1e-15  Score=101.05  Aligned_cols=68  Identities=16%  Similarity=0.273  Sum_probs=63.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ++|||+|||..+++++|.++|.+||.|..+.++.++..    |||||+|.+.++|+.|+..|||..++|+.+
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l   73 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPL   73 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEE
Confidence            68999999999999999999999999999999988553    599999999999999999999999999844

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

Probab=99.62  E-value=5.9e-15  Score=105.41  Aligned_cols=74  Identities=16%  Similarity=0.297  Sum_probs=66.5

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC-----CCCEEEEEecChhhHHHHHHhc-CCCeecCcee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG-----SGTTGIVDYTNYDDMKHAIKKL-DDSEFRNAFS  176 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~-----~~~~~fv~f~~~~~a~~a~~~l-~g~~~~g~~~  176 (299)
                      .......+|||+|||..+++++|+++|.+||.|..|.++.+.     ..+||||+|.+.++|+.|+..| ||..|.|+.+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l   89 (107)
T 2cph_A           10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRL   89 (107)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBC
T ss_pred             ccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEE
Confidence            445567899999999999999999999999999999998772     2469999999999999999999 9999999944

>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=1e-14  Score=102.86  Aligned_cols=81  Identities=19%  Similarity=0.351  Sum_probs=70.2

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC---CEEEEEecChhhHHHHHHhcCCCeecCceeeEEE
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG---TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYV  180 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~  180 (299)
                      ......+|||+|||..+++++|.++|.+||.|..+.++.+..+   +||||+|.+.++|+.|++.|||..|+|+    .+
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~----~l   88 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKEN----II   88 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSC----EE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCE----EE
Confidence            3455689999999999999999999999999999999988732   5999999999999999999999999998    55


Q ss_pred             EecccccC
Q 022301          181 RVREYDHR  188 (299)
Q Consensus       181 ~~~~~~~~  188 (299)
                      .+....+.
T Consensus        89 ~v~~a~~~   96 (100)
T 2do4_A           89 KVAISNSG   96 (100)
T ss_dssp             EEEECCCC
T ss_pred             EEEECCCC
Confidence            55554443

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

Probab=99.62  E-value=3e-14  Score=106.76  Aligned_cols=82  Identities=16%  Similarity=0.194  Sum_probs=71.4

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceeeE
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA  178 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  178 (299)
                      .......+|||+|||..+++++|.++|..||.|..|.++.+..+    |||||+|.+.++|.+|++.|||..|.|+    
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 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNK----  112 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSC----
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCe----
Confidence            34456789999999999999999999999999999999988653    5999999999999999999999999999    


Q ss_pred             EEEecccccC
Q 022301          179 YVRVREYDHR  188 (299)
Q Consensus       179 ~~~~~~~~~~  188 (299)
                      .+.|......
T Consensus       113 ~l~v~~a~~~  122 (139)
T 1u6f_A          113 RLKVALAASG  122 (139)
T ss_dssp             EEEEEESSCC
T ss_pred             EEEEEECCCC
Confidence            5555554443

>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=3.4e-15  Score=101.99  Aligned_cols=71  Identities=20%  Similarity=0.191  Sum_probs=64.9

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .+..+|||+|||..+++++|.++|.+||.|..+.++.+..    .+||||+|.+.++|+.|++.|||..++|+.+
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   79 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI   79 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEE
Confidence            4568999999999999999999999999999999987743    3599999999999999999999999999854

>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=3.2e-15  Score=104.59  Aligned_cols=69  Identities=13%  Similarity=0.257  Sum_probs=64.0

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..+|||+|||..+++++|.++|.+||.|..+.+..+..    .|||||+|.+.++|+.|++.|+|..++|+.+
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   74 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFL   74 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEE
Confidence            47999999999999999999999999999999988754    4699999999999999999999999999844

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

Probab=99.61  E-value=3.4e-15  Score=103.78  Aligned_cols=70  Identities=14%  Similarity=0.220  Sum_probs=62.6

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCe--ecCcee
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSE--FRNAFS  176 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~--~~g~~~  176 (299)
                      ..+..+|||+|||..+++++|.++|.+||.|..+.++..  .|||||+|++.++|..|++.|+|..  |.|+.+
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~--kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i   89 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK--KRQALVEFEDVLGACNAVNYAADNQIYIAGHPA   89 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT--TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC--CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEE
Confidence            346689999999999999999999999999999998854  4699999999999999999999886  779833

>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=99.61  E-value=3e-15  Score=104.91  Aligned_cols=70  Identities=17%  Similarity=0.231  Sum_probs=63.8

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeec--Ccee
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFR--NAFS  176 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~--g~~~  176 (299)
                      ..+..+|||+|||..+++++|.++|.+||.|..+.+..+  .+||||+|.+.++|+.|++.|||..|.  |+.+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l   85 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG--DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRL   85 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS--SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC--CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEE
Confidence            345689999999999999999999999999999998866  569999999999999999999999999  8743

>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=5.2e-15  Score=105.52  Aligned_cols=73  Identities=15%  Similarity=0.220  Sum_probs=65.5

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCee---cCcee
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEF---RNAFS  176 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~---~g~~~  176 (299)
                      ......+|||+|||..+++++|+++|.+||.|..+.++.++.    .+||||+|.+.++|+.|++.|||..+   .|+.+
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            445678999999999999999999999999999999988754    46999999999999999999999987   77743

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.61  E-value=1.1e-15  Score=105.68  Aligned_cols=76  Identities=16%  Similarity=0.261  Sum_probs=65.1

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcC-CeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhc-CCCeecCceeeEEEEe
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAG-DVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKL-DDSEFRNAFSRAYVRV  182 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G-~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l-~g~~~~g~~~~~~~~~  182 (299)
                      .+|||+|||..+++++|.++|.+|| .|..|.++.++.    .|||||+|.+.++|+.|++.+ ++..++|+    .+.+
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr----~i~V   77 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQ----KVSM   77 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTE----EEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCE----EEEE
Confidence            5899999999999999999999999 899999987754    369999999999999999987 56679998    5666


Q ss_pred             cccccC
Q 022301          183 REYDHR  188 (299)
Q Consensus       183 ~~~~~~  188 (299)
                      ..+.++
T Consensus        78 ~~a~~~   83 (91)
T 2lxi_A           78 HYSDPK   83 (91)
T ss_dssp             ECCCSC
T ss_pred             EEcCCC
Confidence            555443

>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=99.61  E-value=2.8e-15  Score=122.10  Aligned_cols=77  Identities=22%  Similarity=0.362  Sum_probs=71.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcC-CeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCC-CceEEEEEcc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYG-PIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFD-GHRLRVELAH   81 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G-~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~-g~~i~v~~~~   81 (299)
                      .++++|||+|||.++++++|+++|+.|| +|..|.+...  .+|||||+|.+.++|.+|+..|||..|. |+.|.|.|+.
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~--~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~  226 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK--DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK  226 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS--STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECS
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC--CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEec
Confidence            3579999999999999999999999999 9999999543  4789999999999999999999999999 9999999986


Q ss_pred             C
Q 022301           82 G   82 (299)
Q Consensus        82 ~   82 (299)
                      .
T Consensus       227 ~  227 (229)
T 2adc_A          227 S  227 (229)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.61  E-value=3.2e-15  Score=107.46  Aligned_cols=82  Identities=13%  Similarity=0.137  Sum_probs=71.1

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHH---HHHHhcCCeeEEEEEeCCCC-------CEEEEEecChhhHHHHHHhcCCCeecC
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLK---DHMRRAGDVCFSQVFRDGSG-------TTGIVDYTNYDDMKHAIKKLDDSEFRN  173 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~---~~f~~~G~v~~~~~~~~~~~-------~~~fv~f~~~~~a~~a~~~l~g~~~~g  173 (299)
                      ......+|||+|||..+++++|.   ++|.+||+|..+.++.+...       |||||+|.+.++|+.|++.|||..|+|
T Consensus        11 r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~g   90 (111)
T 2cpi_A           11 RVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDG   90 (111)
T ss_dssp             CCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             cccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECC
Confidence            34456899999999999999999   99999999999999887642       699999999999999999999999999


Q ss_pred             ceeeEEEEecccccCC
Q 022301          174 AFSRAYVRVREYDHRR  189 (299)
Q Consensus       174 ~~~~~~~~~~~~~~~~  189 (299)
                      +    .+.|.....+.
T Consensus        91 r----~l~V~~a~~k~  102 (111)
T 2cpi_A           91 R----TLKASLGTTKY  102 (111)
T ss_dssp             E----EEEEESCCCCS
T ss_pred             E----EEEEEeccccc
Confidence            9    66666555443

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

Probab=99.61  E-value=3e-14  Score=102.89  Aligned_cols=73  Identities=22%  Similarity=0.326  Sum_probs=66.6

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC---CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG---TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ......+|||+|||..+++++|+++|.+||.|..+.++.+..+   +||||+|.+.++|+.|++.|||..|+|+.+
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   86 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPM   86 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEE
Confidence            3455789999999999999999999999999999999988653   499999999999999999999999999854

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

Probab=99.61  E-value=1.7e-14  Score=101.43  Aligned_cols=77  Identities=19%  Similarity=0.187  Sum_probs=66.9

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEE
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRA--GDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVR  181 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~--G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~  181 (299)
                      ......+|||+|||..+++++|+++|.+|  |.|..+.+..    +||||+|.+.++|+.|+..|||..|.|+    .+.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~~----g~afV~f~~~~~A~~A~~~l~g~~~~g~----~l~   82 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR----DYAFVHFSNREDAVEAMKALNGKVLDGS----PIE   82 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEECS----SEEEEEESSHHHHHHHHHHHSSEEETTE----EEE
T ss_pred             ccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEeC----CeEEEEeCCHHHHHHHHHHhCCCEeCCc----EEE
Confidence            34466899999999999999999999999  8999888763    4999999999999999999999999998    566


Q ss_pred             ecccccC
Q 022301          182 VREYDHR  188 (299)
Q Consensus       182 ~~~~~~~  188 (299)
                      +......
T Consensus        83 v~~a~~~   89 (99)
T 2cpd_A           83 VTLAKPV   89 (99)
T ss_dssp             EECCCCC
T ss_pred             EEECCCC
Confidence            6555443

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

Probab=99.61  E-value=5.7e-15  Score=105.28  Aligned_cols=73  Identities=18%  Similarity=0.312  Sum_probs=66.9

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ......+|||+|||..+++++|.++|..||.|..+.+..+..+    |||||+|.+.++|+.|+..|||..|+|+.+
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   95 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPI   95 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEE
Confidence            3456789999999999999999999999999999999988664    599999999999999999999999999855

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

Probab=99.61  E-value=3.3e-15  Score=105.57  Aligned_cols=67  Identities=18%  Similarity=0.228  Sum_probs=63.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ++|||+|||..+++++|.++|.+||.|..+.+..+ ..+||||+|.+.++|+.|++.|+|..++|+.+
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   67 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRV   67 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-CCCEEEEEECCHHHHHHHHHHHCCCeECCcEE
Confidence            47999999999999999999999999999999988 66799999999999999999999999999954

>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=99.61  E-value=7.7e-15  Score=105.34  Aligned_cols=67  Identities=16%  Similarity=0.193  Sum_probs=61.8

Q ss_pred             CCccEEEEeCCCCC-CCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          106 RSEYRVLVTGLPSS-ASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       106 ~~~~~l~v~nl~~~-~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ....+|||+|||.. +++++|+++|.+||.|..+.+    ..+||||+|.+.++|+.|++.|||..|+|+.+
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i----~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   92 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV----HKGYAFVQYSNERHARAAVLGENGRVLAGQTL   92 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE----ETTEEEEECSSSHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE----eCCEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            34579999999999 999999999999999999998    35699999999999999999999999999844

>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=99.61  E-value=3.5e-15  Score=107.43  Aligned_cols=71  Identities=7%  Similarity=0.071  Sum_probs=63.7

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCC--CeecCcee
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDD--SEFRNAFS  176 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g--~~~~g~~~  176 (299)
                      ...+..+|||+|||+.+++++|+++|.+||.|..+.++.+  .|||||+|++.++|..|++.|++  ..|.|+.+
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~--kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l   99 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG--KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPI   99 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG--GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC--CCEEEEEECCHHHHHHHHHHhccCCceECCeEE
Confidence            3456789999999999999999999999999999999876  46999999999999999999874  68999844

>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=4e-15  Score=106.26  Aligned_cols=77  Identities=16%  Similarity=0.223  Sum_probs=67.1

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEe
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRV  182 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~  182 (299)
                      .......+|||+|||..+++++|.++|.+||.|..+.+.    .|||||+|.+.++|+.|+..|||..++|+    .+.|
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~----kg~afV~f~~~~~A~~Ai~~l~g~~~~g~----~l~V   97 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL----NGFAFVEFEEAESAAKAIEEVHGKSFANQ----PLEV   97 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE----TTEEEEECSSHHHHHHHHHHHTTCEETTE----ECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE----CCEEEEEECCHHHHHHHHHHcCCCEECCe----EEEE
Confidence            344567899999999999999999999999999999998    57999999999999999999999999998    5555


Q ss_pred             ccccc
Q 022301          183 REYDH  187 (299)
Q Consensus       183 ~~~~~  187 (299)
                      .....
T Consensus        98 ~~a~~  102 (108)
T 2jvo_A           98 VYSKL  102 (108)
T ss_dssp             ESCSC
T ss_pred             EEecC
Confidence            54443

>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=6.8e-15  Score=103.52  Aligned_cols=74  Identities=19%  Similarity=0.284  Sum_probs=67.2

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeE--------EEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCe
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCF--------SQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSE  170 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~--------~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~  170 (299)
                      ......++|||+|||..+++++|+++|.+||.|..        +.++.++.+    |||||+|.+.++|+.|++.|||..
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~   87 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   87 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            44556789999999999999999999999999999        999988653    599999999999999999999999


Q ss_pred             ecCcee
Q 022301          171 FRNAFS  176 (299)
Q Consensus       171 ~~g~~~  176 (299)
                      +.|+.+
T Consensus        88 ~~g~~l   93 (99)
T 2la6_A           88 FSGNPI   93 (99)
T ss_dssp             SSSSBC
T ss_pred             eCCcEE
Confidence            999854

>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=99.60  E-value=8.7e-15  Score=105.96  Aligned_cols=72  Identities=8%  Similarity=0.096  Sum_probs=64.9

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCe----eEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDV----CFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v----~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..+..+|||+|||..+++++|.++|.+||.|    ..+.+......|||||+|.+.++|+.|+..|||..|.|+.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l   97 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKIL   97 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEE
Confidence            3456899999999999999999999999998    67777766667899999999999999999999999999944

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

Probab=99.60  E-value=8.6e-15  Score=105.63  Aligned_cols=81  Identities=21%  Similarity=0.369  Sum_probs=69.8

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCee--------EEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCee
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVC--------FSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEF  171 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~--------~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~  171 (299)
                      ......+|||+|||..+++++|+++|.+||.|.        .+.++.+..    .+||||+|.+.++|+.|++.|||..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            345678999999999999999999999999998        688888744    35999999999999999999999999


Q ss_pred             cCceeeEEEEecccccC
Q 022301          172 RNAFSRAYVRVREYDHR  188 (299)
Q Consensus       172 ~g~~~~~~~~~~~~~~~  188 (299)
                      .|+    .+.|......
T Consensus        91 ~g~----~l~V~~a~~~  103 (113)
T 2cpe_A           91 QGS----KLKVSLARKK  103 (113)
T ss_dssp             TTE----ECEEECSSCC
T ss_pred             CCC----EEEEEECCCC
Confidence            998    5555555444

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

Probab=99.60  E-value=6.8e-15  Score=102.48  Aligned_cols=74  Identities=16%  Similarity=0.240  Sum_probs=66.8

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .......+|||+|||..+++++|.++|.+||.|..+.+..++.    .+||||+|.+.++|+.|++.|||..|.|+.+
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   88 (94)
T 2e5h_A           11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVI   88 (94)
T ss_dssp             SCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEE
Confidence            3445678999999999999999999999999999999988754    3699999999999999999999999999844

>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=99.60  E-value=8.2e-15  Score=103.09  Aligned_cols=71  Identities=15%  Similarity=0.216  Sum_probs=64.7

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ...+..+|||+|||..+++++|+++|.+||.|..+.+..+  .+||||+|.+.++|++|++.|||..|.|+.+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~--kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l   81 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD--KGFGFIRLETRTLAEIAKVELDNMPLRGKQL   81 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT--TTEEEEECSSSHHHHHHHHHHTTCCBTTBCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC--CCEEEEEECCHHHHHHHHHHhCCCEeCCceE
Confidence            3446689999999999999999999999999999998865  5699999999999999999999999999844

>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=5.9e-15  Score=104.32  Aligned_cols=70  Identities=20%  Similarity=0.283  Sum_probs=62.2

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCC--eecCcee
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDS--EFRNAFS  176 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~--~~~g~~~  176 (299)
                      ..+..+|||+|||..+++++|+++|.+||.|..+.++.+  .+||||+|.+.++|..|++.|++.  .|.|+.+
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~--kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l   83 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF--KRQALVEFENIDSAKECVTFAADVPVYIAGQQA   83 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT--TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC--CCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            446689999999999999999999999999999988765  579999999999999999998765  4889844

>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=99.60  E-value=1.2e-14  Score=103.86  Aligned_cols=76  Identities=20%  Similarity=0.207  Sum_probs=68.2

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC---CEEEEEecChhhHHHHHHhcCCCeecCceeeE
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG---TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA  178 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  178 (299)
                      ....+..+|||+|||..+++++|+++|.+||.|..+.++.+..+   +||||+|.+.++|+.|++.|||..|.|+.+.+
T Consensus        24 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V  102 (107)
T 3ulh_A           24 AGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI  102 (107)
T ss_dssp             CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            44567789999999999999999999999999999999988632   49999999999999999999999999985543

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

Probab=99.60  E-value=9.9e-15  Score=103.65  Aligned_cols=80  Identities=20%  Similarity=0.201  Sum_probs=69.0

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHh-cCCeeEEEEEeCCCC---CEEEEEecChhhHHHHHHhcCCCe-ecCceeeE
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRR-AGDVCFSQVFRDGSG---TTGIVDYTNYDDMKHAIKKLDDSE-FRNAFSRA  178 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~-~G~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~-~~g~~~~~  178 (299)
                      ...+..+|||+|||..+++++|.++|.+ ||.|..+.++.+..+   +||||+|.+.++|..|++.|+|.. |+|+    
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~----   80 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSK----   80 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSS----
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCE----
Confidence            3456689999999999999999999999 999999999988632   499999999999999999999999 9998    


Q ss_pred             EEEeccccc
Q 022301          179 YVRVREYDH  187 (299)
Q Consensus       179 ~~~~~~~~~  187 (299)
                      .+.+.....
T Consensus        81 ~l~v~~a~~   89 (104)
T 2dhg_A           81 PVRLSVAIP   89 (104)
T ss_dssp             CCCCCBCCC
T ss_pred             eEEEEEccC
Confidence            444444433

>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=99.60  E-value=4.8e-15  Score=109.33  Aligned_cols=81  Identities=20%  Similarity=0.219  Sum_probs=70.3

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCceeeE
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA  178 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  178 (299)
                      ....+..+|||+|||..+++++|+++|.+||.|..|.++.++.    .|||||+|.+.++|+.|++.|+|..|+|+    
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~----  116 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR----  116 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSS----
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCE----
Confidence            3445678999999999999999999999999999999998753    46999999999999999999999999998    


Q ss_pred             EEEeccccc
Q 022301          179 YVRVREYDH  187 (299)
Q Consensus       179 ~~~~~~~~~  187 (299)
                      .+.|.....
T Consensus       117 ~l~V~~a~~  125 (129)
T 2kxn_B          117 RIRVDFSIT  125 (129)
T ss_dssp             CCEESCCSS
T ss_pred             EEEEEEecC
Confidence            555555443

>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=1.4e-15  Score=121.46  Aligned_cols=77  Identities=14%  Similarity=0.216  Sum_probs=67.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCe--eEEEeecC-CCCCceEEEEecChHHHHHHHHhcCCCCCCCc----eEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPI--AHIDLKIP-PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGH----RLR   76 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v--~~i~~~~~-~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~----~i~   76 (299)
                      .++++|||+|||+++|+++|+++|++||.|  ..+.+..+ +..+|||||+|.+.++|..||..|||..|.|.    ++.
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~  200 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYT  200 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEE
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceE
Confidence            357899999999999999999999999999  89998654 34569999999999999999999999999876    577


Q ss_pred             EEEc
Q 022301           77 VELA   80 (299)
Q Consensus        77 v~~~   80 (299)
                      |+++
T Consensus       201 vk~~  204 (205)
T 3tyt_A          201 LKLC  204 (205)
T ss_dssp             CEEE
T ss_pred             EEec
Confidence            7665

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=1.9e-14  Score=102.38  Aligned_cols=82  Identities=13%  Similarity=0.217  Sum_probs=71.5

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceeeE
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA  178 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  178 (299)
                      .......+|||+|||..+++++|+++|.+||.|..|.++.++..    +||||+|.+.++|+.|+.. +|..|+|+    
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-RPHTLDGR----   85 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTE----
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCE----
Confidence            34556789999999999999999999999999999999998654    5999999999999999998 99999998    


Q ss_pred             EEEecccccCC
Q 022301          179 YVRVREYDHRR  189 (299)
Q Consensus       179 ~~~~~~~~~~~  189 (299)
                      .+.|....++.
T Consensus        86 ~l~V~~a~~~~   96 (105)
T 2dh8_A           86 NIDPKPCTPRG   96 (105)
T ss_dssp             EEBCCCSCCSS
T ss_pred             EEEEEEccCCC
Confidence            66666655443

>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=99.60  E-value=1.6e-15  Score=104.81  Aligned_cols=75  Identities=15%  Similarity=0.178  Sum_probs=63.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcC--CeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEe
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAG--DVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRV  182 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G--~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~  182 (299)
                      .+|||+|||..+++++|.++|.+||  .|..+.++.+..+    |||||+|.+.++|+.|++.|||..|+|+    .+.|
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr----~i~V   77 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQ----NPVV   77 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSC----CCEE
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCE----EEEE
Confidence            5799999999999999999999999  9999999998644    4999999999999999999999999999    5555


Q ss_pred             ccccc
Q 022301          183 REYDH  187 (299)
Q Consensus       183 ~~~~~  187 (299)
                      ....+
T Consensus        78 ~~~~~   82 (90)
T 3p5t_L           78 TPSNK   82 (90)
T ss_dssp             CCC--
T ss_pred             EECCC
Confidence            54444

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

Probab=99.60  E-value=1.2e-14  Score=111.19  Aligned_cols=71  Identities=13%  Similarity=0.196  Sum_probs=65.8

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ....+|||.|||..+++++|+++|.+||.|..|.|+.+..+    +||||+|.+.++|++||+.|||..|+|+.+
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l  111 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRII  111 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            45689999999999999999999999999999999988754    499999999999999999999999999944

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

Probab=99.59  E-value=4.6e-15  Score=106.24  Aligned_cols=74  Identities=18%  Similarity=0.219  Sum_probs=66.9

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC--CCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS--GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~--~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .......+|||+|||..+++++|+++|.+||.|..+.+..+..  .|||||+|.+.++|+.|++.|+|..|+|+.+
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   99 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKI   99 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            4455678999999999999999999999999999999987753  4699999999999999999999999999844

>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=99.59  E-value=8.4e-15  Score=102.53  Aligned_cols=70  Identities=16%  Similarity=0.189  Sum_probs=63.0

Q ss_pred             CCCCCccEEEEeCCCC-CCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          103 VSRRSEYRVLVTGLPS-SASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~-~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .......+|||+|||. .+++++|.++|.+||.|..+.+.    .|||||+|.+.++|+.|++.|||..++|+.+
T Consensus        17 ~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~----~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   87 (97)
T 2xnq_A           17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK----NAFGFIQFDNPQSVRDAIEXESQEMNFGKKL   87 (97)
T ss_dssp             --CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC----SSEEEEEESSHHHHHHHHHHHTTSEETTEEC
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe----CCEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            3455678999999998 99999999999999999999884    5699999999999999999999999999844

>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=99.59  E-value=7.6e-15  Score=105.39  Aligned_cols=74  Identities=14%  Similarity=0.175  Sum_probs=66.7

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .......+|||+|||..+++++|.++|.+||.|..+.++.+..    .|||||+|.+.++|+.|+..|||..|+|+.+
T Consensus        21 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   98 (110)
T 1oo0_B           21 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTI   98 (110)
T ss_dssp             CCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEE
Confidence            3445678999999999999999999999999999999988754    3699999999999999999999999999844

>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=99.59  E-value=1.2e-14  Score=103.88  Aligned_cols=74  Identities=16%  Similarity=0.201  Sum_probs=66.9

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .......+|||+|||..+++++|.++|.+||.|..+.++.++..    |||||+|.+.++|+.|++.|+|..|+|+.+
T Consensus        21 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l   98 (108)
T 2jrs_A           21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPM   98 (108)
T ss_dssp             CSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCC
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34456689999999999999999999999999999999988654    599999999999999999999999999944

>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=99.59  E-value=7.9e-15  Score=110.98  Aligned_cols=68  Identities=19%  Similarity=0.253  Sum_probs=63.0

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecC
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRN  173 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g  173 (299)
                      .....|||+||++.+++++|.++|.+||.|..|.+......+||||+|.+.++|+.|++.|||..|.|
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g  111 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYN  111 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSS
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecC
Confidence            34568999999999999999999999999999999877667799999999999999999999999976

>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=1.4e-14  Score=101.08  Aligned_cols=74  Identities=18%  Similarity=0.225  Sum_probs=66.7

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC---CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG---TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .......+|||+|||..+++++|+++|.+||.|..+.+..+..+   +||||+|.+.++|+.|++.|||..|.|+.+
T Consensus        11 ~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   87 (95)
T 2ywk_A           11 AQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPI   87 (95)
T ss_dssp             -CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEE
Confidence            34456789999999999999999999999999999999988653   599999999999999999999999999844

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

Probab=99.59  E-value=1.1e-14  Score=100.96  Aligned_cols=72  Identities=17%  Similarity=0.380  Sum_probs=65.1

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC--CCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS--GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~--~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .....+|||+|||..+++++|+++|.+||.|..+.+..+..  .+||||+|.+.++|+.|++.|||..|+|+.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l   78 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREI   78 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEE
Confidence            44668999999999999999999999999999999987532  3699999999999999999999999999944

>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=99.59  E-value=5.4e-15  Score=102.79  Aligned_cols=76  Identities=14%  Similarity=0.179  Sum_probs=63.5

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCC-eeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCC-CeecCceeeEEEEec
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGD-VCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDD-SEFRNAFSRAYVRVR  183 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~-v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g-~~~~g~~~~~~~~~~  183 (299)
                      ....+|||+|||..+++++|+++|.+||. |..+.+.   ..+||||+|.+.++|+.|++.||| ..|+|+    .+.+.
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---KSGYAFVDYPDQNWAIRAIETLSGKVELHGK----IMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE---ETTEEEECCSCHHHHHHHHHHHTTTCEETTE----ECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc---CCCEEEEEECCHHHHHHHHHHccCCeeECCE----EEEEE
Confidence            45579999999999999999999999999 5555553   346999999999999999999999 999998    44554


Q ss_pred             ccccC
Q 022301          184 EYDHR  188 (299)
Q Consensus       184 ~~~~~  188 (299)
                      .....
T Consensus        79 ~a~~~   83 (93)
T 2cqh_A           79 YSVSK   83 (93)
T ss_dssp             ECCCC
T ss_pred             EccCc
Confidence            44433

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

Probab=99.59  E-value=5e-14  Score=103.32  Aligned_cols=76  Identities=18%  Similarity=0.130  Sum_probs=68.3

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC---CCCEEEEEecChhhHHHHHHhcCCCeecCceeeE
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG---SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA  178 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~---~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  178 (299)
                      ......++|||+|||..+++++|.++|..||.|..+.+..+.   ..|||||+|.+.++|+.|+..|||..|+|+.+.+
T Consensus        30 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  108 (124)
T 2kt5_A           30 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI  108 (124)
T ss_dssp             CCCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            455677899999999999999999999999999999999876   3469999999999999999999999999995433

>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=6.1e-15  Score=104.17  Aligned_cols=81  Identities=16%  Similarity=0.244  Sum_probs=64.7

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEec
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVR  183 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~  183 (299)
                      ......+|||+|||..+++++|+++|.+||.|..+........+||||+|.+.++|++|+..|||..|.|+    .+.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~----~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGR----AIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEEECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTE----EEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCe----EEEEE
Confidence            34567899999999999999999999999988322221223456999999999999999999999999998    55555


Q ss_pred             ccccC
Q 022301          184 EYDHR  188 (299)
Q Consensus       184 ~~~~~  188 (299)
                      .....
T Consensus        87 ~a~~~   91 (101)
T 2fc9_A           87 LQGPR   91 (101)
T ss_dssp             ECSSC
T ss_pred             EcCCC
Confidence            54443

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.59  E-value=3.1e-15  Score=103.95  Aligned_cols=73  Identities=7%  Similarity=0.094  Sum_probs=63.2

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCC--eeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCC----eecC
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGD--VCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDS----EFRN  173 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~--v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~----~~~g  173 (299)
                      ......+|||+|||+.+|+++|.++|++||.  |..|.++.++.    .|||||+|.+.++|+.|++.|||.    .|+|
T Consensus         5 ~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~G   84 (95)
T 2lkz_A            5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDG   84 (95)
T ss_dssp             SSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETT
T ss_pred             cCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECC
Confidence            3445679999999999999999999999995  66888888754    369999999999999999999997    4889


Q ss_pred             cee
Q 022301          174 AFS  176 (299)
Q Consensus       174 ~~~  176 (299)
                      +.+
T Consensus        85 r~i   87 (95)
T 2lkz_A           85 KTI   87 (95)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            843

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

Probab=99.59  E-value=7.5e-15  Score=102.68  Aligned_cols=73  Identities=22%  Similarity=0.323  Sum_probs=66.8

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEE-EEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFS-QVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~-~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ......+|||+|||..+++++|+++|.+||.|..+ .++.++..+.|||+|.+.++|+.|+..|||..|+|+.+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l   84 (96)
T 2e44_A           11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTL   84 (96)
T ss_dssp             CCCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBC
T ss_pred             CCCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEE
Confidence            34456899999999999999999999999999999 58888877789999999999999999999999999954

>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=99.58  E-value=3.1e-15  Score=127.24  Aligned_cols=77  Identities=18%  Similarity=0.323  Sum_probs=67.7

Q ss_pred             CCCCCCeEEEcC--CCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCC---Cc--e
Q 022301            2 SSRASRTLYVGN--LPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFD---GH--R   74 (299)
Q Consensus         2 ~~~~~~~l~V~n--Lp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~---g~--~   74 (299)
                      ++.|+++|||+|  |+..+|+++|.++|++||+|..|.|..   ++|||||+|.+.++|++|+..|||..+.   |+  .
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            568999999999  578999999999999999999998853   5899999999999999999999998773   44  5


Q ss_pred             EEEEEcc
Q 022301           75 LRVELAH   81 (299)
Q Consensus        75 i~v~~~~   81 (299)
                      |.|.|+.
T Consensus        91 ly~~~~~   97 (345)
T 3tht_A           91 LYLNFVE   97 (345)
T ss_dssp             CEEEECS
T ss_pred             EEEEEee
Confidence            7777764

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

Probab=99.58  E-value=4.2e-14  Score=102.47  Aligned_cols=73  Identities=18%  Similarity=0.204  Sum_probs=65.8

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .......+|||.|||..+++++|+++|.+||.|..+.++.++.    .+||||+|.+.++|+.|++.|++ .|.|+.+
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l   88 (116)
T 2cqd_A           12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKA   88 (116)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEEC
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEE
Confidence            4455678999999999999999999999999999999988754    36999999999999999999998 8999844

>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=8.1e-15  Score=102.93  Aligned_cols=73  Identities=14%  Similarity=0.165  Sum_probs=64.2

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .....++|||+|||..+++++|+++|.+||.|..+.++.+...    +||||+|.+.++|+.|++.|||..|+|+.+
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l   87 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKV   87 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEE
Confidence            3445689999999999999999999999999987766666443    599999999999999999999999999844

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

Probab=99.58  E-value=2.7e-14  Score=99.80  Aligned_cols=77  Identities=25%  Similarity=0.384  Sum_probs=65.2

Q ss_pred             CCCCeEEEcCCC-------CCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEE
Q 022301            4 RASRTLYVGNLP-------GDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLR   76 (299)
Q Consensus         4 ~~~~~l~V~nLp-------~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~   76 (299)
                      ...+.|.|.-..       .++++++|+++|++||+|..|.|.  +.++|||||+|.+.++|..|+..+++  +.|++|.
T Consensus         8 ~~~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~--~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~   83 (100)
T 2d9o_A            8 QGTPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS--SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLK   83 (100)
T ss_dssp             CSSCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE--SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCE
T ss_pred             CccceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc--cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEE
Confidence            345677776654       458999999999999999999997  46789999999999999999997554  6799999


Q ss_pred             EEEccCCC
Q 022301           77 VELAHGGR   84 (299)
Q Consensus        77 v~~~~~~~   84 (299)
                      |.|+....
T Consensus        84 V~~a~~~~   91 (100)
T 2d9o_A           84 ISWLEGQP   91 (100)
T ss_dssp             EECSSCCC
T ss_pred             EEEccCCC
Confidence            99987654

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

Probab=99.58  E-value=1.1e-14  Score=102.91  Aligned_cols=68  Identities=13%  Similarity=0.128  Sum_probs=62.9

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCce
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAF  175 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  175 (299)
                      ...++|||+|||..+++++|.++|.+||.|..+.+.  ...+||||+|.+.++|..|+..|||..|+|+.
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~--~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~   92 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY--PEKGCCFIKYDTHEQAAVCIVALANFPFQGRN   92 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE--TTTTEEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe--cCCCEEEEEECCHHHHHHHHHHhCCCeECCeE
Confidence            346899999999999999999999999999999988  44579999999999999999999999999983

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

Probab=99.58  E-value=1.2e-14  Score=101.70  Aligned_cols=73  Identities=16%  Similarity=0.156  Sum_probs=64.4

Q ss_pred             CCCccEEEEeCCCC-CCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEE
Q 022301          105 RRSEYRVLVTGLPS-SASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVR  181 (299)
Q Consensus       105 ~~~~~~l~v~nl~~-~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~  181 (299)
                      ..+..+|||+|||. .+++++|.++|.+||.|..+.+.    .+||||+|.+.++|+.|+..|||..+.|+.+.+...
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~----~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   80 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK----NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVS   80 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE----TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe----CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEc
Confidence            34568999999998 99999999999999999999985    469999999999999999999999999996644443

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

Probab=99.58  E-value=2.9e-14  Score=103.67  Aligned_cols=75  Identities=21%  Similarity=0.290  Sum_probs=67.4

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      .......+|||+|||..+++++|+++|.+||.|..+.++.++.    .|||||+|.+.++|+.|++.|||..|+|+.+.
T Consensus        35 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~  113 (118)
T 2khc_A           35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLK  113 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            3455678999999999999999999999999999999987754    46999999999999999999999999998543

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

Probab=99.57  E-value=1.6e-14  Score=98.65  Aligned_cols=72  Identities=14%  Similarity=0.193  Sum_probs=65.2

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhc-CCCeecCcee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKL-DDSEFRNAFS  176 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l-~g~~~~g~~~  176 (299)
                      +......+|||+|||..+++++|.++|.+||.|..+.+..+  .+||||+|.+.++|..|+..| +|..++|+.+
T Consensus         7 ~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~--kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l   79 (85)
T 2ytc_A            7 GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR--QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRL   79 (85)
T ss_dssp             CSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG--GTEEEEEESSHHHHHHHHHTTTTTCEETTEEC
T ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC--CCEEEEEECCHHHHHHHHHHhcCCeeECCCEE
Confidence            34456689999999999999999999999999999999875  469999999999999999999 9999999854

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.57  E-value=3.4e-14  Score=103.16  Aligned_cols=76  Identities=9%  Similarity=0.080  Sum_probs=63.9

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCE-EEEEecChhhHHHHHHhcCCCeecCceeeEEEEeccc
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTT-GIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVREY  185 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~-~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~~~  185 (299)
                      ....|||+||++.+++++|.++|.+||.|..|.++..  .|| |||+|.+.++|..|++.|||..|.|...  .+.+..+
T Consensus        24 ~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~--~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~--~l~V~~A   99 (124)
T 2e5i_A           24 KVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR--NGIQAMVEFESVLCAQKAKAALNGADIYAGCC--TLKIEYA   99 (124)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES--SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBS--EEEEECC
T ss_pred             cEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC--CCCEEEEEECCHHHHHHHHHHhCCCEecCCCe--EEEEEEe
Confidence            3456789999999999999999999999999998764  375 9999999999999999999999998433  3444444


Q ss_pred             c
Q 022301          186 D  186 (299)
Q Consensus       186 ~  186 (299)
                      .
T Consensus       100 k  100 (124)
T 2e5i_A          100 R  100 (124)
T ss_dssp             S
T ss_pred             c
Confidence            3

>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=99.57  E-value=2.2e-14  Score=98.76  Aligned_cols=74  Identities=18%  Similarity=0.326  Sum_probs=65.6

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEec
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVR  183 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~  183 (299)
                      ..+|||+|||..+++++|.++|.+||.|..+.+..+..    .|||||+|.+.++|+.|+ .|||..+.|+    .+.+.
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-ALDESLFRGR----QIKVI   80 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTE----ECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCc----EEEEE
Confidence            46899999999999999999999999999999998853    359999999999999999 9999999999    45554


Q ss_pred             ccc
Q 022301          184 EYD  186 (299)
Q Consensus       184 ~~~  186 (299)
                      ...
T Consensus        81 ~a~   83 (89)
T 3ucg_A           81 PKR   83 (89)
T ss_dssp             ETT
T ss_pred             Ecc
Confidence            443

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

Probab=99.57  E-value=2.7e-15  Score=102.51  Aligned_cols=70  Identities=19%  Similarity=0.288  Sum_probs=64.3

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCce
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAF  175 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  175 (299)
                      .+..+|||+|||..+++++|+++|.+||.|..+.++.++.    .|||||+|.+.++|+.|++.|||..|.|+.
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   76 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQM   76 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEE
Confidence            3567999999999999999999999999999999988754    469999999999999999999999999973

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

Probab=99.56  E-value=7.8e-15  Score=103.32  Aligned_cols=70  Identities=20%  Similarity=0.209  Sum_probs=64.7

Q ss_pred             CccEEEEeCCCC------CCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecC-ce
Q 022301          107 SEYRVLVTGLPS------SASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRN-AF  175 (299)
Q Consensus       107 ~~~~l~v~nl~~------~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g-~~  175 (299)
                      ..++|||+|||.      .+++++|.++|.+||.|..+.++.++.+    |||||+|.+.++|+.|++.|||..|.| +.
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~   84 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHR   84 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeE
Confidence            457999999999      9999999999999999999999988753    699999999999999999999999999 84


Q ss_pred             e
Q 022301          176 S  176 (299)
Q Consensus       176 ~  176 (299)
                      +
T Consensus        85 l   85 (100)
T 3ns6_A           85 L   85 (100)
T ss_dssp             C
T ss_pred             E
Confidence            4

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

Probab=99.56  E-value=1.7e-14  Score=105.66  Aligned_cols=72  Identities=11%  Similarity=0.139  Sum_probs=63.3

Q ss_pred             CCCccEEEEeCCCCCCCHHHHH----HHHHhcCCeeEEEEEeC-CCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          105 RRSEYRVLVTGLPSSASWQDLK----DHMRRAGDVCFSQVFRD-GSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~----~~f~~~G~v~~~~~~~~-~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..+..+|||+|||..+++++|+    ++|.+||.|..|.+..+ ...|||||+|.+.++|..|+..|||..|.|+.+
T Consensus        26 ~~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           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPL  102 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEE
Confidence            3456899999999999998876    69999999999888653 445799999999999999999999999999955

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

Probab=99.56  E-value=1.2e-13  Score=97.81  Aligned_cols=80  Identities=21%  Similarity=0.328  Sum_probs=67.7

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceeeE
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA  178 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  178 (299)
                      .......+|||+|||..+++++|+++|.+||.|..+.++.++..    |||||+|.+.++|+.|+..  +..|+|+    
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~----   83 (103)
T 2cqg_A           10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGR----   83 (103)
T ss_dssp             CCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTE----
T ss_pred             CccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc--CCeeCCe----
Confidence            34456689999999999999999999999999999999988653    5999999999999999994  6789998    


Q ss_pred             EEEecccccC
Q 022301          179 YVRVREYDHR  188 (299)
Q Consensus       179 ~~~~~~~~~~  188 (299)
                      .+.+.....+
T Consensus        84 ~l~v~~a~~~   93 (103)
T 2cqg_A           84 WCDCKLPNSK   93 (103)
T ss_dssp             EEEEECCCTT
T ss_pred             EEEEEecCCC
Confidence            5555555443

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

Probab=99.56  E-value=4e-14  Score=102.60  Aligned_cols=80  Identities=15%  Similarity=0.253  Sum_probs=69.7

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEE
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVR  181 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~  181 (299)
                      ....+|||+|||..+++++|+++|.+||.|..|.++.++.    .|||||+|.+.++|+.|+.. +|..|+|+    .+.
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-RPHSIDGR----VVE   99 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTE----EEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCE----EEE
Confidence            3568999999999999999999999999999999998754    36999999999999999998 99999998    666


Q ss_pred             ecccccCCC
Q 022301          182 VREYDHRRD  190 (299)
Q Consensus       182 ~~~~~~~~~  190 (299)
                      |.....+..
T Consensus       100 V~~a~~~~~  108 (116)
T 1x4b_A          100 PKRAVAREE  108 (116)
T ss_dssp             EECCSSCCC
T ss_pred             EEECCCCcc
Confidence            666555433

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=9e-14  Score=97.31  Aligned_cols=76  Identities=13%  Similarity=0.188  Sum_probs=65.6

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEecc
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVRE  184 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~~  184 (299)
                      .....+|||+||  .+++++|.++|.+||.|..+.+.  ...+||||+|.+.++|+.|+..|||..|.|+    .+.|..
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~--~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~----~l~v~~   83 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD--PPRNCAFVTYEKMESADQAVAELNGTQVESV----QLKVNI   83 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE--TTTTEEEEEESSHHHHHHHHHHTTTEEETTE----EEEEEC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec--CCCCEEEEEECCHHHHHHHHHHhCCCeECCe----EEEEEE
Confidence            345689999996  89999999999999999999885  4557999999999999999999999999998    566655


Q ss_pred             cccC
Q 022301          185 YDHR  188 (299)
Q Consensus       185 ~~~~  188 (299)
                      ....
T Consensus        84 a~~~   87 (97)
T 1x5p_A           84 ARKQ   87 (97)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            5444

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.56  E-value=7.7e-15  Score=99.20  Aligned_cols=68  Identities=10%  Similarity=0.118  Sum_probs=60.8

Q ss_pred             cEEEEeCCCCCC------CHHHHHHHHHhcCCeeEEEEEeC--CCCCEEEEEecChhhHHHHHHhcCCCeecCc-ee
Q 022301          109 YRVLVTGLPSSA------SWQDLKDHMRRAGDVCFSQVFRD--GSGTTGIVDYTNYDDMKHAIKKLDDSEFRNA-FS  176 (299)
Q Consensus       109 ~~l~v~nl~~~~------~~~~l~~~f~~~G~v~~~~~~~~--~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~-~~  176 (299)
                      ++|||+|||..+      ++++|.++|.+||.|..+.+...  ...|||||+|.+.++|+.|+..|||..++|+ .+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            689999999999      77999999999999999988743  2347999999999999999999999999997 44

>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=2.3e-14  Score=101.23  Aligned_cols=73  Identities=16%  Similarity=0.256  Sum_probs=65.9

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC---CCEEEEEecChhhHHHHHHhcCCCeecCceeeEE
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS---GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY  179 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  179 (299)
                      ....+|||+|||..+++++|.++|.+||+|..|.++.+..   .|||||+|.+.++|+.|+. ++|..|+|+.+.+.
T Consensus         9 ~~~~~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            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLIL   84 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            4568999999999999999999999999999999998754   4699999999999999999 99999999976444

>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=99.56  E-value=7.9e-15  Score=105.98  Aligned_cols=70  Identities=19%  Similarity=0.235  Sum_probs=64.0

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ....+|||+|||..+++++|+++|..||.|..|.++.+..    .|||||+|.+.++|+.|+ .|||..|+|+.+
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l   96 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPI   96 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEE
Confidence            3567999999999999999999999999999999988764    369999999999999999 999999999843

>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=99.56  E-value=4.5e-14  Score=96.78  Aligned_cols=72  Identities=17%  Similarity=0.272  Sum_probs=64.0

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ......+|||+|||..+++++|.++|.+||.|..+.++.++.+    |||||+|.+.++|+.|++ +++..|+|+.+
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i   82 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVI   82 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEE
Confidence            3456689999999999999999999999999999999988653    599999999999999996 58888999844

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

Probab=99.55  E-value=2.5e-14  Score=108.94  Aligned_cols=70  Identities=14%  Similarity=0.084  Sum_probs=64.0

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcC--CeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAG--DVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G--~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ...+|||+|||..+++++|.++|..||  .|..+.++.+..+    |||||+|.+.++|+.||..|||..|+|+.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l  129 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKV  129 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEe
Confidence            457999999999999999999999999  9999999988654    499999999999999999999999999954

>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=99.55  E-value=1.9e-15  Score=112.45  Aligned_cols=113  Identities=11%  Similarity=0.104  Sum_probs=62.4

Q ss_pred             ceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHH
Q 022301           46 GYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDL  125 (299)
Q Consensus        46 g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l  125 (299)
                      ++||.+|..++.+..++..+.... .|...--..                 .............+|||.|||..+++++|
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~-gg~~~g~~~-----------------g~~~~~~~~~~~~~lfV~nLp~~~te~dL   63 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASMT-GGQQMGRGS-----------------GDSEFTVQSTTGHCVHMRGLPYKATENDI   63 (139)
T ss_dssp             -------------------------------------------------------------CCCCEECCSCCTTCCHHHH
T ss_pred             CcccccccCccccchhcccchhcc-CCCCCCCCC-----------------CCcccCCCCCCCCEEEEeCCCCCCCHHHH
Confidence            578999998888877777544332 222110000                 00011123345679999999999999999


Q ss_pred             HHHHHhcCCeeEEEEEeCCC---CCEEEEEecChhhHHHHHHhcCCCeecCceeeE
Q 022301          126 KDHMRRAGDVCFSQVFRDGS---GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA  178 (299)
Q Consensus       126 ~~~f~~~G~v~~~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  178 (299)
                      +++|.+|| |+.|.|+.++.   .|||||+|.+.++|++|| .+|+..|+|+.+.+
T Consensus        64 ~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V  117 (139)
T 2hgn_A           64 YNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIEL  117 (139)
T ss_dssp             HHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCC
T ss_pred             HHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEE
Confidence            99999999 77899887754   469999999999999999 79999999995533

>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=3.7e-14  Score=102.57  Aligned_cols=73  Identities=18%  Similarity=0.203  Sum_probs=65.9

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC-CCEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS-GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      .....+|||+|||..+++++|.++|..||.|..+.++.+.. .|||||+|.+.++|..|+..|||..++|+.+.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   78 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLV   78 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            34568999999999999999999999999999999987654 47999999999999999999999999999553

>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=99.55  E-value=8.4e-15  Score=102.22  Aligned_cols=71  Identities=14%  Similarity=0.157  Sum_probs=62.7

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ....+|||+|||..+++++|+++|.+||.|..+.++.+...    +||||+|.+.++|++|++.|||..|.|+.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l   87 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKV   87 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEE
Confidence            34589999999999999999999999999987777776544    599999999999999999999999999844

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

Probab=99.55  E-value=2.3e-14  Score=102.03  Aligned_cols=71  Identities=11%  Similarity=0.100  Sum_probs=62.6

Q ss_pred             CCCccEEEEeCCCCC-CCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCC--CeecCceee
Q 022301          105 RRSEYRVLVTGLPSS-ASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDD--SEFRNAFSR  177 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~-~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g--~~~~g~~~~  177 (299)
                      ..+..+|||+|||.. +++++|.++|.+||.|..+.++..  .+||||+|.+.++|..|++.|++  ..|.|+.+.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~--kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM--KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT--TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC--CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            456789999999998 999999999999999999999754  57999999999999999998864  568998553

>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=99.55  E-value=1.7e-14  Score=103.50  Aligned_cols=71  Identities=20%  Similarity=0.276  Sum_probs=64.0

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEE
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY  179 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  179 (299)
                      ..++|||+|||..+++++|+++|.+||.|..|.+..  ..+||||+|.+.++|+.|+..|||..|.|+.+.+.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~--~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   79 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE--GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLE   79 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS--SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC--CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            457999999999999999999999999999988874  45699999999999999999999999999966433

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=7.2e-14  Score=97.21  Aligned_cols=72  Identities=18%  Similarity=0.225  Sum_probs=61.7

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCC-EEEEEecChhhHHHHHHhcCCCeecCceeeEEEEeccc
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGT-TGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVREY  185 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~-~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~~~  185 (299)
                      ...+|||+|||..+++++|.++|.+||.|..|  +.+...+ ||||+|.+.++|+.|+. |+|..|+|+    .+.|...
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-QSQHSLGGH----RLRVRPR   79 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCCEEEEEESSHHHHHHHHT-CSCCEETTE----ECCCBCS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCcEEEEEECCHHHHHHHHh-cCCeEECCE----EEEEEEC
Confidence            44699999999999999999999999999987  4443333 99999999999999999 999999998    5555443

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.55  E-value=4.4e-14  Score=102.95  Aligned_cols=77  Identities=19%  Similarity=0.240  Sum_probs=65.2

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCE-EEEEecChhhHHHHHHhcCCCeecCceeeEEEEecc
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTT-GIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVRE  184 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~-~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~~  184 (299)
                      ..-..|||+||++.+++++|.++|.+||+|..|.+.... .++ |||+|.+.++|+.|++.|||..|.|..+  .++++.
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 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-NQFQALLQYADPVSAQHAKLSLDGQNIYNACC--TLRIDF  102 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-TEEEEEEEESCHHHHHHHHHHHTTCEEETTEE--EEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-CCcEEEEEECCHHHHHHHHHHcCCCeecCCCc--EEEEEe
Confidence            345678899999999999999999999999999888755 455 9999999999999999999999998433  344444


Q ss_pred             c
Q 022301          185 Y  185 (299)
Q Consensus       185 ~  185 (299)
                      .
T Consensus       103 a  103 (130)
T 3zzy_A          103 S  103 (130)
T ss_dssp             C
T ss_pred             c
Confidence            3

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=8.3e-14  Score=96.29  Aligned_cols=78  Identities=17%  Similarity=0.247  Sum_probs=67.1

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC---CCEEEEEecChhhHHHHHHhcCCCeecCceeeEEE
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS---GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYV  180 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~  180 (299)
                      ......+|||+|||..+++++|+++|..| .|..+.++.+..   .|||||+|.+.++|+.|+. |||..|+|+    .|
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr----~i   79 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGR----YI   79 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTE----EE
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCc----EE
Confidence            34566899999999999999999999999 999999998843   2599999999999999999 999999999    45


Q ss_pred             Eeccccc
Q 022301          181 RVREYDH  187 (299)
Q Consensus       181 ~~~~~~~  187 (299)
                      .+.....
T Consensus        80 ~v~~a~~   86 (91)
T 2dgw_A           80 EVFREKS   86 (91)
T ss_dssp             EEEEESS
T ss_pred             EEEECCc
Confidence            5544433

>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=99.54  E-value=1.3e-14  Score=103.07  Aligned_cols=71  Identities=25%  Similarity=0.360  Sum_probs=65.2

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ....+|||+|||..+++++|.++|.+||.|..+.++.+...    |||||+|.+.++|+.|++.|||..|+|+.+
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   80 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRAL   80 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCB
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEE
Confidence            34579999999999999999999999999999999988643    599999999999999999999999999954

>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=99.54  E-value=1.1e-14  Score=105.07  Aligned_cols=78  Identities=26%  Similarity=0.345  Sum_probs=67.7

Q ss_pred             CCCCeEEEcCCCC--CC---CHHHHHHHhhhcCCeeEEEeecC-------CCCCceEEEEecChHHHHHHHHhcCCCCCC
Q 022301            4 RASRTLYVGNLPG--DI---REREVEDLFYKYGPIAHIDLKIP-------PRPPGYAFVEFEEARDAEDAIRGRDGYDFD   71 (299)
Q Consensus         4 ~~~~~l~V~nLp~--~~---t~~~l~~~F~~~G~v~~i~~~~~-------~~~~g~afV~F~~~e~A~~A~~~l~~~~~~   71 (299)
                      .++++|+|.||-.  ++   -+++|+++|++||+|..|.|..+       +.++|+|||+|.+.++|.+|+..|||.+|.
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            4899999999932  22   36899999999999999999543       234699999999999999999999999999


Q ss_pred             CceEEEEEcc
Q 022301           72 GHRLRVELAH   81 (299)
Q Consensus        72 g~~i~v~~~~   81 (299)
                      |+.|.|.++.
T Consensus        98 GR~i~v~~~~  107 (118)
T 3ue2_A           98 GRKVVAEVYD  107 (118)
T ss_dssp             TEECEEEEEC
T ss_pred             CcEEEEEEcC
Confidence            9999999975

>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=3.1e-14  Score=101.42  Aligned_cols=65  Identities=18%  Similarity=0.198  Sum_probs=58.5

Q ss_pred             CCCccEEEE--eCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCee
Q 022301          105 RRSEYRVLV--TGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEF  171 (299)
Q Consensus       105 ~~~~~~l~v--~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~  171 (299)
                      ..+..+|||  +||+..+++++|+++|.+||.|..+.++.  ..|||||+|.+.++|++|++.|||.+|
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~--~rgfaFV~f~~~~~A~~Ai~~lnG~~~   88 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP--NKPYSFARYRTTEESKRAYVTLNGKEV   88 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT--TCSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC--CCCEEEEEECCHHHHHHHHHHhCCCEE
Confidence            345678999  66999999999999999999999988764  357999999999999999999999988

>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=4.5e-14  Score=103.60  Aligned_cols=75  Identities=17%  Similarity=0.314  Sum_probs=65.8

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEe
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRV  182 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~  182 (299)
                      ...+|||+|||..+++++|.++|.+||.|..+.++.++.    .|||||+|.+.++|+.|+ .|||..|+|+    .+.|
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-AMDETVFRGR----TIKV  109 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTE----ECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCe----EEEE
Confidence            457999999999999999999999999999999988753    359999999999999999 7999999998    4444


Q ss_pred             cccc
Q 022301          183 REYD  186 (299)
Q Consensus       183 ~~~~  186 (299)
                      ....
T Consensus       110 ~~a~  113 (124)
T 2jwn_A          110 LPKR  113 (124)
T ss_dssp             EESS
T ss_pred             EECC
Confidence            4443

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

Probab=99.54  E-value=3.7e-14  Score=95.89  Aligned_cols=71  Identities=18%  Similarity=0.275  Sum_probs=59.8

Q ss_pred             ccEEEEeCCCCCCCHHH----HHHHHHhcC-CeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEe
Q 022301          108 EYRVLVTGLPSSASWQD----LKDHMRRAG-DVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRV  182 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~----l~~~f~~~G-~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~  182 (299)
                      .+.|||.|||..+++++    |.++|.+|| +|..|      .+|+|||.|.+.++|..|++.|+|..+.|+    .|.+
T Consensus         9 ~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V------tgG~AfV~F~~~esA~~A~~~l~G~~l~gr----~i~v   78 (96)
T 2diu_A            9 HTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI------TGCSAILRFINQDSAERAQKRMENEDVFGN----RIIV   78 (96)
T ss_dssp             SEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC------CTTCEEEEESSHHHHHHHHHHHTTCCSSSS----CCEE
T ss_pred             ceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE------ecCEEEEEECCHHHHHHHHHHhcCCccCCc----eEEE
Confidence            34499999999999887    558999995 99988      238999999999999999999999999999    5555


Q ss_pred             cccccC
Q 022301          183 REYDHR  188 (299)
Q Consensus       183 ~~~~~~  188 (299)
                      ..+...
T Consensus        79 ~~A~~~   84 (96)
T 2diu_A           79 SFTPKN   84 (96)
T ss_dssp             ESSCCS
T ss_pred             EecCCC
Confidence            554443

>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=99.54  E-value=3.6e-14  Score=100.14  Aligned_cols=75  Identities=15%  Similarity=0.233  Sum_probs=64.3

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC---CEEEEEecChhhHHHHHHhcCCCeecCceeeEE
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG---TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY  179 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  179 (299)
                      .......+|||.|||+.+++++|+++|..||. +.|.++.++.+   |||||+|.+.++|++||+ +|+..|+|+.+.+.
T Consensus        10 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~   87 (102)
T 1wez_A           10 FQSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            34456689999999999999999999999994 48999888642   499999999999999995 79999999955443

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

Probab=99.54  E-value=2.4e-14  Score=106.01  Aligned_cols=72  Identities=7%  Similarity=0.135  Sum_probs=64.6

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeE--EEEEeCCC----CCEEEEEecChhhHHHHHHhcCCC----eecC
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCF--SQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDS----EFRN  173 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~--~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~----~~~g  173 (299)
                      ......+|||+|||..+++++|.++|.+||.|..  |.|+.++.    .|||||+|.+. +|..|+..|||.    .|+|
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g   97 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG   97 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC
Confidence            3456789999999999999999999999999966  89988873    36999999999 999999999999    9999


Q ss_pred             cee
Q 022301          174 AFS  176 (299)
Q Consensus       174 ~~~  176 (299)
                      +.+
T Consensus        98 r~l  100 (131)
T 2m2b_A           98 KTI  100 (131)
T ss_dssp             CCC
T ss_pred             EEE
Confidence            954

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

Probab=99.54  E-value=1.4e-14  Score=101.44  Aligned_cols=73  Identities=15%  Similarity=0.196  Sum_probs=63.6

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHH----HHHHhcCCeeEEEEEeC-CCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLK----DHMRRAGDVCFSQVFRD-GSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~----~~f~~~G~v~~~~~~~~-~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ...+..+|||+|||..+++++|.    ++|.+||.|..+.+... ...|||||+|.+.++|..|+..|||..++|+.+
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   81 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEE
Confidence            34567899999999999999999    99999999999988743 234699999999999999999999999999844

>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=1.8e-15  Score=107.05  Aligned_cols=69  Identities=23%  Similarity=0.446  Sum_probs=58.1

Q ss_pred             cCCCCCCCHHHHHHHh------------hhcCCeeEEEeecC--CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEE
Q 022301           12 GNLPGDIREREVEDLF------------YKYGPIAHIDLKIP--PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRV   77 (299)
Q Consensus        12 ~nLp~~~t~~~l~~~F------------~~~G~v~~i~~~~~--~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v   77 (299)
                      .|||.++++++|+++|            ++||+|..|.|..+  +.++|||||+|.+.++|.+|+..|||..|.|+.|.|
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            3444445666666555            99999999999653  567899999999999999999999999999999999


Q ss_pred             EEc
Q 022301           78 ELA   80 (299)
Q Consensus        78 ~~~   80 (299)
                      .|+
T Consensus       101 ~~s  103 (104)
T 1jmt_A          101 ELS  103 (104)
T ss_dssp             EEC
T ss_pred             EEc
Confidence            986

>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=99.54  E-value=3.6e-14  Score=101.67  Aligned_cols=78  Identities=18%  Similarity=0.216  Sum_probs=67.0

Q ss_pred             CCCCCeEEEcCCCC--CC--------CHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCC
Q 022301            3 SRASRTLYVGNLPG--DI--------REREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDG   72 (299)
Q Consensus         3 ~~~~~~l~V~nLp~--~~--------t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g   72 (299)
                      ..++++|.|.|+-.  ..        -+++|+++|++||.|.+|.|..+ ..+|+|||+|.+.++|.+|+..|||.+|.|
T Consensus         4 p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~-~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~G   82 (114)
T 3s6e_A            4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKN-SAQGNVYVKCPSIAAAIAAVNALHGRWFAG   82 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTT-CTTCCEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecC-CCcEEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            46789999999933  21        14578999999999999999654 358999999999999999999999999999


Q ss_pred             ceEEEEEcc
Q 022301           73 HRLRVELAH   81 (299)
Q Consensus        73 ~~i~v~~~~   81 (299)
                      +.|.|.++.
T Consensus        83 R~i~v~~~~   91 (114)
T 3s6e_A           83 KMITAAYVP   91 (114)
T ss_dssp             EECEEEEEC
T ss_pred             EEEEEEEEc
Confidence            999999974

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.54  E-value=1.7e-14  Score=100.85  Aligned_cols=79  Identities=13%  Similarity=0.163  Sum_probs=65.9

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEec
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVR  183 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~  183 (299)
                      ......+|||+|||..+++++|+++|..||.|..+ .......|||||+|.+.++|+.|+..|+|..|+|+    .+.+.
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~----~l~v~   86 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGR----SVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTE----EEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCe----EEEEE
Confidence            34467899999999999999999999999998877 33333456999999999999999999999999998    55555


Q ss_pred             cccc
Q 022301          184 EYDH  187 (299)
Q Consensus       184 ~~~~  187 (299)
                      ....
T Consensus        87 ~a~~   90 (96)
T 1fjc_A           87 YTGE   90 (96)
T ss_dssp             ECSS
T ss_pred             EcCC
Confidence            5443

>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=99.53  E-value=4.7e-14  Score=100.08  Aligned_cols=76  Identities=16%  Similarity=0.163  Sum_probs=65.3

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeE-EEEEeCC---CCCEEEEEecChhhHHHHHHhcCCCeecCceeeE
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCF-SQVFRDG---SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA  178 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~-~~~~~~~---~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  178 (299)
                      +......+|||+|||..+++++|+++|..||.|.. +.++.+.   ..|||||+|.+.++|+.|+.. ++..|+|+.+.+
T Consensus        10 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v   88 (104)
T 1wg5_A           10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEI   88 (104)
T ss_dssp             SSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEE
Confidence            34456789999999999999999999999999987 7777663   346999999999999999998 999999996544


Q ss_pred             E
Q 022301          179 Y  179 (299)
Q Consensus       179 ~  179 (299)
                      .
T Consensus        89 ~   89 (104)
T 1wg5_A           89 F   89 (104)
T ss_dssp             E
T ss_pred             E
Confidence            3

>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=99.53  E-value=2e-14  Score=106.50  Aligned_cols=73  Identities=21%  Similarity=0.282  Sum_probs=65.4

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCC---eeEEEEEeCCCC---CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGD---VCFSQVFRDGSG---TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~---v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      +.....++|||+|||+.+++++|.++|..||.   |..|.++.+..+   |||||+|.+.++|++|++ |||..|+|+.+
T Consensus        39 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i  117 (136)
T 2hgl_A           39 PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYI  117 (136)
T ss_dssp             SSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEE
Confidence            34456789999999999999999999999999   888999888653   599999999999999999 99999999944

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

Probab=99.53  E-value=9e-14  Score=104.21  Aligned_cols=74  Identities=20%  Similarity=0.176  Sum_probs=66.9

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .......+|||+|||..+++++|+++|.+||.|..+.++.++.    .|||||+|.+.++|+.|++.|||..|+|+.+
T Consensus        58 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l  135 (140)
T 2ku7_A           58 GSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI  135 (140)
T ss_dssp             SSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEE
T ss_pred             CCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            4455678999999999999999999999999999999988743    4699999999999999999999999999844

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

Probab=99.53  E-value=3.7e-14  Score=101.04  Aligned_cols=71  Identities=21%  Similarity=0.302  Sum_probs=63.2

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC---CCEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS---GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      .....+|||+|||..+++++|+++|..| .|..|.|+.+..   .|||||+|.+.++|++|| .+||..|+|+.+.
T Consensus        13 ~~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~   86 (109)
T 2dnn_A           13 NPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVE   86 (109)
T ss_dssp             CHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEE
Confidence            3456799999999999999999999999 899999987754   469999999999999999 6999999999443

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

Probab=99.52  E-value=4.7e-14  Score=100.23  Aligned_cols=71  Identities=10%  Similarity=0.113  Sum_probs=62.8

Q ss_pred             CCccEEEEeCCCCCC------CHHHHHHHHHhcCCeeEEEEEeC--CCCCEEEEEecChhhHHHHHHhcCCCeecCc-ee
Q 022301          106 RSEYRVLVTGLPSSA------SWQDLKDHMRRAGDVCFSQVFRD--GSGTTGIVDYTNYDDMKHAIKKLDDSEFRNA-FS  176 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~------~~~~l~~~f~~~G~v~~~~~~~~--~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~-~~  176 (299)
                      ...++|||+|||..+      ++++|.++|.+||.|..+.++..  ...|||||+|.+.++|+.|+..|||..|+|+ .+
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            346799999999999      78999999999999999988732  2347999999999999999999999999996 55

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

Probab=99.52  E-value=1.5e-13  Score=106.99  Aligned_cols=79  Identities=18%  Similarity=0.117  Sum_probs=69.6

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC---CCCEEEEEecChhhHHHHHHhcCCCeecCceeeEE
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG---SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY  179 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~---~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  179 (299)
                      ......++|||+|||..+++++|+++|.+||.|..|.+..+.   ..|||||+|.+.++|+.|++.|||..|+|+.+.+.
T Consensus        83 ~~~~~~~~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           83 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  162 (177)
T ss_dssp             SSCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            344567899999999999999999999999999999998875   33699999999999999999999999999976544


Q ss_pred             EE
Q 022301          180 VR  181 (299)
Q Consensus       180 ~~  181 (299)
                      +.
T Consensus       163 ~a  164 (177)
T 2f3j_A          163 LV  164 (177)
T ss_dssp             EE
T ss_pred             Ee
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=99.52  E-value=7.5e-15  Score=103.46  Aligned_cols=72  Identities=15%  Similarity=0.336  Sum_probs=61.5

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC-----CCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG-----SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~-----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ......++|||+|||..+++++|.++|..|| |..+.++.+.     ..|||||+|.+.++|..|+ .|+|..|+|+.+
T Consensus        14 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l   90 (100)
T 2j76_E           14 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRI   90 (100)
T ss_dssp             ------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEE
Confidence            3445678999999999999999999999999 9999998876     2469999999999999999 899999999854

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

Probab=99.51  E-value=7.3e-14  Score=99.90  Aligned_cols=78  Identities=15%  Similarity=0.227  Sum_probs=64.7

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCceeeEEE
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYV  180 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~  180 (299)
                      .....+|||+|||..+++++|.++|..||.|..+.++.+..    .|||||+|.+.++|..|+..+ |..|+|+    .+
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~----~l   96 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSK----TI   96 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTE----EE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCE----EE
Confidence            34568999999999999999999999999999999998764    369999999999999999986 5999998    45


Q ss_pred             Eeccccc
Q 022301          181 RVREYDH  187 (299)
Q Consensus       181 ~~~~~~~  187 (299)
                      .+.....
T Consensus        97 ~V~~a~~  103 (109)
T 2rs2_A           97 DPKVAFP  103 (109)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            5544433

>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=3.4e-14  Score=118.00  Aligned_cols=80  Identities=23%  Similarity=0.262  Sum_probs=70.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCC-CCCC---CceEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDG-YDFD---GHRLRV   77 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~-~~~~---g~~i~v   77 (299)
                      .+.++|||+|||..+|+++|.++|+.||.|..|.|..  ++.++|||||+|.+.++|..|+..||+ ..+.   +++|.|
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            4678999999999999999999999999999999954  466789999999999999999999954 4444   999999


Q ss_pred             EEccCC
Q 022301           78 ELAHGG   83 (299)
Q Consensus        78 ~~~~~~   83 (299)
                      .++...
T Consensus       174 ~~~~~~  179 (261)
T 3sde_A          174 EPMEQF  179 (261)
T ss_dssp             EECCCE
T ss_pred             eecccc
Confidence            998754

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

Probab=99.51  E-value=3.5e-14  Score=94.40  Aligned_cols=66  Identities=20%  Similarity=0.311  Sum_probs=60.7

Q ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       110 ~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      +|||+|||..+++++|.++|.+||.|..+.++.++.    .|||||+|.+.++|+.|++ |+|..++|+.+
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            489999999999999999999999999999988764    3699999999999999998 99999999854

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

Probab=99.51  E-value=4.9e-14  Score=101.71  Aligned_cols=74  Identities=14%  Similarity=0.130  Sum_probs=64.9

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCe-eEEEEEeCC---CCCEEEEEecChhhHHHHHHhcCCCeecCceeeEE
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDV-CFSQVFRDG---SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY  179 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v-~~~~~~~~~---~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  179 (299)
                      .....+|||+|||..+++++|.++|..||.| ..|.|+.+.   ..|||||+|.+.++|+.||.. ||..|+|+.+.+.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~   89 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVH   89 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEE
Confidence            3456899999999999999999999999999 888888776   336999999999999999997 9999999955433

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

Probab=99.50  E-value=3e-14  Score=95.25  Aligned_cols=68  Identities=16%  Similarity=0.277  Sum_probs=62.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      ++|||+|||..+++++|+++|.+||.|..+.+..++.    .|||||+|.+.++|+.|+..++ ..++|+.+.
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            3799999999999999999999999999999988764    4699999999999999999999 999998553

>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=99.50  E-value=1.8e-13  Score=97.99  Aligned_cols=71  Identities=14%  Similarity=0.246  Sum_probs=62.8

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCC-eeEEEEE-eCC----CCCEEEEEecChhhHHHHHHhcC--CCeecCcee
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGD-VCFSQVF-RDG----SGTTGIVDYTNYDDMKHAIKKLD--DSEFRNAFS  176 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~-v~~~~~~-~~~----~~~~~fv~f~~~~~a~~a~~~l~--g~~~~g~~~  176 (299)
                      ...++|||+|||..+++++|.++|.+||. |..+.++ .+.    ..|||||+|.+.++|..|+..|+  +..++|+.+
T Consensus         6 ~~~~~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            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   84 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeE
Confidence            35689999999999999999999999998 9999887 443    34699999999999999999996  589999844

>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=99.50  E-value=1.1e-13  Score=94.78  Aligned_cols=68  Identities=19%  Similarity=0.303  Sum_probs=61.9

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhc----C-------CeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCc
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRA----G-------DVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNA  174 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~----G-------~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  174 (299)
                      ....+|||+|||..+++++|+++|.+|    |       .|..+.+..+  .|||||+|.+.++|+.|+ .|||..++|+
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~--kg~afV~f~~~~~a~~A~-~l~g~~~~g~   80 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD--KNFAFLEFRSVDETTQAM-AFDGIIFQGQ   80 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS--SSEEEEEESSHHHHHHHG-GGTTCEETTE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC--CcEEEEEcCCHHHHHHHH-hcCCCEECCe
Confidence            356899999999999999999999999    8       8998888765  579999999999999999 9999999998


Q ss_pred             ee
Q 022301          175 FS  176 (299)
Q Consensus       175 ~~  176 (299)
                      .+
T Consensus        81 ~l   82 (87)
T 2hzc_A           81 SL   82 (87)
T ss_dssp             EC
T ss_pred             EE
Confidence            44

>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=99.50  E-value=7.1e-14  Score=102.49  Aligned_cols=76  Identities=22%  Similarity=0.272  Sum_probs=63.6

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCceeeEE
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY  179 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  179 (299)
                      +....++|||+|||..+++++|.++|..||.|..+.++.+..    .|||||+|.+.++|+.||. |||..|+|+.+.+.
T Consensus        21 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~   99 (124)
T 1wel_A           21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVH   99 (124)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            345668999999999999999999999999998744443332    3599999999999999999 99999999966544


Q ss_pred             E
Q 022301          180 V  180 (299)
Q Consensus       180 ~  180 (299)
                      .
T Consensus       100 ~  100 (124)
T 1wel_A          100 P  100 (124)
T ss_dssp             E
T ss_pred             E
Confidence            3

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.50  E-value=1.2e-13  Score=100.22  Aligned_cols=77  Identities=22%  Similarity=0.315  Sum_probs=67.0

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCC---eeEEEEEeCCCC---CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGD---VCFSQVFRDGSG---TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~---v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      +.....++|||+|||..+++++|+++|..||.   |..|.++.+..+   |||||+|.+.++|++||+ |||..|+|+.+
T Consensus        12 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i   90 (118)
T 2db1_A           12 PEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYI   90 (118)
T ss_dssp             SCBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEE
Confidence            33456789999999999999999999999999   889999887653   599999999999999999 99999999955


Q ss_pred             eEEE
Q 022301          177 RAYV  180 (299)
Q Consensus       177 ~~~~  180 (299)
                      .+..
T Consensus        91 ~V~~   94 (118)
T 2db1_A           91 EVFK   94 (118)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            4433

>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=2.2e-13  Score=96.23  Aligned_cols=79  Identities=19%  Similarity=0.300  Sum_probs=64.2

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceeeE
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA  178 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  178 (299)
                      .......+|||+|||..+++++|+++|..|+   .+.++.+...    +||||+|.+.++|+.|++.|||..|.|+    
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~----   82 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGN----   82 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTE----
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCe----
Confidence            3445678999999999999999999999874   4556655433    5999999999999999999999999998    


Q ss_pred             EEEecccccC
Q 022301          179 YVRVREYDHR  188 (299)
Q Consensus       179 ~~~~~~~~~~  188 (299)
                      .+.|....++
T Consensus        83 ~l~V~~a~~~   92 (102)
T 2fc8_A           83 KVTLDWAKPK   92 (102)
T ss_dssp             ECEEEECCCC
T ss_pred             EEEEEEecCC
Confidence            5555555444

>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=99.49  E-value=1.2e-13  Score=112.09  Aligned_cols=73  Identities=14%  Similarity=0.163  Sum_probs=65.3

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcC--CeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceeeEE
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAG--DVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY  179 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G--~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  179 (299)
                      ..++|||+||+..+++++|+++|.+||  .|..|.|+.++.+    |||||+|.+.++|++||+.|||..|.|+.+.+.
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~  145 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVT  145 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEE
Confidence            457899999999999999999999999  9999999998654    499999999999999999999999999965433

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

Probab=99.49  E-value=1.2e-13  Score=94.84  Aligned_cols=67  Identities=10%  Similarity=0.117  Sum_probs=54.7

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeec--Cc
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFR--NA  174 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~--g~  174 (299)
                      ....+.++|||+|||..+++++|+++|++||.|..+.++.+ ..|||||+|.+.++|++    ++|..+.  |.
T Consensus         6 ~~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-srGfaFV~F~~~~~A~~----~~~~~~~~~g~   74 (89)
T 3d2w_A            6 HHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-FRAFAFVTFADDKVAQS----LCGEDLIIKGI   74 (89)
T ss_dssp             -----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-CCSEEEEEESCHHHHHH----HTTCEEEETTE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-CCCEEEEEECCHHHHHH----HcCCCcccCCE
Confidence            34556789999999999999999999999999999999876 56899999999999983    5666655  55

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.48  E-value=1.3e-13  Score=97.27  Aligned_cols=77  Identities=14%  Similarity=0.199  Sum_probs=62.8

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeE---EEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEe
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCF---SQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRV  182 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~---~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~  182 (299)
                      ....+|||+|||..+++++|+++|..||.|..   .........|||||+|.+.++|+.|++ |||..|.|+    .+.|
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-LTGLKVFGN----EIKL   89 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTB----CCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCc----EEEE
Confidence            35689999999999999999999999998765   111223456799999999999999999 999999998    4555


Q ss_pred             ccccc
Q 022301          183 REYDH  187 (299)
Q Consensus       183 ~~~~~  187 (299)
                      .....
T Consensus        90 ~~a~~   94 (101)
T 1fj7_A           90 EKPKG   94 (101)
T ss_dssp             ECCSC
T ss_pred             EEcCC
Confidence            44443

>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=5.6e-14  Score=96.48  Aligned_cols=67  Identities=22%  Similarity=0.325  Sum_probs=61.4

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ...+|||+|||..+++++|+++|.+| .|..+.+.  ...|||||+|.+.++|+.|++.|||..++|+.+
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~--~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l   70 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD--RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDL   70 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE--GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe--CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEE
Confidence            35789999999999999999999999 99998885  556799999999999999999999999999944

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

Probab=99.48  E-value=3.9e-13  Score=96.98  Aligned_cols=70  Identities=19%  Similarity=0.373  Sum_probs=63.6

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC---CEEEEEecChhhHHHHHHhcCCCeecCc
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG---TTGIVDYTNYDDMKHAIKKLDDSEFRNA  174 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~  174 (299)
                      .....+|||+|||..+++++|.++|..||.|..+.++.+..+   +||||+|.+.++|+.|+..|||..|.+.
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~   94 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTP   94 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCC
Confidence            345689999999999999999999999999999999988632   5999999999999999999999999654

>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=99.47  E-value=6e-14  Score=96.79  Aligned_cols=70  Identities=24%  Similarity=0.319  Sum_probs=63.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCceeeEE
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY  179 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  179 (299)
                      .+|||+|||..+++++|.++|.+||.|..+.+..+..    .|||||+|.+.+ |..|+..|||..++|+.+.+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~   75 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVT   75 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEE
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEE
Confidence            5799999999999999999999999999999988754    469999999999 999999999999999965433

>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=99.47  E-value=7.2e-14  Score=99.65  Aligned_cols=74  Identities=9%  Similarity=0.161  Sum_probs=65.3

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCC---eeEEEEEeCCC---CCEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGD---VCFSQVFRDGS---GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~---v~~~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      .....++|||+|||+.+++++|.++|..||.   |..+.++.+..   .|||||+|.+.++|+.|+. +||..|+|+.+.
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            3446689999999999999999999999998   88899987754   4699999999999999999 999999999554


Q ss_pred             E
Q 022301          178 A  178 (299)
Q Consensus       178 ~  178 (299)
                      +
T Consensus        86 V   86 (107)
T 2lmi_A           86 V   86 (107)
T ss_dssp             C
T ss_pred             E
Confidence            3

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.46  E-value=2.4e-13  Score=102.24  Aligned_cols=71  Identities=15%  Similarity=0.136  Sum_probs=61.2

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeE--------EEEE-eCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCF--------SQVF-RDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~--------~~~~-~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .+..+|||+|||..+++++|.++|..||.|..        +.+. .....|||||+|.+.++|..|+..|||..|.|+.+
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l  122 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPM  122 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEE
Confidence            45689999999999999999999999998865        3333 33455799999999999999999999999999844

>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=99.45  E-value=1.4e-13  Score=91.51  Aligned_cols=67  Identities=12%  Similarity=0.201  Sum_probs=60.4

Q ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       110 ~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      +|||+|||..+++++|.++|.+||.|..+.+..++.    .|||||+|.+.++|+.|++. ++..++|+.+.
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCE   71 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEE
Confidence            589999999999999999999999999999987754    46999999999999999995 88999998553

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.44  E-value=5.5e-13  Score=94.17  Aligned_cols=71  Identities=18%  Similarity=0.315  Sum_probs=63.1

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC---CEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG---TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      .....+|||+|||..+++++|.++|..||.|..+.++.+..+   |||||+|.+.++|+.|+.  +|..++|..+.
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~   79 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLK   79 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEE
Confidence            345689999999999999999999999999999999998732   599999999999999999  88888887553

>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=99.44  E-value=1.7e-13  Score=94.02  Aligned_cols=73  Identities=11%  Similarity=0.158  Sum_probs=59.0

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCee--cCceeeEEEEecc
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEF--RNAFSRAYVRVRE  184 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~--~g~~~~~~~~~~~  184 (299)
                      ...+|||+|||..+++++|.++|.+||.|..+.++.+ ..|||||+|.+.++|++|    ++..+  .|.    .+.+..
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----CGEDLIIKGI----SVHISN   74 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-CCSCCEEECSCHHHHHHT----TTCEEEETTE----EEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-CCCEEEEEECCHHHHHHH----hcCCceeCCE----EEEEEe
Confidence            4579999999999999999999999999999999876 567999999999999754    44444  565    555555


Q ss_pred             cccC
Q 022301          185 YDHR  188 (299)
Q Consensus       185 ~~~~  188 (299)
                      ..++
T Consensus        75 a~~~   78 (88)
T 1wf0_A           75 AEPK   78 (88)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            5444

>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=99.44  E-value=3.8e-13  Score=98.08  Aligned_cols=75  Identities=11%  Similarity=0.187  Sum_probs=63.5

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCee--EEEEEeCCC---CCEEEEEecChhhHHHHHHhcCCCeecCceeeE
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVC--FSQVFRDGS---GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA  178 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~--~~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  178 (299)
                      ......+|||+|||+.+++++|+++|..| .|.  .|.|+.++.   .|||||+|.+.++|++|++. ++..|+|+.+.+
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-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIEV  115 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEE
Confidence            34456889999999999999999999999 676  888887754   46999999999999999995 779999996544


Q ss_pred             EE
Q 022301          179 YV  180 (299)
Q Consensus       179 ~~  180 (299)
                      ..
T Consensus       116 ~~  117 (126)
T 2hgm_A          116 FK  117 (126)
T ss_dssp             EE
T ss_pred             EE
Confidence            33

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.44  E-value=3.3e-13  Score=98.16  Aligned_cols=74  Identities=12%  Similarity=0.162  Sum_probs=63.3

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCe----eEEEEEeCCCC---CEEEEEecChhhHHHHHHhcCCCeecCceeeE
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDV----CFSQVFRDGSG---TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA  178 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v----~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  178 (299)
                      ....+|||+|||+.+++++|+++|.+||.|    ..|.|+.+..+   |||||+|.+.++|++||+. |+..|+|+.+.+
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            456899999999999999999999999975    57888877533   5999999999999999996 999999995544


Q ss_pred             EE
Q 022301          179 YV  180 (299)
Q Consensus       179 ~~  180 (299)
                      ..
T Consensus       100 ~~  101 (123)
T 2dha_A          100 FR  101 (123)
T ss_dssp             EE
T ss_pred             EE
Confidence            33

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.13  E-value=1.6e-14  Score=104.63  Aligned_cols=79  Identities=19%  Similarity=0.308  Sum_probs=67.7

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeE--------EEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecC
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCF--------SQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRN  173 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~--------~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g  173 (299)
                      .+..+|||+|||..+++++|+++|.+||.|..        +.++.++.    .|||||+|.+.++|+.|+..|||..|.|
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            35579999999999999999999999999988        78877743    4699999999999999999999999999


Q ss_pred             ceeeEEEEecccccC
Q 022301          174 AFSRAYVRVREYDHR  188 (299)
Q Consensus       174 ~~~~~~~~~~~~~~~  188 (299)
                      +    .+.|.....+
T Consensus        85 ~----~l~V~~a~~~   95 (116)
T 2lcw_A           85 N----PIKVSFATRR   95 (116)
Confidence            8    5555544443

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.40  E-value=1.3e-12  Score=93.54  Aligned_cols=69  Identities=12%  Similarity=0.209  Sum_probs=61.3

Q ss_pred             cEEEEeCC----CCCCCHHHHHHHHHhcCCeeEEEEEeCCCCC----EEEEEecC----hhh----HHHHHH--hcCCCe
Q 022301          109 YRVLVTGL----PSSASWQDLKDHMRRAGDVCFSQVFRDGSGT----TGIVDYTN----YDD----MKHAIK--KLDDSE  170 (299)
Q Consensus       109 ~~l~v~nl----~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~----~~fv~f~~----~~~----a~~a~~--~l~g~~  170 (299)
                      ..|||+||    |+.+++++|+++|..||+|..+.++.|+.+|    ||||+|.+    +++    |..|+.  .|+|..
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            68999999    9999999999999999999999999999885    99999996    433    889988  799999


Q ss_pred             ecCceee
Q 022301          171 FRNAFSR  177 (299)
Q Consensus       171 ~~g~~~~  177 (299)
                      |+|+.+.
T Consensus        83 I~Gr~ir   89 (136)
T 2j8a_A           83 IMGFKFE   89 (136)
T ss_dssp             ETTEEEE
T ss_pred             ecCcEEE
Confidence            9999543

>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=99.40  E-value=4.2e-12  Score=91.16  Aligned_cols=72  Identities=17%  Similarity=0.227  Sum_probs=61.1

Q ss_pred             CCCccEEEEeCCCCCCC-----------HHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecC
Q 022301          105 RRSEYRVLVTGLPSSAS-----------WQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRN  173 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~-----------~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g  173 (299)
                      ..+..+|+|.||.....           +++|.++|.+||.|..+.|......|||||+|.+.++|+.|+..|||..|+|
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            34568999999954432           5899999999999999977544556899999999999999999999999999


Q ss_pred             cee
Q 022301          174 AFS  176 (299)
Q Consensus       174 ~~~  176 (299)
                      +.+
T Consensus        92 r~l   94 (112)
T 2dit_A           92 RQI   94 (112)
T ss_dssp             EEC
T ss_pred             cEE
Confidence            944

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

Probab=99.39  E-value=5.4e-13  Score=96.22  Aligned_cols=60  Identities=15%  Similarity=0.250  Sum_probs=53.4

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC-------CCCEEEEEecChhhHHHHHHhc
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG-------SGTTGIVDYTNYDDMKHAIKKL  166 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~-------~~~~~fv~f~~~~~a~~a~~~l  166 (299)
                      ....+|||+|||..+++++|+++|.+||.|. +.++.+.       ..|||||+|.+.++|+.|++.|
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~   72 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDAC   72 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHS
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhh
Confidence            3457999999999999999999999999999 7776653       3479999999999999999998

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

Probab=99.38  E-value=3.6e-12  Score=90.08  Aligned_cols=74  Identities=14%  Similarity=0.170  Sum_probs=62.4

Q ss_pred             CCccEEEEeCCCC-----CCCHHHHHHHHHhcCCeeEEEEEeCC-----CCCEEEEEecChhhHHHHHHhcCCCeecCce
Q 022301          106 RSEYRVLVTGLPS-----SASWQDLKDHMRRAGDVCFSQVFRDG-----SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAF  175 (299)
Q Consensus       106 ~~~~~l~v~nl~~-----~~~~~~l~~~f~~~G~v~~~~~~~~~-----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  175 (299)
                      .+..+|+|.|+..     +.++++|+++|++||.|..+.|+.++     ..|||||+|.+.++|.+|++.|||..++|+.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            3457899999863     23789999999999999999999864     2479999999999999999999999999996


Q ss_pred             eeEE
Q 022301          176 SRAY  179 (299)
Q Consensus       176 ~~~~  179 (299)
                      +.+.
T Consensus        86 i~v~   89 (105)
T 2pe8_A           86 VKAC   89 (105)
T ss_dssp             CEEE
T ss_pred             EEEE
Confidence            5443

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.36  E-value=3.9e-12  Score=91.09  Aligned_cols=74  Identities=18%  Similarity=0.223  Sum_probs=65.9

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecC-hHHHHHHHHhcC--CCCCCCceEEEEE
Q 022301            4 RASRTLYVGNLPGD-IREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEE-ARDAEDAIRGRD--GYDFDGHRLRVEL   79 (299)
Q Consensus         4 ~~~~~l~V~nLp~~-~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~-~e~A~~A~~~l~--~~~~~g~~i~v~~   79 (299)
                      .+.+.|||+||+.. ++.++|+++|+.||+|..|.|..+.   ..|||.|.+ +++|..|+..||  +..|.|..+++..
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            46899999999999 9999999999999999999997543   379999999 899999999995  6888999888876


Q ss_pred             c
Q 022301           80 A   80 (299)
Q Consensus        80 ~   80 (299)
                      .
T Consensus        93 L   93 (121)
T 1owx_A           93 L   93 (121)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.35  E-value=7.4e-12  Score=98.75  Aligned_cols=71  Identities=17%  Similarity=0.272  Sum_probs=62.4

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC---CEEEEEecChhhHHHHHHhcCCCeecCceeeE
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG---TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA  178 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  178 (299)
                      ...+|||+|||..+++++|.++|.+||.|..|.+..+..+   |||||+|.+.++|+.|+..++ ..++|+.+.+
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V  181 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLI  181 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEE
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEE
Confidence            3579999999999999999999999999999999987543   699999999999999998665 5899996543

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.29  E-value=6.1e-12  Score=101.56  Aligned_cols=65  Identities=14%  Similarity=0.248  Sum_probs=60.1

Q ss_pred             CCCccEEEEeCCCCCC---------CHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCee
Q 022301          105 RRSEYRVLVTGLPSSA---------SWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEF  171 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~---------~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~  171 (299)
                      .....+|||+||+..+         ++++|.++|.+||.|..|.|+..  .|||||+|.+.++|+.|++.|+|..|
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            4467899999999998         79999999999999999999865  46999999999999999999999999

>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=99.27  E-value=1.4e-11  Score=104.81  Aligned_cols=67  Identities=16%  Similarity=0.155  Sum_probs=59.5

Q ss_pred             CCCCccEEEEeC--CCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeec
Q 022301          104 SRRSEYRVLVTG--LPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFR  172 (299)
Q Consensus       104 ~~~~~~~l~v~n--l~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~  172 (299)
                      ...+..+|||+|  |+..+++++|+++|.+||+|..|.+..  ..|||||+|.+.++|++|++.|||.++.
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~--~kgfaFV~f~~~~~A~~Ai~~lnG~~~~   82 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP--NKPYSFARYRTTEESKRAYVTLNGKEVV   82 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT--TCSEEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC--CCCEEEEEECCHHHHHHHHHHhCCCccc
Confidence            345678999999  578899999999999999999887754  5579999999999999999999999984

>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=99.26  E-value=2.1e-11  Score=86.20  Aligned_cols=74  Identities=18%  Similarity=0.188  Sum_probs=61.3

Q ss_pred             CccEEEEeCC--CCCCC--------HHHHHHHHHhcCCeeEEEEEeCC------CCCEEEEEecChhhHHHHHHhcCCCe
Q 022301          107 SEYRVLVTGL--PSSAS--------WQDLKDHMRRAGDVCFSQVFRDG------SGTTGIVDYTNYDDMKHAIKKLDDSE  170 (299)
Q Consensus       107 ~~~~l~v~nl--~~~~~--------~~~l~~~f~~~G~v~~~~~~~~~------~~~~~fv~f~~~~~a~~a~~~l~g~~  170 (299)
                      +...|.|.|+  |..+.        +++|+++|++||.|..+.|+.+.      ..|+|||+|.+.++|.+|+..|||..
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            4568889997  32332        47999999999999999998775      34799999999999999999999999


Q ss_pred             ecCceeeEEE
Q 022301          171 FRNAFSRAYV  180 (299)
Q Consensus       171 ~~g~~~~~~~  180 (299)
                      ++|+.+.+..
T Consensus        84 f~GR~i~v~~   93 (105)
T 3v4m_A           84 FANRVVVTKY   93 (105)
T ss_dssp             ETTEECEEEE
T ss_pred             eCCCEEEEEE
Confidence            9999665443

>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=99.25  E-value=4e-11  Score=85.75  Aligned_cols=76  Identities=12%  Similarity=0.069  Sum_probs=63.0

Q ss_pred             CCccEEEEeCCCCCC----------CHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCce
Q 022301          106 RSEYRVLVTGLPSSA----------SWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAF  175 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~----------~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  175 (299)
                      .+...|.|.|+-...          -+++|.++|++||.|..+.+..+...|+|||+|.+.++|.+|+..|||..++|+.
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~   84 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKM   84 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            345678888863321          2568899999999999999988877789999999999999999999999999997


Q ss_pred             eeEEEE
Q 022301          176 SRAYVR  181 (299)
Q Consensus       176 ~~~~~~  181 (299)
                      +.+...
T Consensus        85 i~v~~~   90 (114)
T 3s6e_A           85 ITAAYV   90 (114)
T ss_dssp             CEEEEE
T ss_pred             EEEEEE
Confidence            655443

>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=99.23  E-value=3.6e-11  Score=86.59  Aligned_cols=74  Identities=14%  Similarity=0.192  Sum_probs=62.0

Q ss_pred             CccEEEEeCCCC--CC---CHHHHHHHHHhcCCeeEEEEEeCCCC--------CEEEEEecChhhHHHHHHhcCCCeecC
Q 022301          107 SEYRVLVTGLPS--SA---SWQDLKDHMRRAGDVCFSQVFRDGSG--------TTGIVDYTNYDDMKHAIKKLDDSEFRN  173 (299)
Q Consensus       107 ~~~~l~v~nl~~--~~---~~~~l~~~f~~~G~v~~~~~~~~~~~--------~~~fv~f~~~~~a~~a~~~l~g~~~~g  173 (299)
                      +..+|+|.|+-.  ++   -+++|++.|.+||+|..|.|+.+..+        |++||+|.+.++|.+|+..|||..++|
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            457889999732  22   37899999999999999999987542        699999999999999999999999999


Q ss_pred             ceeeEEE
Q 022301          174 AFSRAYV  180 (299)
Q Consensus       174 ~~~~~~~  180 (299)
                      +.+.+..
T Consensus        99 R~i~v~~  105 (118)
T 3ue2_A           99 RKVVAEV  105 (118)
T ss_dssp             EECEEEE
T ss_pred             cEEEEEE
Confidence            9665444

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.23  E-value=3.6e-11  Score=80.55  Aligned_cols=74  Identities=16%  Similarity=0.261  Sum_probs=61.7

Q ss_pred             CCCCeEEEcCCC----CCCCH----HHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceE
Q 022301            4 RASRTLYVGNLP----GDIRE----REVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRL   75 (299)
Q Consensus         4 ~~~~~l~V~nLp----~~~t~----~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i   75 (299)
                      -|.-||+|.-++    .+.-+    .+|.+.|.+||+|..++|..     +.+||+|.+.++|.+|+. |||..+.|+.|
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~-----d~~fVtF~d~~sAlaAi~-mnG~~v~Gr~L   78 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVE-----DKMWVTFLEGSSALNVLS-LNGKELLNRTI   78 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECS-----SSEEEEESSHHHHHHGGG-GTTCEETTEEE
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEec-----CCEEEEECChHHHHHHHh-cCCeEeCCeEE
Confidence            466788886665    23333    56999999999999999974     348999999999999999 99999999999


Q ss_pred             EEEEccCC
Q 022301           76 RVELAHGG   83 (299)
Q Consensus        76 ~v~~~~~~   83 (299)
                      +|+++.+.
T Consensus        79 kV~lkt~d   86 (91)
T 2dnr_A           79 TIALKSPS   86 (91)
T ss_dssp             EEEECCCS
T ss_pred             EEEeCCCC
Confidence            99998654

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.18  E-value=9e-11  Score=84.00  Aligned_cols=75  Identities=13%  Similarity=0.180  Sum_probs=65.7

Q ss_pred             CCCCCccEEEEeCCCCC-CCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecC-hhhHHHHHHhc--CCCeecCceeeE
Q 022301          103 VSRRSEYRVLVTGLPSS-ASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTN-YDDMKHAIKKL--DDSEFRNAFSRA  178 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~-~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~-~~~a~~a~~~l--~g~~~~g~~~~~  178 (299)
                      ....++..|+|.||+.. ++.++|+++|++||+|.+|.+..+..  .|||.|.+ ..+|.+|+..|  +|..|.|..+..
T Consensus        13 ~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~--tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~   90 (121)
T 1owx_A           13 LEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK--EGIILFKEKAKEALGKAKDANNGNLQLRNKEVTW   90 (121)
T ss_dssp             CSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS--EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEE
T ss_pred             ccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC--EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEE
Confidence            45567899999999999 99999999999999999999988876  79999999 79999999999  477888875543


Q ss_pred             E
Q 022301          179 Y  179 (299)
Q Consensus       179 ~  179 (299)
                      .
T Consensus        91 e   91 (121)
T 1owx_A           91 E   91 (121)
T ss_dssp             E
T ss_pred             E
Confidence            3

>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=99.15  E-value=1.6e-11  Score=86.68  Aligned_cols=65  Identities=20%  Similarity=0.248  Sum_probs=54.4

Q ss_pred             EeCCCCCCCHHHHHHHH------------HhcCCeeEEEEEeCCC---CCEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          113 VTGLPSSASWQDLKDHM------------RRAGDVCFSQVFRDGS---GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       113 v~nl~~~~~~~~l~~~f------------~~~G~v~~~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      +.||+..+++++|+++|            ++||.|..+.++.+..   .|||||+|.+.++|++|+..|||..++|+.+.
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            45666667777776666            9999999999988753   47999999999999999999999999999553

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

Probab=99.13  E-value=7.8e-10  Score=77.05  Aligned_cols=55  Identities=13%  Similarity=0.102  Sum_probs=47.8

Q ss_pred             CCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCce
Q 022301          118 SSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAF  175 (299)
Q Consensus       118 ~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  175 (299)
                      ..+++++|+++|.+||.|..|.|+ ....|||||+|.+.++|+.|++.+++  +.|+.
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~   81 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-SKKPGTAVVEFATVKAAELAVQNEVG--LVDNP   81 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSB
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCe
Confidence            568999999999999999999988 35667999999999999999998665  45663

>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=99.06  E-value=1.6e-10  Score=77.70  Aligned_cols=72  Identities=17%  Similarity=0.237  Sum_probs=60.5

Q ss_pred             CCCCeEEEcCCCCC-----CCH----HHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCce
Q 022301            4 RASRTLYVGNLPGD-----IRE----REVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHR   74 (299)
Q Consensus         4 ~~~~~l~V~nLp~~-----~t~----~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~   74 (299)
                      -|.-||+|.-++..     .-+    .+|.+.|.+||+|..+++..+     -+||+|.+.++|.+||. |||..+.|+.
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d-----~~fVtF~d~~sAl~AI~-ldG~~v~Gr~   86 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG-----QMLVTFADSHSALSVLD-VDGMKVKGRA   86 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT-----EEEEECSCSHHHHHHHH-GGGSEETTEE
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecC-----cEEEEEcChHHHHHHHh-cCCeeeCCeE
Confidence            56778999777643     222    458999999999999999743     39999999999999999 9999999999


Q ss_pred             EEEEEcc
Q 022301           75 LRVELAH   81 (299)
Q Consensus        75 i~v~~~~   81 (299)
                      |+|.+..
T Consensus        87 L~V~~k~   93 (95)
T 1ufw_A           87 VKISGPS   93 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEeccC
Confidence            9998753

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.02  E-value=1.1e-09  Score=73.32  Aligned_cols=74  Identities=18%  Similarity=0.146  Sum_probs=59.0

Q ss_pred             CccEEEEeCCCC----CCCH----HHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeE
Q 022301          107 SEYRVLVTGLPS----SASW----QDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA  178 (299)
Q Consensus       107 ~~~~l~v~nl~~----~~~~----~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  178 (299)
                      +..+|+|..++.    .+..    .+|.+.|.+||.|..+.+..+    .+||+|.+.++|.+|++ |||..++|+    
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d----~~fVtF~d~~sAlaAi~-mnG~~v~Gr----   76 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED----KMWVTFLEGSSALNVLS-LNGKELLNR----   76 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS----SEEEEESSHHHHHHGGG-GTTCEETTE----
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC----CEEEEECChHHHHHHHh-cCCeEeCCe----
Confidence            446777776652    3333    779999999999999999988    48999999999999999 999999999    


Q ss_pred             EEEecccccCC
Q 022301          179 YVRVREYDHRR  189 (299)
Q Consensus       179 ~~~~~~~~~~~  189 (299)
                      .++|....+.+
T Consensus        77 ~LkV~lkt~dW   87 (91)
T 2dnr_A           77 TITIALKSPSG   87 (91)
T ss_dssp             EEEEEECCCSS
T ss_pred             EEEEEeCCCCc
Confidence            55555554443

>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=98.94  E-value=1.5e-09  Score=87.59  Aligned_cols=77  Identities=25%  Similarity=0.309  Sum_probs=63.2

Q ss_pred             CCCeEEEcCCCC-----CCCHHHHHHHhhhcCCeeEEEeec-------CCCCCceEEEEecChHHHHHHHHhcCCCCCCC
Q 022301            5 ASRTLYVGNLPG-----DIREREVEDLFYKYGPIAHIDLKI-------PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDG   72 (299)
Q Consensus         5 ~~~~l~V~nLp~-----~~t~~~l~~~F~~~G~v~~i~~~~-------~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g   72 (299)
                      .+..|.+.|+-.     .-.+++|.+.|++||+|..+.|..       ++.++|++||+|.+.++|.+|+..|||.+|.|
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            344555555522     234678999999999999999942       23677999999999999999999999999999


Q ss_pred             ceEEEEEcc
Q 022301           73 HRLRVELAH   81 (299)
Q Consensus        73 ~~i~v~~~~   81 (299)
                      +.|.|.++.
T Consensus       203 r~i~~~~~~  211 (222)
T 3dxb_A          203 RKVVAEVYD  211 (222)
T ss_dssp             SBCEEEECC
T ss_pred             eEEEEEEcC
Confidence            999999974

>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=98.83  E-value=8.5e-09  Score=69.37  Aligned_cols=66  Identities=9%  Similarity=0.147  Sum_probs=55.9

Q ss_pred             CCccEEEEeCCCCC-----CCH----HHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          106 RSEYRVLVTGLPSS-----ASW----QDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       106 ~~~~~l~v~nl~~~-----~~~----~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ++..+|+|..++..     +..    .+|.+.|.+||+|..+.+..+.    +||+|.+.++|.+||. |||.+++|+.+
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~----~fVtF~d~~sAl~AI~-ldG~~v~Gr~L   87 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ----MLVTFADSHSALSVLD-VDGMKVKGRAV   87 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE----EEEECSCSHHHHHHHH-GGGSEETTEEE
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc----EEEEEcChHHHHHHHh-cCCeeeCCeEE
Confidence            45578888887642     322    6699999999999999999884    9999999999999999 99999999944

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.77  E-value=4e-08  Score=67.40  Aligned_cols=72  Identities=15%  Similarity=0.155  Sum_probs=65.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhc-----CCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKY-----GPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVE   78 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-----G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~   78 (299)
                      +..++|-|-|||..+++..|..|+..+     |.|..|.+..+   -+-|+|+|.+...|-+|.-.|+|..|.|++|.|.
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD---H~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~g   95 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD---FNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSG   95 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT---TTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC---CCceEEEEccchhhHHHHhhcCCeeecCeEEEec
Confidence            347899999999999999999999999     99999999754   3579999999999999998899999999999985

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.64  E-value=5.1e-07  Score=61.47  Aligned_cols=89  Identities=24%  Similarity=0.339  Sum_probs=71.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhh-----cCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYK-----YGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVE   78 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~-----~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~   78 (299)
                      ...++|.|.|||+.+.++.|.-+|++     =|+|..+....     +-|+|+|.+.+.|+..|. -....|.+..|.|.
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-----~~AvItF~d~~va~rVL~-k~~H~L~~~~LsV~   79 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-----CGGVLTFREPADAERVLA-QADHELHGAQLSLR   79 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-----TEEEEEESSHHHHHHHHT-CSCCBSSSSBCEEE
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-----CcEEEEEcChHHHHHHhc-CCcceecCeEEEEE
Confidence            46789999999999999999999997     25899998863     689999999999999998 44678888999997


Q ss_pred             EccCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCC
Q 022301           79 LAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSAS  121 (299)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~  121 (299)
                      ....                       .....|++.+|++.++
T Consensus        80 P~~~-----------------------~~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           80 PAPP-----------------------RAPARLLLQGLPPGTS   99 (104)
T ss_dssp             ECCC-----------------------CCCCCCCCCSCCCCCC
T ss_pred             cCCC-----------------------CCcceEeeecCCCCCC
Confidence            6432                       2235677777777653

>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=98.58  E-value=4.6e-07  Score=62.04  Aligned_cols=76  Identities=20%  Similarity=0.228  Sum_probs=65.1

Q ss_pred             CCCCCeEEEcCCCCCC-C----HHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEE
Q 022301            3 SRASRTLYVGNLPGDI-R----EREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRV   77 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~-t----~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v   77 (299)
                      +.-.++|+|+||+..+ +    .+.++++|..|+++....+.   ++-.-..|.|.++++|.+|-..||+..|.|..|+|
T Consensus         2 s~~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~l---kSFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            2 SSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF---KSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CSCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEE---TTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CCCCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeec---CcceEEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            3567899999998864 2    25688999999999888886   33447899999999999999999999999999999


Q ss_pred             EEcc
Q 022301           78 ELAH   81 (299)
Q Consensus        78 ~~~~   81 (299)
                      .++.
T Consensus        79 YFgq   82 (104)
T 1wey_A           79 YFAQ   82 (104)
T ss_dssp             ECCC
T ss_pred             EecC
Confidence            9987

>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=98.48  E-value=2.7e-07  Score=74.23  Aligned_cols=61  Identities=16%  Similarity=0.214  Sum_probs=52.7

Q ss_pred             CCHHHHHHHHHhcCCeeEEEEEeCCCC--------CEEEEEecChhhHHHHHHhcCCCeecCceeeEEE
Q 022301          120 ASWQDLKDHMRRAGDVCFSQVFRDGSG--------TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYV  180 (299)
Q Consensus       120 ~~~~~l~~~f~~~G~v~~~~~~~~~~~--------~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~  180 (299)
                      -.+++|.+.|.+||.|..+.+..+...        |++||+|.+.++|.+|+..|||..++|+.+.+..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~  209 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEV  209 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEE
Confidence            357899999999999999999865432        6999999999999999999999999999765443

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.38  E-value=3e-06  Score=58.13  Aligned_cols=68  Identities=13%  Similarity=0.100  Sum_probs=61.8

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhc-----CCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRA-----GDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~-----G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ...+|-+-|||..+++..|..++.++     |.+..+.+..+-.  -|+|+|.+...|-+|.-.|+|.+|+|+.+
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~--GAivef~d~~~AgKasLaL~G~ef~gr~L   92 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFN--GAIIIFRDSKFAAKMLMILNGSQFQGKVI   92 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTT--EEEEECSCHHHHHHHHHHHSSEEETTEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCC--ceEEEEccchhhHHHHhhcCCeeecCeEE
Confidence            35789999999999999999999999     9999988887765  79999999999999999999999999844

>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=98.12  E-value=7.8e-06  Score=55.05  Aligned_cols=65  Identities=15%  Similarity=0.232  Sum_probs=54.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC-----CCCCceEEEEecChHHHHHHHHhcCCCCCC
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEARDAEDAIRGRDGYDFD   71 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~-----~~~~g~afV~F~~~e~A~~A~~~l~~~~~~   71 (299)
                      ++|.|.+||+.+|++++.+.+..+..+....+...     .....-|||.|.+.+++......++|..|.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            57899999999999999999999988776666321     123367999999999999999999998764

>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=1.1e-05  Score=54.16  Aligned_cols=55  Identities=20%  Similarity=0.344  Sum_probs=47.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRD   66 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~   66 (299)
                      ...++| ++|+.....||.++|+.||.|.--+|.     -..|||.|.+++.|..|+..+.
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            467778 999999999999999999977666665     2389999999999999999763

>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=98.02  E-value=1.7e-05  Score=55.89  Aligned_cols=71  Identities=17%  Similarity=0.233  Sum_probs=59.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCC-ceEEEEEc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDG-HRLRVELA   80 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g-~~i~v~~~   80 (299)
                      ..+.|.|-+.|+.. ...|...|.+||+|......   ...++..|.|.+..+|++||. .||..|.| ..|-|.++
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~---~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS---NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC---SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC---CCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            36788899999985 67888999999999998872   335699999999999999999 89999985 55666664

>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=53.97  Aligned_cols=54  Identities=20%  Similarity=0.344  Sum_probs=45.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcC
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRD   66 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~   66 (299)
                      ..++| ++|+.....||.++|+.||.|.--+|.     -..|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv~I~Wid-----DTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNIQISWID-----DTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEEEEEEEE-----TTEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCEEEEEEc-----CCeEEEEecCHHHHHHHHHhcc
Confidence            46777 999999999999999999955544444     2389999999999999999764

>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=97.89  E-value=5.4e-05  Score=51.79  Aligned_cols=71  Identities=14%  Similarity=0.118  Sum_probs=58.9

Q ss_pred             ccEEEEeCCCCCC-C----HHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEE
Q 022301          108 EYRVLVTGLPSSA-S----WQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYV  180 (299)
Q Consensus       108 ~~~l~v~nl~~~~-~----~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~  180 (299)
                      .++|+|+||+..+ .    .+.++++|..|+++......+.-.  =..|.|.+.++|..|-..||+..+.|..+..|.
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR--Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YF   80 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK--RVRINFSNPLSAADARLRLHKTEFLGKEMKLYF   80 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT--EEEEECSSTTHHHHHHHTSTTSEETTEECEEEC
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce--EEEEEeCChHHHHHHHHHhccceecCceeEEEe
Confidence            4789999998865 2    367899999999999887776643  478999999999999999999999999654443

>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=97.73  E-value=0.00027  Score=47.55  Aligned_cols=67  Identities=15%  Similarity=0.361  Sum_probs=57.8

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC------CEEEEEecChhhHHHHHHhcCCCeecCce
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG------TTGIVDYTNYDDMKHAIKKLDDSEFRNAF  175 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~------~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  175 (299)
                      ++|.|.+||+.+|++++.+.+.....+....+......      .-|||.|.+.+++..-.+.++|..+.+..
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            47899999999999999999999998877777666432      27999999999999999999999887654

>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=97.72  E-value=0.0002  Score=50.42  Aligned_cols=67  Identities=15%  Similarity=0.212  Sum_probs=55.5

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCce
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAF  175 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  175 (299)
                      .....-|.|.+.|... ...|..+|.+||.|.....  .....+..|.|.+..+|++||. .||..|+|..
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~--~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~   87 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVM--SNTGNWMHIRYQSKLQARKALS-KDGRIFGESI   87 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEE--CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTE
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEecc--CCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCE
Confidence            3456789999999875 6778889999999998776  3344599999999999999999 6999998754

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.69  E-value=7.3e-05  Score=50.57  Aligned_cols=77  Identities=19%  Similarity=0.244  Sum_probs=54.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC-----CCCCceEEEEecChHHHHHHHHhcCCCCCCCc-----e
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGH-----R   74 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~-----~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~-----~   74 (299)
                      .+-+|.|..||+.+|++++.+.+..+-++....+...     .....-|||.|.+.+++......++|..|.+.     +
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            3567999999999999998888877655433333111     11225789999999999999999999766422     3


Q ss_pred             EEEEEcc
Q 022301           75 LRVELAH   81 (299)
Q Consensus        75 i~v~~~~   81 (299)
                      ..|++|.
T Consensus        88 a~VE~AP   94 (97)
T 2l08_A           88 AVVEFAP   94 (97)
T ss_dssp             EEEEECC
T ss_pred             eEEEecC
Confidence            4566653

>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=97.66  E-value=0.00028  Score=47.47  Aligned_cols=54  Identities=15%  Similarity=0.188  Sum_probs=44.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcC
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLD  167 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~  167 (299)
                      ..++| ++|..+...||.++|..||.|. |..+.|.   .|||.|.+.+.|..|+..+.
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~fggv~-I~WidDT---sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT---SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTTCSCC-CEEEETT---EEEEECSCHHHHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhccCCEE-EEEEcCC---eEEEEecCHHHHHHHHHhcc
Confidence            45555 9999999999999999999554 4444443   89999999999999999763

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.51  E-value=0.00064  Score=46.29  Aligned_cols=63  Identities=22%  Similarity=0.286  Sum_probs=50.8

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHh-----cCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCc
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRR-----AGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNA  174 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~-----~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  174 (299)
                      ...+|.|.|||+.+.++.|.-+|+.     -|.|..++...    .-|+|+|.+...|+..+++ ....|.+.
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~----~~AvItF~d~~va~rVL~k-~~H~L~~~   74 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG----CGGVLTFREPADAERVLAQ-ADHELHGA   74 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET----TEEEEEESSHHHHHHHHTC-SCCBSSSS
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC----CcEEEEEcChHHHHHHhcC-CcceecCe
Confidence            4579999999999999999999998     24788887765    4899999999999999985 22344444

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=97.47  E-value=0.00013  Score=52.16  Aligned_cols=75  Identities=20%  Similarity=0.275  Sum_probs=55.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEE-eec---------------CC-CCCceEEEEecChHHHHHHHHhcC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHID-LKI---------------PP-RPPGYAFVEFEEARDAEDAIRGRD   66 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~-~~~---------------~~-~~~g~afV~F~~~e~A~~A~~~l~   66 (299)
                      +....|.|-+.|+.++ ..|.+.|++||.|.+-. +..               .. ...+...|+|.+..+|.+||. .|
T Consensus         5 ~~e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~N   82 (132)
T 3p3d_A            5 NGELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-EN   82 (132)
T ss_dssp             ---CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TT
T ss_pred             cCceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hC
Confidence            4566778888877755 56778999999987722 110               11 134688999999999999999 99


Q ss_pred             CCCCCCceEEEEEc
Q 022301           67 GYDFDGHRLRVELA   80 (299)
Q Consensus        67 ~~~~~g~~i~v~~~   80 (299)
                      |..|.|.-|-|.+.
T Consensus        83 G~ii~G~mIGV~Py   96 (132)
T 3p3d_A           83 GAVFNGVLLGVIPY   96 (132)
T ss_dssp             TCEETTEECEEEEC
T ss_pred             CeEeCcEEEEEEEC
Confidence            99999987777765

>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=97.40  E-value=0.00033  Score=47.27  Aligned_cols=53  Identities=17%  Similarity=0.188  Sum_probs=43.8

Q ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcC
Q 022301          110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLD  167 (299)
Q Consensus       110 ~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~  167 (299)
                      .++| ++|..+...||.++|..||. ..|..+.+.   .|||.|.+.+.|..|+..+.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fgg-v~I~WidDT---sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT---SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEETT---EEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccCC-EEEEEEcCC---eEEEEecCHHHHHHHHHhcc
Confidence            4555 99999999999999999994 345555553   89999999999999999764

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.99  E-value=0.00039  Score=61.26  Aligned_cols=56  Identities=25%  Similarity=0.313  Sum_probs=43.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHH
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIR   63 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~   63 (299)
                      +.++|+|. .|..+++.+|.++|++||+|.++.+..+.  .-||.|||.+.++|..++.
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            45789996 79999999999999999999999996433  3699999999999998776

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.83  E-value=0.0014  Score=44.22  Aligned_cols=69  Identities=16%  Similarity=0.277  Sum_probs=52.7

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC------CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG------TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~------~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..+|.|..||+.+|++++.+.+...-++....+......      .-|||.|.+.++...-.+.++|..+.+...
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg   83 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKG   83 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTC
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCC
Confidence            468999999999999998888877655433333222211      169999999999999999999999876543

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.42  E-value=0.0039  Score=44.49  Aligned_cols=66  Identities=18%  Similarity=0.263  Sum_probs=48.6

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeE-EEEEe--------------CC---CCCEEEEEecChhhHHHHHHhcCC
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCF-SQVFR--------------DG---SGTTGIVDYTNYDDMKHAIKKLDD  168 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~-~~~~~--------------~~---~~~~~fv~f~~~~~a~~a~~~l~g  168 (299)
                      ....|.|.+.|+... ..+.+.|++||.|.. +.+..              -+   ...+..|.|.+..+|++||. .||
T Consensus         6 ~e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG   83 (132)
T 3p3d_A            6 GELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENG   83 (132)
T ss_dssp             --CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTT
T ss_pred             CceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCC
Confidence            346788889977654 556678999999876 21110              01   23488999999999999999 899


Q ss_pred             CeecCc
Q 022301          169 SEFRNA  174 (299)
Q Consensus       169 ~~~~g~  174 (299)
                      ..|+|.
T Consensus        84 ~ii~G~   89 (132)
T 3p3d_A           84 AVFNGV   89 (132)
T ss_dssp             CEETTE
T ss_pred             eEeCcE
Confidence            999996

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.18  E-value=0.015  Score=51.22  Aligned_cols=56  Identities=13%  Similarity=0.205  Sum_probs=41.8

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHh
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKK  165 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~  165 (299)
                      ...|+|. .|..+++.+|.++|++||+|..+.+..+. +.||.|+|.+.+++..++..
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-GLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-SEEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-CeEEEEEeCCHHHHHHHHhc
Confidence            3578887 68889999999999999999999888654 35999999999999877653

>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=94.77  E-value=0.066  Score=48.07  Aligned_cols=56  Identities=20%  Similarity=0.305  Sum_probs=45.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG   67 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~   67 (299)
                      ..+++|+ +|..+...+|.++|+.||.|.-.++.     ...|||.|.+.+.|..++..++.
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v~V~wid-----dt~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNIQISWID-----DTSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCCEEEECS-----SSEEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCEEEEEEc-----CCeEEEEECCHHHHHHHHHHHHh
Confidence            3577886 99999999999999999965444443     34799999999999999998853

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=91.31  E-value=0.97  Score=28.75  Aligned_cols=68  Identities=19%  Similarity=0.269  Sum_probs=45.1

Q ss_pred             eEEEcCC-CCCCCHHHHHHHhhhcC-----CeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            8 TLYVGNL-PGDIREREVEDLFYKYG-----PIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         8 ~l~V~nL-p~~~t~~~l~~~F~~~G-----~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      +|||..- -..+...+|..++..-+     .|-.|.+.     ..|.||+.... .|..++..|++..+.|+.+.|..+.
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-----DNASYVEILNG-KGPHVLKVMKNTTVKGKQLKVNKAN   75 (76)
T ss_dssp             EEEESCCCC----CHHHHHHHHTSTTCCGGGEEEEEEC-----SSCEEEEECTT-CHHHHHHHHTTCCC---CCCEEECC
T ss_pred             EEEEeCCCccCCCHHHHHHHHHHccCCChhhccEEEEe-----CCcEEEEECHH-HHHHHHHHhccccCcCceEEEEECC
Confidence            5777322 33478888888888655     45666665     45999999765 6778888899999999999987653

>4eyt_A Telomerase associated protein P65; RNA, LA protein, LARP7, RRM, XRRM, RNA binding protein; 2.50A {Tetrahymena thermophila} PDB: 4erd_A

Probab=90.25  E-value=2.6  Score=27.47  Aligned_cols=69  Identities=19%  Similarity=0.235  Sum_probs=52.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      +.+|-|.|-|||..+-..++.-.....|---.|...     -|.|.|.|.+.++-..|+..|-+.  .+.+|.++.
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            467889999999999888888777888866677775     478999999999999998875432  234555544

>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=89.62  E-value=1.1  Score=40.23  Aligned_cols=55  Identities=16%  Similarity=0.221  Sum_probs=44.0

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcC
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLD  167 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~  167 (299)
                      ...++|+ +|..+...+|.++|+.||.| .|..+.+.   .|||.|.+.+.|..++..+.
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            4566665 89999999999999999954 34444332   89999999999999999875

>4eyt_A Telomerase associated protein P65; RNA, LA protein, LARP7, RRM, XRRM, RNA binding protein; 2.50A {Tetrahymena thermophila} PDB: 4erd_A

Probab=88.63  E-value=3.5  Score=26.85  Aligned_cols=56  Identities=16%  Similarity=0.322  Sum_probs=47.9

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhc
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKL  166 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l  166 (299)
                      .++-|.|-|+|..+-..++.-.....|--..|..+..    .|.|.|.+.++..-|+.+|
T Consensus        11 qnclikiinipqgtlkaevvlavrhlgyefycdyidg----qamirfqnsdeqrlaiqkl   66 (129)
T 4eyt_A           11 QNCLIKIINIPQGTLKAEVVLAVRHLGYEFYCDYIDG----QAMIRFQNSDEQRLAIQKL   66 (129)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHTTCCCEEEEECSS----CEEEEESSHHHHHHHHHHH
T ss_pred             hCcEEEEEecCCCceeeeeEEeehhcCeeEeeeeecC----eeEEEecCChHHHHHHHHH
Confidence            4577889999999999888888888898888877655    7999999999999898876

>4e8u_A Putative uncharacterized protein T8P19.180; XS domain, RNA binding protein, RNA directed DNA methylation; 2.70A {Arabidopsis thaliana}

Probab=83.87  E-value=1.5  Score=32.80  Aligned_cols=56  Identities=20%  Similarity=0.230  Sum_probs=39.8

Q ss_pred             eEEEcCCCC-C--------CCHHHHHHHh--hhcCCeeEEEeecCCCCCceEEEEecChHHH-HHHHH
Q 022301            8 TLYVGNLPG-D--------IREREVEDLF--YKYGPIAHIDLKIPPRPPGYAFVEFEEARDA-EDAIR   63 (299)
Q Consensus         8 ~l~V~nLp~-~--------~t~~~l~~~F--~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A-~~A~~   63 (299)
                      ++.|-|+|. .        ....+|.+.|  ..|.++.-..+.......|+|.|+|...-.. ..|+.
T Consensus        14 mgIl~N~~t~~~~dg~~~G~s~~~l~~~~~~~~F~p~kv~~l~~~~Gh~g~aIv~F~~dw~Gf~~A~~   81 (172)
T 4e8u_A           14 KGIVVNIPTTKAQDGRSAGESGSKLRDEYILRGFNPTRVRPLWNYLGHSGTAIVEFNKDWNGLHNGLL   81 (172)
T ss_dssp             EEEEECCCCEECTTSCEECCCSHHHHHHHHHTTCCCSEEEEEECSSBEEEEEEEECCSSHHHHHHHHH
T ss_pred             EEEEEeccccccCCCCccCCCHHHHHHHHHhcCCCCceeEecccCCCCceeEEEEecCChHHHHHHHH
Confidence            456779887 2        4567899977  8999988777755555678999999865443 33444

---

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	299
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-21
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-04
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-19
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	7e-08
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	5e-19
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-06
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-18
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-05
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-18
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-05
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-17
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-06
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	4e-17
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	9e-06
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	7e-17
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-04
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-16
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	0.002
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	9e-05
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-16
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-05
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-16
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-04
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	4e-16
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-05
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	4e-16
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-04
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	6e-16
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	4e-04
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-15
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-15
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-06
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-15
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	0.001
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	4e-15
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	6e-05
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	4e-15
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-04
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-15
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-05
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	5e-15
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	7e-05
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-15
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	8e-15
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	8e-15
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	7e-05
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-14
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	0.001
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-14
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-04
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	3e-14
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	5e-14
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-04
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	7e-14
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-13
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-05
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-13
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	0.002
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-13
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-04
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	3e-13
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-13
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	3e-13
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	0.002
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	6e-13
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	0.002
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	9e-13
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	9e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-12
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-12
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	0.002
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-12
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-12
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-04
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	4e-12
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	4e-12
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	2e-04
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	4e-12
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	5e-12
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-09
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	5e-12
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	6e-12
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	7e-12
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-11
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-11
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-05
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	3e-11
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-11
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	4e-11
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	4e-11
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	3e-04
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 5e-11
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	5e-11
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	6e-11
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	6e-11
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-11
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	1e-10
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-10
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	1e-10
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-10
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	7e-04
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	7e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	1e-06
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	8e-10
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	1e-09
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	2e-09
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	0.001
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	5e-09
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	6e-09
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	1e-08
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	4e-07
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-08
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	3e-08
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-08
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.002
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	6e-08
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-07
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-07
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	8e-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	1e-05
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	9e-06
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	2e-04
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-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 = 84.7 bits (209), Expect = 3e-21
 Identities = 29/91 (31%), Positives = 43/91 (47%)

Query: 1  MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
          +    +R LY+ NLP  I   E+ D+F KYGPI  I +   P   G A+V +E+  DA++
Sbjct: 2  LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKN 61

Query: 61 AIRGRDGYDFDGHRLRVELAHGGRGRSSSDR 91
          A     G++     L V   +  R     D 
Sbjct: 62 ACDHLSGFNVCNRYLVVLYYNANRAFQKMDT 92

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.8 bits (90), Expect = 1e-04
 Identities = 17/90 (18%), Positives = 34/90 (37%), Gaps = 5/90 (5%)

Query: 111 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGT-TGIVDYTNYDDMKHAIKKLDDS 169
           + +  LP   + +++ D   + G +   +V        T  V Y +  D K+A   L   
Sbjct: 10  LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGF 69

Query: 170 EFRNAFSRAYVRVREYDHRRDGSQSPSRGR 199
              N     Y+ V  Y+  R   +  ++ +
Sbjct: 70  NVCN----RYLVVLYYNANRAFQKMDTKKK 95

>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 = 78.5 bits (193), Expect = 3e-19
 Identities = 25/80 (31%), Positives = 39/80 (48%), Gaps = 5/80 (6%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDAEDAI 62
             LYV NLP  I + +++ +F KYG I   ++        P G AFV + +  +A++AI
Sbjct: 6  DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 65

Query: 63 RGRDGYDFDG--HRLRVELA 80
             +    +G    L V LA
Sbjct: 66 SALNNVIPEGGSQPLSVRLA 85

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 47.3 bits (112), Expect = 7e-08
 Identities = 15/79 (18%), Positives = 27/79 (34%), Gaps = 4/79 (5%)

Query: 107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG----SGTTGIVDYTNYDDMKHA 162
            +  + VT LP + +   L     + G +    + RD           V Y   ++ + A
Sbjct: 5   KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 64

Query: 163 IKKLDDSEFRNAFSRAYVR 181
           I  L++           VR
Sbjct: 65  ISALNNVIPEGGSQPLSVR 83

>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 = 78.1 bits (192), Expect = 5e-19
 Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 5/84 (5%)

Query: 3  SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHI----DLKIPPRPPGYAFVEFEEARDA 58
           + +  + V N+P    +RE+ +LF  +G +  +     +       G+ FV+F   +DA
Sbjct: 5  KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 59 EDAIRG-RDGYDFDGHRLRVELAH 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 = 43.8 bits (103), Expect = 1e-06
 Identities = 15/70 (21%), Positives = 34/70 (48%), Gaps = 5/70 (7%)

Query: 105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGT-----TGIVDYTNYDDM 159
           +++  ++LV  +P  A+ +++++     G++   ++ +  +GT      G VD+    D 
Sbjct: 5   KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 160 KHAIKKLDDS 169
           K A   L  S
Sbjct: 65  KKAFNALCHS 74

>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 = 76.9 bits (189), Expect = 1e-18
 Identities = 29/86 (33%), Positives = 43/86 (50%), Gaps = 3/86 (3%)

Query: 4  RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAED 60
          + S TLYVGNL     E ++ +LF K G I  I +   K+     G+ FVE+    DAE+
Sbjct: 5  KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 64

Query: 61 AIRGRDGYDFDGHRLRVELAHGGRGR 86
          A+R  +G   D   +R +   G +  
Sbjct: 65 AMRYINGTRLDDRIIRTDWDAGFKEG 90

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.5 bits (92), Expect = 3e-05
 Identities = 12/85 (14%), Positives = 34/85 (40%), Gaps = 9/85 (10%)

Query: 110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGI----VDYTNYDDMKHAIKK 165
            + V  L    + + + +   ++GD+    +  D    T      V+Y +  D ++A++ 
Sbjct: 9   TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 68

Query: 166 LDDSEFRN-----AFSRAYVRVREY 185
           ++ +   +      +   +   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 = 76.1 bits (187), Expect = 2e-18
 Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 3/77 (3%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDAEDAIRG 64
          +LYVG+L  D+ E  + + F   GPI  I +          GYA+V F++  DAE A+  
Sbjct: 2  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 65 RDGYDFDGHRLRVELAH 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 = 40.7 bits (95), Expect = 1e-05
 Identities = 12/65 (18%), Positives = 23/65 (35%), Gaps = 4/65 (6%)

Query: 113 VTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG----SGTTGIVDYTNYDDMKHAIKKLDD 168
           V  L    +   L +    AG +   +V RD     S     V++    D + A+  ++ 
Sbjct: 5   VGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNF 64

Query: 169 SEFRN 173
              + 
Sbjct: 65  DVIKG 69

>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 = 73.8 bits (181), Expect = 1e-17
 Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPI--AHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRD 66
          L V NL   + + ++++LF ++G +  A +      R  G A V FE   DA  A++  +
Sbjct: 3  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 67 GYDFDGHRLRVELA 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 = 43.4 bits (102), Expect = 1e-06
 Identities = 14/67 (20%), Positives = 27/67 (40%), Gaps = 3/67 (4%)

Query: 110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGI---VDYTNYDDMKHAIKKL 166
           ++LV+ L    S  D+++     G +  + V  D SG +     V +    D   A+K+ 
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 61

Query: 167 DDSEFRN 173
           +      
Sbjct: 62  NGVPLDG 68

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 72.3 bits (177), Expect = 4e-17
 Identities = 27/82 (32%), Positives = 40/82 (48%), Gaps = 3/82 (3%)

Query: 5  ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDAEDA 61
          ++  L V  LP D+ +RE+  LF   GPI    +    +     GYAFV+F    D++ A
Sbjct: 1  SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 60

Query: 62 IRGRDGYDFDGHRLRVELAHGG 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 = 41.1 bits (96), Expect = 9e-06
 Identities = 18/71 (25%), Positives = 28/71 (39%), Gaps = 4/71 (5%)

Query: 107 SEYRVLVTGLPSSASWQDLKDHMRRAGDV----CFSQVFRDGSGTTGIVDYTNYDDMKHA 162
           S   ++V  LP   + ++L    R  G +             S     VD+T+  D + A
Sbjct: 1   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 60

Query: 163 IKKLDDSEFRN 173
           IK L+    RN
Sbjct: 61  IKVLNGITVRN 71

>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 = 71.9 bits (176), Expect = 7e-17
 Identities = 11/75 (14%), Positives = 31/75 (41%), Gaps = 4/75 (5%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDAEDAIRGR 65
          +++G L     +  + + F ++G +    +   P      G+ FV F +    +  +  +
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 66 DGYDFDGHRLRVELA 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 = 36.1 bits (83), Expect = 4e-04
 Identities = 11/60 (18%), Positives = 26/60 (43%), Gaps = 4/60 (6%)

Query: 110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD----GSGTTGIVDYTNYDDMKHAIKK 165
           ++ + GL    + + L+++  + G+V    V RD     S   G V + +   +   + +
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

>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 = 70.8 bits (173), Expect = 2e-16
 Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 2/84 (2%)

Query: 4  RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIR 63
          RA+RTL   NL  +I E E++++F     I  +      +  G A++EF+   DAE  + 
Sbjct: 14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVS--QDGKSKGIAYIEFKSEADAEKNLE 71

Query: 64 GRDGYDFDGHRLRVELAHGGRGRS 87
           + G + DG  + +       G  
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 = 34.6 bits (79), Expect = 0.002
 Identities = 9/68 (13%), Positives = 26/68 (38%), Gaps = 1/68 (1%)

Query: 106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKK 165
           R+   +L   L  + +  +LK+    A ++          G    +++ +  D +  +++
Sbjct: 14  RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKG-IAYIEFKSEADAEKNLEE 72

Query: 166 LDDSEFRN 173
              +E   
Sbjct: 73  KQGAEIDG 80

>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 = 20/79 (25%), Positives = 34/79 (43%), Gaps = 3/79 (3%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
          SS  + T+Y G +   + ++ +   F  +G I  I +       GY+FV F     A  A
Sbjct: 14 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRV---FPEKGYSFVRFSTHESAAHA 70

Query: 62 IRGRDGYDFDGHRLRVELA 80
          I   +G   +GH ++    
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 = 38.4 bits (89), Expect = 9e-05
 Identities = 12/70 (17%), Positives = 26/70 (37%), Gaps = 2/70 (2%)

Query: 104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAI 163
           S      V   G+ S  + Q ++      G +   +VF +       V ++ ++   HAI
Sbjct: 14  SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE--KGYSFVRFSTHESAAHAI 71

Query: 164 KKLDDSEFRN 173
             ++ +    
Sbjct: 72  VSVNGTTIEG 81

>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 = 70.4 bits (172), Expect = 2e-16
 Identities = 27/75 (36%), Positives = 34/75 (45%), Gaps = 3/75 (4%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGR 65
             L+VGNLP DI E E+  LF KYG    +      +  G+ F+  E    AE A    
Sbjct: 8  RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF---IHKDKGFGFIRLETRTLAEIAKVEL 64

Query: 66 DGYDFDGHRLRVELA 80
          D     G +LRV  A
Sbjct: 65 DNMPLRGKQLRVRFA 79

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.1 bits (96), Expect = 1e-05
 Identities = 12/64 (18%), Positives = 24/64 (37%), Gaps = 2/64 (3%)

Query: 110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDS 169
           R+ V  LP   + ++++    + G     +VF       G +        + A  +LD+ 
Sbjct: 10  RLFVGNLPPDITEEEMRKLFEKYG--KAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNM 67

Query: 170 EFRN 173
             R 
Sbjct: 68  PLRG 71

>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 = 70.4 bits (172), Expect = 3e-16
 Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 6/79 (7%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPG------YAFVEFEEARDAEDAI 62
          L++ NL     E  ++ +F K G I    +       G      + FVE+++   A+ A+
Sbjct: 1  LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 63 RGRDGYDFDGHRLRVELAH 81
          +   G+  DGH+L V ++ 
Sbjct: 61 KQLQGHTVDGHKLEVRISE 79

>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 = 37.3 bits (86), Expect = 2e-04
 Identities = 11/68 (16%), Positives = 24/68 (35%), Gaps = 7/68 (10%)

Query: 113 VTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTT-------GIVDYTNYDDMKHAIKK 165
           +  L  S + + LK    + G +    + +  +          G V+Y   +  + A+K+
Sbjct: 3   IKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQ 62

Query: 166 LDDSEFRN 173
           L       
Sbjct: 63  LQGHTVDG 70

>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 = 69.8 bits (170), Expect = 4e-16
 Identities = 14/77 (18%), Positives = 31/77 (40%), Gaps = 3/77 (3%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIA---HIDLKIPPRPPGYAFVEFEEARDAEDAIR 63
           TL++ N P    +R + DL      +A    +          +A+++     DA   + 
Sbjct: 2  CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 64 GRDGYDFDGHRLRVELA 80
            +G   +G+ 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 = 40.2 bits (93), Expect = 2e-05
 Identities = 12/70 (17%), Positives = 32/70 (45%), Gaps = 4/70 (5%)

Query: 108 EYRVLVTGLPSSASWQDLKDHMRRAGDV----CFSQVFRDGSGTTGIVDYTNYDDMKHAI 163
           E  + +T  P S + ++++D ++    V        +  + S     +D T+ +D ++ +
Sbjct: 1   ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 60

Query: 164 KKLDDSEFRN 173
           +KL+  +   
Sbjct: 61  EKLNGLKIEG 70

>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 = 69.6 bits (170), Expect = 4e-16
 Identities = 14/75 (18%), Positives = 36/75 (48%), Gaps = 4/75 (5%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDAEDAIRGR 65
          ++VG L  D  E ++ + F  +G +  I+L +  +     G+ F+ F+E    +  +  +
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 66 DGYDFDGHRLRVELA 80
            ++    +  +++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 = 37.3 bits (86), Expect = 2e-04
 Identities = 7/60 (11%), Positives = 24/60 (40%), Gaps = 4/60 (6%)

Query: 110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFR----DGSGTTGIVDYTNYDDMKHAIKK 165
           ++ V GL      + ++++    G+V   ++      +       + +   + +K  ++K
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

>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 = 69.4 bits (169), Expect = 6e-16
 Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 4/76 (5%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDL----KIPPRPPGYAFVEFEEARDAEDAIRG 64
          +++GNL  +I E+ + D F  +G I                GYAF+ F     ++ AI  
Sbjct: 1  IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 65 RDGYDFDGHRLRVELA 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 = 36.3 bits (83), Expect = 4e-04
 Identities = 9/68 (13%), Positives = 22/68 (32%), Gaps = 5/68 (7%)

Query: 111 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGT-----TGIVDYTNYDDMKHAIKK 165
           + +  L      + L D     G +  +        T        +++ ++D    AI+ 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 166 LDDSEFRN 173
           ++     N
Sbjct: 61  MNGQYLCN 68

>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 = 68.9 bits (168), Expect = 1e-15
 Identities = 26/94 (27%), Positives = 48/94 (51%), Gaps = 9/94 (9%)

Query: 4  RASRTLYVGNLPGDIREREVE----DLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAE 59
          R + T+Y+ NL   I++ E++     +F ++G I  I +    +  G AFV F+E   A 
Sbjct: 1  RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 60

Query: 60 DAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHS 93
          +A+R   G+ F    +R++ A     ++ SD  +
Sbjct: 61 NALRSMQGFPFYDKPMRIQYA-----KTDSDIIA 89

>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 = 68.9 bits (168), Expect = 1e-15
 Identities = 50/85 (58%), Positives = 61/85 (71%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
          +      +YVGNLP DIR +++ED+FYKYG I  IDLK     P +AFVEFE+ RDAEDA
Sbjct: 10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDA 69

Query: 62 IRGRDGYDFDGHRLRVELAHGGRGR 86
          + GRDGYD+DG+RLRVE    GRG 
Sbjct: 70 VYGRDGYDYDGYRLRVEFPRSGRGT 94

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.5 bits (102), Expect = 2e-06
 Identities = 14/79 (17%), Positives = 31/79 (39%), Gaps = 1/79 (1%)

Query: 96  SSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG-SGTTGIVDYT 154
             G  RG +  ++ R+ V  LP     +D++D   + G +    +           V++ 
Sbjct: 2   GGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFE 61

Query: 155 NYDDMKHAIKKLDDSEFRN 173
           +  D + A+   D  ++  
Sbjct: 62  DPRDAEDAVYGRDGYDYDG 80

>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 = 67.8 bits (165), Expect = 2e-15
 Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 5/84 (5%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPI---AHIDLKIPPRPPGYAFVEFEEARDA 58
          +S     LYV  LP  + ++E+E LF +YG I     +  ++     G  F+ F++  +A
Sbjct: 2  ASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEA 61

Query: 59 EDAIRGRDGYDFDG--HRLRVELA 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 = 35.0 bits (80), Expect = 0.001
 Identities = 14/76 (18%), Positives = 30/76 (39%), Gaps = 4/76 (5%)

Query: 110 RVLVTGLPSSASWQDLKDHMRRAGDV----CFSQVFRDGSGTTGIVDYTNYDDMKHAIKK 165
            + V+GLP + + ++L+    + G +             S   G + +    + + AIK 
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 166 LDDSEFRNAFSRAYVR 181
           L+  +   A     V+
Sbjct: 68  LNGQKPSGATEPITVK 83

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 67.4 bits (164), Expect = 4e-15
 Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 3/82 (3%)

Query: 3  SRASRTLYVGNLPGDIREREVEDLFYKYGPI---AHIDLKIPPRPPGYAFVEFEEARDAE 59
          S     L+V ++  + +E E+++ F  YG I        +      GYA VE+E  + A 
Sbjct: 4  SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 63

Query: 60 DAIRGRDGYDFDGHRLRVELAH 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 = 38.9 bits (90), Expect = 6e-05
 Identities = 11/69 (15%), Positives = 27/69 (39%), Gaps = 4/69 (5%)

Query: 109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD----GSGTTGIVDYTNYDDMKHAIK 164
           + + VT +   A   ++++     G++    +  D     S    +V+Y  +     A +
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 165 KLDDSEFRN 173
            L+ +E   
Sbjct: 68  ALNGAEIMG 76

>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 = 67.4 bits (164), Expect = 4e-15
 Identities = 25/78 (32%), Positives = 37/78 (47%), Gaps = 3/78 (3%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIA---HIDLKIPPRPPGYAFVEFEEARDAEDAI 62
            T+YVG L   + E  + +LF + GP+        ++  +  GY FVEF    DA+ AI
Sbjct: 9  DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 68

Query: 63 RGRDGYDFDGHRLRVELA 80
          +  D     G  +RV  A
Sbjct: 69 KIMDMIKLYGKPIRVNKA 86

>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 = 37.7 bits (87), Expect = 2e-04
 Identities = 16/73 (21%), Positives = 26/73 (35%), Gaps = 4/73 (5%)

Query: 105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGD----VCFSQVFRDGSGTTGIVDYTNYDDMK 160
           R  +  V V GL    S   L +   +AG                   G V++ + +D  
Sbjct: 6   RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDAD 65

Query: 161 HAIKKLDDSEFRN 173
           +AIK +D  +   
Sbjct: 66  YAIKIMDMIKLYG 78

>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 = 67.1 bits (163), Expect = 4e-15
 Identities = 24/79 (30%), Positives = 34/79 (43%), Gaps = 4/79 (5%)

Query: 6  SRT-LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDAEDA 61
          S+T L V  LP ++ + E   LF   G I    L          GY FV + + +DAE A
Sbjct: 1  SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 62 IRGRDGYDFDGHRLRVELA 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 = 39.3 bits (91), Expect = 4e-05
 Identities = 14/71 (19%), Positives = 31/71 (43%), Gaps = 4/71 (5%)

Query: 107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHA 162
           S+  ++V  LP + + ++ +      G++   ++ RD         G V+Y +  D + A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 163 IKKLDDSEFRN 173
           I  L+    + 
Sbjct: 61  INTLNGLRLQT 71

>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 = 67.0 bits (163), Expect = 5e-15
 Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 3/75 (4%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDAEDAI 62
          +  L V  L     ER++ ++F KYGPIA + +    +     G+AFV FE   DA++A 
Sbjct: 9  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 68

Query: 63 RGRDGYDFDGHRLRV 77
             +G + DG R+RV
Sbjct: 69 ERANGMELDGRRIRV 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.5 bits (89), Expect = 7e-05
 Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 4/68 (5%)

Query: 110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG----SGTTGIVDYTNYDDMKHAIKK 165
            + V GL    + +DL++   + G +    +  D     S     V + N DD K A ++
Sbjct: 11  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 166 LDDSEFRN 173
            +  E   
Sbjct: 71  ANGMELDG 78

>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 = 66.8 bits (163), Expect = 6e-15
 Identities = 28/94 (29%), Positives = 44/94 (46%), Gaps = 11/94 (11%)

Query: 6  SRTLYVGNLPGD-IREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRG 64
          +  +++GNL    +++ +VE +F KYG I    +       G+AFV++   R+A  A+ G
Sbjct: 15 NSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-----HKGFAFVQYVNERNARAAVAG 69

Query: 65 RDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
           DG    G  L + LA            S  SSG
Sbjct: 70 EDGRMIAGQVLDINLA-----AEPKVNRSGPSSG 98

>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 = 66.5 bits (162), Expect = 8e-15
 Identities = 17/82 (20%), Positives = 33/82 (40%), Gaps = 5/82 (6%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDA 58
          + + +  L V  LP    E+++++ F  +G +  + +K   +     G+ FV F E    
Sbjct: 4  AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 63

Query: 59 EDAIRGRDGYDFDGHRLRVELA 80
             +  R     DG     +L 
Sbjct: 64 VKVMSQRHM--IDGRWCDCKLP 83

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.6 bits (162), Expect = 8e-15
 Identities = 27/83 (32%), Positives = 40/83 (48%), Gaps = 4/83 (4%)

Query: 1  MSSRASRTLYVGNLPGDIREREVEDLFYKYGPI---AHIDLKIPPRPPGYAFVEFEEARD 57
          M++   R LYVG L  ++ ++ +   F  +G I            +  G+AFVEFE A D
Sbjct: 1  MATT-KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 59

Query: 58 AEDAIRGRDGYDFDGHRLRVELA 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 = 38.5 bits (89), Expect = 7e-05
 Identities = 14/68 (20%), Positives = 24/68 (35%), Gaps = 4/68 (5%)

Query: 110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG----SGTTGIVDYTNYDDMKHAIKK 165
            + V GL      + L       GD+   Q+  D           V++   +D   AI  
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 166 LDDSEFRN 173
           +++SE   
Sbjct: 67  MNESELFG 74

>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 = 65.8 bits (160), Expect = 1e-14
 Identities = 28/77 (36%), Positives = 36/77 (46%), Gaps = 1/77 (1%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI-PPRPPGYAFVEFEEARDAEDAIRG 64
           RTLYVGNL  D+ E  +  LF + GP     +         Y FVEF E RDA  A+  
Sbjct: 8  PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAA 67

Query: 65 RDGYDFDGHRLRVELAH 81
           +G    G  ++V  A 
Sbjct: 68 MNGRKILGKEVKVNWAT 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 = 35.4 bits (81), Expect = 0.001
 Identities = 7/66 (10%), Positives = 19/66 (28%), Gaps = 2/66 (3%)

Query: 110 RVLVTGLPSSASWQDLKDHMRRAGDV--CFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLD 167
            + V  L    +   +     + G    C        +     V++  + D   A+  ++
Sbjct: 10  TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 69

Query: 168 DSEFRN 173
             +   
Sbjct: 70  GRKILG 75

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.4 bits (159), Expect = 2e-14
 Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 3/85 (3%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAI 62
          +  L++G LP  + + +V++L   +GP+   +L          GYAF E+ +    + AI
Sbjct: 1  AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60

Query: 63 RGRDGYDFDGHRLRVELAHGGRGRS 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 = 37.7 bits (87), Expect = 2e-04
 Identities = 10/69 (14%), Positives = 28/69 (40%), Gaps = 4/69 (5%)

Query: 109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFR----DGSGTTGIVDYTNYDDMKHAIK 164
           +++ + GLP+  +   +K+ +   G +    + +      S      +Y + +    AI 
Sbjct: 2   HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61

Query: 165 KLDDSEFRN 173
            L+  +  +
Sbjct: 62  GLNGMQLGD 70

>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 = 64.7 bits (157), Expect = 3e-14
 Identities = 25/75 (33%), Positives = 34/75 (45%), Gaps = 3/75 (4%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGR 65
           + LYV NL     E  +E  F    P A   +K   +   YAFV F    DA +A++  
Sbjct: 8  VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK---KIRDYAFVHFSNREDAVEAMKAL 64

Query: 66 DGYDFDGHRLRVELA 80
          +G   DG  + V LA
Sbjct: 65 NGKVLDGSPIEVTLA 79

>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 = 64.0 bits (155), Expect = 5e-14
 Identities = 14/75 (18%), Positives = 28/75 (37%), Gaps = 4/75 (5%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDAEDAIRGR 65
          ++VG L  +    +V+  F ++G +    L          G+ FV FE     E      
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 66 DGYDFDGHRLRVELA 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 = 37.4 bits (86), Expect = 2e-04
 Identities = 14/79 (17%), Positives = 32/79 (40%), Gaps = 9/79 (11%)

Query: 110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG----SGTTGIVDYTNYDDMKHAIKK 165
           ++ V GL  + + +D+K +  + G V  + +  D         G V + + D ++    +
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-E 59

Query: 166 LDDSEFRNAFSRAYVRVRE 184
           +   E  N      V  ++
Sbjct: 60  IHFHEINN----KMVECKK 74

>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 = 64.0 bits (155), Expect = 7e-14
 Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 2/76 (2%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGR 65
          S TL++ N+P  + E +++ LF   G +     K   +    A ++     +A  A+   
Sbjct: 10 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF-KFFQKDRKMALIQMGSVEEAVQALIDL 68

Query: 66 DGYDF-DGHRLRVELA 80
            +D  + H LRV  +
Sbjct: 69 HNHDLGENHHLRVSFS 84

>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 = 63.6 bits (154), Expect = 1e-13
 Identities = 19/80 (23%), Positives = 31/80 (38%), Gaps = 7/80 (8%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP-----GYAFVEFEEARDAEDAI 62
           L++G +P   +  E+ +   K        +            G+AFVE+E  R A  A 
Sbjct: 3  RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 63 RG--RDGYDFDGHRLRVELA 80
          R          GH++ 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 = 2e-05
 Identities = 9/69 (13%), Positives = 26/69 (37%), Gaps = 6/69 (8%)

Query: 110 RVLVTGLPSSASWQDLKDHMRRAGDVC------FSQVFRDGSGTTGIVDYTNYDDMKHAI 163
           R+ + G+P     +++ + + +  +         S   +  +     V+Y ++     A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 164 KKLDDSEFR 172
           +KL     +
Sbjct: 63  RKLMPGRIQ 71

>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 = 62.8 bits (152), Expect = 2e-13
 Identities = 27/78 (34%), Positives = 39/78 (50%), Gaps = 3/78 (3%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPI---AHIDLKIPPRPPGYAFVEFEEARDAEDAI 62
          + T+ V NL  D RE ++++LF  +G I        K   +  G+AF+ F    DA  AI
Sbjct: 8  NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 67

Query: 63 RGRDGYDFDGHRLRVELA 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 = 34.3 bits (78), Expect = 0.002
 Identities = 12/73 (16%), Positives = 24/73 (32%), Gaps = 4/73 (5%)

Query: 105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD----GSGTTGIVDYTNYDDMK 160
                 + VT L       DL++  R  G +    + +D     S     + +   +D  
Sbjct: 5   ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAA 64

Query: 161 HAIKKLDDSEFRN 173
            AI  +    + +
Sbjct: 65  RAIAGVSGFGYDH 77

>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 = 61.9 bits (150), Expect = 2e-13
 Identities = 17/75 (22%), Positives = 38/75 (50%), Gaps = 4/75 (5%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDAEDAIRGR 65
          +++G L  D  +++++D F K+G +    LK+ P      G+ FV F+E+   +  +  +
Sbjct: 2  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-Q 60

Query: 66 DGYDFDGHRLRVELA 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 = 35.3 bits (81), Expect = 8e-04
 Identities = 12/62 (19%), Positives = 27/62 (43%), Gaps = 4/62 (6%)

Query: 110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD----GSGTTGIVDYTNYDDMKHAIKK 165
           ++ + GL    + +DLKD+  + G+V    +  D     S   G V +   + +   + +
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 166 LD 167
            +
Sbjct: 61  KE 62

>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 = 62.0 bits (150), Expect = 3e-13
 Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 5/79 (6%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
          + R   TLYV     D+    +   F  +G I  +       P   AFV +E+   A+ A
Sbjct: 1  APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLS---MDPPRNCAFVTYEKMESADQA 55

Query: 62 IRGRDGYDFDGHRLRVELA 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 = 62.4 bits (151), Expect = 3e-13
 Identities = 25/96 (26%), Positives = 42/96 (43%), Gaps = 9/96 (9%)

Query: 3  SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAI 62
          S  S  ++VG   GD+ E E+ + F +YG    +D+ IP     +AFV F + + A+   
Sbjct: 2  SSGSSGVFVGRCTGDMTEDELREFFSQYGD--VMDVFIPKPFRAFAFVTFADDQIAQSLC 59

Query: 63 RGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
             +     G  + +  A         + +S  SSG
Sbjct: 60 --GEDLIIKGISVHISNA-----EPKHNSNSGPSSG 88

>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 = 62.5 bits (151), Expect = 3e-13
 Identities = 24/94 (25%), Positives = 39/94 (41%), Gaps = 11/94 (11%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP-----------RPPGYAFVEFEE 54
           +  +YV  L   +   ++ D F + G +        P           +P G A V +E+
Sbjct: 8   NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 67

Query: 55  ARDAEDAIRGRDGYDFDGHRLRVELAHGGRGRSS 88
              A+ A+   DG DF G +L+V LA      +S
Sbjct: 68  PPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS 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 = 34.8 bits (79), Expect = 0.002
 Identities = 15/81 (18%), Positives = 26/81 (32%), Gaps = 12/81 (14%)

Query: 105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD------------GSGTTGIVD 152
                 + V GL  S +  DL D  ++ G V  ++                       V 
Sbjct: 5   DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 64

Query: 153 YTNYDDMKHAIKKLDDSEFRN 173
           Y +    K A++  D  +F+ 
Sbjct: 65  YEDPPTAKAAVEWFDGKDFQG 85

>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 = 63.0 bits (152), Expect = 6e-13
 Identities = 29/100 (29%), Positives = 44/100 (44%), Gaps = 3/100 (3%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRP---PGYAFVEFEEARDA 58
                R L V  +P  + E ++  LF +YGPI  + +          GY FV+F+    A
Sbjct: 38  EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSA 97

Query: 59  EDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
           + AI G +G++    RL+V LA  G  R          +G
Sbjct: 98  QQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGNG 137

>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 = 35.7 bits (81), Expect = 0.002
 Identities = 15/95 (15%), Positives = 28/95 (29%), Gaps = 6/95 (6%)

Query: 110 RVLVTGLPSSASWQDLKDHM----RRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKK 165
            ++V  +P++     L+                      S   G V + +    + AI  
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103

Query: 166 LDDSEFRNAFSRAYVRVREYDHRRDGSQSPSRGRS 200
           L+     N   R  V +    H+R G        +
Sbjct: 104 LNGFNILN--KRLKVALAASGHQRPGIAGAVGDGN 136

>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 = 60.8 bits (147), Expect = 9e-13
 Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 1/80 (1%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP-GYAFVEFEEARDAED 60
          S    + L+V N+P   R+ ++  +F ++G I  +++    R   G+ FV FE + DA+ 
Sbjct: 7  SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADR 66

Query: 61 AIRGRDGYDFDGHRLRVELA 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 = 38.5 bits (89), Expect = 9e-05
 Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 2/72 (2%)

Query: 104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD--GSGTTGIVDYTNYDDMKH 161
           S+ +  R+ V+ +P      DL+    + G +   ++  +  GS   G V + N  D   
Sbjct: 7   SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADR 66

Query: 162 AIKKLDDSEFRN 173
           A +KL  +    
Sbjct: 67  AREKLHGTVVEG 78

>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 = 60.9 bits (147), Expect = 1e-12
 Identities = 29/96 (30%), Positives = 37/96 (38%), Gaps = 9/96 (9%)

Query: 3  SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAI 62
          S  S  + V NLP D   +EV DL   Y            R    AFV       A++AI
Sbjct: 2  SSGSSGILVKNLPQDSNCQEVHDLLKDYDLKY----CYVDRNKRTAFVTLLNGEQAQNAI 57

Query: 63 RGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
          +    Y F G  L V+L       + +   S  SSG
Sbjct: 58 QMFHQYSFRGKDLIVQLQ-----PTDALLCSGPSSG 88

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.9 bits (147), Expect = 1e-12
 Identities = 26/96 (27%), Positives = 52/96 (54%), Gaps = 3/96 (3%)

Query: 4   RASRTLYVGNLPGDIREREVEDLFYKYGPIA---HIDLKIPPRPPGYAFVEFEEARDAED 60
           R+ R+++VGN+P +  E +++D+F + GP+     +  +   +P GY F E+++   A  
Sbjct: 6   RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65

Query: 61  AIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHS 96
           A+R  +G +F G  LRV+ A   + +       + +
Sbjct: 66  AMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGA 101

>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 = 34.7 bits (79), Expect = 0.002
 Identities = 22/98 (22%), Positives = 37/98 (37%), Gaps = 8/98 (8%)

Query: 106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGT----TGIVDYTNYDDMKH 161
           RS   V V  +P  A+ + LKD     G V   ++  D         G  +Y + +    
Sbjct: 6   RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65

Query: 162 AIKKLDDSEFRNAFSRAYVRVREYDHRRDGSQSPSRGR 199
           A++ L+  EF        +RV      ++  +  S G 
Sbjct: 66  AMRNLNGREFSG----RALRVDNAASEKNKEELKSLGT 99

>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 = 59.3 bits (143), Expect = 3e-12
 Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 4/77 (5%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIR 63
          + ++VG +  D  E  + D F +YG I  I++   +   +  G+AFV F++  D+ D I 
Sbjct: 3  KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIV 61

Query: 64 GRDGYDFDGHRLRVELA 80
           +  +  +GH   V  A
Sbjct: 62 IQKYHTVNGHNCEVRKA 78

>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 = 59.7 bits (144), Expect = 3e-12
 Identities = 30/94 (31%), Positives = 41/94 (43%), Gaps = 3/94 (3%)

Query: 3  SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHI---DLKIPPRPPGYAFVEFEEARDAE 59
          S  S  L+V NL     E ++E LF  YGP++ +      +  +P G+AFV F     A 
Sbjct: 5  SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAV 64

Query: 60 DAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHS 93
           A    DG  F G  L V  +   +  S S   S
Sbjct: 65 KAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSS 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 = 37.8 bits (87), Expect = 2e-04
 Identities = 24/111 (21%), Positives = 39/111 (35%), Gaps = 18/111 (16%)

Query: 93  SSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQV----FRDGSGTT 148
           SS SSG GR         + V  L  ++S +DL+      G +                 
Sbjct: 2   SSGSSGSGR---------LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGF 52

Query: 149 GIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVREYDHRRDGSQS-PSRG 198
             V +   +    A  ++D   F+       + V     +++ SQS PS G
Sbjct: 53  AFVTFMFPEHAVKAYAEVDGQVFQG----RMLHVLPSTIKKEASQSGPSSG 99

>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 = 59.8 bits (144), Expect = 4e-12
 Identities = 23/100 (23%), Positives = 36/100 (36%), Gaps = 10/100 (10%)

Query: 7   RTLYVGNLPGDIREREVEDLF---YKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIR 63
             ++VG LP    +  +   F           I  +   +  GY FV   +   AE A +
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 70

Query: 64  GRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGV 103
             +    DG +  V LA+ G       +  S  +G   GV
Sbjct: 71  DPNPI-IDGRKANVNLAYLGA------KPRSLQTGFAIGV 103

>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 = 59.3 bits (143), Expect = 4e-12
 Identities = 15/78 (19%), Positives = 32/78 (41%), Gaps = 4/78 (5%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP---GYAFVEFEEARDAEDAI 62
           R L++G L  +  E  + + + ++G +    +   P      G+ FV F    + + A+
Sbjct: 20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 79

Query: 63 RGRDGYDFDGHRLRVELA 80
               +  DG  +  + A
Sbjct: 80 AA-RPHSIDGRVVEPKRA 96

>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 = 22/82 (26%), Positives = 33/82 (40%), Gaps = 3/82 (3%)

Query: 2  SSRAS--RTLYVGNLPGDIREREVEDLFYKYGPIAHIDL-KIPPRPPGYAFVEFEEARDA 58
          S R S    +++ NL   I  + + D F  +G I    +        GY FV FE    A
Sbjct: 2  SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAA 61

Query: 59 EDAIRGRDGYDFDGHRLRVELA 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 = 37.7 bits (87), Expect = 2e-04
 Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 3/73 (4%)

Query: 104 SRRS-EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD--GSGTTGIVDYTNYDDMK 160
            R+S    + +  L  S   + L D     G++   +V  D  GS   G V +   +  +
Sbjct: 3   LRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAE 62

Query: 161 HAIKKLDDSEFRN 173
            AI+K++     +
Sbjct: 63  RAIEKMNGMLLND 75

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 4e-12
 Identities = 14/77 (18%), Positives = 31/77 (40%), Gaps = 4/77 (5%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDAEDAIR 63
          R L++G L  +  +  +   F ++G +    +   P      G+ FV +    + + A+ 
Sbjct: 7  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66

Query: 64 GRDGYDFDGHRLRVELA 80
              +  DG  +  + A
Sbjct: 67 A-RPHKVDGRVVEPKRA 82

>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 = 61.6 bits (148), Expect = 5e-12
 Identities = 21/167 (12%), Positives = 54/167 (32%), Gaps = 21/167 (12%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDAEDAI 62
            R L++G L  +  +  +   F ++G +    +   P      G+ FV +    + + A+
Sbjct: 6   LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 65

Query: 63  RGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASW 122
             R                         + +       R  +  +  ++ V G+      
Sbjct: 66  NARPHKVDGRVV--------------EPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEE 111

Query: 123 QDLKDHMRRAGDVCFSQVFRDGSGTT----GIVDYTNYDDMKHAIKK 165
             L+D+  + G +   ++  D           V + ++D +   + +
Sbjct: 112 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 158

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.5 bits (127), Expect = 3e-09
 Identities = 20/92 (21%), Positives = 41/92 (44%), Gaps = 4/92 (4%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARD 57
            +    + ++VG +  D  E  + D F +YG I  I++       +  G+AFV F++   
Sbjct: 92  GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 151

Query: 58  AEDAIRGRDGYDFDGHRLRVELAHGGRGRSSS 89
            +  +  +  +  +GH   V  A   +  +S+
Sbjct: 152 VDKIVI-QKYHTVNGHNCEVRKALSKQEMASA 182

>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 = 59.2 bits (143), Expect = 5e-12
 Identities = 20/91 (21%), Positives = 34/91 (37%), Gaps = 12/91 (13%)

Query: 3  SRASRTLYVGNL--PGDIR---------EREVEDLFYKYGPIAHIDLKIPPRPPGYAFVE 51
           R  R + + N+  P D             ++     K+G I  +       P G A V 
Sbjct: 5  MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLL-LFDRHPDGVASVS 63

Query: 52 FEEARDAEDAIRGRDGYDFDGHRLRVELAHG 82
          F +  +A+  I+  DG  F G ++  +   G
Sbjct: 64 FRDPEEADYCIQTLDGRWFGGRQITAQAWDG 94

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.6 bits (141), Expect = 6e-12
 Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 3/77 (3%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR--PPGYAFVEFEEARDAEDAIR 63
          +R++Y+   P D    ++++     G + +I ++        G  FV F+    A+  + 
Sbjct: 6  NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE 65

Query: 64 GRDGYDFDGHRLRVELA 80
             G  +    L +   
Sbjct: 66 -TPGQKYKETDLLILFK 81

>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 = 58.2 bits (140), Expect = 7e-12
 Identities = 20/81 (24%), Positives = 33/81 (40%), Gaps = 4/81 (4%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDG 67
           LY+GNL   +   ++  LF          +       GYAFV++ +   A  AI    G
Sbjct: 3  KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL---LKSGYAFVDYPDQNWAIRAIETLSG 59

Query: 68 -YDFDGHRLRVELAHGGRGRS 87
            +  G  + V+ +   + RS
Sbjct: 60 KVELHGKIMEVDYSVSKKLRS 80

>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 = 58.2 bits (140), Expect = 1e-11
 Identities = 15/82 (18%), Positives = 33/82 (40%), Gaps = 6/82 (7%)

Query: 1  MSSRASRTLYV--GNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDA 58
            S A+++L V  G L   +   ++  +  K G +  +     P    Y+F  +    ++
Sbjct: 13 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALL---MPPNKPYSFARYRTTEES 69

Query: 59 EDAIRGRDGYD-FDGHRLRVEL 79
          + A    +G +  D    ++ L
Sbjct: 70 KRAYVTLNGKEVVDDLGQKITL 91

>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 = 56.7 bits (136), Expect = 2e-11
 Identities = 16/71 (22%), Positives = 27/71 (38%), Gaps = 3/71 (4%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIA---HIDLKIPPRPPGYAFVEFEEARDAEDAIRGR 65
          LY+  L     ++++  L   YG I     I  K   +  GY FV+F+    A+ A+   
Sbjct: 1  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 66 DGYDFDGHRLR 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 = 40.1 bits (93), Expect = 2e-05
 Identities = 13/66 (19%), Positives = 25/66 (37%), Gaps = 4/66 (6%)

Query: 111 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG----SGTTGIVDYTNYDDMKHAIKKL 166
           + + GL    + QDL    +  G +  ++   D         G VD+ +    + A+  L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 167 DDSEFR 172
             S  +
Sbjct: 61  KASGVQ 66

>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 = 57.0 bits (137), Expect = 3e-11
 Identities = 23/87 (26%), Positives = 38/87 (43%), Gaps = 4/87 (4%)

Query: 3   SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAE 59
            R +RT++   L   IR R++ED F   G +  + +   +   R  G A+VEF E +   
Sbjct: 15  ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP 74

Query: 60  DAIRGRDGYDFDGHRLRVELAHGGRGR 86
               G  G    G  + V+ +   + R
Sbjct: 75  -LAIGLTGQRLLGVPIIVQASQAEKNR 100

>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 = 56.7 bits (136), Expect = 3e-11
 Identities = 30/91 (32%), Positives = 45/91 (49%), Gaps = 4/91 (4%)

Query: 1  MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPP---GYAFVEFEEARD 57
          M+S     L+VG L  D  E+ +E +F KYG I+ + +          G+ FV FE   D
Sbjct: 1  MASD-EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDD 59

Query: 58 AEDAIRGRDGYDFDGHRLRVELAHGGRGRSS 88
          A+DA+   +G   DG ++RV+ A       S
Sbjct: 60 AKDAMMAMNGKSVDGRQIRVDQAGKSSDNRS 90

>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 = 57.1 bits (137), Expect = 4e-11
 Identities = 21/106 (19%), Positives = 41/106 (38%), Gaps = 3/106 (2%)

Query: 6   SRTLYVGNL-PGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRG 64
           +  L V NL P  +  + +  LF  YG +  +  KI       A V+  +   A+ A+  
Sbjct: 2   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRV--KILFNKKENALVQMADGNQAQLAMSH 59

Query: 65  RDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGRGVSRRSEYR 110
            +G+   G  +R+ L+     +   +        +  G S    ++
Sbjct: 60  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFK 105

>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 = 56.2 bits (135), Expect = 4e-11
 Identities = 18/78 (23%), Positives = 30/78 (38%), Gaps = 3/78 (3%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIA---HIDLKIPPRPPGYAFVEFEEARDAEDAI 62
             + V N+P  +   E+ D FY Y  I     +       P G A V FE   +A  A+
Sbjct: 9  PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAV 68

Query: 63 RGRDGYDFDGHRLRVELA 80
             +       ++++ L 
Sbjct: 69 IDLNDRPIGSRKVKLVLG 86

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.0 bits (85), Expect = 3e-04
 Identities = 11/78 (14%), Positives = 26/78 (33%), Gaps = 4/78 (5%)

Query: 100 GRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG----SGTTGIVDYTN 155
           G    +     + V  +P + S  ++ D       +  S   +           +V + +
Sbjct: 1   GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 60

Query: 156 YDDMKHAIKKLDDSEFRN 173
            D+   A+  L+D    +
Sbjct: 61  RDEATAAVIDLNDRPIGS 78

>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 = 56.6 bits (136), Expect = 5e-11
 Identities = 15/73 (20%), Positives = 31/73 (42%), Gaps = 2/73 (2%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDL--KIPPRPPGYAFVEFEEARDAEDAIRGRD 66
           + +     +  E    ++  KYG +  +++   +     G  +V+F    DAE A+   +
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLN 89

Query: 67  GYDFDGHRLRVEL 79
              F+G  +  EL
Sbjct: 90  NRWFNGQPIHAEL 102

>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 = 56.2 bits (135), Expect = 5e-11
 Identities = 16/78 (20%), Positives = 37/78 (47%), Gaps = 3/78 (3%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP---RPPGYAFVEFEEARDAEDAI 62
             L++ +LP +  ++++  +F  +G +    + I         + FV ++    A+ AI
Sbjct: 18 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 77

Query: 63 RGRDGYDFDGHRLRVELA 80
          +  +G+     RL+V+L 
Sbjct: 78 QSMNGFQIGMKRLKVQLK 95

>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 = 55.9 bits (134), Expect = 6e-11
 Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 6/80 (7%)

Query: 6  SRTLYVGNLPGD-IREREVEDLFYKYGPI----AHIDLKIPPRPPGYAFVEFEEARDAED 60
           R + + NL  + + E  + + F  +G I         K        AF+ FE    AE 
Sbjct: 4  GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 61 AIRGRDGYDFDGHRLRVELA 80
          A++  +        + V LA
Sbjct: 64 ALQ-MNRSLLGNREISVSLA 82

>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 = 55.6 bits (133), Expect = 6e-11
 Identities = 19/74 (25%), Positives = 30/74 (40%), Gaps = 2/74 (2%)

Query: 8  TLYVGNLPGDIREREVEDLFYKYGPIAHIDL-KIPPRPPGYAFVEFEEARDAEDAIRGRD 66
          T+ V NLP    + +V   F   GPI H+D+     +   +A +EF     A  AI  + 
Sbjct: 2  TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KT 60

Query: 67 GYDFDGHRLRVELA 80
                + + V   
Sbjct: 61 HKVVGQNEIIVSHL 74

>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 = 55.9 bits (134), Expect = 6e-11
 Identities = 22/88 (25%), Positives = 34/88 (38%), Gaps = 9/88 (10%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP--------RPPGYAFVEFEEARDA 58
          R LYVGN+P  I E  + D F     +  +              +   +AF+EF    + 
Sbjct: 2  RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 59 EDAIRGRDGYDFDGHRLRVELAHGGRGR 86
            A+   DG  F G  L++   H  +  
Sbjct: 62 TQAMA-FDGIIFQGQSLKIRRPHDYQPL 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 = 54.5 bits (130), Expect = 1e-10
 Identities = 20/72 (27%), Positives = 27/72 (37%), Gaps = 4/72 (5%)

Query: 9  LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
          + +  LPGD+  +EV DL   Y     +      +  G AFV       AE AI      
Sbjct: 1  ILIRGLPGDVTNQEVHDLLSDY----ELKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQS 56

Query: 69 DFDGHRLRVELA 80
                L V+L 
Sbjct: 57 RLRERELSVQLQ 68

>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 = 55.2 bits (132), Expect = 1e-10
 Identities = 18/84 (21%), Positives = 35/84 (41%), Gaps = 9/84 (10%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGP---IAHIDLKIPPRPPGYAFVEFEEARDAEDAI 62
           +T+++ NL  D  E  + ++  ++G    +  +         G AF +F     A+  +
Sbjct: 8  GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 67

Query: 63 RG------RDGYDFDGHRLRVELA 80
                    G   DG +L+V+LA
Sbjct: 68 AAASLEAEGGGLKLDGRQLKVDLA 91

>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 = 55.2 bits (132), Expect = 1e-10
 Identities = 21/85 (24%), Positives = 36/85 (42%), Gaps = 3/85 (3%)

Query: 6   SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDAEDAI 62
           ++ LY+ NL   + ER++  LF ++       ++         G AF+ F     A  A+
Sbjct: 18  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 77

Query: 63  RGRDGYDFDGHRLRVELAHGGRGRS 87
              +GY   G  L +E     + RS
Sbjct: 78  HLVNGYKLYGKILVIEFGKNKKQRS 102

>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 = 54.7 bits (131), Expect = 2e-10
 Identities = 21/85 (24%), Positives = 37/85 (43%), Gaps = 5/85 (5%)

Query: 3  SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAI 62
          +  +  L+VG L  +     +   F ++G I  ID     +   +A++++E    A+ A 
Sbjct: 14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTID---HVKGDSFAYIQYESLDAAQAAC 70

Query: 63 RGRDGYDFDG--HRLRVELAHGGRG 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 = 36.2 bits (83), Expect = 7e-04
 Identities = 20/90 (22%), Positives = 31/90 (34%), Gaps = 4/90 (4%)

Query: 93  SSHSSGR-GRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIV 151
           SS SSG+ G G +  +  R+ V GL  + S   L     R        +      +   +
Sbjct: 2   SSGSSGKIGYGKANPTT-RLWVGGLGPNTSLAALAREFDR--FGSIRTIDHVKGDSFAYI 58

Query: 152 DYTNYDDMKHAIKKLDDSEFRNAFSRAYVR 181
            Y + D  + A  K+          R  V 
Sbjct: 59  QYESLDAAQAACAKMRGFPLGGPDRRLRVD 88

>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 = 53.5 bits (128), Expect = 7e-10
 Identities = 15/90 (16%), Positives = 31/90 (34%), Gaps = 3/90 (3%)

Query: 7  RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRD 66
            + V NL   +    +  +F K+G +  I           A +++ +   A+ A    D
Sbjct: 8  LRIIVENLFYPVTLDVLHQIFSKFGTVLKIIT-FTKNNQFQALLQYADPVSAQHAKLSLD 66

Query: 67 GYDF--DGHRLRVELAHGGRGRSSSDRHSS 94
          G +       LR++ +         +   S
Sbjct: 67 GQNIYNACCTLRIDFSKLTSLNVKYNNDKS 96

>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 = 44.6 bits (105), Expect = 1e-06
 Identities = 19/113 (16%), Positives = 35/113 (30%), Gaps = 19/113 (16%)

Query: 110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDS 169
           R++V  L    +   L     + G V     F   +    ++ Y +    +HA   LD  
Sbjct: 9   RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQ 68

Query: 170 EFRNAFSRAYVRVREYDHRRDGSQSPSRGRSYSRGRSESRSRSRSRGRSYSRS 222
              NA     +                    +S+  S +   +  + R Y+R 
Sbjct: 69  NIYNACCTLRI-------------------DFSKLTSLNVKYNNDKSRDYTRP 102

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.3 bits (127), Expect = 8e-10
 Identities = 17/92 (18%), Positives = 25/92 (27%), Gaps = 8/92 (8%)

Query: 3  SRASRTLYVGNLPGDIRE-----REVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARD 57
          S  S  L       D+        + E LF  Y            +      + F     
Sbjct: 2  SSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF---KSFKRVRINFSNPLS 58

Query: 58 AEDAIRGRDGYDFDGHRLRVELAHGGRGRSSS 89
          A DA       +F G  +++  A      SS 
Sbjct: 59 AADARLRLHKTEFLGKEMKLYFAQTLHIGSSH 90

>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 = 52.2 bits (124), Expect = 1e-09
 Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 3/76 (3%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGR 65
          ++ L++ NLP +  E  +  LF ++     +   + P     AFVEF     +  A    
Sbjct: 8  NQILFLTNLPEETNEMMLSMLFNQFPGFKEVR--LVPNRHDIAFVEFTTELQSNAAKEAL 65

Query: 66 DGYDFD-GHRLRVELA 80
           G+     H +++  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 = 51.7 bits (123), Expect = 2e-09
 Identities = 16/79 (20%), Positives = 26/79 (32%), Gaps = 2/79 (2%)

Query: 4  RASRTLYVGNLPGDIREREVEDLFYKYGPIAH--IDLKIPPRPPGYAFVEFEEARDAEDA 61
          +    LY+ NLP  + E+E+E++   +G +    I         G  F   E     E  
Sbjct: 16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAV 75

Query: 62 IRGRDGYDFDGHRLRVELA 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 = 35.5 bits (81), Expect = 0.001
 Identities = 13/85 (15%), Positives = 32/85 (37%), Gaps = 6/85 (7%)

Query: 95  HSSGRGRGVSRRSE---YRVLVTGLPSSASWQDLKDHMRRAGDVC---FSQVFRDGSGTT 148
            +SG    ++++ E     + ++ LP S   Q+L++ ++  G V      +     S   
Sbjct: 2   KASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGV 61

Query: 149 GIVDYTNYDDMKHAIKKLDDSEFRN 173
           G     + +  +  I   +    + 
Sbjct: 62  GFARMESTEKCEAVIGHFNGKFIKT 86

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 50.3 bits (119), Expect = 5e-09
 Identities = 16/80 (20%), Positives = 32/80 (40%), Gaps = 3/80 (3%)

Query: 3  SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPP--RPPGYAFVEFEEARDAED 60
          S     L++GNL  +    E++    +      + +          + +V+FE A D E 
Sbjct: 10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEK 69

Query: 61 AIRGRDGYDFDGHRLRVELA 80
          A+    G    G+ +++E  
Sbjct: 70 ALE-LTGLKVFGNEIKLEKP 88

>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 = 50.2 bits (119), Expect = 6e-09
 Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 5/83 (6%)

Query: 1  MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
          M    SR L++  LPG++ E EV  L   +G + +I      +    AF+E      A  
Sbjct: 3  MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNIL---MLKGKNQAFLELATEEAAIT 59

Query: 61 AIRGR--DGYDFDGHRLRVELAH 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 = 49.4 bits (117), Expect = 1e-08
 Identities = 46/103 (44%), Positives = 64/103 (62%), Gaps = 7/103 (6%)

Query: 96  SSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTN 155
           S   G   +RRS++RVLV+GLP S SWQDLKDHMR AGDVC++ V +D     G+V+Y  
Sbjct: 3   SGSSGGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD---GMGMVEYLR 59

Query: 156 YDDMKHAIKKLDDSEFRNAFSRAYVRVREYDHRRDGSQSPSRG 198
            +DM++A++KLDD++FR+                + S  PS G
Sbjct: 60  KEDMEYALRKLDDTKFRSHE----GETSYIRVYPERSSGPSSG 98

>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 = 45.2 bits (106), Expect = 4e-07
 Identities = 18/91 (19%), Positives = 29/91 (31%), Gaps = 4/91 (4%)

Query: 2  SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
          + R+   + V  LP     ++++D   +             +  G   VE+    D E A
Sbjct: 11 TRRSDFRVLVSGLPPSGSWQDLKDHMREA----GDVCYADVQKDGMGMVEYLRKEDMEYA 66

Query: 62 IRGRDGYDFDGHRLRVELAHGGRGRSSSDRH 92
          +R  D   F  H            RSS    
Sbjct: 67 LRKLDDTKFRSHEGETSYIRVYPERSSGPSS 97

>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 = 49.3 bits (117), Expect = 2e-08
 Identities = 20/94 (21%), Positives = 38/94 (40%), Gaps = 4/94 (4%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARD 57
           +      T ++GNLP D+ E  +++ F      A    + P       G+ + EFE+   
Sbjct: 10  LPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDS 69

Query: 58  AEDAIRGRDGYDFDGHRLRVELAHGGRGRSSSDR 91
              A+   +       R+RV++A   + + S   
Sbjct: 70  LLSALS-LNEESLGNKRIRVDVADQAQDKDSGPS 102

>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 = 48.2 bits (114), Expect = 3e-08
 Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 6/83 (7%)

Query: 2  SSRASRTLYVGNLP-GDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAED 60
               R +++ +   G     ++  L   +G I++            AF+E     DA+ 
Sbjct: 4  RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHL---ILNKINEAFIEMATTEDAQA 60

Query: 61 AIRGR--DGYDFDGHRLRVELAH 81
          A+           G  +RV L+ 
Sbjct: 61 AVDYYTTTPALVFGKPVRVHLSQ 83

>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 = 48.6 bits (115), Expect = 3e-08
 Identities = 19/97 (19%), Positives = 36/97 (37%), Gaps = 3/97 (3%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
               S  ++V  L   + E ++ +   K+G I ++ +    R    A VEFE    A++ 
Sbjct: 11  KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR---QALVEFENIDSAKEC 67

Query: 62  IRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
           +             +    +    R +   +S  SSG
Sbjct: 68  VTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGPSSG 104

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.2 bits (80), Expect = 0.002
 Identities = 24/105 (22%), Positives = 36/105 (34%), Gaps = 4/105 (3%)

Query: 96  SSGRGRGVSRRSEYRVL-VTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYT 154
           SSG      + S   V+ V GL  S    DL + + +        V         +V++ 
Sbjct: 2   SSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEK--FGTICYVMMMPFKRQALVEFE 59

Query: 155 NYDDMKHAIKKLDDSEFRNAFSRAYVRVREYDH-RRDGSQSPSRG 198
           N D  K  +    D     A  +A+          R G+  PS G
Sbjct: 60  NIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGPSSG 104

>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 = 47.9 bits (113), Expect = 6e-08
 Identities = 15/97 (15%), Positives = 29/97 (29%), Gaps = 4/97 (4%)

Query: 3   SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPR---PPGYAFVEFEEARDAE 59
           + A    ++ N+P  I + +V           +    +        G A V+F+   DA 
Sbjct: 5   NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDAR 64

Query: 60  DAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHS 96
            + R       +G    V +      R       +  
Sbjct: 65  KSER-LHRKKLNGREAFVHVVTLEDMREIEKNPPAQG 100

>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 = 46.0 bits (108), Expect = 2e-07
 Identities = 16/80 (20%), Positives = 31/80 (38%), Gaps = 9/80 (11%)

Query: 7  RTLYVGNLPGDIRE---REVEDLFYKYGPIAHIDL------KIPPRPPGYAFVEFEEARD 57
            ++V  L   + +    +  + F K+G I  + +           P   A+V +  + D
Sbjct: 9  NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 58 AEDAIRGRDGYDFDGHRLRV 77
          A  AI+  +    DG  L+ 
Sbjct: 69 ALRAIQCVNNVVVDGRTLKA 88

>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 = 46.5 bits (109), Expect = 2e-07
 Identities = 23/98 (23%), Positives = 38/98 (38%), Gaps = 3/98 (3%)

Query: 2   SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDA 61
           S R+   +   NLP      E+++ F ++G +  +   + P     A VEF E  +A  A
Sbjct: 6   SGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRV---LLPEGGITAIVEFLEPLEARKA 62

Query: 62  IRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSGR 99
            R      F    L +E A  G   ++  +  S     
Sbjct: 63  FRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQP 100

>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 = 44.6 bits (105), Expect = 8e-07
 Identities = 19/90 (21%), Positives = 35/90 (38%), Gaps = 15/90 (16%)

Query: 6  SRTLYVGNL--PGDIRERE-----VEDLFYKYGPIAHI-DLKIP-------PRPPGYAFV 50
          +  L + N+  P ++ + E     VED+  +      +  ++IP           G  FV
Sbjct: 4  TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFV 63

Query: 51 EFEEARDAEDAIRGRDGYDFDGHRLRVELA 80
          EF    D + A++G  G  F    +  +  
Sbjct: 64 EFTSVFDCQKAMQGLTGRKFANRVVVTKYC 93

>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 = 45/93 (48%), Positives = 63/93 (67%), Gaps = 7/93 (7%)

Query: 110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDS 169
           RV+V+GLP S SWQDLKDHMR AGDVC++ V+RD    TG+V++   +DM +A++KLD++
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNT 58

Query: 170 EFRNAFSRAYVRVREYDHRRDGSQSPSRGRSYS 202
           +FR+              + DG +SPS GRS S
Sbjct: 59  KFRS----HEGETAYIRVKVDGPRSPSYGRSRS 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 = 40.6 bits (94), Expect = 1e-05
 Identities = 21/93 (22%), Positives = 28/93 (30%), Gaps = 9/93 (9%)

Query: 9   LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY 68
           + V  LP     ++++D   +                G   VEF    D   A+R  D  
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREA----GDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNT 58

Query: 69  DFDGHRLRVELAHGGRGRSSSDRHSSHSSGRGR 101
            F  H            R   D   S S GR R
Sbjct: 59  KFRSHEGETAYI-----RVKVDGPRSPSYGRSR 86

>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 = 41.1 bits (96), Expect = 9e-06
 Identities = 11/70 (15%), Positives = 21/70 (30%), Gaps = 5/70 (7%)

Query: 6  SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGR 65
             + V   P       +   F +YG I             +  + ++    A  A+  +
Sbjct: 4  DTWVTVFGFPQASAS-YILLQFAQYGNILKHV---MSNTGNWMHIRYQSKLQARKALS-K 58

Query: 66 DGYDFDGHRL 75
          DG  F    +
Sbjct: 59 DGRIFGESIM 68

>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 = 16/104 (15%), Positives = 33/104 (31%), Gaps = 11/104 (10%)

Query: 7   RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFV-EFEEARDAEDAIRGR 65
              + G+L       ++  LF  +G I  ID     R      +   E+A++A    +  
Sbjct: 12  LLKFSGDLDDQTCREDLHILFSNHGEIKWIDF---VRGAKEGIILFKEKAKEALGKAKDA 68

Query: 66  DGYDFDGHRLRVELAHGG-------RGRSSSDRHSSHSSGRGRG 102
           +  +       V               +   D+  S +  + +G
Sbjct: 69  NNGNLQLRNKEVTWEVLEGEVEKEALKKIIEDQQESLNKWKSKG 112

>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 = 37.9 bits (87), Expect = 2e-04
 Identities = 14/108 (12%), Positives = 32/108 (29%), Gaps = 9/108 (8%)

Query: 111 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTN-YDDMKHAIKKLDDS 169
                L      +DL       G+     +        GI+ +     +     K  ++ 
Sbjct: 14  KFSGDLDDQTCREDLHILFSNHGE--IKWIDFVRGAKEGIILFKEKAKEALGKAKDANNG 71

Query: 170 EFRNAFSRAYVRVREYDHRRDGSQSPSRGRSYSRGRSESRSRSRSRGR 217
             +         V E +  ++        +     + ES ++ +S+GR
Sbjct: 72  NLQLRNKEVTWEVLEGEVEKE------ALKKIIEDQQESLNKWKSKGR 113

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.6 bits (89), Expect = 1e-04
 Identities = 21/99 (21%), Positives = 35/99 (35%), Gaps = 7/99 (7%)

Query: 1   MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLK-IPPRPPGYAFVEFEEARDAE 59
             S     +++  LP    E ++ + F    P+          R  G A VEF    DA 
Sbjct: 10  FQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAV 69

Query: 60  DAIRGRDGYDFDGHRLRVELAHGGRGRSSSDRHSSHSSG 98
            A+  +D  +     + + L       ++    S  SSG
Sbjct: 70  AAMA-KDKANMQHRYVELFLN-----STAGTSGSGPSSG 102

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	299
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.97
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.88
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.88
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.87
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.87
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.87
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.87
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.86
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.86
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.86
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.86
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.86
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.86
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.86
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.85
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.85
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.85
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.85
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.85
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.85
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.85
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.85
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.84
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.84
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.84
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.84
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.84
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.84
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.84
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.84
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.84
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.83
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.83
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.83
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.83
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.83
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.83
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.83
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.82
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.82
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.82
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.82
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.82
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.82
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.82
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.82
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.82
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.82
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.82
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.82
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.82
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.82
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.82
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.82
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.82
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.81
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.81
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.81
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.81
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.81
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.8
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.8
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.8
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.8
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.8
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.8
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.78
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.78
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.78
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.77
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.77
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.77
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.77
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.77
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.76
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.76
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.75
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.72
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.72
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.72
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.71
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.71
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.7
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.7
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.69
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.69
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.69
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.69
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.69
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.69
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.69
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.69
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.68
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.68
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.68
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.67
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.67
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.67
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.67
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.67
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.66
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.66
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.66
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.66
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.66
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.65
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.65
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.65
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.64
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.64
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.63
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.63
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.63
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.62
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	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
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.62
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.62
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.62
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.62
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.62
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.62
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.62
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.62
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.62
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.61
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.61
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.61
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.61
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.6
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.6
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.6
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.6
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.6
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.6
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.6
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.59
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.59
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.59
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.59
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.59
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.58
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.58
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.58
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.58
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.57
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.57
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.57
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.56
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.56
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.56
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.56
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.55
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.54
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.53
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.52
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.51
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.51
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.49
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.47
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.46
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.46
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.46
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.44
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.44
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.39
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.35
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.33
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.29
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	99.26
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.13
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	98.13
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	98.12
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.99
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.81
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.65
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.55
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	97.07
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.89
d1m1ha2	101	N-utilization substance G protein NusG, N-terminal	83.48

>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=2.6e-29  Score=196.68  Aligned_cols=155  Identities=14%  Similarity=0.292  Sum_probs=131.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      ++|||+|||+++|+++|.++|++||+|..+.+..   ++.++|||||+|.+.++|..|+. +++..+.+..+.+......
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            7999999999999999999999999999999854   46778999999999999999999 6777777888877765433


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhH
Q 022301           84 RGRSSSDRHSSHSSGRGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDM  159 (299)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a  159 (299)
                      .....             ........+|||+|||..+++++|.++|..||.|..+.+..+...    |||||+|.+.++|
T Consensus        86 ~~~~~-------------~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A  152 (183)
T d1u1qa_          86 EDSQR-------------PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV  152 (183)
T ss_dssp             TGGGS-------------TTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHH
T ss_pred             ccccc-------------cccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHH
Confidence            22111             122334578999999999999999999999999999999987654    4999999999999


Q ss_pred             HHHHHhcCCCeecCcee
Q 022301          160 KHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       160 ~~a~~~l~g~~~~g~~~  176 (299)
                      ..|+. +++..++|+.+
T Consensus       153 ~~Al~-~~~~~~~G~~i  168 (183)
T d1u1qa_         153 DKIVI-QKYHTVNGHNC  168 (183)
T ss_dssp             HHHHT-SSCEEETTEEE
T ss_pred             HHHHH-hCCCeECCEEE
Confidence            99997 79999999843

>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=7.1e-23  Score=137.72  Aligned_cols=77  Identities=34%  Similarity=0.533  Sum_probs=72.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      +++|||+|||+++|+++|.++|++||+|..+.|..   ++.++|||||+|.+.++|+.|+..|||..|.|+.|.|.|+++
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            67899999999999999999999999999999943   567889999999999999999999999999999999999864

>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=1.2e-22  Score=145.55  Aligned_cols=82  Identities=33%  Similarity=0.539  Sum_probs=77.6

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            1 MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         1 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      |+...+++|||+|||.++|+++|.++|+.||+|..|.+..++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
T Consensus         2 ~pp~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   81 (114)
T d2f9da1           2 LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYY   81 (114)
T ss_dssp             CCTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             cccCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            56678899999999999999999999999999999999888888999999999999999999999999999999999997


Q ss_pred             cC
Q 022301           81 HG   82 (299)
Q Consensus        81 ~~   82 (299)
                      ..
T Consensus        82 ~~   83 (114)
T d2f9da1          82 NA   83 (114)
T ss_dssp             CH
T ss_pred             CC
Confidence            53

>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=99.87  E-value=2e-22  Score=138.43  Aligned_cols=80  Identities=35%  Similarity=0.505  Sum_probs=74.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      +.++||||+|||+++|+++|.++|+.||+|.+|.|..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.|+
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   4667899999999999999999999999999999999998


Q ss_pred             cCC
Q 022301           81 HGG   83 (299)
Q Consensus        81 ~~~   83 (299)
                      ...
T Consensus        85 ~~~   87 (93)
T d1h2vz_          85 AGF   87 (93)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            643

>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=3.1e-22  Score=138.24  Aligned_cols=81  Identities=59%  Similarity=1.046  Sum_probs=76.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      ..++++|||+|||+++|+++|+++|..||.|..+.+..+...++||||+|.+.++|+.||..|||..|.|++|+|.|++.
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            36788999999999999999999999999999999987778899999999999999999999999999999999999875


Q ss_pred             C
Q 022301           83 G   83 (299)
Q Consensus        83 ~   83 (299)
                      .
T Consensus        91 ~   91 (95)
T d1x4aa1          91 G   91 (95)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=4.4e-22  Score=136.71  Aligned_cols=81  Identities=31%  Similarity=0.484  Sum_probs=74.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      +++++|||+|||.++|+++|+++|++||+|..|.|..   ++.++|||||+|.+.++|+.|+..|||..|.|+.|.|.++
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            5578999999999999999999999999999999954   4678999999999999999999999999999999999998


Q ss_pred             cCCC
Q 022301           81 HGGR   84 (299)
Q Consensus        81 ~~~~   84 (299)
                      ....
T Consensus        87 ~~~~   90 (93)
T d1x5ua1          87 SAHN   90 (93)
T ss_dssp             TTTS
T ss_pred             CCCC
Confidence            7543

>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=99.87  E-value=2.3e-22  Score=137.14  Aligned_cols=80  Identities=34%  Similarity=0.597  Sum_probs=74.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ..++||||+|||+++|+++|.++|+.||+|..|.|..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a   82 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   82 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            6789999999999999999999999999999999954   4678999999999999999999999999999999999998


Q ss_pred             cCC
Q 022301           81 HGG   83 (299)
Q Consensus        81 ~~~   83 (299)
                      .+.
T Consensus        83 ~p~   85 (89)
T d2cqba1          83 KPM   85 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=99.86  E-value=8.7e-22  Score=135.51  Aligned_cols=82  Identities=26%  Similarity=0.472  Sum_probs=75.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec----CCCCCceEEEEecChHHHHHHHHhc-CCCCCCCceEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI----PPRPPGYAFVEFEEARDAEDAIRGR-DGYDFDGHRLRV   77 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~----~~~~~g~afV~F~~~e~A~~A~~~l-~~~~~~g~~i~v   77 (299)
                      ..++++|||+|||+++++++|.++|+.||.|..|.|..    ++.++|||||+|.+.++|..|+..| ||..|.|+.|.|
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            36789999999999999999999999999999999943    4678999999999999999999998 899999999999


Q ss_pred             EEccCCC
Q 022301           78 ELAHGGR   84 (299)
Q Consensus        78 ~~~~~~~   84 (299)
                      .|+....
T Consensus        85 ~~A~~~~   91 (94)
T d2cpha1          85 EWADSEV   91 (94)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCC
Confidence            9997654

>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=9.5e-22  Score=134.32  Aligned_cols=81  Identities=35%  Similarity=0.517  Sum_probs=73.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC-CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~-~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      +.+++||||+|||.++|+++|.++|+.||+|..|.|..+ ...+|||||+|.+.++|..|+..|||..|.|+.|+|.|+.
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            366799999999999999999999999999999999654 3458999999999999999999999999999999999987


Q ss_pred             CC
Q 022301           82 GG   83 (299)
Q Consensus        82 ~~   83 (299)
                      ..
T Consensus        85 ~~   86 (90)
T d2cqia1          85 TP   86 (90)
T ss_dssp             CT
T ss_pred             CC
Confidence            53

>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=99.86  E-value=7.7e-22  Score=134.99  Aligned_cols=83  Identities=35%  Similarity=0.610  Sum_probs=75.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEE
Q 022301            1 MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRV   77 (299)
Q Consensus         1 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v   77 (299)
                      |+ .+..+|||+|||+++|+++|+++|++||+|..+.+..   ++.++|||||+|.++++|+.|+..|||..|.|+.|.|
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 MA-SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRV   79 (90)
T ss_dssp             CC-CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEE
T ss_pred             CC-CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            54 5677799999999999999999999999999998743   4678999999999999999999999999999999999


Q ss_pred             EEccCCC
Q 022301           78 ELAHGGR   84 (299)
Q Consensus        78 ~~~~~~~   84 (299)
                      .++....
T Consensus        80 ~~a~~~~   86 (90)
T d1x5sa1          80 DQAGKSS   86 (90)
T ss_dssp             EEEECCC
T ss_pred             EEcCCCC
Confidence            9986544

>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=99.86  E-value=1.7e-21  Score=135.57  Aligned_cols=82  Identities=34%  Similarity=0.519  Sum_probs=75.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      +.++++|||+|||+++|+++|.++|.+||+|..|.|..   ++.++|||||+|.+.++|+.||..|||..|.|+.|.|.+
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            46788999999999999999999999999999999954   467899999999999999999999999999999999999


Q ss_pred             ccCCC
Q 022301           80 AHGGR   84 (299)
Q Consensus        80 ~~~~~   84 (299)
                      +....
T Consensus        85 a~~~~   89 (99)
T d1whwa_          85 STIKK   89 (99)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            87654

>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=99.86  E-value=5.2e-22  Score=133.45  Aligned_cols=77  Identities=29%  Similarity=0.484  Sum_probs=71.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      .++|||+|||+++++++|.++|++||+|..|.|..   ++..+|||||+|.+.++|+.|+..|||..|.|+.|.|.|+++
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   357789999999999999999999999999999999999864

>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=4.4e-22  Score=136.04  Aligned_cols=80  Identities=35%  Similarity=0.588  Sum_probs=74.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .++++|||+|||.++|+++|.++|+.||+|..|.|..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.|+
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            5778999999999999999999999999999999954   4677899999999999999999999999999999999999


Q ss_pred             cCC
Q 022301           81 HGG   83 (299)
Q Consensus        81 ~~~   83 (299)
                      ++.
T Consensus        86 kp~   88 (90)
T d2cq0a1          86 KPS   88 (90)
T ss_dssp             SCC
T ss_pred             eCC
Confidence            753

>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=99.86  E-value=6.1e-22  Score=132.68  Aligned_cols=77  Identities=18%  Similarity=0.306  Sum_probs=68.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      .|||||+|||+++|+++|.++|+.||+|..+.+..   .+.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+
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            48999999999999999999999999998877733   467889999999999999999999999999999999999864

>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=99.85  E-value=6.6e-22  Score=134.44  Aligned_cols=80  Identities=28%  Similarity=0.490  Sum_probs=73.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      +.+.++|||+|||.++|+++|.++|+.||+|..|.|..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|+|
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~   83 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            35678999999999999999999999999999999954   467789999999999999999999999999999999999


Q ss_pred             ccC
Q 022301           80 AHG   82 (299)
Q Consensus        80 ~~~   82 (299)
                      +..
T Consensus        84 a~~   86 (88)
T d1rk8a_          84 CFV   86 (88)
T ss_dssp             SEE
T ss_pred             ecC
Confidence            864

>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=99.85  E-value=1.4e-21  Score=129.60  Aligned_cols=74  Identities=27%  Similarity=0.495  Sum_probs=69.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         8 ~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      .|||+|||+++++++|+++|++||+|..+.|..  ++.++|||||+|.+.++|+.|+..|||..|.|++|.|.++.
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            599999999999999999999999999999954  57788999999999999999999999999999999999874

>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=99.85  E-value=2.5e-21  Score=132.94  Aligned_cols=82  Identities=24%  Similarity=0.477  Sum_probs=74.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC-CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~-~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ....++|||+|||+++|+++|.++|+.||+|..|.+..+ +.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~   87 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT   87 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            356789999999999999999999999999999999654 3468999999999999999999999999999999999997


Q ss_pred             CCC
Q 022301           82 GGR   84 (299)
Q Consensus        82 ~~~   84 (299)
                      +..
T Consensus        88 ~r~   90 (93)
T d2cq3a1          88 ARV   90 (93)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            543

>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=1.1e-21  Score=132.44  Aligned_cols=78  Identities=32%  Similarity=0.593  Sum_probs=70.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCC--ceEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDG--HRLRV   77 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g--~~i~v   77 (299)
                      +..+++|||+|||+++|+++|+++|++||+|..+.|..   ++.++|||||+|.+.++|..|+..|||..+.|  .+|.|
T Consensus         3 s~k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V   82 (85)
T d1fxla2           3 SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV   82 (85)
T ss_dssp             GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEE
Confidence            34568899999999999999999999999999999954   46788999999999999999999999999987  56999


Q ss_pred             EEc
Q 022301           78 ELA   80 (299)
Q Consensus        78 ~~~   80 (299)
                      .||
T Consensus        83 ~~A   85 (85)
T d1fxla2          83 KFA   85 (85)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            885

>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=99.85  E-value=1.8e-21  Score=131.32  Aligned_cols=78  Identities=28%  Similarity=0.586  Sum_probs=72.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      .+|||+|||+++|+++|.++|++||+|..|.|..   ++.++|||||+|.++++|..|+..|||..|.|+.|.|.++...
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            4799999999999999999999999999999954   4788999999999999999999999999999999999999754


Q ss_pred             C
Q 022301           84 R   84 (299)
Q Consensus        84 ~   84 (299)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.85  E-value=7.5e-22  Score=131.74  Aligned_cols=74  Identities=32%  Similarity=0.513  Sum_probs=69.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         8 ~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      +|||+|||+++|+++|.++|+.||+|..|.|..   ++.++|||||+|.++++|..|+..|||..|.|+.|+|.|++
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            699999999999999999999999999999954   36678999999999999999999999999999999999985

>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=132.89  Aligned_cols=79  Identities=24%  Similarity=0.396  Sum_probs=72.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC-CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~-~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      +..+|||+|||+++|+++|+++|+.||.|..+.|..+ +.++|||||+|.+.++|..|+..|||..|.|+.|.|.++...
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            4568999999999999999999999999999999654 456899999999999999999999999999999999998754

>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=134.88  Aligned_cols=80  Identities=30%  Similarity=0.572  Sum_probs=73.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHH----HhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            4 RASRTLYVGNLPGDIREREVED----LFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~----~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      +|++||||+|||+++++++|++    +|++||+|..|.+..++.++|||||+|.+.++|..|+..|||..|.|+.|.|.|
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    689999999999977777889999999999999999999999999999999999


Q ss_pred             ccCC
Q 022301           80 AHGG   83 (299)
Q Consensus        80 ~~~~   83 (299)
                      ++..
T Consensus        81 ak~~   84 (91)
T d1nu4a_          81 AKTD   84 (91)
T ss_dssp             CSSC
T ss_pred             eCCC
Confidence            8753

>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=1.1e-21  Score=129.45  Aligned_cols=73  Identities=15%  Similarity=0.404  Sum_probs=68.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      |+|||+|||+++|+++|+++|++||+|..+.|..   ++.++|||||+|.++++|++|+. +|+..|.|+.|.|..|
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            7899999999999999999999999999999954   46789999999999999999998 8999999999999876

>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=99.84  E-value=1.3e-21  Score=131.67  Aligned_cols=74  Identities=38%  Similarity=0.630  Sum_probs=68.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRV   77 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v   77 (299)
                      .++++|||+|||+++|+++|+++|++||+|..|.|..   ++.++|||||+|.+.++|..|+..|||..|.|+.|+|
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            4678999999999999999999999999999999854   3677899999999999999999999999999999987

>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=99.84  E-value=2.1e-21  Score=135.64  Aligned_cols=81  Identities=20%  Similarity=0.479  Sum_probs=73.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .+.++|||+|||+++|+++|.++|+.||.|..+.+..   ++.++|||||+|.+.++|..||..|||..|.|+.|.|.|+
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            4568899999999999999999999999999999854   4677899999999999999999999999999999999998


Q ss_pred             cCCC
Q 022301           81 HGGR   84 (299)
Q Consensus        81 ~~~~   84 (299)
                      ....
T Consensus        96 ~~k~   99 (102)
T d2cpza1          96 RSKN   99 (102)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            7543

>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=3.4e-21  Score=130.13  Aligned_cols=77  Identities=34%  Similarity=0.578  Sum_probs=70.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCC--ceEEEE
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDG--HRLRVE   78 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g--~~i~v~   78 (299)
                      ..+++|||+|||+++++++|.++|++||+|..+.|..   ++.++|||||+|.+.++|..|+..|||..+.|  ++|.|.
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            4567899999999999999999999999999999954   46788999999999999999999999999876  889999


Q ss_pred             Ec
Q 022301           79 LA   80 (299)
Q Consensus        79 ~~   80 (299)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>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=99.84  E-value=7.1e-21  Score=127.85  Aligned_cols=77  Identities=22%  Similarity=0.411  Sum_probs=70.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCC-CceEEEEEcc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFD-GHRLRVELAH   81 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~-g~~i~v~~~~   81 (299)
                      +.|++||||+|||.++|+++|.++|+.||+|..|.+..+  .+|||||+|.+.++|..|+..|||..|. |+.|.|.|++
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN--RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT--TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc--cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            468899999999999999999999999999999999643  3689999999999999999999998885 6899999985

>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=99.84  E-value=4.9e-21  Score=129.34  Aligned_cols=77  Identities=35%  Similarity=0.538  Sum_probs=71.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCCC
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGGR   84 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~~   84 (299)
                      ..++|||+|||.++++++|.++|+.||+|.+|.+..   .++||||+|.+.++|..|+..|||..|.|+.|.|.|+....
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 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK---DKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEET---TTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeec---ccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            457899999999999999999999999999999973   47899999999999999999999999999999999987543

>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=5.1e-21  Score=131.97  Aligned_cols=77  Identities=23%  Similarity=0.460  Sum_probs=71.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      .++++|||+|||.++++++|+++|++||+|..|.|..+   +|||||+|.+.++|..|+..|||..|.|+.|+|.|++..
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            45689999999999999999999999999999999844   899999999999999999999999999999999998653

>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=99.84  E-value=4.3e-21  Score=136.73  Aligned_cols=78  Identities=27%  Similarity=0.341  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      +.++||||+|||+++++++|.++|..||+|..|.|.   ..+|||||+|.+.++|..|++.|||..|.|+.|.|.|+...
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 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP---EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC---SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee---ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            567899999999999999999999999999999985   45789999999999999999999999999999999998654


Q ss_pred             C
Q 022301           84 R   84 (299)
Q Consensus        84 ~   84 (299)
                      .
T Consensus        85 ~   85 (111)
T d1whxa_          85 V   85 (111)
T ss_dssp             T
T ss_pred             c
Confidence            4

>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=7.9e-21  Score=140.79  Aligned_cols=82  Identities=33%  Similarity=0.654  Sum_probs=74.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ...++|||+|||+++|+++|+++|+.||+|..|.|..   ++.++|||||+|.+.++|..||..|||..|.|+.|.|.++
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            3457899999999999999999999999999999954   4677899999999999999999999999999999999998


Q ss_pred             cCCCC
Q 022301           81 HGGRG   85 (299)
Q Consensus        81 ~~~~~   85 (299)
                      .....
T Consensus       120 ~~~~~  124 (139)
T d1u6fa1         120 ASGHQ  124 (139)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            75543

>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=1.4e-20  Score=131.61  Aligned_cols=79  Identities=25%  Similarity=0.429  Sum_probs=71.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ..++|||+|||+++|+++|.++|+.||+|.+|.|..   ++.++|||||+|.+.++|..|++.+|+ .|.|+.|.|.++.
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            346799999999999999999999999999999954   467899999999999999999998776 7999999999987


Q ss_pred             CCC
Q 022301           82 GGR   84 (299)
Q Consensus        82 ~~~   84 (299)
                      ...
T Consensus        88 ~~~   90 (103)
T d2cqda1          88 LGA   90 (103)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            554

>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=1.2e-20  Score=128.34  Aligned_cols=78  Identities=22%  Similarity=0.343  Sum_probs=70.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCC-CCceEEEEEccC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDF-DGHRLRVELAHG   82 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~-~g~~i~v~~~~~   82 (299)
                      -|++||||+|||.++|+++|.++|+.||.|..+.+.. +..++||||+|.+.++|..|+..|||..| .|+.|+|.|++.
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~-~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~   86 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF-QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS   86 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC-SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee-ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCC
Confidence            4688999999999999999999999999998887743 34578999999999999999999999888 589999999864

>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=4.1e-21  Score=134.97  Aligned_cols=78  Identities=33%  Similarity=0.700  Sum_probs=72.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      +.+||||+|||+++|+++|.++|+.||+|..|.|..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.
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            457899999999999999999999999999999954   46678999999999999999999999999999999999986


Q ss_pred             C
Q 022301           82 G   82 (299)
Q Consensus        82 ~   82 (299)
                      .
T Consensus        87 ~   87 (104)
T d1p1ta_          87 S   87 (104)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=2.1e-20  Score=132.57  Aligned_cols=78  Identities=21%  Similarity=0.353  Sum_probs=71.0

Q ss_pred             CCCeEEEcCCCC-CCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            5 ASRTLYVGNLPG-DIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         5 ~~~~l~V~nLp~-~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      .+++|||+|||+ .+|+++|.++|+.||+|..|.|..+.  +|||||+|.+.++|..|+..|||..|.|+.|.|.|++..
T Consensus         1 g~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~--kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~   78 (109)
T d2adca1           1 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK--KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   78 (109)
T ss_dssp             CCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT--SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc--cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            478999999965 59999999999999999999997653  789999999999999999999999999999999998754


Q ss_pred             C
Q 022301           84 R   84 (299)
Q Consensus        84 ~   84 (299)
                      .
T Consensus        79 ~   79 (109)
T d2adca1          79 N   79 (109)
T ss_dssp             C
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=99.83  E-value=4.9e-21  Score=129.49  Aligned_cols=78  Identities=23%  Similarity=0.356  Sum_probs=68.9

Q ss_pred             CCCCeEEEcCCCCCCC-HHHHHHHhhhcCCeeEEEeec----CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEE
Q 022301            4 RASRTLYVGNLPGDIR-EREVEDLFYKYGPIAHIDLKI----PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVE   78 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t-~~~l~~~F~~~G~v~~i~~~~----~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~   78 (299)
                      -..++|||+|||+++| +++|.++|++||+|..|.|..    ++.++|||||+|.+.++|..|+. |||..|.|+.|.|.
T Consensus         2 ~e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~   80 (86)
T d2ghpa3           2 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVS   80 (86)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEE
T ss_pred             CCCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEE
Confidence            3578999999999986 556999999999999999843    46788999999999999999996 99999999999999


Q ss_pred             EccC
Q 022301           79 LAHG   82 (299)
Q Consensus        79 ~~~~   82 (299)
                      ++..
T Consensus        81 ~a~~   84 (86)
T d2ghpa3          81 LADK   84 (86)
T ss_dssp             ECCC
T ss_pred             EcCC
Confidence            9864

>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=99.83  E-value=8.1e-21  Score=132.07  Aligned_cols=76  Identities=29%  Similarity=0.454  Sum_probs=70.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      +.+||||+|||.++|+++|+++|+.||+|.+|.|..   ++.++|||||+|.+.++|.+|+. |||..|.|+.|.|.++.
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            357999999999999999999999999999999954   47899999999999999999996 99999999999999875

>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=99.83  E-value=9.4e-21  Score=128.83  Aligned_cols=79  Identities=22%  Similarity=0.420  Sum_probs=70.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ..+++|||+|||+++|+++|.++|+.||+|..|.|..   ++.++|||||+|.+.++|.+||..++  .|.|+.|.|.++
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~~--~l~Gr~i~v~~a   83 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH--MIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCE--EETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcCC--ccCCEEeEEEeC
Confidence            5788999999999999999999999999999999954   47788999999999999999999543  789999999998


Q ss_pred             cCCC
Q 022301           81 HGGR   84 (299)
Q Consensus        81 ~~~~   84 (299)
                      ....
T Consensus        84 ~~k~   87 (90)
T d2cqga1          84 NSKQ   87 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            6543

>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=99.83  E-value=4e-21  Score=134.66  Aligned_cols=82  Identities=24%  Similarity=0.434  Sum_probs=75.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEee---cCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLK---IPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~---~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      ..|+++|||+|||.++++++|+++|..||.|..+.+.   .++.++|||||+|.+.++|..|+..|||..|.|+.|.|.|
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   94 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF   94 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            3578999999999999999999999999999888774   3578899999999999999999999999999999999999


Q ss_pred             ccCCC
Q 022301           80 AHGGR   84 (299)
Q Consensus        80 ~~~~~   84 (299)
                      ++...
T Consensus        95 ak~k~   99 (102)
T d2cpxa1          95 GKNKK   99 (102)
T ss_dssp             CCCCS
T ss_pred             CCCcc
Confidence            97543

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=1.2e-20  Score=124.05  Aligned_cols=71  Identities=23%  Similarity=0.560  Sum_probs=65.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEE
Q 022301            8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVEL   79 (299)
Q Consensus         8 ~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~   79 (299)
                      .|||+|||+++|+++|.++|++||+|..+.|..   ++.++|||||+|.++++|++|+. +++..|.|+.|.|..
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~r   74 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKR   74 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeE
Confidence            489999999999999999999999999999954   46789999999999999999998 899999999999854

>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=99.82  E-value=1.2e-20  Score=126.80  Aligned_cols=76  Identities=18%  Similarity=0.392  Sum_probs=69.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ..++|||+|||+++|+++|.++|+.||+|..+.|..   ++.++|||||+|.+.++|.+|+. +++..|.|+.|.|..|.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            346899999999999999999999999999999954   47789999999999999999998 79999999999998774

>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=99.82  E-value=1.8e-20  Score=126.81  Aligned_cols=76  Identities=33%  Similarity=0.441  Sum_probs=70.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      ..++|||+|||+++|+++|.++|+.||.|..+.+.   .++|||||+|.+.++|..|+..|||..|.|+.|.|.|+++.
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~---~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~   82 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK---KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV   82 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE---ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc---cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCC
Confidence            45899999999999999999999999999888875   45899999999999999999999999999999999998743

>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=99.82  E-value=1.2e-20  Score=126.85  Aligned_cols=75  Identities=25%  Similarity=0.456  Sum_probs=67.8

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhcCCeeEE-Eeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            9 LYVGNLPGDIREREVEDLFYKYGPIAHI-DLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         9 l~V~nLp~~~t~~~l~~~F~~~G~v~~i-~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      |||+|||+++|+++|.++|++||+|..+ .+..   ++.++|||||+|.+.++|..|+..|||..|.|++|.|.++...
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            8999999999999999999999998664 4533   4678899999999999999999999999999999999998754

>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=99.82  E-value=2.2e-20  Score=131.17  Aligned_cols=81  Identities=26%  Similarity=0.521  Sum_probs=70.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec----CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEE
Q 022301            2 SSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI----PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRV   77 (299)
Q Consensus         2 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~----~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v   77 (299)
                      ...|+++|||+|||+++|+++|+++|+.|| |..+.+..    ++.++|||||+|.+.++|++|+. ||+..|.|+.|.|
T Consensus        11 p~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V   88 (104)
T d1wi8a_          11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRV   88 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEE
Confidence            356789999999999999999999999999 66776633    35678999999999999987775 9999999999999


Q ss_pred             EEccCCC
Q 022301           78 ELAHGGR   84 (299)
Q Consensus        78 ~~~~~~~   84 (299)
                      .++....
T Consensus        89 ~~a~~~~   95 (104)
T d1wi8a_          89 DVADQAQ   95 (104)
T ss_dssp             EECCCCC
T ss_pred             EECCCCC
Confidence            9987654

>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=1.4e-20  Score=130.16  Aligned_cols=75  Identities=32%  Similarity=0.606  Sum_probs=69.1

Q ss_pred             CCCCeEEEcCCC-CCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            4 RASRTLYVGNLP-GDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         4 ~~~~~l~V~nLp-~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      ..+++|||+||| ..+++++|+++|.+||+|..|.|.     +|||||+|.+.++|+.||..|||..|.|+.|.|.++..
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            456889999997 568889999999999999999996     79999999999999999999999999999999999865


Q ss_pred             C
Q 022301           83 G   83 (299)
Q Consensus        83 ~   83 (299)
                      .
T Consensus        88 ~   88 (98)
T d1wf2a_          88 P   88 (98)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=1.4e-20  Score=131.16  Aligned_cols=77  Identities=19%  Similarity=0.394  Sum_probs=70.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      .++|||+|||+++|+++|+++|.+||+|..+.|..   ++.++|||||+|.+.++|..|+. ++|..|.|+.|.|.++.+
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            37899999999999999999999999999999954   46789999999999999999997 899999999999998865


Q ss_pred             C
Q 022301           83 G   83 (299)
Q Consensus        83 ~   83 (299)
                      .
T Consensus        99 k   99 (103)
T d1x4ba1          99 R   99 (103)
T ss_dssp             C
T ss_pred             c
Confidence            4

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=2e-20  Score=124.33  Aligned_cols=75  Identities=25%  Similarity=0.457  Sum_probs=69.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      ..++||||+||+  +|+++|.++|++||+|..|.+.   ..++||||+|.+.++|..|+..|||..|.|+.|+|.|+...
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--MTPTLLRGAFSPFGNIIDLSMD---PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeec---cCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            567899999996  9999999999999999999997   34789999999999999999999999999999999999643

>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=5.2e-21  Score=133.48  Aligned_cols=79  Identities=19%  Similarity=0.310  Sum_probs=71.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      +.+.++|||+|||+++|+++|.++|+.||+|..+.+..  ++.++|||||+|.+.++|.+|+..|||..|.|+++.|.++
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            45678999999999999999999999999999998844  4567899999999999999999999999999999888665


Q ss_pred             c
Q 022301           81 H   81 (299)
Q Consensus        81 ~   81 (299)
                      .
T Consensus        95 ~   95 (101)
T d1x5oa1          95 E   95 (101)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.82  E-value=6.7e-21  Score=126.90  Aligned_cols=75  Identities=24%  Similarity=0.394  Sum_probs=67.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCC-CCCCceEEEEEccCCC
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY-DFDGHRLRVELAHGGR   84 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~-~~~g~~i~v~~~~~~~   84 (299)
                      ++|||+|||.++|+++|.++|++||.|..+.+.   ..+|||||+|.+.++|..|+..|||. .|.|+.|.|.|+.+..
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 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL---LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK   77 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE---EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEe---cccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcC
Confidence            479999999999999999999999999777664   34789999999999999999999996 5999999999987543

>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=4e-20  Score=125.60  Aligned_cols=81  Identities=21%  Similarity=0.318  Sum_probs=72.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhc--CCCCCCCceEEEE
Q 022301            1 MSSRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGR--DGYDFDGHRLRVE   78 (299)
Q Consensus         1 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l--~~~~~~g~~i~v~   78 (299)
                      |...|+++|||+|||+++|+++|+++|++||.|..+.+.   ..++||||+|.+.++|..|+..|  ++..+.|++|.|.
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 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILML---KGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   79 (88)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEE---TTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccc---ccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEE
Confidence            456899999999999999999999999999999999997   34689999999999999999865  5778999999999


Q ss_pred             EccCCC
Q 022301           79 LAHGGR   84 (299)
Q Consensus        79 ~~~~~~   84 (299)
                      |++...
T Consensus        80 ~sk~~~   85 (88)
T d2cq1a1          80 YSNHKE   85 (88)
T ss_dssp             ECSCSS
T ss_pred             ECCCCC
Confidence            997543

>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=99.82  E-value=2.1e-20  Score=126.27  Aligned_cols=74  Identities=27%  Similarity=0.521  Sum_probs=67.6

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC---C---CCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP---P---RPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         9 l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~---~---~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      |||+|||+++|+++|.++|++||+|..+.|..+   +   .++|||||+|.+.++|..|+..|||..|.|+.|.|.++..
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            899999999999999999999999999999442   2   2478999999999999999999999999999999999854

>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=99.82  E-value=4.6e-20  Score=127.57  Aligned_cols=78  Identities=27%  Similarity=0.512  Sum_probs=71.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCC--ceEEEEEc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDG--HRLRVELA   80 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g--~~i~v~~~   80 (299)
                      +.|+++|||+|||+++++++|+++|++||+|..|.+..   .++||||+|.+.++|..|+..||+..|.|  ..|+|.|+
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~---~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~a   90 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK---GDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFA   90 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECS---SSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEEC
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeec---cccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeC
Confidence            36789999999999999999999999999999999963   47899999999999999999999999986  58999998


Q ss_pred             cCC
Q 022301           81 HGG   83 (299)
Q Consensus        81 ~~~   83 (299)
                      +..
T Consensus        91 k~~   93 (97)
T d1whya_          91 KSG   93 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            753

>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=1.8e-20  Score=123.06  Aligned_cols=73  Identities=26%  Similarity=0.345  Sum_probs=66.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC-CCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-PRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~-~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      +||||+|||+++++++|+++|..||+|..|.|..+ +...+||||+|.++++|.+|+. ||+..|.|+.|.|..+
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            58999999999999999999999999999999543 4557899999999999999997 9999999999999864

>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=2e-20  Score=126.89  Aligned_cols=78  Identities=32%  Similarity=0.425  Sum_probs=68.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      +.++++|||+|||+++++++|+++|.+|| +..+.+.   ..++||||+|.+.++|+.|+..|||..|.|+.|.|+++..
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            35688999999999999999999999999 3334442   3478999999999999999999999999999999999865


Q ss_pred             CC
Q 022301           83 GR   84 (299)
Q Consensus        83 ~~   84 (299)
                      ..
T Consensus        78 ~~   79 (88)
T d1wg1a_          78 DA   79 (88)
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=99.82  E-value=1.5e-20  Score=123.20  Aligned_cols=72  Identities=19%  Similarity=0.496  Sum_probs=66.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         8 ~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .|||+|||+++|+++|+++|++||+|..|.|..   ++.++|||||+|.+.++|++||. +++..|.|+.|.|..|
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            599999999999999999999999999999954   46789999999999999999998 6888999999998764

>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=99.82  E-value=2.2e-20  Score=124.41  Aligned_cols=74  Identities=26%  Similarity=0.541  Sum_probs=68.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      -++|||+|||+++|+++|+++|+.||.|..+.+..   ++.++|||||+|.++++|.+|+. |||..|.|+.|.|..|
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            47899999999999999999999999999999954   45678999999999999999997 9999999999999875

>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=99.81  E-value=2.1e-20  Score=125.89  Aligned_cols=76  Identities=17%  Similarity=0.378  Sum_probs=70.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      .+++|||+|||.++|+++|.++|+.||+|..|.|..  ++.++|||||+|.++++|.+||. ++|..|.|+.|.|.+..
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            468999999999999999999999999999999953  46678999999999999999997 89999999999999864

>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=99.81  E-value=6.1e-20  Score=127.62  Aligned_cols=80  Identities=23%  Similarity=0.485  Sum_probs=71.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcC------CCCCCCce
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRD------GYDFDGHR   74 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~------~~~~~g~~   74 (299)
                      .+.++|||+|||+++|+++|+++|..||+|..+.+..   ++.++|||||+|.+.++|..|+..||      |..|.|+.
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            4578999999999999999999999999999999954   35678999999999999999999887      56688999


Q ss_pred             EEEEEccCC
Q 022301           75 LRVELAHGG   83 (299)
Q Consensus        75 i~v~~~~~~   83 (299)
                      |.|.++...
T Consensus        86 l~v~~a~~k   94 (98)
T d1x4ha1          86 LKVDLAVTR   94 (98)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEECCCC
Confidence            999998653

>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=99.81  E-value=2.7e-20  Score=122.75  Aligned_cols=72  Identities=21%  Similarity=0.377  Sum_probs=66.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         8 ~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .|||+|||+++|+++|.++|+.||.|..+.+..   ++.+++||||+|.+.++|.+|++ |||..|.|++|.|.+|
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            489999999999999999999999999999843   46788999999999999999998 9999999999999875

>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=99.81  E-value=3.7e-20  Score=129.44  Aligned_cols=82  Identities=27%  Similarity=0.474  Sum_probs=71.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEE--------Eeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCC
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHI--------DLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFD   71 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i--------~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~   71 (299)
                      +..+++|||+|||.++|+++|.++|..||+|..+        .+..   ++..+|||||+|.+.++|..|+..|||..|.
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~   84 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   84 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEEC
Confidence            3568899999999999999999999999998543        3322   3677899999999999999999999999999


Q ss_pred             CceEEEEEccCCC
Q 022301           72 GHRLRVELAHGGR   84 (299)
Q Consensus        72 g~~i~v~~~~~~~   84 (299)
                      |+.|.|.++....
T Consensus        85 gr~i~V~~a~~~~   97 (101)
T d2cpea1          85 GSKLKVSLARKKP   97 (101)
T ss_dssp             TEECEEECSSCCC
T ss_pred             CEEEEEEEcCCCC
Confidence            9999999997543

>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=9.2e-21  Score=128.42  Aligned_cols=72  Identities=22%  Similarity=0.273  Sum_probs=66.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      ++|||+|||+++|+++|+++|++||+|..+.+..    .|||||+|.+.++|++||..|||..|.|+.|.|.++..
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~----~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~   72 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR----DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   72 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT----TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc----cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEec
Confidence            5799999999999999999999999999999864    37999999999999999999999999999999887653

>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=99.80  E-value=1.3e-20  Score=130.20  Aligned_cols=79  Identities=28%  Similarity=0.443  Sum_probs=71.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      .++++|||+|||.++|+++|+++|..||.|..+..  ++.+++||||+|.+.++|..|+..|||..|.|+.|.|.|+.+.
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 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ--DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK   91 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE--TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee--cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCC
Confidence            56799999999999999999999999999877654  4567899999999999999999999999999999999998765


Q ss_pred             C
Q 022301           84 R   84 (299)
Q Consensus        84 ~   84 (299)
                      .
T Consensus        92 ~   92 (96)
T d1fjca_          92 G   92 (96)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=1.2e-19  Score=125.38  Aligned_cols=79  Identities=24%  Similarity=0.341  Sum_probs=69.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhhcCC-eeEEEeec----CCCCCceEEEEecChHHHHHHHHhcCC--CCCCCceEEEE
Q 022301            6 SRTLYVGNLPGDIREREVEDLFYKYGP-IAHIDLKI----PPRPPGYAFVEFEEARDAEDAIRGRDG--YDFDGHRLRVE   78 (299)
Q Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~G~-v~~i~~~~----~~~~~g~afV~F~~~e~A~~A~~~l~~--~~~~g~~i~v~   78 (299)
                      ||.|||+|||.++|+++|.++|+.||+ |..+.|..    ++.++|||||+|.+.++|..|+..|++  ..+.|+.|.|.
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            688999999999999999999999996 89999854    356889999999999999999999875  44579999999


Q ss_pred             EccCCC
Q 022301           79 LAHGGR   84 (299)
Q Consensus        79 ~~~~~~   84 (299)
                      |+.+..
T Consensus        81 ~A~p~~   86 (96)
T d2disa1          81 WAEPEI   86 (96)
T ss_dssp             ESCSSC
T ss_pred             EcCCCC
Confidence            997544

>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=99.80  E-value=6.6e-21  Score=130.05  Aligned_cols=78  Identities=21%  Similarity=0.342  Sum_probs=70.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEe--ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL--KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~--~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      ....+|||+|||+++|+++|+++|..||.|..+.|  ..++.++|||||+|.+.++|+.||+ |||..|.|+.|.|.+++
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            35568999999999999999999999999988877  3357889999999999999999997 99999999999999986


Q ss_pred             C
Q 022301           82 G   82 (299)
Q Consensus        82 ~   82 (299)
                      .
T Consensus        90 ~   90 (91)
T d1fjeb1          90 G   90 (91)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.80  E-value=4.8e-19  Score=124.03  Aligned_cols=79  Identities=19%  Similarity=0.216  Sum_probs=71.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhc--CCCCCCCceEEEEEc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGR--DGYDFDGHRLRVELA   80 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l--~~~~~~g~~i~v~~~   80 (299)
                      ..++++|||+|||.++|+++|.++|..||+|..|.+.   ..+++|||+|.+.++|+.|+..|  ++..+.|++|.|.|+
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~---~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s   88 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMM---PFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYS   88 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEE---TTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEE---ecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEc
Confidence            3689999999999999999999999999999999997   35789999999999999999977  567788999999999


Q ss_pred             cCCC
Q 022301           81 HGGR   84 (299)
Q Consensus        81 ~~~~   84 (299)
                      ....
T Consensus        89 ~~~~   92 (104)
T d1wexa_          89 TSKR   92 (104)
T ss_dssp             SSSS
T ss_pred             CCCc
Confidence            7644

>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=99.80  E-value=1.9e-19  Score=118.02  Aligned_cols=71  Identities=28%  Similarity=0.425  Sum_probs=64.7

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         9 l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      |||+|||+++++++|+++|++|| +..+.+.   ..+|||||+|.+.++|.+|+..|||..+.|++|.|.++...
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 5556554   56899999999999999999999999999999999998643

>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=99.80  E-value=5.9e-20  Score=124.66  Aligned_cols=78  Identities=23%  Similarity=0.418  Sum_probs=70.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccC
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHG   82 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~   82 (299)
                      +.++++|||+|||+++|+++|+++|++||+|..|.+..  .+++||||+|.+.++|+.|+.  ++..|.|+.|.|.++.+
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            46789999999999999999999999999999998753  457899999999999999985  77889999999999865


Q ss_pred             CC
Q 022301           83 GR   84 (299)
Q Consensus        83 ~~   84 (299)
                      ..
T Consensus        78 k~   79 (88)
T d1wf0a_          78 KH   79 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.78  E-value=5.5e-20  Score=124.93  Aligned_cols=74  Identities=24%  Similarity=0.413  Sum_probs=66.1

Q ss_pred             CCCeEEEcCCCCCCCHHHH---HHHhhhcCCeeEEEeecC---C---CCCceEEEEecChHHHHHHHHhcCCCCCCCceE
Q 022301            5 ASRTLYVGNLPGDIREREV---EDLFYKYGPIAHIDLKIP---P---RPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRL   75 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l---~~~F~~~G~v~~i~~~~~---~---~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i   75 (299)
                      ..++|||+|||+++++++|   .++|++||+|..|.|..+   +   ...|||||+|.+.++|..|+..|||..|.|+.|
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   778999999999999543   2   334899999999999999999999999999999


Q ss_pred             EEE
Q 022301           76 RVE   78 (299)
Q Consensus        76 ~v~   78 (299)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            873

>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=99.78  E-value=1.9e-19  Score=124.42  Aligned_cols=76  Identities=22%  Similarity=0.292  Sum_probs=70.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEccCC
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAHGG   83 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~~~   83 (299)
                      ....+|||+|||+++++++|+++|+.||+|..+.|..    +|||||+|.+.++|+.||+.|||..|.|+.|.|.++...
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            5677899999999999999999999999999999963    589999999999999999999999999999999998643

>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=99.78  E-value=7.7e-19  Score=123.01  Aligned_cols=80  Identities=16%  Similarity=0.204  Sum_probs=70.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEe---ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~---~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .+..+|||+|||+++|+++|+++|..||.|..+.+   ..++.++|||||+|.++++|++|+. ||+..|.|+.|.|.++
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            35568999999999999999999999999877544   2346788999999999999999997 9999999999999998


Q ss_pred             cCCC
Q 022301           81 HGGR   84 (299)
Q Consensus        81 ~~~~   84 (299)
                      ....
T Consensus        92 ~~~~   95 (104)
T d1wg5a_          92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            7554

>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=99.77  E-value=4.1e-19  Score=123.90  Aligned_cols=80  Identities=21%  Similarity=0.305  Sum_probs=69.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEe--ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            3 SRASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL--KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~--~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      +....+|||+|||+++|+++|+++|..||.| .|.+  ..++..+|||||+|.++++|+.|+. ||+..|.|+.|.|.++
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~~~-~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s   89 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccCcc-eeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            3566799999999999999999999999854 5555  3356778999999999999999997 9999999999999998


Q ss_pred             cCCC
Q 022301           81 HGGR   84 (299)
Q Consensus        81 ~~~~   84 (299)
                      ....
T Consensus        90 ~~~~   93 (102)
T d1weza_          90 STAG   93 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7543

>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=1.9e-19  Score=121.73  Aligned_cols=77  Identities=25%  Similarity=0.389  Sum_probs=67.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeE-EEe--ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAH-IDL--KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-i~~--~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ...++|||+|||+++++++|+++|..||.|.. +.+  ..++.++|+|||+|.+.++|.+|+..||+..|.|++|.|.++
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34566999999999999999999999999855 334  445778899999999999999999999999999999999874

>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=9.1e-20  Score=119.02  Aligned_cols=68  Identities=21%  Similarity=0.427  Sum_probs=62.9

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEE
Q 022301            9 LYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLR   76 (299)
Q Consensus         9 l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~   76 (299)
                      |||+|||.++|+++|.++|+.||+|..+.+..   ++.++|||||+|.+.++|+.|+..|||..|.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            89999999999999999999999999998844   467889999999999999999999999999998763

>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=4.6e-19  Score=125.08  Aligned_cols=80  Identities=18%  Similarity=0.213  Sum_probs=70.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCC--CCceEEEEEcc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDF--DGHRLRVELAH   81 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~--~g~~i~v~~~~   81 (299)
                      .+..+|||+|||+++|+++|+++|++||.|..|.|... ..+|||||+|.+.++|+.|+..|||..|  .|..|.|.|++
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            56678999999999999999999999999999999644 3478999999999999999999999988  47889999986


Q ss_pred             CCC
Q 022301           82 GGR   84 (299)
Q Consensus        82 ~~~   84 (299)
                      ...
T Consensus        84 ~~~   86 (108)
T d2adba1          84 LTS   86 (108)
T ss_dssp             SCS
T ss_pred             Ccc
Confidence            544

>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=99.77  E-value=6.4e-19  Score=122.02  Aligned_cols=77  Identities=26%  Similarity=0.342  Sum_probs=69.6

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHH--hcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGD-IREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIR--GRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~-~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~--~l~~~~~~g~~i~v~~~   80 (299)
                      .++++|||+|||.+ +|+++|.++|+.||+|..|.+..   .+|||||+|.+.++|..|+.  .+++..|.|+.|.|.++
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 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR---MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLS   92 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET---TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEee---cCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEc
Confidence            56789999999985 89999999999999999999973   47899999999999999997  47889999999999998


Q ss_pred             cCC
Q 022301           81 HGG   83 (299)
Q Consensus        81 ~~~   83 (299)
                      ...
T Consensus        93 ~~~   95 (99)
T d1x4fa1          93 EKY   95 (99)
T ss_dssp             CSC
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=6.8e-19  Score=119.29  Aligned_cols=78  Identities=18%  Similarity=0.161  Sum_probs=70.2

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhc--CCCCCCCceEEEEE
Q 022301            3 SRASRTLYVGNLPGD-IREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGR--DGYDFDGHRLRVEL   79 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~-~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l--~~~~~~g~~i~v~~   79 (299)
                      .+++++|||+|||.. +|++||.++|++||+|..|.+..   .+++|||+|.+.++|..|+..|  ++..+.|++|.|.|
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 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN---KINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHL   81 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECS---SSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeec---cceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEE
Confidence            578999999999986 88999999999999999999973   3679999999999999999965  67889999999999


Q ss_pred             ccCC
Q 022301           80 AHGG   83 (299)
Q Consensus        80 ~~~~   83 (299)
                      ++..
T Consensus        82 s~~~   85 (89)
T d1x4da1          82 SQKY   85 (89)
T ss_dssp             ECCC
T ss_pred             CCCc
Confidence            8743

>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=99.76  E-value=6.9e-19  Score=122.65  Aligned_cols=80  Identities=19%  Similarity=0.178  Sum_probs=71.3

Q ss_pred             CCCCCeEEEcCCCCCC-C----HHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEE
Q 022301            3 SRASRTLYVGNLPGDI-R----EREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRV   77 (299)
Q Consensus         3 ~~~~~~l~V~nLp~~~-t----~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v   77 (299)
                      +.++++|||+||+.++ +    .++|.++|++||+|.++.+.   .+++||||+|.+.++|..|+..|||..|.|+.|+|
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 SSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF---KSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CSCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEE---TTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CCCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEe---cCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEE
Confidence            4678999999999986 3    35699999999999999997   45789999999999999999999999999999999


Q ss_pred             EEccCCCC
Q 022301           78 ELAHGGRG   85 (299)
Q Consensus        78 ~~~~~~~~   85 (299)
                      .|+.....
T Consensus        79 ~~a~~~~~   86 (104)
T d1weya_          79 YFAQTLHI   86 (104)
T ss_dssp             ECCCCSSC
T ss_pred             eecccCCC
Confidence            99975543

>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=7.1e-19  Score=123.08  Aligned_cols=77  Identities=18%  Similarity=0.217  Sum_probs=68.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeE-EEe--ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAH-IDL--KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-i~~--~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ....+|||+|||+++|+++|.++|..||.|.. +.+  ..++.++|||||+|.+.++|+.||. ||+..|.|+.|.|.++
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEEC
Confidence            45678999999999999999999999998865 444  3457889999999999999999997 9999999999999886


Q ss_pred             c
Q 022301           81 H   81 (299)
Q Consensus        81 ~   81 (299)
                      .
T Consensus        85 ~   85 (103)
T d2cpya1          85 T   85 (103)
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=99.72  E-value=2.6e-18  Score=116.09  Aligned_cols=65  Identities=55%  Similarity=1.039  Sum_probs=60.6

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      +.|||+|||..+++++|+++|++||.|..+.+..+   |||||+|.+.++|+.||..|||..|.|+.+
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~---g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i   65 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTKFRSHEG   65 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT---SEEEEEESSHHHHHHHHHHHTTCBCCCTTS
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc---ceeeEEeCCHHHHHHHHHHhCCCEECCcEe
Confidence            36999999999999999999999999999998655   699999999999999999999999999854

>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=1.5e-18  Score=123.12  Aligned_cols=76  Identities=22%  Similarity=0.296  Sum_probs=67.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEe---ecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDL---KIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~---~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ...++|||+|||+++|+++|.++|+.||.|..+.+   ..++.++|||||+|.+.++|.+|+. |||..|.|+.|.|..+
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            56779999999999999999999999998855322   4567889999999999999999997 9999999999999876

>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=99.72  E-value=1.6e-19  Score=123.14  Aligned_cols=75  Identities=29%  Similarity=0.515  Sum_probs=65.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEee--------cCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEE
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLK--------IPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVE   78 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~--------~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~   78 (299)
                      ++|||+|||.++|+++|.++|+.||.|..+.+.        .++.++|||||+|.++++|+.|+. |||..|.|+.|.|.
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            689999999999999999999999988766652        235678999999999999999996 99999999999997


Q ss_pred             EccC
Q 022301           79 LAHG   82 (299)
Q Consensus        79 ~~~~   82 (299)
                      .++.
T Consensus        81 r~k~   84 (90)
T d1u2fa_          81 RPHD   84 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            6543

>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=99.71  E-value=2.1e-17  Score=110.50  Aligned_cols=74  Identities=26%  Similarity=0.328  Sum_probs=66.2

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEec
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVR  183 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~  183 (299)
                      +++|||+|||..+++++|.++|++||.|..+.+..++..    +||||+|.+.++|+.|++.|||..+.|+    .+.+.
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 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNK----RLKVS   77 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTE----ECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCE----EEEEE
Confidence            478999999999999999999999999999999887654    4999999999999999999999999998    44444


Q ss_pred             cc
Q 022301          184 EY  185 (299)
Q Consensus       184 ~~  185 (299)
                      .+
T Consensus        78 ~a   79 (82)
T d1b7fa1          78 YA   79 (82)
T ss_dssp             EC
T ss_pred             Ec
Confidence            44

>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=99.71  E-value=5.3e-17  Score=108.67  Aligned_cols=71  Identities=20%  Similarity=0.236  Sum_probs=65.1

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .+..+|||+|||..+++++|+++|++||.|..+.++.++.+    |||||+|.+.++|+.|+..|||..|+|+.+
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i   81 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI   81 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEe
Confidence            35679999999999999999999999999999999988654    499999999999999999999999999843

>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=99.70  E-value=2.1e-17  Score=114.47  Aligned_cols=66  Identities=18%  Similarity=0.316  Sum_probs=60.7

Q ss_pred             CCCCCCeEEEcC--CCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCC
Q 022301            2 SSRASRTLYVGN--LPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDF   70 (299)
Q Consensus         2 ~~~~~~~l~V~n--Lp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~   70 (299)
                      ++.|+++|+|.|  ||.++|+++|+++|++||.|..|.+..   .++||||+|.+.++|..|+..|||..+
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 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP---NKPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT---TCSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeecc---CccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            568999999955  999999999999999999999999974   478999999999999999999999876

>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=99.70  E-value=1.2e-16  Score=111.07  Aligned_cols=79  Identities=22%  Similarity=0.266  Sum_probs=69.4

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceeeEEEE
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVR  181 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~  181 (299)
                      +++++|||+|||..+++++|.++|..||.|..+.++.+..+    |||||+|.+.++|+.|++.|||..|.|+    .|.
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~----~i~   91 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMK----RLK   91 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTE----ECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCE----EEE
Confidence            34678999999999999999999999999999999988654    4999999999999999999999999998    555


Q ss_pred             ecccccC
Q 022301          182 VREYDHR  188 (299)
Q Consensus       182 ~~~~~~~  188 (299)
                      |..+.++
T Consensus        92 V~~a~~k   98 (102)
T d2cpza1          92 VQLKRSK   98 (102)
T ss_dssp             EECCCCS
T ss_pred             EEEeCCC
Confidence            5555443

>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=99.69  E-value=9.8e-17  Score=108.47  Aligned_cols=71  Identities=14%  Similarity=0.191  Sum_probs=64.8

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..+++|||+|||..+++++|.++|.+||.|..+.++.++.+    |||||+|.+.++|+.|+..|||..|.|+.+
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l   79 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTI   79 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            35689999999999999999999999999999999988654    499999999999999999999999999844

>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=9.4e-17  Score=107.28  Aligned_cols=68  Identities=19%  Similarity=0.348  Sum_probs=63.2

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ++|||+|||..+++++|.++|++||.|..+.++.+...    |||||+|.+.++|+.|+..|||..|+|+.+
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l   74 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTI   74 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            57999999999999999999999999999999987654    499999999999999999999999999843

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

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

Probab=99.69  E-value=6.9e-17  Score=110.37  Aligned_cols=71  Identities=24%  Similarity=0.236  Sum_probs=64.7

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ....+|||+|||..+++++|+++|.+||.|..+.++.++.+    |||||+|.+.++|+.|++.|||..|+|+.+
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   81 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPI   81 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34579999999999999999999999999999999887543    599999999999999999999999999844

>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=99.69  E-value=1.5e-16  Score=108.69  Aligned_cols=70  Identities=13%  Similarity=0.186  Sum_probs=65.1

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..++|||+|||..+++++|.++|.+||+|..+.++.++.+    |||||+|.+.++|+.|++.|||..|+|+.+
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i   79 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRII   79 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            4579999999999999999999999999999999988765    399999999999999999999999999954

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=1.6e-16  Score=107.85  Aligned_cols=76  Identities=11%  Similarity=0.115  Sum_probs=67.3

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC--CEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEecc
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG--TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVRE  184 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~--~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~~  184 (299)
                      ...+|||+|||..+++++|.++|+.||+|..+.+..+..+  +||||+|.+.++|..|+..|||..|.|+    .+.+..
T Consensus         7 ~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~----~i~v~~   82 (90)
T d2cqia1           7 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGK----EVKVNW   82 (90)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTE----EEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCE----EEEEEE
Confidence            3468999999999999999999999999999999877544  5999999999999999999999999998    555554


Q ss_pred             cc
Q 022301          185 YD  186 (299)
Q Consensus       185 ~~  186 (299)
                      +.
T Consensus        83 a~   84 (90)
T d2cqia1          83 AT   84 (90)
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=99.69  E-value=1e-16  Score=107.68  Aligned_cols=70  Identities=20%  Similarity=0.359  Sum_probs=64.1

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .+++|||+|||..+++++|+++|++||+|..+.++.++..    |||||+|.+.++|..|++.|||..+.|...
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~   78 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATE   78 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCE
Confidence            4578999999999999999999999999999999988654    499999999999999999999999998643

>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=4e-17  Score=110.74  Aligned_cols=77  Identities=19%  Similarity=0.293  Sum_probs=68.2

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC--CCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEeccc
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS--GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVREY  185 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~--~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~~~  185 (299)
                      ..+|||+|||..+++++|+++|.+||.|..+.++.+..  .|||||+|.+.++|+.|++.|||..|+|+    .|.|..+
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 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR----KVFVGRF   83 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTE----EEEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCE----EEEEEEC
Confidence            35799999999999999999999999999999988764  36999999999999999999999999998    5666555


Q ss_pred             ccC
Q 022301          186 DHR  188 (299)
Q Consensus       186 ~~~  188 (299)
                      ..+
T Consensus        84 ~~~   86 (89)
T d1cvja2          84 KSR   86 (89)
T ss_dssp             CCT
T ss_pred             CCC
Confidence            443

>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=99.69  E-value=2.1e-16  Score=109.33  Aligned_cols=78  Identities=17%  Similarity=0.158  Sum_probs=68.2

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEe
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRV  182 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~  182 (299)
                      ..++|||+|||..+++++|.++|.+||.|..+.++.+..+    |||||+|.+.++|+.|++.|||..|+|+    .|.|
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr----~i~V   82 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGR----MLHV   82 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSC----EEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCE----EEEE
Confidence            4568999999999999999999999999999999887543    5999999999999999999999999999    5555


Q ss_pred             cccccC
Q 022301          183 REYDHR  188 (299)
Q Consensus       183 ~~~~~~  188 (299)
                      .....+
T Consensus        83 ~~a~~~   88 (99)
T d1whwa_          83 LPSTIK   88 (99)
T ss_dssp             EECCCC
T ss_pred             EECCCC
Confidence            554443

>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=1.3e-16  Score=105.80  Aligned_cols=67  Identities=16%  Similarity=0.173  Sum_probs=63.0

Q ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       110 ~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .|||+|||..+++++|.++|.+||+|..+.++.++.+    |||||+|.+.++|..|++.|+|..+.|+.+
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i   72 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPV   72 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEEC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            6999999999999999999999999999999998764    499999999999999999999999999843

>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=99.68  E-value=1.7e-16  Score=104.73  Aligned_cols=69  Identities=22%  Similarity=0.249  Sum_probs=63.3

Q ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC---CEEEEEecChhhHHHHHHhcCCCeecCceeeE
Q 022301          110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG---TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA  178 (299)
Q Consensus       110 ~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  178 (299)
                      .|||+|||+.+++++|.++|.+||.|..+.+..+..+   |||||+|.+.++|+.|++.|||..++|+.+.+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V   73 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI   73 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            5999999999999999999999999999999877543   59999999999999999999999999996543

>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=2.6e-16  Score=107.48  Aligned_cols=80  Identities=20%  Similarity=0.287  Sum_probs=69.5

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC--CEEEEEecChhhHHHHHHhcCCCeecCceeeEEEE
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG--TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVR  181 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~--~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~  181 (299)
                      ......+|||+|||..+++++|.++|.+||+|..+.++.+..+  |||||+|.+.++|..|+..|||..|+|+    .+.
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~----~l~   82 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGR----KIE   82 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTE----ECE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCE----EEE
Confidence            3445678999999999999999999999999999999887643  6999999999999999999999999998    555


Q ss_pred             eccccc
Q 022301          182 VREYDH  187 (299)
Q Consensus       182 ~~~~~~  187 (299)
                      +..+.+
T Consensus        83 V~~A~~   88 (93)
T d2cq3a1          83 VNNATA   88 (93)
T ss_dssp             EEECCS
T ss_pred             EEecCc
Confidence            555444

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.67  E-value=1.4e-15  Score=112.08  Aligned_cols=78  Identities=17%  Similarity=0.219  Sum_probs=68.8

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceeeEEEE
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVR  181 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~  181 (299)
                      ....+|||+|||..+++++|.++|++||.|..+.++.+..+    |||||+|.+.++|..||+.|||..|+|+    .|.
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr----~l~  115 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNK----RLK  115 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSC----EEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCE----EEE
Confidence            34568999999999999999999999999999999988654    4999999999999999999999999999    555


Q ss_pred             eccccc
Q 022301          182 VREYDH  187 (299)
Q Consensus       182 ~~~~~~  187 (299)
                      |..+..
T Consensus       116 V~~a~~  121 (139)
T d1u6fa1         116 VALAAS  121 (139)
T ss_dssp             EEESSC
T ss_pred             EEEcCC
Confidence            555443

>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=3.5e-16  Score=107.31  Aligned_cols=79  Identities=16%  Similarity=0.241  Sum_probs=68.4

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC-CCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEE
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG-SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVR  181 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~-~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~  181 (299)
                      +....+++|||+|||..+++++|+++|..||.|..+.+..+. ..+||||+|.+.++|+.||+.|||..|.|+    .+.
T Consensus         9 p~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~----~l~   84 (95)
T d1x4aa1           9 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGY----RLR   84 (95)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTE----ECE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCE----EEE
Confidence            445566789999999999999999999999999998887654 346999999999999999999999999999    555


Q ss_pred             eccc
Q 022301          182 VREY  185 (299)
Q Consensus       182 ~~~~  185 (299)
                      |..+
T Consensus        85 V~~a   88 (95)
T d1x4aa1          85 VEFP   88 (95)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            5544

>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=1.7e-16  Score=107.82  Aligned_cols=76  Identities=16%  Similarity=0.226  Sum_probs=67.6

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEe
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRV  182 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~  182 (299)
                      ...+|||+|||..+++++|.++|++||.|..+.++.+...    |||||+|.+.++|..|++.|||..|+|+    .+.+
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 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHL----ILNV   82 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTE----ECEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCE----EEEE
Confidence            4578999999999999999999999999999999988654    4999999999999999999999999999    5555


Q ss_pred             cccc
Q 022301          183 REYD  186 (299)
Q Consensus       183 ~~~~  186 (299)
                      ..+.
T Consensus        83 ~~ak   86 (90)
T d2cq0a1          83 EWAK   86 (90)
T ss_dssp             EESS
T ss_pred             Eeee
Confidence            4443

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.67  E-value=1.5e-16  Score=109.53  Aligned_cols=73  Identities=55%  Similarity=0.994  Sum_probs=65.5

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeE
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA  178 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  178 (299)
                      +......+|||.|||..+++++|.++|.+||+|..+.+..+   |||||+|.+.++|++||+.|||..|.|+.+.+
T Consensus        10 ~~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~~---g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v   82 (98)
T d1wg4a_          10 PTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD---GMGMVEYLRKEDMEYALRKLDDTKFRSHEGET   82 (98)
T ss_dssp             CCCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEETT---TEEEEEESSHHHHHHHHHHHSSEEEECTTSCE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhhccccccccccc---ceEEEEECCHHHHHHHHHHhCCCEeCCeEEEE
Confidence            44456788999999999999999999999999999998753   69999999999999999999999999987543

>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=99.67  E-value=2.9e-16  Score=111.74  Aligned_cols=72  Identities=18%  Similarity=0.182  Sum_probs=65.4

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC-CCEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS-GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~-~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      ..+.+|||+|||..+++++|.++|++||.|..|.+..+.. .|||||+|.+.++|..|++.|||..|+|+.+.
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~   77 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLV   77 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            3467999999999999999999999999999999987643 57999999999999999999999999999553

>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=2.9e-16  Score=107.78  Aligned_cols=68  Identities=16%  Similarity=0.269  Sum_probs=63.1

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..++|||+|||..+++++|.++|.+||.|..+.+..+  .|||||+|.+.++|..|+..|||..|+|+.+
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~--kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l   84 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE--KGYSFVRFSTHESAAHAIVSVNGTTIEGHVV   84 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT--TTEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec--ceEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            3478999999999999999999999999999999876  5699999999999999999999999999843

>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=99.66  E-value=3.1e-16  Score=105.39  Aligned_cols=71  Identities=18%  Similarity=0.300  Sum_probs=63.4

Q ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC-------CEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEec
Q 022301          111 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG-------TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVR  183 (299)
Q Consensus       111 l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~-------~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~  183 (299)
                      |||+|||..+++++|.++|++||+|..+.++.++.+       |||||+|.+.++|+.|++.|||..|+|+    .+.|.
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 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGH----KLEVR   76 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTE----ECEEE
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCE----EEEEE
Confidence            799999999999999999999999999999877543       4899999999999999999999999999    45554


Q ss_pred             cc
Q 022301          184 EY  185 (299)
Q Consensus       184 ~~  185 (299)
                      .+
T Consensus        77 ~a   78 (85)
T d2cpfa1          77 IS   78 (85)
T ss_dssp             CS
T ss_pred             EC
Confidence            43

>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=99.66  E-value=1.5e-16  Score=106.75  Aligned_cols=68  Identities=15%  Similarity=0.275  Sum_probs=63.3

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..|||+|||..+++++|.++|++||+|..+.++.++.    .|||||+|.+.++|..|+..|||..|+|+.+
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l   73 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKL   73 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            4799999999999999999999999999999998765    3699999999999999999999999999944

>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=99.66  E-value=1.2e-16  Score=108.24  Aligned_cols=76  Identities=21%  Similarity=0.208  Sum_probs=67.2

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEec
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVR  183 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~  183 (299)
                      ..+|||+|||..+++++|.++|++||+|..+.++.++.    .|||||+|.+.++|+.|++.|||..|+|+    .+.+.
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 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGR----TIRVN   80 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTE----EEEEE
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCE----EEEEE
Confidence            46899999999999999999999999999999987754    35999999999999999999999999998    55555


Q ss_pred             cccc
Q 022301          184 EYDH  187 (299)
Q Consensus       184 ~~~~  187 (299)
                      .+.+
T Consensus        81 ~a~p   84 (89)
T d2cqba1          81 LAKP   84 (89)
T ss_dssp             ECCC
T ss_pred             EeCC
Confidence            5443

>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=99.66  E-value=2.6e-16  Score=106.48  Aligned_cols=70  Identities=17%  Similarity=0.258  Sum_probs=64.1

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCee-cCcee
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEF-RNAFS  176 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~-~g~~~  176 (299)
                      +..+|||+|||..+++++|.++|..||.|..+.+......+||||+|.+.++|..|+..|||..| +|+.+
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l   79 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHL   79 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEE
Confidence            45789999999999999999999999999998888887788999999999999999999999998 47743

>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=99.65  E-value=5.4e-16  Score=104.11  Aligned_cols=69  Identities=19%  Similarity=0.315  Sum_probs=63.2

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCc
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNA  174 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~  174 (299)
                      ..+++|||+|||..+++++|.++|++||+|..+.++.++..    |||||+|.+.++|..|++.|||..+.|.
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   76 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGG   76 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCC
Confidence            34578999999999999999999999999999999988654    4999999999999999999999999873

>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=99.65  E-value=2.4e-16  Score=104.89  Aligned_cols=68  Identities=18%  Similarity=0.248  Sum_probs=59.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC----CCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG----SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ++|||+|||..+++++|.++|+.||.|..+.++.+.    ..|||||+|.+.++|+.|++.|||..++|+.+
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i   73 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTL   73 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            689999999999999999999999999877765443    34699999999999999999999999999944

>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=99.65  E-value=3.6e-16  Score=106.95  Aligned_cols=72  Identities=17%  Similarity=0.313  Sum_probs=64.2

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC-----CCCEEEEEecChhhHHHHHHhc-CCCeecCcee
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG-----SGTTGIVDYTNYDDMKHAIKKL-DDSEFRNAFS  176 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~-----~~~~~fv~f~~~~~a~~a~~~l-~g~~~~g~~~  176 (299)
                      .....+|||+|||..+++++|.++|.+||.|..+.++.+.     ..|||||+|.+.++|..|++.| ||..|+|+.+
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l   82 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRL   82 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEE
Confidence            3455789999999999999999999999999999997763     2469999999999999999998 8999999844

>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=99.64  E-value=2e-16  Score=111.25  Aligned_cols=76  Identities=18%  Similarity=0.232  Sum_probs=67.1

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEE
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVR  181 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~  181 (299)
                      .+...|||+|||..+|+++|.++|++||.|..+.+..++..|||||+|.+.++|+.|+..|||..|.+......+.
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~   80 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            3457899999999999999999999999999999999888889999999999999999999999996554433343

>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=5.5e-16  Score=106.71  Aligned_cols=69  Identities=17%  Similarity=0.212  Sum_probs=61.0

Q ss_pred             CCCCccEEEEeCCC-CCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          104 SRRSEYRVLVTGLP-SSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       104 ~~~~~~~l~v~nl~-~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      +.....+|||+||+ ..+++++|+++|.+||.|..+.+.    .+||||+|.+.++|+.|++.|||..|.|+.+
T Consensus        11 ~~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~----rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l   80 (98)
T d1wf2a_          11 PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH----KGFAFVQYVNERNARAAVAGEDGRMIAGQVL   80 (98)
T ss_dssp             CSSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE----TEEEEEEESSHHHHHHHHHTTTTCEETTEEC
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe----CCeEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34455789999997 568899999999999999999984    4599999999999999999999999999944

>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=99.63  E-value=8.7e-16  Score=104.33  Aligned_cols=70  Identities=24%  Similarity=0.350  Sum_probs=63.5

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      ..+|||+|||..+++++|+++|.+||.|..+.++.+...    |||||+|.+.++|+.|++.|||..|+|+.+.
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~   78 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIR   78 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCE
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            357999999999999999999999999999988876543    5999999999999999999999999999553

>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=99.63  E-value=7.3e-16  Score=100.61  Aligned_cols=67  Identities=18%  Similarity=0.204  Sum_probs=61.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC--CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG--TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~--~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ++|||+|||..+++++|+++|..||+|..+.+..++.+  +||||+|.+.++|++|+. ++|..|+|+.+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i   69 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEI   69 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEECCEEE
Confidence            47999999999999999999999999999999888765  499999999999999995 89999999844

>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=99.63  E-value=2e-15  Score=102.05  Aligned_cols=75  Identities=23%  Similarity=0.338  Sum_probs=64.2

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEe
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRV  182 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~  182 (299)
                      ...+|||+|||..+++++|.++|+.||.|..+.++.++.+    |||||+|.+.++|+.||+.++  .|+|+    .+.+
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~~--~l~Gr----~i~v   80 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH--MIDGR----WCDC   80 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCE--EETTE----EEEE
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcCC--ccCCE----EeEE
Confidence            4578999999999999999999999999999999998764    499999999999999998644  78998    5555


Q ss_pred             ccccc
Q 022301          183 REYDH  187 (299)
Q Consensus       183 ~~~~~  187 (299)
                      ..+..
T Consensus        81 ~~a~~   85 (90)
T d2cqga1          81 KLPNS   85 (90)
T ss_dssp             ECCCT
T ss_pred             EeCCC
Confidence            44433

>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=3.4e-16  Score=110.77  Aligned_cols=71  Identities=18%  Similarity=0.266  Sum_probs=62.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecCh-HHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEA-RDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~-e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      ..+||+|||..+|+++|+++|++||+|.+|.|.   ..+|||||.|.+. ++|..|+..||+..+.+..+.|.+.
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~---~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~   83 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFV---RGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   83 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECC---TTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEe---cCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEe
Confidence            456999999999999999999999999999997   4589999999996 7899999999999888777777665

>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=99.62  E-value=2e-15  Score=105.03  Aligned_cols=69  Identities=19%  Similarity=0.225  Sum_probs=62.1

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..++|||+|||..+++++|.++|++||.|..+.++.+..    .|||||+|.+.++|+.|++.+++ .|+|+.+
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l   81 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKA   81 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEEC
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEE
Confidence            346799999999999999999999999999999988764    36999999999999999999886 7999844

>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=1.6e-17  Score=115.63  Aligned_cols=73  Identities=21%  Similarity=0.327  Sum_probs=66.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec--CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            8 TLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI--PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         8 ~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~--~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .++|.+++.++++++|.++|++||+|..|.|..  ++.++|||||+|.+.++|.+|+..|||.+|.|+.|.|+|+
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            356677777888999999999999999999943  4678899999999999999999999999999999999986

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=4e-16  Score=103.32  Aligned_cols=75  Identities=17%  Similarity=0.213  Sum_probs=64.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCC-eecCceeeEEEEeccccc
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDS-EFRNAFSRAYVRVREYDH  187 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~-~~~g~~~~~~~~~~~~~~  187 (299)
                      ++|||+|||..+++++|.++|.+||.|..+.+...  .|||||+|.+.++|+.|++.|||. .++|+    .+.|..+.+
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--SGYAFVDYPDQNWAIRAIETLSGKVELHGK----IMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE--TTEEEECCSCHHHHHHHHHHHTTTCEETTE----ECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc--cceEEEEECCHHHHHHHHHHhCCCeEECCE----EEEEEEcCC
Confidence            47999999999999999999999999987777665  469999999999999999999996 69998    555555544


Q ss_pred             CC
Q 022301          188 RR  189 (299)
Q Consensus       188 ~~  189 (299)
                      +.
T Consensus        76 k~   77 (80)
T d2cqha1          76 KK   77 (80)
T ss_dssp             CC
T ss_pred             cC
Confidence            43

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.62  E-value=1.3e-15  Score=104.78  Aligned_cols=76  Identities=18%  Similarity=0.233  Sum_probs=66.0

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEec
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVR  183 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~  183 (299)
                      .+..+|||+|||..+++++|+++|++||.|..+.+..+  .+||||+|.+.++|+.|++.|||..|.|......+...
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--DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFA   90 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS--SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEEC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc--ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeC
Confidence            35689999999999999999999999999999988765  45999999999999999999999999986554444443

>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=99.62  E-value=5.6e-16  Score=119.95  Aligned_cols=78  Identities=24%  Similarity=0.500  Sum_probs=71.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeec---CCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301            4 RASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKI---PPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~---~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .+.++|||+|||.++|+++|.++|+.||.|..+.|..   ++.++|||||+|.+.++|..|+. +++..|.|+.|.|.++
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            5678999999999999999999999999999999854   36778999999999999999998 8998999999999987


Q ss_pred             cC
Q 022301           81 HG   82 (299)
Q Consensus        81 ~~   82 (299)
                      .+
T Consensus       174 ~~  175 (183)
T d1u1qa_         174 LS  175 (183)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.62  E-value=1.1e-15  Score=102.10  Aligned_cols=69  Identities=12%  Similarity=0.089  Sum_probs=62.0

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeec-Cc
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFR-NA  174 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~-g~  174 (299)
                      .+++.+|||+|||..+++++|.++|++||.|..+.+..+. .|||||+|.+.++|..|++.|||..|. |+
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-~g~afV~f~~~~~A~~A~~~l~g~~~~~~~   74 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-HDIAFVEFTTELQSNAAKEALQGFKITPTH   74 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-CSCEEEEESSHHHHHHHHHHHTTCBSSTTC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-ceeEEEecCCHHHHHHHHHHhCCcEeCCCc
Confidence            3456799999999999999999999999999999987654 469999999999999999999999985 45

>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=99.62  E-value=2e-15  Score=100.85  Aligned_cols=69  Identities=17%  Similarity=0.315  Sum_probs=62.9

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      ..+|||+|||..+++++|.++|++||.|..+.++.+..+    |||||+|.+.++|++|++ ++|..|+|+.+.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~   78 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVE   78 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECE
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEE
Confidence            468999999999999999999999999999999988764    499999999999999997 699999999543

>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=99.62  E-value=7.8e-16  Score=100.58  Aligned_cols=66  Identities=17%  Similarity=0.293  Sum_probs=60.3

Q ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       110 ~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .|||+|||..+++++|.++|++||+|..+.+..++.+    |||||+|.+.++|+.|++ +++..|+|+.+
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i   70 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVI   70 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEE
Confidence            4899999999999999999999999999999987643    599999999999999997 79999999843

>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=99.62  E-value=4e-15  Score=100.04  Aligned_cols=75  Identities=17%  Similarity=0.146  Sum_probs=65.4

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEecccc
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVREYD  186 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~~~~  186 (299)
                      ...+|||+|||..+++++|.++|.+||.|..+.+...  .|||||+|.+.++|..|+..|||..|.|+    .+.+..+.
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--RDYAFVHFSNREDAVEAMKALNGKVLDGS----PIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--SSEEEEEESSHHHHHHHHHHHSSEEETTE----EEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEccc--cEEEEEEeCCHHHHHHHHHHcCCCEECCE----EEEEEecc
Confidence            3468999999999999999999999999988877654  46999999999999999999999999999    56665554


Q ss_pred             c
Q 022301          187 H  187 (299)
Q Consensus       187 ~  187 (299)
                      +
T Consensus        81 P   81 (86)
T d2cpda1          81 P   81 (86)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.62  E-value=1.4e-15  Score=107.57  Aligned_cols=69  Identities=20%  Similarity=0.302  Sum_probs=62.9

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      ..++|||+|||..+++++|.++|.+||+|..|.+..  ..+||||+|.+.++|..|++.|||..|.|+.+.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~--~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~   77 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE--GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLY   77 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS--SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec--cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEE
Confidence            457999999999999999999999999999988753  457999999999999999999999999999663

>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=99.62  E-value=8.5e-16  Score=102.69  Aligned_cols=66  Identities=15%  Similarity=0.265  Sum_probs=58.8

Q ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEE-EEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          111 VLVTGLPSSASWQDLKDHMRRAGDVCFS-QVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       111 l~v~nl~~~~~~~~l~~~f~~~G~v~~~-~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      |||+|||..+++++|.++|.+||.|..+ .++.+..    .|||||+|.+.++|+.|++.|+|..++|+.+
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l   71 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPI   71 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEEC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEE
Confidence            7999999999999999999999998654 6666643    3699999999999999999999999999944

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.61  E-value=1.1e-15  Score=102.65  Aligned_cols=67  Identities=16%  Similarity=0.238  Sum_probs=62.3

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .++|||+|||..+++++|.++|.+||+|..+.+..+  .+||||+|.+.++|..|+..|||..|.|+.+
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~--k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l   74 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD--KGFGFIRLETRTLAEIAKVELDNMPLRGKQL   74 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT--TTEEEEECSSSHHHHHHHHHHTTCCBTTBCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc--cceEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            467999999999999999999999999999999866  4699999999999999999999999999854

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.61  E-value=3e-16  Score=106.15  Aligned_cols=70  Identities=16%  Similarity=0.184  Sum_probs=63.2

Q ss_pred             CccEEEEeCCCCCCCHHHH---HHHHHhcCCeeEEEEEeCCCC-------CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          107 SEYRVLVTGLPSSASWQDL---KDHMRRAGDVCFSQVFRDGSG-------TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l---~~~f~~~G~v~~~~~~~~~~~-------~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..+.|||+|||+.+++++|   .++|.+||+|..+.++.++..       +||||+|.+.++|+.|++.|||..++|+.+
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            3468999999999999999   778999999999999987533       599999999999999999999999999954

>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=99.61  E-value=2.1e-15  Score=104.56  Aligned_cols=76  Identities=16%  Similarity=0.246  Sum_probs=66.6

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEec
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVR  183 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~  183 (299)
                      ..+|||+|||+.+++++|+++|.+||.|..+.|..++.    .|||||+|.+.++|+.|++ ++|..|+|+    .|.|.
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-ARPHSIDGR----VVEPK   94 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTE----EEEEE
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCE----EEEEE
Confidence            46899999999999999999999999999999988754    3699999999999999996 799999999    66665


Q ss_pred             ccccC
Q 022301          184 EYDHR  188 (299)
Q Consensus       184 ~~~~~  188 (299)
                      .+.++
T Consensus        95 ~a~~k   99 (103)
T d1x4ba1          95 RAVAR   99 (103)
T ss_dssp             CCSSC
T ss_pred             ECccc
Confidence            55443

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=1.1e-15  Score=100.89  Aligned_cols=66  Identities=12%  Similarity=0.149  Sum_probs=60.0

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .+.+|||+||+  +++++|.++|++||.|..+.+..+  .+||||+|.+.++|..|+..|||..++|+.+
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~--~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   69 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP--RNCAFVTYEKMESADQAVAELNGTQVESVQL   69 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT--TTEEEEECSSHHHHHHHHHHHTTCBCSSCBC
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC--CCEEEEEEcccHHHHHHHHHhCCCEECCEEE
Confidence            45799999986  899999999999999999988755  4699999999999999999999999999944

>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=99.60  E-value=7.8e-16  Score=100.95  Aligned_cols=68  Identities=16%  Similarity=0.274  Sum_probs=61.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      +.|||+|||..+++++|+++|.+||+|..+.++.++.+    |||||+|.+.++|++|++ +++..|+|+.+.
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            46999999999999999999999999999999887653    599999999999999997 799999998553

>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=99.60  E-value=1.3e-15  Score=106.32  Aligned_cols=69  Identities=23%  Similarity=0.337  Sum_probs=64.0

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..+|||+|||..+++++|.++|++||+|..+.++.++.+    |||||+|.+.++|+.|++.|||..|.|+.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i   80 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRAL   80 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCB
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            357999999999999999999999999999999988764    499999999999999999999999999854

>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=99.60  E-value=1.4e-15  Score=107.28  Aligned_cols=68  Identities=16%  Similarity=0.162  Sum_probs=62.3

Q ss_pred             ccEEEEeCCCC-CCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          108 EYRVLVTGLPS-SASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       108 ~~~l~v~nl~~-~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      +.+|||+||++ .+++++|.++|+.||.|..+.|+.+. .|||||+|.+.++|..|++.|||..|.|+.+
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-kg~afV~f~~~~~A~~ai~~lng~~l~g~~l   70 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-KENALVQMADGNQAQLAMSHLNGHKLHGKPI   70 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-SCCEEEEESCHHHHHHHHHHHTTCBCSSSBC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-cceEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            46899999965 59999999999999999999998875 4699999999999999999999999999944

>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=6.1e-16  Score=105.02  Aligned_cols=77  Identities=14%  Similarity=0.208  Sum_probs=64.8

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEe---CCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEE
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFR---DGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVR  181 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~---~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~  181 (299)
                      ....++|||+|||..+++++|+++|..||.|..+.++.   ....|||||+|.+.++|+.||+ |||..|+|+    .+.
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-LTGLKVFGN----EIK   84 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTE----EEE
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCE----EEE
Confidence            34567999999999999999999999999887665543   3455799999999999999996 999999999    666


Q ss_pred             ecccc
Q 022301          182 VREYD  186 (299)
Q Consensus       182 ~~~~~  186 (299)
                      +..+.
T Consensus        85 V~~ak   89 (91)
T d1fjeb1          85 LEKPK   89 (91)
T ss_dssp             EECCC
T ss_pred             EEecC
Confidence            65543

>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=1e-15  Score=105.83  Aligned_cols=69  Identities=17%  Similarity=0.223  Sum_probs=62.7

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ...+|||+|||..+++++|.++|..||.|..+.++.+..+    |||||+|.+.++|+.|++ |||..|.|+.+
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l   89 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPI   89 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEE
Confidence            3468999999999999999999999999999999987543    599999999999999995 99999999844

>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=99.60  E-value=2.7e-15  Score=104.23  Aligned_cols=80  Identities=21%  Similarity=0.373  Sum_probs=65.8

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCee--------EEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeec
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVC--------FSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFR  172 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~--------~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~  172 (299)
                      .....+|||+|||..+++++|.++|..||.|.        .+.+..+..    .+||||+|.+.++|..|++.|||..|+
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~   84 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   84 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEEC
Confidence            34568999999999999999999999999874        344445433    359999999999999999999999999


Q ss_pred             CceeeEEEEecccccC
Q 022301          173 NAFSRAYVRVREYDHR  188 (299)
Q Consensus       173 g~~~~~~~~~~~~~~~  188 (299)
                      |+    .|.|..+..+
T Consensus        85 gr----~i~V~~a~~~   96 (101)
T d2cpea1          85 GS----KLKVSLARKK   96 (101)
T ss_dssp             TE----ECEEECSSCC
T ss_pred             CE----EEEEEEcCCC
Confidence            99    5666555443

>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=99.60  E-value=1.5e-15  Score=102.45  Aligned_cols=66  Identities=21%  Similarity=0.304  Sum_probs=56.9

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..+|||+|||..+++++|+++|.+|| +..+.+.  ...+||||+|.+.++|+.|++.|||..|.|+.+
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~--~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l   70 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD--RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDL   70 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEE--GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeeee--ccCCceEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            46899999999999999999999999 3333333  345699999999999999999999999999944

>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=99.59  E-value=4.7e-15  Score=98.02  Aligned_cols=67  Identities=12%  Similarity=0.250  Sum_probs=61.4

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .+|||+|||..+++++|+++|++||.|..+.+..++.+    |||||+|.+.++|.+|+. ++|..|+|+.+
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i   73 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNC   73 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEE
Confidence            58999999999999999999999999999999988655    499999999999999985 89999999954

>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=99.59  E-value=1.1e-15  Score=100.09  Aligned_cols=67  Identities=19%  Similarity=0.308  Sum_probs=60.7

Q ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       110 ~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      .|||+|||..+++++|.++|++||.|..+.+..++..    +||||+|.+.++|+.|++ +||..|+|+.+.
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            4899999999999999999999999999988777644    499999999999999997 999999999543

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=4.1e-16  Score=101.29  Aligned_cols=65  Identities=20%  Similarity=0.323  Sum_probs=60.6

Q ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCce
Q 022301          111 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAF  175 (299)
Q Consensus       111 l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  175 (299)
                      |||+|||..+++++|.++|.+||.|..+.+..++.+    |||||+|.+.++|+.|++.|||..|+|+.
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            799999999999999999999999999999887643    59999999999999999999999999974

>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=99.59  E-value=1.4e-15  Score=104.42  Aligned_cols=80  Identities=13%  Similarity=0.177  Sum_probs=66.4

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEecc
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVRE  184 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~~  184 (299)
                      .....+|||+|||..+++++|.++|.+||.|..+.. .....+||||+|.+.++|+.|++.|||..|+|+    .|.+..
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr----~i~V~~   87 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGR----SVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTE----EEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-cCccccEEEEEeCCHHHHHHHHHHcCCCEECCE----EEEEEE
Confidence            345689999999999999999999999999876643 223446999999999999999999999999999    666655


Q ss_pred             cccCC
Q 022301          185 YDHRR  189 (299)
Q Consensus       185 ~~~~~  189 (299)
                      ..++.
T Consensus        88 a~~k~   92 (96)
T d1fjca_          88 TGEKG   92 (96)
T ss_dssp             CSSSC
T ss_pred             eCCCC
Confidence            54443

>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=1.8e-15  Score=104.16  Aligned_cols=79  Identities=27%  Similarity=0.422  Sum_probs=68.4

Q ss_pred             CCCCeEEEcCC--CCCCC---------HHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCC
Q 022301            4 RASRTLYVGNL--PGDIR---------EREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDG   72 (299)
Q Consensus         4 ~~~~~l~V~nL--p~~~t---------~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g   72 (299)
                      +.+++|+|.||  |.++.         +++|.+.|++||.|..|.+.. +..+|+|||+|.++++|..|+..|||..|.|
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 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFD-RHPDGVASVSFRDPEEADYCIQTLDGRWFGG   84 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEET-TCTTCEEEEECSCHHHHHHHHHHSTTCEETT
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccC-CCCccEEEEEECCHHHHHHHHHHhCCcEECC
Confidence            67899999999  55432         367999999999999998854 3567999999999999999999999999999


Q ss_pred             ceEEEEEccCC
Q 022301           73 HRLRVELAHGG   83 (299)
Q Consensus        73 ~~i~v~~~~~~   83 (299)
                      ++|.|.++.+.
T Consensus        85 r~i~v~~~~g~   95 (99)
T d2dita1          85 RQITAQAWDGT   95 (99)
T ss_dssp             EECEEEECCSC
T ss_pred             EEEEEEEeCCc
Confidence            99999998643

>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=99.58  E-value=5.5e-15  Score=102.41  Aligned_cols=70  Identities=19%  Similarity=0.348  Sum_probs=63.5

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC---CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG---TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..++|||+|||..+++++|.++|++||.|..+.+..+..+   |||||+|.+.++|++|++.|||..|.|+.+
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            4578999999999999999999999999999988877543   499999999999999999999999999743

>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=99.58  E-value=6.9e-15  Score=101.53  Aligned_cols=77  Identities=9%  Similarity=0.162  Sum_probs=65.8

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcC------CCeecCcee
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLD------DSEFRNAFS  176 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~------g~~~~g~~~  176 (299)
                      .+.+|||+|||..+++++|.++|.+||.|..+.+..+..    .|||||+|.+.++|..|++.|+      |..|.|+  
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr--   84 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR--   84 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC--
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE--
Confidence            457899999999999999999999999999998887754    3699999999999999999886      6677787  


Q ss_pred             eEEEEeccccc
Q 022301          177 RAYVRVREYDH  187 (299)
Q Consensus       177 ~~~~~~~~~~~  187 (299)
                        .+.+..+..
T Consensus        85 --~l~v~~a~~   93 (98)
T d1x4ha1          85 --QLKVDLAVT   93 (98)
T ss_dssp             --EEEEECCCC
T ss_pred             --EEEEEECCC
Confidence              566655544

>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=99.58  E-value=1.7e-15  Score=98.64  Aligned_cols=66  Identities=11%  Similarity=0.175  Sum_probs=59.6

Q ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC----CEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          110 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG----TTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       110 ~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~----~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .|||+|||..+++++|+++|++||.|..+.++.++.+    |||||+|.+.++|++|++ +++..|+|+.+
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            4899999999999999999999999999999988643    599999999999999997 47778999854

>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=99.58  E-value=9.5e-15  Score=101.89  Aligned_cols=70  Identities=16%  Similarity=0.336  Sum_probs=58.9

Q ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCC-----CCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          105 RRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDG-----SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       105 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~-----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..+.++|||+|||..+++++|+++|+.|| |+.+.++.+.     ..|||||+|.+.++|++|+ .|||..|+|+.+
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l   86 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRI   86 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEE
Confidence            44568999999999999999999999999 6666666553     2359999999999998776 599999999944

>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=2e-15  Score=99.51  Aligned_cols=72  Identities=17%  Similarity=0.224  Sum_probs=62.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCce-EEEEEcc
Q 022301            5 ASRTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHR-LRVELAH   81 (299)
Q Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~-i~v~~~~   81 (299)
                      +.+.|+|++||++++++.| ++|++||+|.++.+.   ..++||||+|.++++|++||. |||..|.|+. |.|..+.
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~---~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS---NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC---SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEec---CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            4678999999999986555 689999999999885   447899999999999999997 9999999985 4687764

>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=99.57  E-value=7.8e-16  Score=107.20  Aligned_cols=78  Identities=8%  Similarity=0.052  Sum_probs=65.8

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeC----CCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEE
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD----GSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVR  181 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~----~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~  181 (299)
                      .+..+|||+|||..+++++|.++|.+||.|..+.+..+    ...+||||+|.+.++|..|++.|||..|.|+.    |.
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~----l~   91 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKI----LV   91 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCB----CE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEE----EE
Confidence            34679999999999999999999999999887666543    34579999999999999999999999999984    44


Q ss_pred             eccccc
Q 022301          182 VREYDH  187 (299)
Q Consensus       182 ~~~~~~  187 (299)
                      +..+..
T Consensus        92 V~~ak~   97 (102)
T d2cpxa1          92 IEFGKN   97 (102)
T ss_dssp             EEECCC
T ss_pred             EEeCCC
Confidence            444443

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.57  E-value=7.7e-15  Score=95.64  Aligned_cols=63  Identities=24%  Similarity=0.345  Sum_probs=56.0

Q ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          111 VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       111 l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      |||+|||.++++++|+++|.+|| +..+.+  +...|||||+|.+.++|+.|++.|||..+.|+.+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~--~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l   63 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV--DKYKGTAFVTLLNGEQAEAAINTFHQSRLREREL   63 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE--ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEE
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee--cccceeEEEEECCHHHHHHHHHHhCCccCCCCEE
Confidence            79999999999999999999999 444443  4566799999999999999999999999999944

>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=4.1e-15  Score=99.84  Aligned_cols=75  Identities=13%  Similarity=0.191  Sum_probs=62.2

Q ss_pred             CccEEEEeCCCCCCC-HHHHHHHHHhcCCeeEEEEEeCC-----CCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEE
Q 022301          107 SEYRVLVTGLPSSAS-WQDLKDHMRRAGDVCFSQVFRDG-----SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYV  180 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~-~~~l~~~f~~~G~v~~~~~~~~~-----~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~  180 (299)
                      ...+|||+|||..++ +++|.++|++||.|..+.+..+.     ..|||||+|.+.++|+.|++ |||..|+|+    .+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr----~l   77 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNR----EI   77 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTE----EE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCE----EE
Confidence            357999999999976 55699999999999999986542     23599999999999999996 999999999    55


Q ss_pred             Eecccc
Q 022301          181 RVREYD  186 (299)
Q Consensus       181 ~~~~~~  186 (299)
                      .+..+.
T Consensus        78 ~V~~a~   83 (86)
T d2ghpa3          78 SVSLAD   83 (86)
T ss_dssp             EEEECC
T ss_pred             EEEEcC
Confidence            554443

>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=99.56  E-value=5.7e-15  Score=99.28  Aligned_cols=72  Identities=13%  Similarity=0.127  Sum_probs=61.7

Q ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCeeE-EEEEeCCC---CCEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          106 RSEYRVLVTGLPSSASWQDLKDHMRRAGDVCF-SQVFRDGS---GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       106 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~-~~~~~~~~---~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      +..+.|+|.|||..+++++|.++|..||.|.. +.+..+..   .|+|||+|.+.++|+.|++.|||..|.|+.+.
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~   82 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVK   82 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEE
Confidence            34578999999999999999999999999865 44554433   35999999999999999999999999999553

>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=99.56  E-value=1.8e-14  Score=96.36  Aligned_cols=69  Identities=17%  Similarity=0.284  Sum_probs=62.7

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC---CEEEEEecChhhHHHHHHhcCCCeecCceee
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG---TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSR  177 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~  177 (299)
                      ..+|||+|||..+++++|.++|..||.|..+.+..+..+   |||||+|.+.++|+.|++ ++|..+.|+.+.
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~   77 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLL   77 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECE
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEE
Confidence            468999999999999999999999999999999887654   599999999999999996 799999998553

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=1.1e-14  Score=101.05  Aligned_cols=75  Identities=15%  Similarity=0.233  Sum_probs=62.7

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC---CEEEEEecChhhHHHHHHhcCCCeecCceeeEE
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG---TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY  179 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  179 (299)
                      .....+.+|||.|||+++|+++|+++|..||. +.+.++.+..+   |||||+|.+.++|+.|++ ||+..|+|+.+.+.
T Consensus        10 ~~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~   87 (102)
T d1weza_          10 FQSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             CcCCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            34456679999999999999999999999984 46666666543   599999999999999986 89999999955443

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=3.4e-15  Score=100.73  Aligned_cols=75  Identities=12%  Similarity=0.152  Sum_probs=63.8

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCceeeEEEEecccc
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAYVRVREYD  186 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~~~~~~~~  186 (299)
                      ...+|||+|||..+++++|+++|.+||.|..+.+... ..+||||+|.+.++|+.|+.  ++..|+|+    .+.+..+.
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--EDLIIKGI----SVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-CCSCCEEECSCHHHHHHTTT--CEEEETTE----EEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec-cCceEEEEECCHHHHHHHHh--CCCEECCE----EeEEEeCC
Confidence            4579999999999999999999999999999877544 45699999999999999985  78889998    56666554


Q ss_pred             cC
Q 022301          187 HR  188 (299)
Q Consensus       187 ~~  188 (299)
                      ++
T Consensus        77 ~k   78 (88)
T d1wf0a_          77 PK   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.54  E-value=4.2e-15  Score=103.42  Aligned_cols=78  Identities=26%  Similarity=0.440  Sum_probs=67.5

Q ss_pred             CCCCeEEEcCC--CCCCC--------HHHHHHHhhhcCCeeEEEeecC-----CCCCceEEEEecChHHHHHHHHhcCCC
Q 022301            4 RASRTLYVGNL--PGDIR--------EREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEARDAEDAIRGRDGY   68 (299)
Q Consensus         4 ~~~~~l~V~nL--p~~~t--------~~~l~~~F~~~G~v~~i~~~~~-----~~~~g~afV~F~~~e~A~~A~~~l~~~   68 (299)
                      .|+++|.|.||  |..+.        .++|++.|++||.|..|.|..+     ....|+|||+|.+.++|..|+..|||.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            68999999999  55543        3568999999999999999543     234589999999999999999999999


Q ss_pred             CCCCceEEEEEcc
Q 022301           69 DFDGHRLRVELAH   81 (299)
Q Consensus        69 ~~~g~~i~v~~~~   81 (299)
                      .|.|+.|.|.++.
T Consensus        82 ~f~gR~v~v~f~~   94 (104)
T d1o0pa_          82 KFANRVVVTKYCD   94 (104)
T ss_dssp             CSSSSCCEEEEEC
T ss_pred             EECCeEEEEEEcC
Confidence            9999999999974

>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=7.4e-15  Score=99.73  Aligned_cols=70  Identities=14%  Similarity=0.185  Sum_probs=60.9

Q ss_pred             CccEEEEeCCCCCCCHHHHHH----HHHhcCCeeEEEEEeC-CCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          107 SEYRVLVTGLPSSASWQDLKD----HMRRAGDVCFSQVFRD-GSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~----~f~~~G~v~~~~~~~~-~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ++.+|||+|||..+++++|++    +|.+||+|..+.+... ...|||||+|.+.++|..|+..|||..++|+.+
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l   76 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   76 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            357999999999999998864    5899999999887653 235799999999999999999999999999844

>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=99.52  E-value=5.6e-14  Score=97.77  Aligned_cols=75  Identities=12%  Similarity=0.112  Sum_probs=62.1

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCC----CCEEEEEecChhhHHHHHHhcCCCeecCceeeE
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGS----GTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA  178 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~----~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  178 (299)
                      +.......|||.|||+.+++++|+++|..+|.|..+.++.+..    .|||||+|.+.++|++|++ +|+..|+|+.+.+
T Consensus        10 ~~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V   88 (104)
T d1wg5a_          10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEI   88 (104)
T ss_dssp             SSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEE
Confidence            3444556899999999999999999999999888755544433    3699999999999999996 9999999996543

>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=99.51  E-value=5e-14  Score=94.90  Aligned_cols=71  Identities=8%  Similarity=0.072  Sum_probs=62.7

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhc--CCCeecCcee
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKL--DDSEFRNAFS  176 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l--~g~~~~g~~~  176 (299)
                      ...+..+|||+|||..+++++|.++|.+||.|..+.+..+.  +||||+|.+.++|+.|++.+  ++..+.|+.+
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~--~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l   76 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK--NQAFLELATEEAAITMVNYYSAVTPHLRNQPI   76 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTT--TEEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccc--eEEEEEeCCHHHHHHHHHHHccCCCccCCCEE
Confidence            34567899999999999999999999999999999887654  59999999999999999865  6778999854

>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=99.51  E-value=1.8e-13  Score=95.08  Aligned_cols=71  Identities=18%  Similarity=0.242  Sum_probs=61.7

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhc--CCCeecCcee
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKL--DDSEFRNAFS  176 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l--~g~~~~g~~~  176 (299)
                      ...+..+|||.|||..+++++|.++|..||.|..+.+...  .++|||+|.+.++|+.|+..|  ++..+.|+.+
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~--k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l   83 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF--KRQALVEFENIDSAKECVTFAADVPVYIAGQQA   83 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT--TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec--ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEE
Confidence            3456789999999999999999999999999999988754  469999999999999999987  5566778844

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.49  E-value=4.8e-14  Score=97.03  Aligned_cols=72  Identities=11%  Similarity=0.101  Sum_probs=62.9

Q ss_pred             CCCCccEEEEeCCCCC-CCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHH--hcCCCeecCceee
Q 022301          104 SRRSEYRVLVTGLPSS-ASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIK--KLDDSEFRNAFSR  177 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~-~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~--~l~g~~~~g~~~~  177 (299)
                      ....+.+|||+|||.. +++++|.++|+.||.|..+.++.+.  ++|||+|.+.++|..|++  .+++..+.|+.+.
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k--~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~   88 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK--SQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   88 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTT--TEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecC--CcEEEEecchHHHHHHHHHHhcCCceECCEEEE
Confidence            3445689999999985 8999999999999999999998654  699999999999999998  5788899999553

>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=99.47  E-value=1.1e-13  Score=94.72  Aligned_cols=76  Identities=14%  Similarity=0.252  Sum_probs=62.0

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCC-eeEEEEEeCC-----CCCEEEEEecChhhHHHHHHhcCCC--eecCceeeEEE
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGD-VCFSQVFRDG-----SGTTGIVDYTNYDDMKHAIKKLDDS--EFRNAFSRAYV  180 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~-v~~~~~~~~~-----~~~~~fv~f~~~~~a~~a~~~l~g~--~~~g~~~~~~~  180 (299)
                      +.|||+|||..+++++|.++|.+||+ |..+.++.+.     ..|||||+|.+.++|..|++.|++.  .+.|+    .+
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~----~i   77 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGH----QI   77 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTB----CC
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCE----EE
Confidence            67999999999999999999999996 8888887663     2369999999999999999999754  44677    44


Q ss_pred             EecccccC
Q 022301          181 RVREYDHR  188 (299)
Q Consensus       181 ~~~~~~~~  188 (299)
                      .|..+.+.
T Consensus        78 ~V~~A~p~   85 (96)
T d2disa1          78 AVDWAEPE   85 (96)
T ss_dssp             EEEESCSS
T ss_pred             EEEEcCCC
Confidence            45544443

>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=99.46  E-value=6.9e-14  Score=98.60  Aligned_cols=76  Identities=22%  Similarity=0.265  Sum_probs=62.1

Q ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEE-EeCCCC---CEEEEEecChhhHHHHHHhcCCCeecCceeeEE
Q 022301          104 SRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQV-FRDGSG---TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY  179 (299)
Q Consensus       104 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~-~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  179 (299)
                      +....++|||+|||+.+++++|.++|..||.+..+.+ ..+..+   |||||+|.+.++|+.|++ |||..|+|+.+.+.
T Consensus        14 ~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~   92 (112)
T d1wela1          14 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVH   92 (112)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEE
T ss_pred             CCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEE
Confidence            3446679999999999999999999999998865433 333322   599999999999999996 99999999976544


Q ss_pred             E
Q 022301          180 V  180 (299)
Q Consensus       180 ~  180 (299)
                      .
T Consensus        93 ~   93 (112)
T d1wela1          93 P   93 (112)
T ss_dssp             E
T ss_pred             E
Confidence            3

>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=99.46  E-value=1.7e-13  Score=94.43  Aligned_cols=66  Identities=17%  Similarity=0.181  Sum_probs=58.4

Q ss_pred             CCccEEEEeC--CCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecC
Q 022301          106 RSEYRVLVTG--LPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRN  173 (299)
Q Consensus       106 ~~~~~l~v~n--l~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g  173 (299)
                      .+..+|+|.|  ||..+|+++|+++|.+||.|..+.+..++  +||||+|.+.++|..|+..|||..|..
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k--~~aFV~f~~~e~A~~A~~~lng~~i~~   83 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK--PYSFARYRTTEESKRAYVTLNGKEVVD   83 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTC--SCEEEEESSHHHHHHHHHHTTTCEEEC
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCc--cEEEEEECCHHHHHHHHHHhCCCCCCC
Confidence            4456888865  99999999999999999999998877654  599999999999999999999998843

>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=99.46  E-value=7.9e-14  Score=96.62  Aligned_cols=68  Identities=13%  Similarity=0.079  Sum_probs=59.8

Q ss_pred             CccEEEEeCCCCCC-C----HHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          107 SEYRVLVTGLPSSA-S----WQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       107 ~~~~l~v~nl~~~~-~----~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ...+|||+||+..+ +    .++|+++|..||.|+.+.++..  .+||||+|.+.++|..|+..|||..|+|+.+
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~--~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS--FKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT--TTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC--CCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            45789999999876 3    3679999999999999998854  4599999999999999999999999999944

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=1.2e-13  Score=95.99  Aligned_cols=72  Identities=15%  Similarity=0.152  Sum_probs=60.5

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeE-EEEEeCC---CCCEEEEEecChhhHHHHHHhcCCCeecCceeeEE
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCF-SQVFRDG---SGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRAY  179 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~-~~~~~~~---~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~~  179 (299)
                      ...+|||+|||+.+++++|.++|..||.|.. +.+..+.   ..|||||+|.+.++|+.|++ |||..|+|+.+.+.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~   82 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVH   82 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEE
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEE
Confidence            3468999999999999999999999998875 4444443   34699999999999999996 99999999955443

>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=99.44  E-value=1.4e-13  Score=92.71  Aligned_cols=69  Identities=7%  Similarity=0.054  Sum_probs=61.0

Q ss_pred             CCccEEEEeCCCCC-CCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhc--CCCeecCcee
Q 022301          106 RSEYRVLVTGLPSS-ASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKL--DDSEFRNAFS  176 (299)
Q Consensus       106 ~~~~~l~v~nl~~~-~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l--~g~~~~g~~~  176 (299)
                      .+..+|||+|||.. +|++||.++|++||.|..+.+..++  ++|||+|++.++|..|++.|  ++..+.|+.+
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k--~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l   77 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI--NEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   77 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS--SCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc--eEEEEEEcchhhHHHHHHHHhhCCCccCCceE
Confidence            45578999999986 7899999999999999999998765  49999999999999999965  7888999854

>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=99.39  E-value=6.8e-13  Score=93.45  Aligned_cols=75  Identities=12%  Similarity=0.157  Sum_probs=65.0

Q ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecCh-hhHHHHHHhcCCCeecCceeeEEEEec
Q 022301          107 SEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNY-DDMKHAIKKLDDSEFRNAFSRAYVRVR  183 (299)
Q Consensus       107 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~-~~a~~a~~~l~g~~~~g~~~~~~~~~~  183 (299)
                      ....+||+|||..+|+++|.++|.+||+|..|.|+.+  .+||||.|.+. ++|..|+..|++..+.+......+.+.
T Consensus        10 g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~--kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          10 GCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG--AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT--CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             CCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC--CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            3466799999999999999999999999999999865  46999999996 789999999999999988766555553

>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=99.35  E-value=4.5e-14  Score=95.59  Aligned_cols=67  Identities=12%  Similarity=0.157  Sum_probs=56.8

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEE---------eCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVF---------RDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~---------~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..|||+|||..+++++|.++|..||.|..+.+.         .....|||||+|.+.++|+.|++ |||..+.|+.+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l   77 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSL   77 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEE
Confidence            479999999999999999999999987654432         22345799999999999999985 99999999944

>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=99.33  E-value=2.3e-12  Score=88.36  Aligned_cols=78  Identities=18%  Similarity=0.307  Sum_probs=65.0

Q ss_pred             CCccEEEEeCC--CCCC---------CHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCc
Q 022301          106 RSEYRVLVTGL--PSSA---------SWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNA  174 (299)
Q Consensus       106 ~~~~~l~v~nl--~~~~---------~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~  174 (299)
                      ....+|+|.|+  |.++         ..++|.+.|.+||.|..+.+..+...|+|||+|.+.++|..|+..|||..++|+
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr   85 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGR   85 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETTE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEECCE
Confidence            34578999998  4432         136889999999999999999998889999999999999999999999999999


Q ss_pred             eeeEEEEeccccc
Q 022301          175 FSRAYVRVREYDH  187 (299)
Q Consensus       175 ~~~~~~~~~~~~~  187 (299)
                          .|.+..+.+
T Consensus        86 ----~i~v~~~~g   94 (99)
T d2dita1          86 ----QITAQAWDG   94 (99)
T ss_dssp             ----ECEEEECCS
T ss_pred             ----EEEEEEeCC
Confidence                455544433

>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=99.29  E-value=3.3e-12  Score=83.77  Aligned_cols=64  Identities=17%  Similarity=0.212  Sum_probs=55.4

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCce
Q 022301          108 EYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAF  175 (299)
Q Consensus       108 ~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~  175 (299)
                      .+-|+|.++|+.++++.| ++|.+||+|..+.+..+  .+||||+|.+.++|++||. +||..|+|+.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~--~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~   67 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT--GNWMHIRYQSKLQARKALS-KDGRIFGESI   67 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS--SSEEEEEESSHHHHHHHHT-TTTCEETTTE
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC--CCEEEEEEcccHHHHHHHh-cCCCeECCcE
Confidence            467999999999886655 57999999999887544  4699999999999999996 9999999974

>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=99.26  E-value=3.9e-13  Score=93.02  Aligned_cols=70  Identities=14%  Similarity=0.076  Sum_probs=61.5

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCC---CEEEEEecChhhHHHHHHhcCCCeecCceeeE
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSG---TTGIVDYTNYDDMKHAIKKLDDSEFRNAFSRA  178 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~---~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~~~  178 (299)
                      ..++|.+++..+++++|.++|++||+|..+.|+.+..+   |+|||+|.+.++|..|+..|||..++|+.+.+
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v  100 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHA  100 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCE
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEE
Confidence            35777788888899999999999999999999876543   69999999999999999999999999996543

>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=99.13  E-value=2.7e-11  Score=83.70  Aligned_cols=74  Identities=19%  Similarity=0.227  Sum_probs=60.9

Q ss_pred             CccEEEEeCC--CCCCC--------HHHHHHHHHhcCCeeEEEEEeCCCC------CEEEEEecChhhHHHHHHhcCCCe
Q 022301          107 SEYRVLVTGL--PSSAS--------WQDLKDHMRRAGDVCFSQVFRDGSG------TTGIVDYTNYDDMKHAIKKLDDSE  170 (299)
Q Consensus       107 ~~~~l~v~nl--~~~~~--------~~~l~~~f~~~G~v~~~~~~~~~~~------~~~fv~f~~~~~a~~a~~~l~g~~  170 (299)
                      +...|.|.|+  +..+.        .++|++.|.+||.|..+.|..+...      |++||+|.+.++|..|+..|||..
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            4568899998  44432        4678999999999999999775433      699999999999999999999999


Q ss_pred             ecCceeeEEE
Q 022301          171 FRNAFSRAYV  180 (299)
Q Consensus       171 ~~g~~~~~~~  180 (299)
                      ++|+.+.+..
T Consensus        83 f~gR~v~v~f   92 (104)
T d1o0pa_          83 FANRVVVTKY   92 (104)
T ss_dssp             SSSSCCEEEE
T ss_pred             ECCeEEEEEE
Confidence            9999765443

>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=98.13  E-value=7.5e-06  Score=49.61  Aligned_cols=60  Identities=22%  Similarity=0.321  Sum_probs=52.9

Q ss_pred             HHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEcc
Q 022301           22 EVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELAH   81 (299)
Q Consensus        22 ~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~~   81 (299)
                      -|.+.|..+|+|..+.+.......-.|-|...+.++|..|+..|+-..|+++.|.|.++.
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            366788999999999996655556689999999999999999999999999999999874

>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=98.12  E-value=3.7e-06  Score=54.76  Aligned_cols=65  Identities=15%  Similarity=0.232  Sum_probs=55.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecC-----CCCCceEEEEecChHHHHHHHHhcCCCCCC
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIP-----PRPPGYAFVEFEEARDAEDAIRGRDGYDFD   71 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~-----~~~~g~afV~F~~~e~A~~A~~~l~~~~~~   71 (299)
                      ++|.|..||+.+|++++.+.++..|++....+...     .....-|||.|.+.+++......++|..|.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            57899999999999999999999999988777332     122357999999999999999999998774

>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=97.99  E-value=7.4e-06  Score=52.31  Aligned_cols=54  Identities=20%  Similarity=0.423  Sum_probs=48.7

Q ss_pred             HHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCCCCCCceEEEEEc
Q 022301           21 REVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGYDFDGHRLRVELA   80 (299)
Q Consensus        21 ~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~~~~g~~i~v~~~   80 (299)
                      .+|.+.|..||+|.-|++.     .+...|+|.+-+.|.+|+. |+|..+.|+.|+|...
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            3588899999999999997     4578999999999999999 9999999999999753

>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=97.81  E-value=8.2e-05  Score=48.25  Aligned_cols=68  Identities=15%  Similarity=0.348  Sum_probs=58.9

Q ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCC------EEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          109 YRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGT------TGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       109 ~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~------~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ++|.|..||+.+|++++.+.+...|.+........+...      -|||.|.+.++...-.+.++|..+.+...
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g   75 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKG   75 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCC
Confidence            579999999999999999999999999888777664331      79999999999999999999999876543

>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=97.65  E-value=0.00013  Score=46.45  Aligned_cols=50  Identities=8%  Similarity=0.223  Sum_probs=45.4

Q ss_pred             HHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          122 WQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       122 ~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      ..+|.+.|..||+|.-+.+..+    ..+|+|.+-+.|.+|+. ++|.++.|+.+
T Consensus        38 ~~~Llq~l~~~GeViLvRFv~d----~mwVTF~dG~SAL~al~-l~g~~v~G~~l   87 (95)
T d1ufwa_          38 RTELMQTLGSYGTIVLVRINQG----QMLVTFADSHSALSVLD-VDGMKVKGRAV   87 (95)
T ss_dssp             HHHHHHHHHHHSCCSEEEEETT----EEEEECSCSHHHHHHHH-GGGSEETTEEE
T ss_pred             HHHHHHHHhhCCeEEEEEEeCC----eEEEEECCcHHHHHHhc-cCCeEEcceEE
Confidence            4678899999999999999888    78999999999999998 99999999854

>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=97.55  E-value=0.0002  Score=43.20  Aligned_cols=55  Identities=18%  Similarity=0.159  Sum_probs=47.5

Q ss_pred             HHHHHHHHHhcCCeeEEEEEeCCCCC-EEEEEecChhhHHHHHHhcCCCeecCcee
Q 022301          122 WQDLKDHMRRAGDVCFSQVFRDGSGT-TGIVDYTNYDDMKHAIKKLDDSEFRNAFS  176 (299)
Q Consensus       122 ~~~l~~~f~~~G~v~~~~~~~~~~~~-~~fv~f~~~~~a~~a~~~l~g~~~~g~~~  176 (299)
                      .+.|...|.++|.|..+.+....... .|-|...+.++|..|+..||...|+++.+
T Consensus        10 qq~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI   65 (73)
T d2dgxa1          10 QQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKI   65 (73)
T ss_dssp             HHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             HHHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEE
Confidence            45577889999999999987665543 89999999999999999999999999844

>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=97.07  E-value=0.00084  Score=43.43  Aligned_cols=55  Identities=16%  Similarity=0.262  Sum_probs=47.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhhcCCeeEEEeecCCCCCceEEEEecChHHHHHHHHhcC
Q 022301            7 RTLYVGNLPGDIREREVEDLFYKYGPIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRD   66 (299)
Q Consensus         7 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~   66 (299)
                      .-||.-.+|......||.++|++||.|.--.|..     .-|||...+.++|..++..+.
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            3477779999999999999999999998888863     389999999999999988544

>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=96.89  E-value=0.0031  Score=40.72  Aligned_cols=61  Identities=15%  Similarity=0.161  Sum_probs=49.5

Q ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEeCCCCCEEEEEecChhhHHHHHHhcC
Q 022301          103 VSRRSEYRVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGSGTTGIVDYTNYDDMKHAIKKLD  167 (299)
Q Consensus       103 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~fv~f~~~~~a~~a~~~l~  167 (299)
                      .+.+.-..+|.-..|..+...||.++|..||.|.-..|...    .|||...+.++|+.++..+.
T Consensus        10 d~~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswIddT----Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          10 DLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDDT----SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEEETT----EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCCcceeEEEeCCcccchhHHHHHhcCCCceEEEEecCc----eEEEEecCHHHHHHHHHHhc
Confidence            34455567888899999999999999999999876666322    89999999999888887543

>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=83.48  E-value=2  Score=27.46  Aligned_cols=48  Identities=13%  Similarity=0.109  Sum_probs=34.3

Q ss_pred             HHHHHHhhhcC---CeeEEEeecCCCCCceEEEEecChHHHHHHHHhcCCC
Q 022301           21 REVEDLFYKYG---PIAHIDLKIPPRPPGYAFVEFEEARDAEDAIRGRDGY   68 (299)
Q Consensus        21 ~~l~~~F~~~G---~v~~i~~~~~~~~~g~afV~F~~~e~A~~A~~~l~~~   68 (299)
                      +.|.......|   .|..+.++......||.||++.-.+++..++....|.
T Consensus        24 ~~l~~~~~~~~l~~~i~~v~VP~~klfPGYvfV~~~~~~~~~~~Ir~t~gV   74 (101)
T d1m1ha2          24 ENLLKVLELEGLKDLVDEVIVPANKIFPGYILIKAHMNDKLLMAIEKTPHV   74 (101)
T ss_dssp             HHHHHHHHHTTCGGGEEEEECSSCSSSTTEEEEEECCCHHHHHHHHTSTTE
T ss_pred             HHHHHHHHHcCchhhhHHHhccchhcCCCEEEEEEEeCchHHHHHhcCCCE
Confidence            34554444444   4677777655567899999999988988888877663