Psyllid ID: psy14476

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300---
Protein Sequence
MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAPQMRPSGQTAQGFPNIPQFRSAPRASTGQTVIRGANMSARPITGQSTMGPRGGGPMQAPGPASVSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGVQAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQAKQAAVKKE
Secondary Structure (PSIPRED)
cccccccccEEEEEcccHHHHHHHHHHHcccEEccccEEEEEcccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccHHHHHHHHHccccHHHHHHcccccccHHHHHccccHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccccccccEEEEcccHHHHHHHHHHHcccEcccccEEEHHHHcHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHcccHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHccccHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
msedgrskgfgfvcfsspeeATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIANMRMQQMgqlfqpgstggyfvptlpqpqrfygptqmtqirpqprwaaapqmrpsgqtaqgfpnipqfrsaprastgqtvirganmsarpitgqstmgprgggpmqapgpasvsaagrqtggynkypvrnpgtqpqaqiggiqpaaaGVQAVhvqgqepltstmLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQAKQAAVKKE
Flexible Loop (DISEMBL)
msedgrskgfgfvcfsspEEATKAVTemngriigSKPLYVALAQRKEDRKAHLASQYMQRIANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAPQMRPSGQTAQGFPNIPQFRSAPRASTGQTvirganmsarpitGQSTMGPRGGGPMQAPGPASVSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGVQAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQakqaavkke
Low Complexity Region (SEG)
MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAPQMRPSGQTAQGFPNIPQFRSAPRASTGQTVIRGANMSARPITGQSTMGPRGGGPMQAPGPASVSAAGRQTGGYNKYPVRNPGTqpqaqiggiqpaaagvqavhvqgqEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEavavlqahqakqaavkkE
Disordered region (IsUnstruct)
*********FGFVCFS*******AVTEMNGRIIGSKPLYVALAQ************Y***I**********LFQ**STGGYFVPTL*******************************************************************************************************************************************************LGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHN***************************
Disordered Region (DISOPRED)
****GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVAL**************************************************************************************************************************************************************************************************MLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAV**************
Disordered Region (DISEMBL)
********GFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR********ASQYMQRIANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAPQMRPSGQTAQGFPNIPQFRSAPRASTGQTVIRGANMSARPITGQSTM*******************GRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGVQAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQ************
Disordered Region (DISPRO)
******SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAPQMRPSGQTAQGFPNIPQFRSAPRASTGQTVIRGANMSARPITGQSTMGPRGGGPMQAPGPASVSAAGRQTGGYNKYPVRNPGTQ**********************QEPLTST**AAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQAKQA*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAPQMRPSGQTAQGFPNIPQFRSAPRASTGQTVIRGANMSARPITGQSTMGPRGGGPMQAPGPASVSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGVQAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHxxxxxxxxxxxxxxxxxxxxxQAAVKKE
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	303	2.2.26 [Sep-21-2011]
Q13310	644	Polyadenylate-binding pro	yes	N/A	0.937	0.440	0.548	8e-78
Q5R8F7	636	Polyadenylate-binding pro	no	N/A	0.940	0.448	0.547	2e-75
P29341	636	Polyadenylate-binding pro	no	N/A	0.940	0.448	0.547	2e-75
P11940	636	Polyadenylate-binding pro	no	N/A	0.940	0.448	0.547	2e-75
P61286	636	Polyadenylate-binding pro	no	N/A	0.940	0.448	0.547	2e-75
Q9EPH8	636	Polyadenylate-binding pro	no	N/A	0.914	0.435	0.546	3e-74
P21187	634	Polyadenylate-binding pro	yes	N/A	0.933	0.446	0.481	7e-73
Q6IP09	633	Polyadenylate-binding pro	N/A	N/A	0.933	0.447	0.537	2e-72
P20965	633	Polyadenylate-binding pro	N/A	N/A	0.910	0.436	0.554	1e-71
Q9H361	631	Polyadenylate-binding pro	no	N/A	0.914	0.438	0.526	5e-70

>sp|Q13310|PABP4_HUMAN Polyadenylate-binding protein 4 OS=Homo sapiens GN=PABPC4 PE=1 SV=1

 Score =  290 bits (742), Expect = 8e-78,   Method: Compositional matrix adjust.
 Identities = 180/328 (54%), Positives = 206/328 (62%), Gaps = 44/328 (13%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           M EDGRSKGFGFVCFSSPEEATKAVTEMNGRI+GSKPLYVALAQRKE+RKAHL +QYMQR
Sbjct: 326 MLEDGRSKGFGFVCFSSPEEATKAVTEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQR 385

Query: 61  IANMRMQQMGQL---FQPGSTGGYFVPTLPQPQR---FYGPTQMTQIRPQPRWAAAPQMR 114
           +A MR      +   FQP + GGYFVP +PQ Q    +Y P Q+ Q+RP PRW       
Sbjct: 386 VAGMRALPANAILNQFQPAA-GGYFVPAVPQAQGRPPYYTPNQLAQMRPNPRWQ------ 438

Query: 115 PSGQTAQGFPNIPQFRSAPRASTGQTVIRGANMSARPITGQSTMGPRGGGPMQAPGPASV 174
             G   QGF  +P   SA R S  +  +R    +      +  M   G G  Q     S 
Sbjct: 439 -QGGRPQGFQGMP---SAIRQSGPRPTLRHLAPTGSECPDRLAMDFGGAGAAQQGLTDSC 494

Query: 175 SAAGRQTGGYN------------------KY--PVRNPGTQPQAQIGGIQPAAAGVQAVH 214
            + G  T   N                  KY   VR+P   P      IQP  A   AVH
Sbjct: 495 QSGGVPTAVQNLAPRAAVAAAAPRAVAPYKYASSVRSP--HP-----AIQPLQAPQPAVH 547

Query: 215 VQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLE 274
           VQGQEPLT++MLAAA PQEQKQMLGERLFPLIQ M+  LAGKITGMLLEIDN+ELL+MLE
Sbjct: 548 VQGQEPLTASMLAAAPPQEQKQMLGERLFPLIQTMHSNLAGKITGMLLEIDNSELLHMLE 607

Query: 275 HNESLKSKVEEAVAVLQAHQAKQAAVKK 302
             ESL+SKV+EAVAVLQAH AK+ A +K
Sbjct: 608 SPESLRSKVDEAVAVLQAHHAKKEAAQK 635

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo.
Homo sapiens (taxid: 9606)

>sp|Q5R8F7|PABP1_PONAB Polyadenylate-binding protein 1 OS=Pongo abelii GN=PABPC1 PE=2 SV=1

 Score =  282 bits (722), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 173/316 (54%), Positives = 211/316 (66%), Gaps = 31/316 (9%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           M E GRSKGFGFVCFSSPEEATKAVTEMNGRI+ +KPLYVALAQRKE+R+AHL +QYMQR
Sbjct: 326 MMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQR 385

Query: 61  IANMRM--QQMGQLFQPGSTGGYFVPTLPQPQR---FYGPTQMTQIRPQPRWAAAPQMRP 115
           +A++R     +   +QP    GYF+  +PQ Q    +Y P+Q+ Q+RP PRW A      
Sbjct: 386 MASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRAAYYPPSQIAQLRPSPRWTA------ 439

Query: 116 SGQTAQGFPNIP-QFR-SAPRASTGQTVIRGAN------MSARPITGQST--MGPRGGGP 165
            G     F N+P   R +APR     + +R A+      MS + +   ST  MGPR    
Sbjct: 440 QGARPHPFQNMPGAIRPAAPRPPF--STMRPASSQVPRVMSTQRVANTSTQTMGPRPAAA 497

Query: 166 MQAPGPASVSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGVQAVHVQGQEPLTSTM 225
             A  PA  +    +     + P ++   QPQ  +   QPA      VHVQGQEPLT++M
Sbjct: 498 AAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQ--QPA------VHVQGQEPLTASM 549

Query: 226 LAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEE 285
           LA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ESL+SKV+E
Sbjct: 550 LASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDE 609

Query: 286 AVAVLQAHQAKQAAVK 301
           AVAVLQAHQAK+AA K
Sbjct: 610 AVAVLQAHQAKEAAQK 625

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Pongo abelii (taxid: 9601)

>sp|P29341|PABP1_MOUSE Polyadenylate-binding protein 1 OS=Mus musculus GN=Pabpc1 PE=1 SV=2

 Score =  282 bits (721), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 173/316 (54%), Positives = 211/316 (66%), Gaps = 31/316 (9%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           M E GRSKGFGFVCFSSPEEATKAVTEMNGRI+ +KPLYVALAQRKE+R+AHL +QYMQR
Sbjct: 326 MMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQR 385

Query: 61  IANMRM--QQMGQLFQPGSTGGYFVPTLPQPQR---FYGPTQMTQIRPQPRWAAAPQMRP 115
           +A++R     +   +QP    GYF+  +PQ Q    +Y P+Q+ Q+RP PRW A      
Sbjct: 386 MASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRAAYYPPSQIAQLRPSPRWTA------ 439

Query: 116 SGQTAQGFPNIP-QFR-SAPRASTGQTVIRGAN------MSARPITGQST--MGPRGGGP 165
            G     F N+P   R +APR     + +R A+      MS + +   ST  MGPR    
Sbjct: 440 QGARPHPFQNMPGAIRPAAPRPPF--STMRPASSQVPRVMSTQRVANTSTQTMGPRPAAA 497

Query: 166 MQAPGPASVSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGVQAVHVQGQEPLTSTM 225
             A  PA  +    +     + P ++   QPQ  +   QPA      VHVQGQEPLT++M
Sbjct: 498 AAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQ--QPA------VHVQGQEPLTASM 549

Query: 226 LAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEE 285
           LA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ESL+SKV+E
Sbjct: 550 LASAPPQEQKQMLGERLFPLIQAMHPSLAGKITGMLLEIDNSELLHMLESPESLRSKVDE 609

Query: 286 AVAVLQAHQAKQAAVK 301
           AVAVLQAHQAK+AA K
Sbjct: 610 AVAVLQAHQAKEAAQK 625

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Mus musculus (taxid: 10090)

>sp|P11940|PABP1_HUMAN Polyadenylate-binding protein 1 OS=Homo sapiens GN=PABPC1 PE=1 SV=2

 Score =  282 bits (721), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 173/316 (54%), Positives = 211/316 (66%), Gaps = 31/316 (9%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           M E GRSKGFGFVCFSSPEEATKAVTEMNGRI+ +KPLYVALAQRKE+R+AHL +QYMQR
Sbjct: 326 MMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQR 385

Query: 61  IANMRM--QQMGQLFQPGSTGGYFVPTLPQPQR---FYGPTQMTQIRPQPRWAAAPQMRP 115
           +A++R     +   +QP    GYF+  +PQ Q    +Y P+Q+ Q+RP PRW A      
Sbjct: 386 MASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRAAYYPPSQIAQLRPSPRWTA------ 439

Query: 116 SGQTAQGFPNIP-QFR-SAPRASTGQTVIRGAN------MSARPITGQST--MGPRGGGP 165
            G     F N+P   R +APR     + +R A+      MS + +   ST  MGPR    
Sbjct: 440 QGARPHPFQNMPGAIRPAAPRPPF--STMRPASSQVPRVMSTQRVANTSTQTMGPRPAAA 497

Query: 166 MQAPGPASVSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGVQAVHVQGQEPLTSTM 225
             A  PA  +    +     + P ++   QPQ  +   QPA      VHVQGQEPLT++M
Sbjct: 498 AAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQ--QPA------VHVQGQEPLTASM 549

Query: 226 LAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEE 285
           LA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ESL+SKV+E
Sbjct: 550 LASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDE 609

Query: 286 AVAVLQAHQAKQAAVK 301
           AVAVLQAHQAK+AA K
Sbjct: 610 AVAVLQAHQAKEAAQK 625

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Homo sapiens (taxid: 9606)

>sp|P61286|PABP1_BOVIN Polyadenylate-binding protein 1 OS=Bos taurus GN=PABPC1 PE=2 SV=1

 Score =  282 bits (721), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 173/316 (54%), Positives = 211/316 (66%), Gaps = 31/316 (9%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           M E GRSKGFGFVCFSSPEEATKAVTEMNGRI+ +KPLYVALAQRKE+R+AHL +QYMQR
Sbjct: 326 MMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQR 385

Query: 61  IANMRM--QQMGQLFQPGSTGGYFVPTLPQPQR---FYGPTQMTQIRPQPRWAAAPQMRP 115
           +A++R     +   +QP    GYF+  +PQ Q    +Y P+Q+ Q+RP PRW A      
Sbjct: 386 MASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRAAYYPPSQIAQLRPSPRWTA------ 439

Query: 116 SGQTAQGFPNIP-QFR-SAPRASTGQTVIRGAN------MSARPITGQST--MGPRGGGP 165
            G     F N+P   R +APR     + +R A+      MS + +   ST  MGPR    
Sbjct: 440 QGARPHPFQNMPGAIRPAAPRPPF--STMRPASSQVPRVMSTQRVANTSTQTMGPRPAAA 497

Query: 166 MQAPGPASVSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGVQAVHVQGQEPLTSTM 225
             A  PA  +    +     + P ++   QPQ  +   QPA      VHVQGQEPLT++M
Sbjct: 498 AAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQ--QPA------VHVQGQEPLTASM 549

Query: 226 LAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEE 285
           LA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ESL+SKV+E
Sbjct: 550 LASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDE 609

Query: 286 AVAVLQAHQAKQAAVK 301
           AVAVLQAHQAK+AA K
Sbjct: 610 AVAVLQAHQAKEAAQK 625

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Bos taurus (taxid: 9913)

>sp|Q9EPH8|PABP1_RAT Polyadenylate-binding protein 1 OS=Rattus norvegicus GN=Pabpc1 PE=2 SV=1

 Score =  278 bits (712), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 177/324 (54%), Positives = 210/324 (64%), Gaps = 47/324 (14%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           M E GRSKGFGFVCFSSPEEATKAVTEMNGRI+ +KPLYVALAQRKE+R+AHL +QYMQR
Sbjct: 326 MMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQR 385

Query: 61  IANMRM--QQMGQLFQPGSTGGYFVPTLPQPQR---FYGPTQMTQIRPQPRWAAAPQMRP 115
           +A++R     +   +QP    GYF+  +PQ Q    +Y P+Q+ Q+RP PRW A      
Sbjct: 386 MASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRAAYYPPSQIAQLRPSPRWTA------ 439

Query: 116 SGQTAQGFPNIP-QFR-SAPRASTGQTVIRGAN------MSARPITGQST--MGPRGGGP 165
            G     F N+P   R +APR     + +R A+      MS + +   ST  MGPR    
Sbjct: 440 QGARPHPFQNMPGAIRPAAPRPPF--STMRPASSQVPRVMSTQRVANTSTQTMGPRPAAA 497

Query: 166 MQAPG------PASVSAAGRQTGGYNKYPVRNP--GTQPQAQIGGIQPAAAGVQAVHVQG 217
             A        P    AAG          VRNP      Q Q+   QPA      VHVQG
Sbjct: 498 ATAATPAVRTVPQYKYAAG----------VRNPQQHLNAQPQVTMQQPA------VHVQG 541

Query: 218 QEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNE 277
           QEPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  E
Sbjct: 542 QEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPSLAGKITGMLLEIDNSELLHMLESPE 601

Query: 278 SLKSKVEEAVAVLQAHQAKQAAVK 301
           SL+SKV+EAVAVLQAHQAK+AA K
Sbjct: 602 SLRSKVDEAVAVLQAHQAKEAAQK 625

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Rattus norvegicus (taxid: 10116)

>sp|P21187|PABP_DROME Polyadenylate-binding protein OS=Drosophila melanogaster GN=pAbp PE=1 SV=3

 Score =  274 bits (700), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 158/328 (48%), Positives = 201/328 (61%), Gaps = 45/328 (13%)

Query: 2   SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRI 61
            E+GRSKGFGFVCF++  EAT AVTE+NGR++GSKPLYVALAQRKE+RKAHLASQYM+ +
Sbjct: 321 DEEGRSKGFGFVCFNAASEATCAVTELNGRVVGSKPLYVALAQRKEERKAHLASQYMRHM 380

Query: 62  ANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAPQMRPSGQTAQ 121
             MRMQQ+GQ++QP +  G+FVPTLP  QRF+G    TQ+R  PRW   PQ+RP      
Sbjct: 381 TGMRMQQLGQIYQPNAASGFFVPTLPSNQRFFGSQVATQMRNTPRW--VPQVRPPAAIQG 438

Query: 122 GFPNI----------------------------PQFRSAPRASTGQTVIRGANMSARPIT 153
                                            PQ +    A+     +R  N  AR IT
Sbjct: 439 VQAGAAAAGGFQGTAGAVPTQFRSAAAGARGAQPQVQGTHAAAAAANNMR--NTGARAIT 496

Query: 154 GQSTMGPRGGGPMQAPGPASVSAAGRQTGGYNKYP--VRNPGTQPQAQIGGIQPAAAGVQ 211
           GQ T  P     MQ PG      A ++T  Y KY   +RNP   P  Q+   QP    +Q
Sbjct: 497 GQQTAAPN----MQIPGAQIAGGAQQRTSNY-KYTSNMRNP---PVPQLHQTQPIPQQLQ 548

Query: 212 AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 271
               +  E L +++LA A+PQEQKQ+LGERL+P+I+ M+  LAGKITGMLLEI+N+ELL+
Sbjct: 549 G---KNSEKLIASLLANAKPQEQKQILGERLYPMIEHMHANLAGKITGMLLEIENSELLH 605

Query: 272 MLEHNESLKSKVEEAVAVLQAHQAKQAA 299
           M+E  E+LK+KVEEAVAVLQ H+  + A
Sbjct: 606 MIEDQEALKAKVEEAVAVLQVHRVTEPA 633

Binds the poly(A) tail of mRNA.

Drosophila melanogaster (taxid: 7227)

>sp|Q6IP09|PABPB_XENLA Polyadenylate-binding protein 1-B OS=Xenopus laevis GN=pabpc1-b PE=2 SV=1

 Score =  273 bits (697), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 170/316 (53%), Positives = 204/316 (64%), Gaps = 33/316 (10%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           M E GRSKGFGFVCFSSPEEATKAVTEMNGRI+ +KPLYVALAQRKE+R+AHL +QYMQR
Sbjct: 326 MMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQR 385

Query: 61  IANMRMQQ-MGQLFQPGSTGGYFVPTLPQPQR---FYGPTQMTQIRPQPRWAA------- 109
           +A++R+   +   +QP  +  YF+  +P  Q    +Y P Q+ Q+RP PRW A       
Sbjct: 386 MASVRVPNPVINPYQPPPSS-YFMAAIPPAQNRAAYYPPGQIAQLRPSPRWTAQGARPHP 444

Query: 110 ----APQMRPSGQTAQGFPNIPQFRSAPRASTGQTVIRGANMSARPITGQSTMGPRGGGP 165
               A  +RPS      F  +      PR  + Q V   AN      T   TMGPR    
Sbjct: 445 FQNMAGAIRPSAPRPPTFSTMRPTSQVPRVMSAQRV---AN------TSTQTMGPRPTTA 495

Query: 166 MQAPGPASVSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGVQAVHVQGQEPLTSTM 225
             A   A  +    +     +   ++  TQPQ  +   QPA      VHVQGQEPLT++M
Sbjct: 496 AAAATSAVRTVPQYKYAAGVRNTQQHLNTQPQVAMQ--QPA------VHVQGQEPLTASM 547

Query: 226 LAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEE 285
           LAAA PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ESL+SKV+E
Sbjct: 548 LAAAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDE 607

Query: 286 AVAVLQAHQAKQAAVK 301
           AVAVLQAHQAK+AA K
Sbjct: 608 AVAVLQAHQAKEAAQK 623

Binds the poly(A) tail of mRNA. Prevents mRNA deadenylation and confers poly(A) stability. Stimulates the translation of mRNAs to which it is bound, acting, at least in part, with dazl.

Xenopus laevis (taxid: 8355)

>sp|P20965|PABPA_XENLA Polyadenylate-binding protein 1-A OS=Xenopus laevis GN=pabpc1-a PE=1 SV=3

 Score =  270 bits (689), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 179/323 (55%), Positives = 211/323 (65%), Gaps = 47/323 (14%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           M E GRSKGFGFVCFSSPEEATKAVTEMNGRI+ +KPLYVALAQRKE+R+AHL +QYMQR
Sbjct: 326 MMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQR 385

Query: 61  IANMRMQQ-MGQLFQPGSTGGYFVPTLPQPQR---FYGPTQMTQIRPQPRWAAAPQMRPS 116
           +A++R+   +   +QP  +  YF+  +P  Q    +Y P Q+ Q+RP PRW A       
Sbjct: 386 MASVRVPNPVINPYQPPPSS-YFMAAIPPAQNRAAYYPPGQIAQLRPSPRWTA------Q 438

Query: 117 GQTAQGFPNIP-QFR-SAPRASTGQTVIRGAN-----MSARPITGQST--MGPRGGGPMQ 167
           G     F N+P   R +APR  T  T+   +N     MSA+ +   ST  MGPR      
Sbjct: 439 GARPHPFQNMPGAIRPTAPRPPTFSTMRPASNQVPRVMSAQRVANTSTQTMGPRPTTAAA 498

Query: 168 APG------PASVSAAGRQTGGYNKYPVRNP---GTQPQAQIGGIQPAAAGVQAVHVQGQ 218
           A        P    AAG          VRN     TQPQ  +   QPA      VHVQGQ
Sbjct: 499 AAASAVRAVPQYKYAAG----------VRNQQHLNTQPQVAMQ--QPA------VHVQGQ 540

Query: 219 EPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNES 278
           EPLT++MLAAA PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ES
Sbjct: 541 EPLTASMLAAAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPES 600

Query: 279 LKSKVEEAVAVLQAHQAKQAAVK 301
           L+SKV+EAVAVLQAHQAK+AA K
Sbjct: 601 LRSKVDEAVAVLQAHQAKEAAQK 623

Binds the poly(A) tail of mRNA. Prevents mRNA deadenylation and confers poly(A) stability. Stimulates the translation of mRNAs to which it is bound, acting, at least in part, with dazl.

Xenopus laevis (taxid: 8355)

>sp|Q9H361|PABP3_HUMAN Polyadenylate-binding protein 3 OS=Homo sapiens GN=PABPC3 PE=1 SV=2

 Score =  264 bits (675), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 168/319 (52%), Positives = 203/319 (63%), Gaps = 42/319 (13%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           M E GRSKGFGFVCFSSPEEATKAVTEMNGRI+ +KPLYVALAQRKE+R+A+L ++YMQR
Sbjct: 326 MMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAYLTNEYMQR 385

Query: 61  IANMRMQQMGQLFQPGSTGGYFVPTLPQPQR---FYGPTQMTQIRPQPRWAAAP------ 111
           +A++R        Q     GYF+  +PQ Q    +Y P+Q+ ++RP PRW A        
Sbjct: 386 MASVRAVPN----QRAPPSGYFMTAVPQTQNHAAYYPPSQIARLRPSPRWTAQGARPHPF 441

Query: 112 QMRPSGQTAQGFPNIPQFRSAPRASTGQTVI---RGANMSARPITGQSTMGPRGGGPMQA 168
           Q +PS     G P +P     P +S    V+   R AN S +      T+GPR      A
Sbjct: 442 QNKPSA-IRPGAPRVPFSTMRPASSQVPRVMSTQRVANTSTQ------TVGPRPAAAAAA 494

Query: 169 PGPASVSAAGRQTGGYNKYP--VRNP----GTQPQAQIGGIQPAAAGVQAVHVQGQEPLT 222
               +V    R      KY   VRNP      QPQ  +  +        AVHVQGQE LT
Sbjct: 495 AATPAVRTVPRY-----KYAAGVRNPQQHRNAQPQVTMQQL--------AVHVQGQETLT 541

Query: 223 STMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSK 282
           ++ LA+A PQ+QKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELLYMLE  ESL+SK
Sbjct: 542 ASRLASAPPQKQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLYMLESPESLRSK 601

Query: 283 VEEAVAVLQAHQAKQAAVK 301
           V+EAVAVLQAHQAK+A  K
Sbjct: 602 VDEAVAVLQAHQAKEATQK 620

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism. Binds poly(A) with a slightly lower affinity as compared to PABPC1.

Homo sapiens (taxid: 9606)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	303
340719920	609	PREDICTED: polyadenylate-binding protein	0.973	0.484	0.700	1e-106
340719918	630	PREDICTED: polyadenylate-binding protein	0.973	0.468	0.700	1e-106
350408508	601	PREDICTED: polyadenylate-binding protein	0.970	0.489	0.701	1e-106
350408504	630	PREDICTED: polyadenylate-binding protein	0.970	0.466	0.701	1e-106
380019828	630	PREDICTED: polyadenylate-binding protein	0.970	0.466	0.701	1e-106
328782034	601	PREDICTED: polyadenylate-binding protein	0.970	0.489	0.701	1e-105
383862667	630	PREDICTED: polyadenylate-binding protein	0.970	0.466	0.698	1e-105
383862671	601	PREDICTED: polyadenylate-binding protein	0.970	0.489	0.698	1e-105
389608229	619	polyA-binding protein [Papilio xuthus]	0.927	0.453	0.679	1e-104
389610655	611	polyA-binding protein [Papilio polytes]	0.927	0.459	0.679	1e-104

>gi|340719920|ref|XP_003398392.1| PREDICTED: polyadenylate-binding protein 1-like isoform 2 [Bombus terrestris]

 Score =  391 bits (1004), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 218/311 (70%), Positives = 242/311 (77%), Gaps = 16/311 (5%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           M E+GRSKGFGFVCFS+PEEATKAVTEMNGRII +KPLYVALAQRKEDRKAHLASQYMQR
Sbjct: 307 MMEEGRSKGFGFVCFSAPEEATKAVTEMNGRIIVTKPLYVALAQRKEDRKAHLASQYMQR 366

Query: 61  IANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAP-QMRPSGQT 119
           +ANMRMQQMGQ+FQPG  G YFVPT+PQPQRFYGP QM QIR  PRW A P Q+RP+ QT
Sbjct: 367 LANMRMQQMGQIFQPGGAGNYFVPTIPQPQRFYGPAQMAQIRTTPRWPAQPNQVRPNAQT 426

Query: 120 -AQGFPNIPQ-FRSAPRASTGQTVIRGANMSARPITGQSTMGPRGGGPMQA---PGPA-S 173
            + GF  +   FR+APRA T Q     + +SARPITGQ T+   GG  MQ+    GPA  
Sbjct: 427 GSSGFATMQGPFRAAPRAPTAQPGAMRSTLSARPITGQQTV---GGANMQSRSMAGPAVG 483

Query: 174 VSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGVQAVHVQGQEPLTSTMLAAAQPQE 233
           VSA  R +       +RNP   PQA    I       QAVH+QGQEPLT++MLAAA PQE
Sbjct: 484 VSAQSRPSNYKYTSNMRNP---PQAM--AIPTPTPVQQAVHIQGQEPLTASMLAAAPPQE 538

Query: 234 QKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAH 293
           QKQMLGERLFPLIQ MYP+L GKITGMLLEIDN+ELL+MLEHNESLK+KVEEAVAVLQAH
Sbjct: 539 QKQMLGERLFPLIQCMYPQLTGKITGMLLEIDNSELLHMLEHNESLKAKVEEAVAVLQAH 598

Query: 294 QAKQA-AVKKE 303
           QAKQA A KKE
Sbjct: 599 QAKQAVASKKE 609

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340719918|ref|XP_003398391.1| PREDICTED: polyadenylate-binding protein 1-like isoform 1 [Bombus terrestris]

 Score =  390 bits (1003), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 218/311 (70%), Positives = 242/311 (77%), Gaps = 16/311 (5%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           M E+GRSKGFGFVCFS+PEEATKAVTEMNGRII +KPLYVALAQRKEDRKAHLASQYMQR
Sbjct: 328 MMEEGRSKGFGFVCFSAPEEATKAVTEMNGRIIVTKPLYVALAQRKEDRKAHLASQYMQR 387

Query: 61  IANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAP-QMRPSGQT 119
           +ANMRMQQMGQ+FQPG  G YFVPT+PQPQRFYGP QM QIR  PRW A P Q+RP+ QT
Sbjct: 388 LANMRMQQMGQIFQPGGAGNYFVPTIPQPQRFYGPAQMAQIRTTPRWPAQPNQVRPNAQT 447

Query: 120 -AQGFPNIPQ-FRSAPRASTGQTVIRGANMSARPITGQSTMGPRGGGPMQA---PGPA-S 173
            + GF  +   FR+APRA T Q     + +SARPITGQ T+   GG  MQ+    GPA  
Sbjct: 448 GSSGFATMQGPFRAAPRAPTAQPGAMRSTLSARPITGQQTV---GGANMQSRSMAGPAVG 504

Query: 174 VSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGVQAVHVQGQEPLTSTMLAAAQPQE 233
           VSA  R +       +RNP   PQA    I       QAVH+QGQEPLT++MLAAA PQE
Sbjct: 505 VSAQSRPSNYKYTSNMRNP---PQAM--AIPTPTPVQQAVHIQGQEPLTASMLAAAPPQE 559

Query: 234 QKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAH 293
           QKQMLGERLFPLIQ MYP+L GKITGMLLEIDN+ELL+MLEHNESLK+KVEEAVAVLQAH
Sbjct: 560 QKQMLGERLFPLIQCMYPQLTGKITGMLLEIDNSELLHMLEHNESLKAKVEEAVAVLQAH 619

Query: 294 QAKQA-AVKKE 303
           QAKQA A KKE
Sbjct: 620 QAKQAVASKKE 630

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350408508|ref|XP_003488428.1| PREDICTED: polyadenylate-binding protein 1-like isoform 3 [Bombus impatiens]

 Score =  389 bits (1000), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 219/312 (70%), Positives = 243/312 (77%), Gaps = 18/312 (5%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           M E+GRSKGFGFVCFS+PEEATKAVTEMNGRII +KPLYVALAQRKEDRKAHLASQYMQR
Sbjct: 299 MMEEGRSKGFGFVCFSAPEEATKAVTEMNGRIIVTKPLYVALAQRKEDRKAHLASQYMQR 358

Query: 61  IANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAP-QMRPSGQT 119
           +ANMRMQQMGQ+FQPG  G YFVPT+PQPQRFYGP QM QIR  PRW A P Q+RP+ QT
Sbjct: 359 LANMRMQQMGQIFQPGGAGNYFVPTIPQPQRFYGPAQMAQIRTTPRWPAQPNQVRPNAQT 418

Query: 120 -AQGFPNIPQ-FRSAPRASTGQTVIRGANMSARPITGQSTMGPRGGGPMQ---APGPA-S 173
            + GF  +   FR+APRA T Q     + +SARPITGQ T+   GG  MQ     GPA  
Sbjct: 419 GSSGFATMQGPFRAAPRAPTAQPGAMRSTLSARPITGQQTV---GGANMQNRSMAGPAVG 475

Query: 174 VSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGV-QAVHVQGQEPLTSTMLAAAQPQ 232
           V+A  R +       +RNP   PQA      PA   V QAVH+QGQEPLT++MLAAA PQ
Sbjct: 476 VTAQSRPSNYKYTSNMRNP---PQAM---AIPAPTPVQQAVHIQGQEPLTASMLAAAPPQ 529

Query: 233 EQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQA 292
           EQKQMLGERLFPLIQ MYP+L GKITGMLLEIDN+ELL+MLEHNESLK+KVEEAVAVLQA
Sbjct: 530 EQKQMLGERLFPLIQCMYPQLTGKITGMLLEIDNSELLHMLEHNESLKAKVEEAVAVLQA 589

Query: 293 HQAKQA-AVKKE 303
           HQAKQA A KKE
Sbjct: 590 HQAKQAVASKKE 601

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350408504|ref|XP_003488426.1| PREDICTED: polyadenylate-binding protein 1-like isoform 1 [Bombus impatiens]

 Score =  389 bits (1000), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 219/312 (70%), Positives = 243/312 (77%), Gaps = 18/312 (5%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           M E+GRSKGFGFVCFS+PEEATKAVTEMNGRII +KPLYVALAQRKEDRKAHLASQYMQR
Sbjct: 328 MMEEGRSKGFGFVCFSAPEEATKAVTEMNGRIIVTKPLYVALAQRKEDRKAHLASQYMQR 387

Query: 61  IANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAP-QMRPSGQT 119
           +ANMRMQQMGQ+FQPG  G YFVPT+PQPQRFYGP QM QIR  PRW A P Q+RP+ QT
Sbjct: 388 LANMRMQQMGQIFQPGGAGNYFVPTIPQPQRFYGPAQMAQIRTTPRWPAQPNQVRPNAQT 447

Query: 120 -AQGFPNIPQ-FRSAPRASTGQTVIRGANMSARPITGQSTMGPRGGGPMQ---APGPA-S 173
            + GF  +   FR+APRA T Q     + +SARPITGQ T+   GG  MQ     GPA  
Sbjct: 448 GSSGFATMQGPFRAAPRAPTAQPGAMRSTLSARPITGQQTV---GGANMQNRSMAGPAVG 504

Query: 174 VSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGV-QAVHVQGQEPLTSTMLAAAQPQ 232
           V+A  R +       +RNP   PQA      PA   V QAVH+QGQEPLT++MLAAA PQ
Sbjct: 505 VTAQSRPSNYKYTSNMRNP---PQAM---AIPAPTPVQQAVHIQGQEPLTASMLAAAPPQ 558

Query: 233 EQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQA 292
           EQKQMLGERLFPLIQ MYP+L GKITGMLLEIDN+ELL+MLEHNESLK+KVEEAVAVLQA
Sbjct: 559 EQKQMLGERLFPLIQCMYPQLTGKITGMLLEIDNSELLHMLEHNESLKAKVEEAVAVLQA 618

Query: 293 HQAKQA-AVKKE 303
           HQAKQA A KKE
Sbjct: 619 HQAKQAVASKKE 630

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380019828|ref|XP_003693803.1| PREDICTED: polyadenylate-binding protein 1-like [Apis florea]

 Score =  389 bits (999), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 219/312 (70%), Positives = 241/312 (77%), Gaps = 18/312 (5%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           M E+GRSKGFGFVCFS+PEEATKAVTEMNGRII +KPLYVALAQRKEDRKAHLASQYMQR
Sbjct: 328 MMEEGRSKGFGFVCFSAPEEATKAVTEMNGRIIVTKPLYVALAQRKEDRKAHLASQYMQR 387

Query: 61  IANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAP-QMRPSGQT 119
           +ANMRMQQMGQ+FQPG  G YFVPT+PQPQRFYGP QM QIR  PRW A P Q+RP+ QT
Sbjct: 388 LANMRMQQMGQIFQPGGAGNYFVPTIPQPQRFYGPAQMAQIRTTPRWPAQPNQVRPNAQT 447

Query: 120 -AQGFPNIPQ-FRSAPRASTGQTVIRGANMSARPITGQSTMGPRGGGPMQ---APGPA-S 173
            + GF  +   FR+APRA T Q       +SARPITGQ  +   GG  MQ     GPA  
Sbjct: 448 GSSGFATMQGPFRAAPRAPTAQAGTMRNTLSARPITGQQAV---GGANMQNRSMAGPAVG 504

Query: 174 VSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGV-QAVHVQGQEPLTSTMLAAAQPQ 232
           VSA  R +       +RNP   PQA      PA   V QAVH+QGQEPLT++MLAAA PQ
Sbjct: 505 VSAQSRPSNYKYTSNMRNP---PQAM---AIPAPTPVQQAVHIQGQEPLTASMLAAAPPQ 558

Query: 233 EQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQA 292
           EQKQMLGERLFPLIQ MYP+L GKITGMLLEIDN+ELL+MLEHNESLK+KVEEAVAVLQA
Sbjct: 559 EQKQMLGERLFPLIQCMYPQLTGKITGMLLEIDNSELLHMLEHNESLKAKVEEAVAVLQA 618

Query: 293 HQAKQA-AVKKE 303
           HQAKQA A KKE
Sbjct: 619 HQAKQAVASKKE 630

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328782034|ref|XP_396057.4| PREDICTED: polyadenylate-binding protein 1-like isoform 1 [Apis mellifera]

 Score =  389 bits (998), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 219/312 (70%), Positives = 241/312 (77%), Gaps = 18/312 (5%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           M E+GRSKGFGFVCFS+PEEATKAVTEMNGRII +KPLYVALAQRKEDRKAHLASQYMQR
Sbjct: 299 MMEEGRSKGFGFVCFSAPEEATKAVTEMNGRIIVTKPLYVALAQRKEDRKAHLASQYMQR 358

Query: 61  IANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAP-QMRPSGQT 119
           +ANMRMQQMGQ+FQPG  G YFVPT+PQPQRFYGP QM QIR  PRW A P Q+RP+ QT
Sbjct: 359 LANMRMQQMGQIFQPGGAGNYFVPTIPQPQRFYGPAQMAQIRTTPRWPAQPNQVRPNAQT 418

Query: 120 -AQGFPNIPQ-FRSAPRASTGQTVIRGANMSARPITGQSTMGPRGGGPMQ---APGPA-S 173
            + GF  +   FR+APRA T Q       +SARPITGQ  +   GG  MQ     GPA  
Sbjct: 419 GSSGFATMQGPFRAAPRAPTAQAGTMRNTLSARPITGQQAV---GGANMQNRSMAGPAVG 475

Query: 174 VSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGV-QAVHVQGQEPLTSTMLAAAQPQ 232
           VSA  R +       +RNP   PQA      PA   V QAVH+QGQEPLT++MLAAA PQ
Sbjct: 476 VSAQSRPSNYKYTSNMRNP---PQAM---AIPAPTPVQQAVHIQGQEPLTASMLAAAPPQ 529

Query: 233 EQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQA 292
           EQKQMLGERLFPLIQ MYP+L GKITGMLLEIDN+ELL+MLEHNESLK+KVEEAVAVLQA
Sbjct: 530 EQKQMLGERLFPLIQCMYPQLTGKITGMLLEIDNSELLHMLEHNESLKAKVEEAVAVLQA 589

Query: 293 HQAKQA-AVKKE 303
           HQAKQA A KKE
Sbjct: 590 HQAKQAVASKKE 601

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383862667|ref|XP_003706805.1| PREDICTED: polyadenylate-binding protein 1-like isoform 1 [Megachile rotundata]

 Score =  388 bits (997), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 218/312 (69%), Positives = 240/312 (76%), Gaps = 18/312 (5%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           M EDGRSKGFGFVCFS+PEEATKAVTEMNGRII +KPLYVALAQRKEDRKAHLASQYMQR
Sbjct: 328 MMEDGRSKGFGFVCFSAPEEATKAVTEMNGRIIVTKPLYVALAQRKEDRKAHLASQYMQR 387

Query: 61  IANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAP-QMRPSGQT 119
           +ANMRMQQMGQ+F PG  G YFVPT+PQPQRFYGP QM QIR  PRW A P Q+RP+ QT
Sbjct: 388 LANMRMQQMGQMFPPGGAGNYFVPTIPQPQRFYGPAQMAQIRATPRWPAQPNQVRPNAQT 447

Query: 120 AQ-GFPNIPQ-FRSAPRASTGQTVIRGANMSARPITGQSTMGPRGGGPMQA---PGPA-S 173
              GF  +   FR+ PRA T Q     + +SARPITGQ  +   GG  MQ+    GPA  
Sbjct: 448 GNSGFATMQGPFRTTPRAPTAQAGTMRSTLSARPITGQQAV---GGANMQSRSMAGPAVG 504

Query: 174 VSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGV-QAVHVQGQEPLTSTMLAAAQPQ 232
           VSA  R +       +RNP   PQA      PA   V QAVH+QGQEPLT++MLAAA PQ
Sbjct: 505 VSAQSRPSNYKYTSNMRNP---PQAM---AIPAPTPVQQAVHIQGQEPLTASMLAAAPPQ 558

Query: 233 EQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQA 292
           EQKQMLGERLFPLIQ MYP+L GKITGMLLEIDN+ELL+MLEHNESLK+KVEEAVAVLQA
Sbjct: 559 EQKQMLGERLFPLIQCMYPQLTGKITGMLLEIDNSELLHMLEHNESLKAKVEEAVAVLQA 618

Query: 293 HQAKQA-AVKKE 303
           HQAKQA A KKE
Sbjct: 619 HQAKQAVASKKE 630

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383862671|ref|XP_003706807.1| PREDICTED: polyadenylate-binding protein 1-like isoform 3 [Megachile rotundata]

 Score =  388 bits (997), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 218/312 (69%), Positives = 240/312 (76%), Gaps = 18/312 (5%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           M EDGRSKGFGFVCFS+PEEATKAVTEMNGRII +KPLYVALAQRKEDRKAHLASQYMQR
Sbjct: 299 MMEDGRSKGFGFVCFSAPEEATKAVTEMNGRIIVTKPLYVALAQRKEDRKAHLASQYMQR 358

Query: 61  IANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAP-QMRPSGQT 119
           +ANMRMQQMGQ+F PG  G YFVPT+PQPQRFYGP QM QIR  PRW A P Q+RP+ QT
Sbjct: 359 LANMRMQQMGQMFPPGGAGNYFVPTIPQPQRFYGPAQMAQIRATPRWPAQPNQVRPNAQT 418

Query: 120 AQ-GFPNIPQ-FRSAPRASTGQTVIRGANMSARPITGQSTMGPRGGGPMQA---PGPA-S 173
              GF  +   FR+ PRA T Q     + +SARPITGQ  +   GG  MQ+    GPA  
Sbjct: 419 GNSGFATMQGPFRTTPRAPTAQAGTMRSTLSARPITGQQAV---GGANMQSRSMAGPAVG 475

Query: 174 VSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGV-QAVHVQGQEPLTSTMLAAAQPQ 232
           VSA  R +       +RNP   PQA      PA   V QAVH+QGQEPLT++MLAAA PQ
Sbjct: 476 VSAQSRPSNYKYTSNMRNP---PQAM---AIPAPTPVQQAVHIQGQEPLTASMLAAAPPQ 529

Query: 233 EQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQA 292
           EQKQMLGERLFPLIQ MYP+L GKITGMLLEIDN+ELL+MLEHNESLK+KVEEAVAVLQA
Sbjct: 530 EQKQMLGERLFPLIQCMYPQLTGKITGMLLEIDNSELLHMLEHNESLKAKVEEAVAVLQA 589

Query: 293 HQAKQA-AVKKE 303
           HQAKQA A KKE
Sbjct: 590 HQAKQAVASKKE 601

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|389608229|dbj|BAM17726.1| polyA-binding protein [Papilio xuthus]

 Score =  384 bits (986), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 208/306 (67%), Positives = 235/306 (76%), Gaps = 25/306 (8%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           M EDGRSKGFGFVCFSSPEEATKAVTEMNGRI+G+KPLYVALAQRKEDRKAHL SQYMQR
Sbjct: 328 MLEDGRSKGFGFVCFSSPEEATKAVTEMNGRIVGTKPLYVALAQRKEDRKAHLTSQYMQR 387

Query: 61  IANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAPQMRPSGQT- 119
           +A+MRMQQMGQ+FQPG TGGYFVPT+P  QRFYGP QMTQIRP PRW A P +RP+ Q+ 
Sbjct: 388 MASMRMQQMGQIFQPGGTGGYFVPTIPPAQRFYGPAQMTQIRPSPRWTAQPAVRPNAQSA 447

Query: 120 AQGFPNI-PQFRSAPRASTGQTVIRGANMSARPITGQSTMGPRGGGPMQAPGPASVSAAG 178
           A  +PN+ P FR APR    Q  +R ++M ARPITGQ   G      ++AP    V  +G
Sbjct: 448 ASAYPNMQPPFRPAPRGP-AQAALR-SSMGARPITGQQ--GVATASSIRAP---IVPQSG 500

Query: 179 RQTGGYNKYPVRN-PGTQPQAQIGGIQPAAAGVQAVHVQGQEPLTSTMLAAAQPQEQKQM 237
           R  G      +RN P  QP               AVH+QGQEPLT+TMLAAA  QEQKQM
Sbjct: 501 RPAGYKYTSNMRNPPAPQP---------------AVHIQGQEPLTTTMLAAAPLQEQKQM 545

Query: 238 LGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQAKQ 297
           LGERLFPLIQRM+P+LAGKITGMLLEIDN+ELL+MLEH ESLK+KV+EAVAVLQAHQAKQ
Sbjct: 546 LGERLFPLIQRMHPDLAGKITGMLLEIDNSELLHMLEHGESLKAKVDEAVAVLQAHQAKQ 605

Query: 298 AAVKKE 303
            A KK+
Sbjct: 606 QATKKD 611

Source: Papilio xuthus

Species: Papilio xuthus

Genus: Papilio

Family: Papilionidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|389610655|dbj|BAM18939.1| polyA-binding protein [Papilio polytes]

 Score =  384 bits (986), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 208/306 (67%), Positives = 235/306 (76%), Gaps = 25/306 (8%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           M EDGRSKGFGFVCFSSPEEATKAVTEMNGRI+G+KPLYVALAQRKEDRKAHL SQYMQR
Sbjct: 328 MLEDGRSKGFGFVCFSSPEEATKAVTEMNGRIVGTKPLYVALAQRKEDRKAHLTSQYMQR 387

Query: 61  IANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAPQMRPSGQT- 119
           +A+MRMQQMGQ+FQPG TGGYFVPT+P  QRFYGP QMTQIRP PRW A P +RP+ Q+ 
Sbjct: 388 MASMRMQQMGQIFQPGGTGGYFVPTIPPAQRFYGPAQMTQIRPSPRWTAQPAVRPNAQSA 447

Query: 120 AQGFPNI-PQFRSAPRASTGQTVIRGANMSARPITGQSTMGPRGGGPMQAPGPASVSAAG 178
           A  +PN+ P FR APR    Q  +R ++M ARPITGQ   G      ++AP    V  +G
Sbjct: 448 ASAYPNMQPPFRPAPRGP-AQAALR-SSMGARPITGQQ--GVATAASIRAP---IVPQSG 500

Query: 179 RQTGGYNKYPVRN-PGTQPQAQIGGIQPAAAGVQAVHVQGQEPLTSTMLAAAQPQEQKQM 237
           R  G      +RN P  QP               AVH+QGQEPLT+TMLAAA  QEQKQM
Sbjct: 501 RPAGYKYTSNMRNPPAPQP---------------AVHIQGQEPLTTTMLAAAPLQEQKQM 545

Query: 238 LGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQAKQ 297
           LGERLFPLIQRM+P+LAGKITGMLLEIDN+ELL+MLEH ESLK+KV+EAVAVLQAHQAKQ
Sbjct: 546 LGERLFPLIQRMHPDLAGKITGMLLEIDNSELLHMLEHGESLKAKVDEAVAVLQAHQAKQ 605

Query: 298 AAVKKE 303
            A KK+
Sbjct: 606 QATKKD 611

Source: Papilio polytes

Species: Papilio polytes

Genus: Papilio

Family: Papilionidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

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	303
UNIPROTKB|D4AC21	588	Pabpc4 "Protein Pabpc4" [Rattu	0.491	0.253	0.570	1.1e-67
UNIPROTKB|E1C903	630	PABPC4 "Uncharacterized protei	0.891	0.428	0.552	1.5e-67
ZFIN|ZDB-GENE-030131-9663	637	pabpc4 "poly(A) binding protei	0.897	0.427	0.542	1.1e-66
ZFIN|ZDB-GENE-030131-3238	634	pabpc1a "poly A binding protei	0.900	0.430	0.542	1.5e-65
UNIPROTKB|D4AC14	631	Pabpc4 "Protein Pabpc4" [Rattu	0.891	0.427	0.542	5.2e-65
UNIPROTKB|E2R9I0	631	PABPC4 "Uncharacterized protei	0.891	0.427	0.542	6.7e-65
UNIPROTKB|F1SV06	631	PABPC4 "Uncharacterized protei	0.891	0.427	0.542	8.5e-65
UNIPROTKB|Q13310	644	PABPC4 "Polyadenylate-binding	0.894	0.420	0.527	6.9e-63
ZFIN|ZDB-GENE-050308-1	634	pabpc1b "poly A binding protei	0.891	0.425	0.525	1.1e-62
UNIPROTKB|H0Y5F5	550	PABPC4 "Polyadenylate-binding	0.920	0.507	0.511	2.3e-62

UNIPROTKB|D4AC21 Pabpc4 "Protein Pabpc4" [Rattus norvegicus (taxid:10116)]

 Score = 417 (151.9 bits), Expect = 1.1e-67, Sum P(3) = 1.1e-67
 Identities = 93/163 (57%), Positives = 109/163 (66%)

Query:     1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
             M EDGRSKGFGFVCFSSPEEATKAVTEMNGRI+GSKPLYVALAQRKE+RKAHL +QYMQR
Sbjct:   255 MLEDGRSKGFGFVCFSSPEEATKAVTEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQR 314

Query:    61 IANMRMQQMGQL---FQPGSTGGYFVPTLPQPQR---FYGPTQMTQIRPQPRWAAAPQMR 114
             +A MR      +   FQP + GGYFVP +PQ Q    +Y P Q+ Q+RP PRW      R
Sbjct:   315 VAGMRALPANAILNQFQPAA-GGYFVPAVPQAQGRPPYYTPNQLAQMRPNPRWQQGG--R 371

Query:   115 PSGQTAQGFPNIPQFRSAPRASTGQTVIRGANMSAR--PITGQ 155
             P G   QG P+  + +S PR +       G   ++R  P T Q
Sbjct:   372 PQG--FQGMPSALR-QSGPRPALRHLAPTGNAPASRGLPTTAQ 411

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|E1C903 PABPC4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 686 (246.5 bits), Expect = 1.5e-67, P = 1.5e-67
 Identities = 163/295 (55%), Positives = 188/295 (63%)

Query:     1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
             M EDGRSKGFGFVCFSSPEEATKAVTEMNGRI+GSKPLYVALAQRKE+RKAHL +QYMQR
Sbjct:   326 MLEDGRSKGFGFVCFSSPEEATKAVTEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQR 385

Query:    61 IANMRMQQMGQL---FQPGSTGGYFVPTLPQPQR---FYGPTQMTQIRPQPRWAAAPQMR 114
             IA MR      +   FQP + GGYF+P +PQ Q    +Y P QM Q+RP PRW      R
Sbjct:   386 IAGMRALPANTIINQFQPAA-GGYFMPAVPQAQSRPTYYAPNQMAQMRPNPRWQQGG--R 442

Query:   115 PSGQTAQGFPNIPQFRSAPRASTGQTVIRGANMSAR--PITGQSTMGPRGGGPMQAPGPA 172
             P G   QG PN  + +S PR +       G   ++R  P++ Q  +G    G   AP P 
Sbjct:   443 PQG--FQGMPNAMR-QSGPRPALRHLAPAGTAPASRGLPVSAQR-VGVTTAGQSLAPRPP 498

Query:   173 SVSAAGRQTGGYNKYP--VRNPGTXXXXXXXXXXXXXXXXXXXXXXXXEPLTSTMLAAAQ 230
               + A R    Y KY   VR+P                          EPLT++MLAAA 
Sbjct:   499 VAAPAPRAVPPY-KYASSVRSPHPPVQPLQAPQPAVHVQGQ-------EPLTASMLAAAP 550

Query:   231 PQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEE 285
             PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ESL+SKVEE
Sbjct:   551 PQEQKQMLGERLFPLIQAMHPSLAGKITGMLLEIDNSELLHMLESPESLRSKVEE 605

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0008143 "poly(A) RNA binding" evidence=IEA

GO:0008266 "poly(U) RNA binding" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=IEA

ZFIN|ZDB-GENE-030131-9663 pabpc4 "poly(A) binding protein, cytoplasmic 4 (inducible form)" [Danio rerio (taxid:7955)]

 Score = 678 (243.7 bits), Expect = 1.1e-66, P = 1.1e-66
 Identities = 160/295 (54%), Positives = 185/295 (62%)

Query:     1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
             M E+GRSKGFGFVCFSSPEEATKAVTEMNGRI+GSKPLYVALAQRKE+RKAHL +QYMQR
Sbjct:   327 MLEEGRSKGFGFVCFSSPEEATKAVTEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQR 386

Query:    61 IANMRMQQMGQL---FQPGSTGGYFVPTLPQPQR---FYGPTQMTQIRPQPRWAAAPQMR 114
             IA MR      +   FQP   GGYF+P +PQ Q    +Y P Q+TQ+RP PRW    Q  
Sbjct:   387 IAGMRAMPANAIINQFQPA--GGYFMPAVPQAQNRTTYYAPNQLTQMRPNPRWQ---QQG 441

Query:   115 PSGQTA-QGFPNIPQFRSAPRASTGQTVIRGANMSARPI-TGQSTMGPRGGGPMQAPGPA 172
               GQ   QG P+  + +  PRA+        +N   R + TG   +G  G G    P PA
Sbjct:   442 GRGQGGFQGMPSSLR-QPGPRANIRHLAPNASNQGPRGMPTGAQRVG--GTGQPMGPRPA 498

Query:   173 SVSAAGRQTGGYNKYP--VRNPGTXXXXXXXXXXXXXXXXXXXXXXXXEPLTSTMLAAAQ 230
                   R    Y KY   +RN                           EPLT++MLAAA 
Sbjct:   499 MGMTTPRAMPPY-KYASTIRN----TQPQVVQPIALQQAQPAVHVQGQEPLTASMLAAAP 553

Query:   231 PQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEE 285
             PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE +ESL+SKVEE
Sbjct:   554 PQEQKQMLGERLFPLIQAMHPSLAGKITGMLLEIDNSELLHMLESHESLRSKVEE 608

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

ZFIN|ZDB-GENE-030131-3238 pabpc1a "poly A binding protein, cytoplasmic 1 a" [Danio rerio (taxid:7955)]

 Score = 667 (239.9 bits), Expect = 1.5e-65, P = 1.5e-65
 Identities = 160/295 (54%), Positives = 184/295 (62%)

Query:     1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
             M E GRSKGFGFVCFSSPEEATKAVTEMNGRI+ +KPLYVALAQRKE+R+AHL SQYMQR
Sbjct:   326 MMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTSQYMQR 385

Query:    61 IANMRMQQMGQL--FQPGSTGGYFVPTLPQPQR---FYGPTQMTQIRPQPRWAAAPQMRP 115
             +A++R      L  +QP    GYF+  +PQ Q    +Y  +Q+ Q+RP PRWA    +RP
Sbjct:   386 MASVRAVPNPVLNPYQPAPPSGYFMAAIPQAQNRAAYYPTSQLAQLRPSPRWATQG-VRP 444

Query:   116 SGQTAQGFPNIPQFRSAPRASTGQTVIRGANMSARPIT----GQSTMGPRGGGPMQAPGP 171
               Q  Q  PN     SAPR  T   V R A+   R +T    G   MGPR      A GP
Sbjct:   445 --QHFQNMPNAAVRPSAPRPQTFNPV-RPASQVPRMMTSQRMGSQAMGPRPAAAGAATGP 501

Query:   172 ASVSAAGRQTGGYNKYP-VRNPGTXXXXXXXXXXXXXXXXXXXXXXXXEPLTSTMLAAAQ 230
             A V    R    Y   P VRNP                          EPLT++MLAAA 
Sbjct:   502 AQV----RGVPQYKYAPGVRNP----QQRMPTQPQVPMQQPAVHVQGQEPLTASMLAAAP 553

Query:   231 PQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEE 285
             PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ESL+SKV+E
Sbjct:   554 PQEQKQMLGERLFPLIQNMHPSLAGKITGMLLEIDNSELLHMLESPESLRSKVDE 608

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0007507 "heart development" evidence=IMP

UNIPROTKB|D4AC14 Pabpc4 "Protein Pabpc4" [Rattus norvegicus (taxid:10116)]

 Score = 662 (238.1 bits), Expect = 5.2e-65, P = 5.2e-65
 Identities = 160/295 (54%), Positives = 186/295 (63%)

Query:     1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
             M EDGRSKGFGFVCFSSPEEATKAVTEMNGRI+GSKPLYVALAQRKE+RKAHL +QYMQR
Sbjct:   326 MLEDGRSKGFGFVCFSSPEEATKAVTEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQR 385

Query:    61 IANMRMQQMGQL---FQPGSTGGYFVPTLPQPQR---FYGPTQMTQIRPQPRWAAAPQMR 114
             +A MR      +   FQP + GGYFVP +PQ Q    +Y P Q+ Q+RP PRW      R
Sbjct:   386 VAGMRALPANAILNQFQPAA-GGYFVPAVPQAQGRPPYYTPNQLAQMRPNPRWQQGG--R 442

Query:   115 PSGQTAQGFPNIPQFRSAPRASTGQTVIRGANMSAR--PITGQSTMGPRGGGPMQAPGPA 172
             P G   QG P+  + +S PR +       G   ++R  P T Q  +G     P  AP   
Sbjct:   443 PQG--FQGMPSALR-QSGPRPALRHLAPTGNAPASRGLPTTAQR-VGVPTAVPNLAPRAT 498

Query:   173 SVSAAGRQTGGYNKYP--VRNPGTXXXXXXXXXXXXXXXXXXXXXXXXEPLTSTMLAAAQ 230
               +AA R    Y KY   VR+P                          EPLT++MLAAA 
Sbjct:   499 VAAAAPRAVAPY-KYASNVRSPHPAIQPLQAPQPAVHVQGQ-------EPLTASMLAAAP 550

Query:   231 PQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEE 285
             PQEQKQMLGERLFPLIQ M+  LAGKITGMLLEIDN+ELL+MLE  ESL+SKV+E
Sbjct:   551 PQEQKQMLGERLFPLIQTMHSNLAGKITGMLLEIDNSELLHMLESPESLRSKVDE 605

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|E2R9I0 PABPC4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 661 (237.7 bits), Expect = 6.7e-65, P = 6.7e-65
 Identities = 160/295 (54%), Positives = 186/295 (63%)

Query:     1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
             M EDGRSKGFGFVCFSSPEEATKAVTEMNGRI+GSKPLYVALAQRKE+RKAHL +QYMQR
Sbjct:   326 MLEDGRSKGFGFVCFSSPEEATKAVTEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQR 385

Query:    61 IANMRMQQMGQL---FQPGSTGGYFVPTLPQPQR---FYGPTQMTQIRPQPRWAAAPQMR 114
             +A MR      +   FQP + GGYFVP +PQ Q    +Y P Q+ Q+RP PRW      R
Sbjct:   386 VAGMRALPANAILNQFQPAA-GGYFVPAVPQAQGRPPYYTPNQLAQMRPNPRWQQGG--R 442

Query:   115 PSGQTAQGFPNIPQFRSAPRASTGQTVIRGANMSAR--PITGQSTMGPRGGGPMQAPGPA 172
             P G   QG P+  + +S PR +       G   ++R  P T Q    P     + AP  A
Sbjct:   443 PQG--FQGMPSAIR-QSGPRPALRHLAPTGNAPASRGLPTTAQRVGVPTAVQTL-APRAA 498

Query:   173 SVSAAGRQTGGYNKYP--VRNPGTXXXXXXXXXXXXXXXXXXXXXXXXEPLTSTMLAAAQ 230
               +AA R    Y KY   VR+P                          EPLT++MLAAA 
Sbjct:   499 VAAAAPRAVAPY-KYASSVRSPHPAIQPLQAPQPAVHVQGQ-------EPLTASMLAAAP 550

Query:   231 PQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEE 285
             PQEQKQMLGERLFPLIQ M+  LAGKITGMLLEIDN+ELL+MLE  ESL+SKV+E
Sbjct:   551 PQEQKQMLGERLFPLIQTMHSNLAGKITGMLLEIDNSELLHMLESPESLRSKVDE 605

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0008266 "poly(U) RNA binding" evidence=IEA

GO:0008143 "poly(A) RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1SV06 PABPC4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 660 (237.4 bits), Expect = 8.5e-65, P = 8.5e-65
 Identities = 160/295 (54%), Positives = 186/295 (63%)

Query:     1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
             M EDGRSKGFGFVCFSSPEEATKAVTEMNGRI+GSKPLYVALAQRKE+RKAHL +QYMQR
Sbjct:   326 MLEDGRSKGFGFVCFSSPEEATKAVTEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQR 385

Query:    61 IANMRMQQMGQL---FQPGSTGGYFVPTLPQPQR---FYGPTQMTQIRPQPRWAAAPQMR 114
             +A MR      +   FQP + GGYFVP +PQ Q    +Y P Q+ Q+RP PRW      R
Sbjct:   386 VAGMRALPANAILNQFQPAA-GGYFVPAVPQAQGRPPYYTPNQLAQMRPNPRWQQGG--R 442

Query:   115 PSGQTAQGFPNIPQFRSAPRASTGQTVIRGANMSAR--PITGQSTMGPRGGGPMQAPGPA 172
             P G   QG P+  + +S PR +       G   ++R  P T Q    P     + AP  A
Sbjct:   443 PQG--FQGMPSAIR-QSGPRPALRHLAPTGNAPASRGLPTTAQRVGVPTAVQNL-APRAA 498

Query:   173 SVSAAGRQTGGYNKYP--VRNPGTXXXXXXXXXXXXXXXXXXXXXXXXEPLTSTMLAAAQ 230
               +AA R    Y KY   VR+P                          EPLT++MLAAA 
Sbjct:   499 VATAAPRAVAPY-KYASSVRSPHPAIQPLQAPQPAVHVQGQ-------EPLTASMLAAAP 550

Query:   231 PQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEE 285
             PQEQKQMLGERLFPLIQ M+  LAGKITGMLLEIDN+ELL+MLE  ESL+SKV+E
Sbjct:   551 PQEQKQMLGERLFPLIQTMHSNLAGKITGMLLEIDNSELLHMLESPESLRSKVDE 605

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0008266 "poly(U) RNA binding" evidence=IEA

GO:0008143 "poly(A) RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q13310 PABPC4 "Polyadenylate-binding protein 4" [Homo sapiens (taxid:9606)]

 Score = 642 (231.1 bits), Expect = 6.9e-63, P = 6.9e-63
 Identities = 162/307 (52%), Positives = 188/307 (61%)

Query:     1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
             M EDGRSKGFGFVCFSSPEEATKAVTEMNGRI+GSKPLYVALAQRKE+RKAHL +QYMQR
Sbjct:   326 MLEDGRSKGFGFVCFSSPEEATKAVTEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQR 385

Query:    61 IANMRMQQMGQL---FQPGSTGGYFVPTLPQPQR---FYGPTQMTQIRPQPRWAAAPQMR 114
             +A MR      +   FQP + GGYFVP +PQ Q    +Y P Q+ Q+RP PRW      R
Sbjct:   386 VAGMRALPANAILNQFQPAA-GGYFVPAVPQAQGRPPYYTPNQLAQMRPNPRWQQGG--R 442

Query:   115 PSGQTAQGFPNIPQFRSAPRASTGQTVIRGANMSARPI-----TGQSTMG-----PRGGG 164
             P G   QG P+  + +S PR +       G+    R        G +  G       GG 
Sbjct:   443 PQG--FQGMPSAIR-QSGPRPTLRHLAPTGSECPDRLAMDFGGAGAAQQGLTDSCQSGGV 499

Query:   165 P--MQ--APGPASVSAAGRQTGGYNKYP--VRNPGTXXXXXXXXXXXXXXXXXXXXXXXX 218
             P  +Q  AP  A  +AA R    Y KY   VR+P                          
Sbjct:   500 PTAVQNLAPRAAVAAAAPRAVAPY-KYASSVRSPHPAIQPLQAPQPAVHVQGQ------- 551

Query:   219 EPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNES 278
             EPLT++MLAAA PQEQKQMLGERLFPLIQ M+  LAGKITGMLLEIDN+ELL+MLE  ES
Sbjct:   552 EPLTASMLAAAPPQEQKQMLGERLFPLIQTMHSNLAGKITGMLLEIDNSELLHMLESPES 611

Query:   279 LKSKVEE 285
             L+SKV+E
Sbjct:   612 LRSKVDE 618

GO:0000166 "nucleotide binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0008143 "poly(A) RNA binding" evidence=IDA

GO:0008266 "poly(U) RNA binding" evidence=IDA

GO:0010494 "cytoplasmic stress granule" evidence=IDA

GO:0017130 "poly(C) RNA binding" evidence=IDA

GO:0006401 "RNA catabolic process" evidence=TAS

GO:0006396 "RNA processing" evidence=TAS

GO:0006412 "translation" evidence=TAS

GO:0007596 "blood coagulation" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

ZFIN|ZDB-GENE-050308-1 pabpc1b "poly A binding protein, cytoplasmic 1 b" [Danio rerio (taxid:7955)]

 Score = 640 (230.4 bits), Expect = 1.1e-62, P = 1.1e-62
 Identities = 156/297 (52%), Positives = 186/297 (62%)

Query:     1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
             M + GRSKGFGFVCFSSPEEATKAVTEMNGRI+ +KPLYVALAQRKE+R+AHL +QYMQR
Sbjct:   326 MMDGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQR 385

Query:    61 IANMRMQQMGQL--FQPGSTGGYFVPTLPQPQR---FYGPTQMTQIRPQPRWAAAPQMRP 115
             +A++R      +  +QP    GYF+  +PQ Q    +Y  +Q+ Q+RP PRW     +RP
Sbjct:   386 MASVRAVPNPVINPYQPAPPSGYFMAAIPQAQNRAAYYPTSQLAQLRPSPRWTTQG-VRP 444

Query:   116 SGQTAQGFPNIP-QFR-SAPRASTGQTVIRGANMSARPITGQ----STMGPRGGGPMQAP 169
                  Q F N+P   R SAPR  T  T+ R A+   R ++ Q     TMGPR   P  A 
Sbjct:   445 -----QHFQNMPGTMRPSAPRPQTFSTM-RPASQVPRMMSTQRVATQTMGPR---PSTAA 495

Query:   170 GPASVSAAGRQTGGYNKYP-VRNPGTXXXXXXXXXXXXXXXXXXXXXXXXEPLTSTMLAA 228
               AS     R    Y   P VRNP                          EPLT++MLAA
Sbjct:   496 AAASAPPV-RGVPQYKYAPSVRNP----QQHMNTQPQVTMQQPAVHVQGQEPLTASMLAA 550

Query:   229 AQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEE 285
             A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ESL+SKV+E
Sbjct:   551 APPQEQKQMLGERLFPLIQNMHPSLAGKITGMLLEIDNSELLHMLESPESLRSKVDE 607

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|H0Y5F5 PABPC4 "Polyadenylate-binding protein 4" [Homo sapiens (taxid:9606)]

 Score = 637 (229.3 bits), Expect = 2.3e-62, P = 2.3e-62
 Identities = 155/303 (51%), Positives = 181/303 (59%)

Query:     1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
             M EDGRSKGFGFVCFSSPEEATKAVTEMNGRI+GSKPLYVALAQRKE+RKAHL +QYMQR
Sbjct:   228 MLEDGRSKGFGFVCFSSPEEATKAVTEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQR 287

Query:    61 IANMRMQQMGQL---FQPGSTGGYFVPTLPQPQR---FYGPTQMTQIRPQPRWAAAPQMR 114
             +A MR      +   FQP + GGYFVP +PQ Q    +Y P Q+ Q+RP PRW      R
Sbjct:   288 VAGMRALPANAILNQFQPAA-GGYFVPAVPQAQGRPPYYTPNQLAQMRPNPRWQQGG--R 344

Query:   115 PSGQTAQGFPNIPQFRSAPR------ASTGQT-VIRGANMSARPITGQS----TMGPRGG 163
             P G   QG P+  + +S PR      A TG     RG   + + +  +      M   G 
Sbjct:   345 PQG--FQGMPSAIR-QSGPRPTLRHLAPTGNAPASRGLPTTTQRVGSECPDRLAMDFGGA 401

Query:   164 GPMQAPGPASVSAAGRQTGGYNKYP-VRNPGTXXXXXXXXXXXXXXXXXXXXXXXXEPLT 222
             G  Q     S  + G  T   N  P                               +PLT
Sbjct:   402 GAAQQGLTDSCQSGGVPTAVQNLAPRAAVAAAAPRAVAPYKYASSVRSPHPAIQPLQPLT 461

Query:   223 STMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSK 282
             ++MLAAA PQEQKQMLGERLFPLIQ M+  LAGKITGMLLEIDN+ELL+MLE  ESL+SK
Sbjct:   462 ASMLAAAPPQEQKQMLGERLFPLIQTMHSNLAGKITGMLLEIDNSELLHMLESPESLRSK 521

Query:   283 VEE 285
             V+E
Sbjct:   522 VDE 524

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

---

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)
Q13310	PABP4_HUMAN	No assigned EC number	0.5487	0.9372	0.4409	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	303
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-72
pfam00658	72	pfam00658, PABP, Poly-adenylate binding protein, u	1e-38
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	3e-30
smart00517	64	smart00517, PolyA, C-terminal domain of Poly(A)-bi	1e-28
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-18
smart00360	73	smart00360, RRM, RNA recognition motif	2e-11
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	6e-11
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	7e-11
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	3e-10
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-09
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	2e-09
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	5e-09
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	6e-09
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	7e-09
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-08
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	2e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-08
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	3e-08
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	4e-08
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	6e-08
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	7e-08
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	8e-08
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	9e-08
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	2e-07
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-07
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	3e-07
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	4e-07
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-07
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	9e-07
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	9e-07
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	9e-07
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	9e-07
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	1e-06
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	3e-06
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	3e-06
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	6e-06
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	9e-06
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	9e-06
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-05
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	2e-05
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-05
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	2e-05
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	3e-05
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	3e-05
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	3e-05
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	3e-05
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	4e-05
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	4e-05
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	5e-05
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	5e-05
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	8e-05
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	9e-05
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-04
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	1e-04
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	1e-04
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	1e-04
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	1e-04
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	1e-04
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	2e-04
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	3e-04
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	3e-04
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	3e-04
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	3e-04
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	3e-04
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	4e-04
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	4e-04
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	4e-04
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	5e-04
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	5e-04
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	5e-04
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	5e-04
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	6e-04
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	7e-04
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	8e-04
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	0.001
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	0.001
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	0.001
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	0.001
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	0.001
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.002
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	0.002
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	0.002
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	0.002
cd12374	85	cd12374, RRM_UHM_SPF45_PUF60, RNA recognition moti	0.002
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	0.002
cd12647	96	cd12647, RRM_UHM_SPF45, RNA recognition motif in U	0.002
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	0.002
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	0.002
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	0.002
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	0.002
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	0.002
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	0.002
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	0.002
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	0.002
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.003
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	0.003
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	0.003
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	0.003
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	0.003
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	0.003
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	0.003
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	0.003
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	0.003
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	0.004
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	0.004
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	0.004
cd12515	75	cd12515, RRM5_RBM12_like, RNA recognition motif 5	0.004
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	0.004
cd12439	79	cd12439, RRM_TRMT2A, RNA recognition motif in tRNA	0.004

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

 Score =  231 bits (590), Expect = 6e-72
 Identities = 113/291 (38%), Positives = 144/291 (49%), Gaps = 47/291 (16%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           + E G S+GFGFVCFS+PEEA +AVTEM+GR++G KPLYVALAQRKE R+AHL  Q+MQ 
Sbjct: 319 LDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQFMQL 378

Query: 61  IANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAPQMRPSGQTA 120
              MR   MG     G+ G         P    GP Q    +P      +    P G   
Sbjct: 379 QPRMRQLPMGSPM-GGAMG-------QPPYYGQGPQQQFNGQPLGWPRMSMMPTPMGPGG 430

Query: 121 QGFPNIPQFRSAPRASTGQTVIRGANMSARPITGQSTMGPRGGGPMQAPGPASVSAAGRQ 180
              PN      AP  +                  Q+        P+  P           
Sbjct: 431 PLRPNGL----APMNAVRAP----------SRNAQNAAQKPPMQPVMYPP---------- 466

Query: 181 TGGYNKYPVRNPGTQPQAQIGGIQPAAAGVQAVHVQGQEPLTSTMLAAAQPQEQKQMLGE 240
              Y   P+     QPQ+                  GQ    + +LA+A PQ QKQ+LGE
Sbjct: 467 --NYQSLPLSQDLPQPQS-------------TASQGGQNKKLAQVLASATPQMQKQVLGE 511

Query: 241 RLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQ 291
           RLFPL++ + P LA KITGMLLE+DN+ELL++LE  E LKSKV+EA+ VL+
Sbjct: 512 RLFPLVEAIEPALAAKITGMLLEMDNSELLHLLESPELLKSKVDEALEVLK 562

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|201378 pfam00658, PABP, Poly-adenylate binding protein, unique domain

 Score =  130 bits (330), Expect = 1e-38
 Identities = 55/72 (76%), Positives = 68/72 (94%)

Query: 219 EPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNES 278
           EPLT++ LAAA PQEQKQMLGERL+PLIQ M+PELAGKITGMLLE+DN+ELL++LE +E+
Sbjct: 1   EPLTASALAAAPPQEQKQMLGERLYPLIQAMHPELAGKITGMLLEMDNSELLHLLESDEA 60

Query: 279 LKSKVEEAVAVL 290
           LK+KV+EA+AVL
Sbjct: 61  LKAKVDEALAVL 72

The region featured in this family is found towards the C-terminus of poly(A)-binding proteins (PABPs). These are eukaryotic proteins that, through their binding of the 3' poly(A) tail on mRNA, have very important roles in the pathways of gene expression. They seem to provide a scaffold on which other proteins can bind and mediate processes such as export, translation and turnover of the transcripts. Moreover, they may act as antagonists to the binding of factors that allow mRNA degradation, regulating mRNA longevity. PABPs are also involved in nuclear transport. PABPs interact with poly(A) tails via RNA-recognition motifs (pfam00076). Note that the PABP C-terminal region is also found in members of the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains - these are also included in this family. Length = 72

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

 Score =  108 bits (273), Expect = 3e-30
 Identities = 41/43 (95%), Positives = 41/43 (95%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR 45
          E GRSKGFGFVCFSSPEEATKAVTEMNGRIIG KPLYVALAQR
Sbjct: 37 EKGRSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVALAQR 79

This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 79

>gnl|CDD|197769 smart00517, PolyA, C-terminal domain of Poly(A)-binding protein

 Score =  104 bits (261), Expect = 1e-28
 Identities = 42/63 (66%), Positives = 55/63 (87%)

Query: 231 PQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVL 290
           PQEQKQ LGERL+P +Q + PELAGKITGMLLE+DN+ELL++LE  E L++KV+EA+ VL
Sbjct: 2   PQEQKQALGERLYPKVQALEPELAGKITGMLLEMDNSELLHLLESPELLRAKVDEALEVL 61

Query: 291 QAH 293
           ++H
Sbjct: 62  KSH 64

Present also in Drosophila hyperplastics discs protein. Involved in homodimerisation (either directly or indirectly). Length = 64

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

 Score = 77.6 bits (192), Expect = 2e-18
 Identities = 24/44 (54%), Positives = 32/44 (72%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
          ++G+SKGFGFV F + E A KAV E+NG+ +  K LYV  AQ+K
Sbjct: 37 DEGKSKGFGFVNFENHEAAQKAVEELNGKEVNGKKLYVGRAQKK 80

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

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

 Score = 58.8 bits (143), Expect = 2e-11
 Identities = 19/38 (50%), Positives = 26/38 (68%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYV 40
          E G+SKGF FV F S E+A KA+  +NG+ +  +PL V
Sbjct: 36 ETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

Length = 73

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

 Score = 57.2 bits (139), Expect = 6e-11
 Identities = 16/39 (41%), Positives = 27/39 (69%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVA 41
          E+G SKG+GFV F + E A +A+ ++NG ++  K ++V 
Sbjct: 38 ENGGSKGYGFVHFETEEAAVRAIEKVNGMLLNDKKVFVG 76

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

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

 Score = 56.9 bits (138), Expect = 7e-11
 Identities = 19/40 (47%), Positives = 27/40 (67%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYV 40
            +DG+SKGF FV F SPE+A KA+  +NG+ +  + L V
Sbjct: 32 RDKDGKSKGFAFVEFESPEDAEKALEALNGKELDGRKLKV 71

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

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

 Score = 55.3 bits (134), Expect = 3e-10
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPL 38
          G+SKG+GFV FS P +  KA+ EMNG+ +G++P+
Sbjct: 45 GKSKGYGFVSFSDPNDYLKAMKEMNGKYVGNRPI 78

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

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

 Score = 53.4 bits (129), Expect = 1e-09
 Identities = 18/37 (48%), Positives = 24/37 (64%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLY 39
          E GRSKGF FV F   E+A KA+  +NG+ +G + L 
Sbjct: 34 ETGRSKGFAFVEFEDEEDAEKALEALNGKELGGRELR 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|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 20/39 (51%), Positives = 27/39 (69%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
          GRSKG+GFV F   +E  +A+TEMNG    S+P+ V+ A
Sbjct: 41 GRSKGYGFVRFGDEDERDRALTEMNGVYCSSRPMRVSPA 79

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

>gnl|CDD|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 = 51.9 bits (125), Expect = 5e-09
 Identities = 18/36 (50%), Positives = 23/36 (63%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYV 40
          G+SK FGFV + +PE A  A+  MNG  +G K L V
Sbjct: 37 GQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRLKV 72

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

 Score = 55.7 bits (133), Expect = 6e-09
 Identities = 32/133 (24%), Positives = 49/133 (36%), Gaps = 12/133 (9%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ-----RKEDRKAHLASQY 57
           E G+S+GF FV F S E A KA+ E+NG+ +  +PL V  AQ     R E      AS  
Sbjct: 152 ETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFA 211

Query: 58  MQ--RIANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAPQMRP 115
            +  R   + +++   L+            L    +  G      + P           P
Sbjct: 212 KKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSK-----DGKIP 266

Query: 116 SGQTAQGFPNIPQ 128
             ++  G      
Sbjct: 267 KSRSFVGNEASKD 279

Length = 306

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

 Score = 51.5 bits (124), Expect = 7e-09
 Identities = 17/41 (41%), Positives = 27/41 (65%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR 45
          G S+GFGFV F S E+A  A+ ++NG+ +  + + V  A+R
Sbjct: 40 GESRGFGFVTFESVEDADAAIRDLNGKELEGRVIKVEKAKR 80

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

 Score = 50.5 bits (121), Expect = 1e-08
 Identities = 19/41 (46%), Positives = 29/41 (70%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
          E GRS+GFG+V F SPE+A KA+  M+G+ +  +P+ V  +
Sbjct: 36 ETGRSRGFGYVDFESPEDAKKAIEAMDGKELDGRPINVDFS 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|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 50.0 bits (120), Expect = 2e-08
 Identities = 19/40 (47%), Positives = 24/40 (60%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYV 40
             DGRSKGFG V F SPE+A +A+   NG  +  + L V
Sbjct: 32 TDNDGRSKGFGTVLFESPEDAQRAIEMFNGYDLEGRELEV 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 54.4 bits (131), Expect = 3e-08
 Identities = 19/57 (33%), Positives = 34/57 (59%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQY 57
             E+G+S+G+GFV F   E A  A+ ++NG ++  K +YV    +K +R+A    ++
Sbjct: 122 TDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLKKF 178

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

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

 Score = 49.6 bits (119), Expect = 3e-08
 Identities = 19/46 (41%), Positives = 27/46 (58%), Gaps = 1/46 (2%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
            +DGRSKGFG V F++ E A KA  E +G  +  + + V LA  +
Sbjct: 33 QDDDGRSKGFGHVEFATEEGAQKA-LEKSGEELLGREIRVDLATER 77

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

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

 Score = 49.0 bits (117), Expect = 4e-08
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPL 38
          GRS+G+GFV F S ++A  A+ EMNG+ +GS+P+
Sbjct: 38 GRSRGYGFVSFRSQQDAENAINEMNGKWLGSRPI 71

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

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

 Score = 48.8 bits (117), Expect = 6e-08
 Identities = 19/42 (45%), Positives = 26/42 (61%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ 44
          E GRS+GFGFV   + EEA  A+ ++NG   G + L V  A+
Sbjct: 36 ETGRSRGFGFVEMETAEEANAAIEKLNGTDFGGRTLTVNEAR 77

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|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 48.8 bits (117), Expect = 7e-08
 Identities = 20/44 (45%), Positives = 30/44 (68%), Gaps = 1/44 (2%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNG-RIIGSKPLYVALA 43
          + ++G S+G+GFV FS   E  +A+TEM G   +G KP+ V+LA
Sbjct: 36 LDQNGNSRGYGFVRFSDESEQKRALTEMQGASGLGGKPIRVSLA 79

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 48.4 bits (116), Expect = 8e-08
 Identities = 18/40 (45%), Positives = 24/40 (60%)

Query: 4  DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
          DG+S+ FGFV F S E+A +AV   N   I +  + V LA
Sbjct: 37 DGKSRRFGFVGFKSEEDAQQAVKYFNKTFIDTSKISVELA 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|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 48.1 bits (115), Expect = 9e-08
 Identities = 15/34 (44%), Positives = 23/34 (67%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPL 38
          G+SKG+GFV F   E+A  A+  MNG+ +G + +
Sbjct: 38 GKSKGYGFVSFVKKEDAENAIQSMNGQWLGGRAI 71

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

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

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 16/45 (35%), Positives = 29/45 (64%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE 47
          + G SKGF F+ + S E +  A+  MNG+ + ++P+ V+ A +K+
Sbjct: 39 DTGNSKGFAFISYDSFEASDAAIEAMNGQYLCNRPITVSYAFKKD 83

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

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

 Score = 46.9 bits (112), Expect = 3e-07
 Identities = 17/39 (43%), Positives = 27/39 (69%)

Query: 2  SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYV 40
           E GRSKG+GF+ F+  E+A KA+ ++NG  +  +P+ V
Sbjct: 34 PETGRSKGYGFIQFADAEDAKKALEQLNGFELAGRPIKV 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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 46.4 bits (111), Expect = 3e-07
 Identities = 17/38 (44%), Positives = 23/38 (60%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
          +  GF FV FS+ E A KAV  +NG + G +PL V  +
Sbjct: 19 KKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 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|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 46.6 bits (111), Expect = 4e-07
 Identities = 15/36 (41%), Positives = 22/36 (61%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPL 38
          + GR KGFG+V FSS E A  A+  + G  +  +P+
Sbjct: 35 DSGRPKGFGYVEFSSQEAAQAALDALGGTDLLGRPV 70

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

>gnl|CDD|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 = 46.5 bits (111), Expect = 4e-07
 Identities = 19/39 (48%), Positives = 24/39 (61%)

Query: 2  SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYV 40
           E  RSKGF FV F  PE A KA +E++G I   + L+V
Sbjct: 35 KETKRSKGFAFVSFMFPEHAVKAYSELDGSIFQGRLLHV 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|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 45.7 bits (109), Expect = 9e-07
 Identities = 13/43 (30%), Positives = 25/43 (58%)

Query: 4  DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
            + +GFG+V F+  E+A +A+ E      G + ++V  A++K
Sbjct: 37 SKKCRGFGYVTFALEEDAKRALEEKKKTKFGGRKIHVEFAKKK 79

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

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

 Score = 45.7 bits (109), Expect = 9e-07
 Identities = 16/39 (41%), Positives = 23/39 (58%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
          G+ +G+ FV F + EEA KA+  +NG+    K L V  A
Sbjct: 41 GQPRGYCFVTFETKEEAEKALKSLNGKTALGKKLVVRWA 79

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

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

 Score = 45.4 bits (108), Expect = 9e-07
 Identities = 16/39 (41%), Positives = 24/39 (61%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
          G+S G+GFV +    +A KA+  +NG  I +K L V+ A
Sbjct: 39 GQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRLKVSYA 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|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 45.6 bits (109), Expect = 9e-07
 Identities = 15/30 (50%), Positives = 23/30 (76%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNG 30
          + E G++KG+ FV F++PEEA +AV  +NG
Sbjct: 43 VDETGKTKGYAFVEFATPEEAKEAVKALNG 72

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

 Score = 44.9 bits (107), Expect = 1e-06
 Identities = 18/40 (45%), Positives = 26/40 (65%)

Query: 4  DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
          DG+ KGF FV F+S  +A KA+  +NG+ I  +P+ V  A
Sbjct: 36 DGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGRPVAVDWA 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|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 44.2 bits (105), Expect = 3e-06
 Identities = 17/39 (43%), Positives = 25/39 (64%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
          G SKG+GFV ++S   A KA  +++G+ IG + L V  A
Sbjct: 38 GESKGYGFVEYASKASALKAKNQLDGKQIGGRKLQVDWA 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|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family

 Score = 43.7 bits (104), Expect = 3e-06
 Identities = 14/40 (35%), Positives = 23/40 (57%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVAL 42
            GRS+G   V F   E+A +A+ + NG ++  +P+ V L
Sbjct: 36 RSGRSEGTADVVFEKREDAERAIKQFNGVLLDGQPMQVEL 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|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 43.0 bits (102), Expect = 6e-06
 Identities = 15/31 (48%), Positives = 19/31 (61%)

Query: 8  KGFGFVCFSSPEEATKAVTEMNGRIIGSKPL 38
          KG+GFV F + E+A  AV   NGR I  + L
Sbjct: 35 KGYGFVQFDNEEDARAAVAGENGREIAGQKL 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|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 = 42.6 bits (101), Expect = 9e-06
 Identities = 14/41 (34%), Positives = 20/41 (48%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
          + G+ KG+GF  F   E A  A+  +NG     + L V  A
Sbjct: 35 DTGKPKGYGFCEFEDIETAASAIRNLNGYEFNGRALRVDFA 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|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 42.7 bits (101), Expect = 9e-06
 Identities = 14/37 (37%), Positives = 25/37 (67%)

Query: 4  DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYV 40
          +G+S+G G V F  P EA +A++  NG+++  +P+ V
Sbjct: 35 EGKSRGMGVVQFEHPIEAVQAISMFNGQMLFDRPMRV 71

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

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

 Score = 46.0 bits (109), Expect = 1e-05
 Identities = 21/55 (38%), Positives = 28/55 (50%)

Query: 2   SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQ 56
            E GRSKGFGF+ F   EEA +A+  MNG  +  +P+ V  AQ          + 
Sbjct: 222 PETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAANTF 276

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

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 15/36 (41%), Positives = 23/36 (63%)

Query: 8  KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
          K + FV F   ++A KA+ EMNG+ +   P+ V+LA
Sbjct: 35 KDYAFVHFEERDDAVKAMEEMNGKELEGSPIEVSLA 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|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 42.1 bits (99), Expect = 2e-05
 Identities = 15/39 (38%), Positives = 24/39 (61%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
          G S+G+GFV FS   +  +A+ EM G   G +P+ ++ A
Sbjct: 41 GVSRGYGFVRFSDENDQQRALIEMQGVYCGGRPMRISTA 79

This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 80

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

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 11/33 (33%), Positives = 18/33 (54%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPL 38
          + KG+ FV F + E A  A+  +NG  I  + +
Sbjct: 34 KDKGYAFVRFDTHEAAATAIVAVNGTSINGQTV 66

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

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 14/41 (34%), Positives = 25/41 (60%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR 45
           RS G+ +V F +P +A +A+  +N  +I  KP+ +  +QR
Sbjct: 38 RRSLGYAYVNFQNPADAERALDTLNFDVIKGKPIRIMWSQR 78

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

 Score = 41.2 bits (97), Expect = 3e-05
 Identities = 17/39 (43%), Positives = 25/39 (64%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
          G S GFGFV + S E+A +A+  +NG  + +K + VA A
Sbjct: 39 GYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRIKVAYA 77

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

>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 41.1 bits (96), Expect = 3e-05
 Identities = 15/40 (37%), Positives = 28/40 (70%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVAL 42
          +DG+S+G G V F  P EA +A++  NG+++  +P++V +
Sbjct: 36 KDGKSRGIGTVTFEQPIEAVQAISMFNGQLLFDRPMHVKM 75

This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

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

 Score = 41.0 bits (97), Expect = 3e-05
 Identities = 13/29 (44%), Positives = 21/29 (72%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGR 31
          E G+S+GF FV F + E+A +A+ ++NG 
Sbjct: 36 ETGQSRGFAFVTFHTREDAERAIEKLNGF 64

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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 44.6 bits (105), Expect = 3e-05
 Identities = 32/96 (33%), Positives = 44/96 (45%), Gaps = 7/96 (7%)

Query: 5   GRSKGFGFVCFSSPEEATKAVTEMNGRII--GSKPLYVALAQRKEDRKAHLASQYMQRIA 62
           G  +G  FV F+  EEA +A++ +N  I   GS+PL V LA+     KAH    YM ++ 
Sbjct: 232 GTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGKAKAH---HYMSQMG 288

Query: 63  NMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQM 98
           +  M  MG      + G       P P  F G   M
Sbjct: 289 HGNMGNMGHGNMGMAGGS--GMNPPNPPAFMGMNNM 322

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

>gnl|CDD|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 = 41.0 bits (96), Expect = 4e-05
 Identities = 17/43 (39%), Positives = 27/43 (62%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR 45
          E  RS+GFGFV F +P++A  A+  MNG+ +  + + V  A +
Sbjct: 37 ETQRSRGFGFVTFENPDDAKDAMMAMNGKSVDGRQIRVDQAGK 79

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

 Score = 40.6 bits (96), Expect = 4e-05
 Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 4/36 (11%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTE----MNGRIIGSK 36
          GRS+GFGFV F+ P    K +      ++GR I  K
Sbjct: 37 GRSRGFGFVTFADPSSVDKVLAAKPHVLDGREIDPK 72

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

>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 16/38 (42%), Positives = 21/38 (55%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYV 40
            G+ K FGF  F  PE A +A+  +NG  +G K L V
Sbjct: 37 STGKLKAFGFCEFEDPEGALRALRLLNGLELGGKKLLV 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 = 40.5 bits (95), Expect = 5e-05
 Identities = 16/39 (41%), Positives = 26/39 (66%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
          G+S G+GFV +  PE+A KA+  +NG  + +K + V+ A
Sbjct: 40 GQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKTIKVSYA 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|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 39.9 bits (94), Expect = 8e-05
 Identities = 15/40 (37%), Positives = 23/40 (57%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR 45
          + K  GFV F   E A +A+ E+NG  +    L V+LA++
Sbjct: 36 KEKNCGFVTFEKMESADRAIAELNGTTVQGVQLKVSLARK 75

This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif. . Length = 75

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

 Score = 39.9 bits (94), Expect = 9e-05
 Identities = 17/33 (51%), Positives = 22/33 (66%), Gaps = 1/33 (3%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNG-RIIGSK 36
          GRS+GFGFV F S E+A +A   +NG  I G +
Sbjct: 38 GRSRGFGFVYFESVEDAKEAKERLNGMEIDGRR 70

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

 Score = 41.6 bits (97), Expect = 1e-04
 Identities = 18/44 (40%), Positives = 28/44 (63%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
           E GRS+GFGFV F+    AT A++EM+G+ +  + + V  A  +
Sbjct: 71  ETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDR 114

Length = 144

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

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 15/30 (50%), Positives = 20/30 (66%)

Query: 2  SEDGRSKGFGFVCFSSPEEATKAVTEMNGR 31
           +  + KG+GFV F SPE A KA+  +NGR
Sbjct: 36 KKTNKCKGYGFVDFDSPEAALKAIEGLNGR 65

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 12/41 (29%), Positives = 26/41 (63%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVA 41
          ++ +G+ +GF FV +++ E+A +A   +NG  +   P+ V+
Sbjct: 37 IAPNGQPRGFAFVEYATAEDAEEAQQALNGHSLQGSPIRVS 77

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|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 = 39.5 bits (93), Expect = 1e-04
 Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 1/40 (2%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYV 40
            +DGR  G  +V F+SPE+A +A+   +   +G + + V
Sbjct: 34 YDDDGRPTGEAYVEFASPEDARRALR-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|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 17/39 (43%), Positives = 24/39 (61%), Gaps = 2/39 (5%)

Query: 7  SKGFGFVCFSSPEEATKAVTEMNGRIIGS--KPLYVALA 43
          SKG  +V F+    A +A+ EMNG+ +G   KPL V +A
Sbjct: 43 SKGVAYVKFAKASSAARAMEEMNGKCLGGDTKPLKVLIA 81

This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

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

 Score = 39.3 bits (92), Expect = 1e-04
 Identities = 13/25 (52%), Positives = 16/25 (64%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMN 29
          G  KGF F+ F +PEEA KA   +N
Sbjct: 38 GDIKGFAFIEFETPEEAQKACKHLN 62

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

 Score = 39.1 bits (91), Expect = 2e-04
 Identities = 15/39 (38%), Positives = 22/39 (56%)

Query: 7  SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR 45
          S GFGFV F + E+A  A+  M+G ++    L V  + R
Sbjct: 46 SMGFGFVGFKTKEQAQAALKAMDGFVLDGHTLVVKFSHR 84

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

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 1/40 (2%)

Query: 4  DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
           G+S+G+GFV F   E A +A  + N  I G K   V LA
Sbjct: 38 TGKSRGYGFVTFKDKESAERACKDPNPIIDGRK-ANVNLA 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|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 38.5 bits (89), Expect = 3e-04
 Identities = 15/40 (37%), Positives = 27/40 (67%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVAL 42
          +DG+S+G G V F  P EA +A++  NG+ +  +P++V +
Sbjct: 36 KDGKSRGMGTVTFEQPIEAVQAISMFNGQFLFDRPMHVKM 75

This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 38.5 bits (90), Expect = 3e-04
 Identities = 11/27 (40%), Positives = 20/27 (74%)

Query: 7  SKGFGFVCFSSPEEATKAVTEMNGRII 33
          SKGFGFV F++  +A +A  +++G ++
Sbjct: 39 SKGFGFVTFANSADADRAREKLHGTVV 65

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

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 14/29 (48%), Positives = 19/29 (65%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIG 34
          RS+GFGF+ FSS +EA +A+      I G
Sbjct: 42 RSRGFGFITFSSADEADEAMEAQPHSIDG 70

This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 79

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

 Score = 38.3 bits (89), Expect = 3e-04
 Identities = 14/45 (31%), Positives = 29/45 (64%)

Query: 2  SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
           E G S+G+GFV F+  E+A +A+ ++  + +  + L + +A+R+
Sbjct: 35 PETGESRGYGFVTFAMLEDAQEALAKLKNKKLHGRILRLDIAERR 79

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

>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 38.1 bits (88), Expect = 4e-04
 Identities = 23/49 (46%), Positives = 27/49 (55%), Gaps = 5/49 (10%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
          E+G+SKG G V F SPE A KA   MNG  I  + + V L     DR A
Sbjct: 34 ENGKSKGCGTVRFDSPESAEKACRLMNGIKINGREIDVRL-----DRNA 77

This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 77

>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 38.5 bits (89), Expect = 4e-04
 Identities = 17/44 (38%), Positives = 25/44 (56%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
          + KGFGFV  ++ EEA  A+  +NG  +G K L V+    K  +
Sbjct: 41 KCKGFGFVTMTNYEEAAMAIASLNGYRLGDKILQVSFKTSKSHK 84

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

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

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 1/35 (2%)

Query: 8  KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVAL 42
           GF FV F     A  A+ ++NG  +G + + V+L
Sbjct: 45 NGFAFVTFKDASSAENAL-QLNGTELGGRKISVSL 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|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 38.0 bits (88), Expect = 5e-04
 Identities = 20/49 (40%), Positives = 27/49 (55%), Gaps = 5/49 (10%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
          E+G+SKG G V F SPE A +A   MNG  +  + + V +     DR A
Sbjct: 34 ENGKSKGCGVVRFESPEVAERACRMMNGYKLNGREIDVRI-----DRNA 77

This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 77

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

 Score = 37.7 bits (88), Expect = 5e-04
 Identities = 13/38 (34%), Positives = 18/38 (47%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVAL 42
          G+SKGF +V F+S   A     ++ GR    K   V  
Sbjct: 39 GKSKGFAYVEFASEAAAAAVKEKLEGREFNGKKCVVTY 76

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

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

 Score = 38.0 bits (89), Expect = 5e-04
 Identities = 12/24 (50%), Positives = 15/24 (62%)

Query: 7  SKGFGFVCFSSPEEATKAVTEMNG 30
          S G+GFV F S E A KA+  + G
Sbjct: 46 SMGYGFVEFKSKEAAQKALKRLQG 69

This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 82

>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 37.6 bits (87), Expect = 5e-04
 Identities = 19/35 (54%), Positives = 23/35 (65%), Gaps = 1/35 (2%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEM-NGRIIGSK 36
          + G SKGFGFV FSS E+A  A   M +G I G+K
Sbjct: 34 DTGSSKGFGFVDFSSEEDAKAAKEAMEDGEIDGNK 68

This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 78

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

 Score = 37.1 bits (87), Expect = 6e-04
 Identities = 14/39 (35%), Positives = 24/39 (61%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLY 39
          +    R +GF FV F+SPE+A  A+ ++NG ++  + L 
Sbjct: 31 VRNKDRPRGFAFVEFASPEDAEAALKKLNGLVLDGRTLR 69

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

>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 37.3 bits (87), Expect = 7e-04
 Identities = 14/39 (35%), Positives = 23/39 (58%)

Query: 2  SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYV 40
          ++DG+ + FGFV + + EEA KA+   N   I +  + V
Sbjct: 35 TKDGKFRKFGFVGYKTEEEAQKALKHFNNSFIDTSKITV 73

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|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 37.2 bits (86), Expect = 8e-04
 Identities = 15/39 (38%), Positives = 25/39 (64%)

Query: 2  SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYV 40
             G SKG+GFV +   + A +A +++ G+ +GS+ LYV
Sbjct: 35 ETTGHSKGYGFVEYMKKDSAARAKSDLLGKQLGSRTLYV 73

This subgroup corresponds to the RRM2 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 77

>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 19/43 (44%), Positives = 26/43 (60%), Gaps = 1/43 (2%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
          M+E GR KG  FV F S E ATKA+  +NG ++  KP+ +   
Sbjct: 41 MTE-GRMKGQAFVTFPSEEIATKALNLVNGYVLKGKPMVIQFG 82

This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear. . Length = 82

>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 15/40 (37%), Positives = 26/40 (65%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ 44
          G+S G+GFV +  P +A KA+  +NG  + +K + V+ A+
Sbjct: 42 GQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTIKVSYAR 81

This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 36.8 bits (85), Expect = 0.001
 Identities = 18/36 (50%), Positives = 21/36 (58%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYV 40
           +SK FGFV F +P  A  A+  MNG  IG K L V
Sbjct: 43 NQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKV 78

This subgroup corresponds to the RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 79

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

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 14/37 (37%), Positives = 20/37 (54%)

Query: 9  GFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR 45
          GF FV F  P +A  AV  ++GR I    + V L++ 
Sbjct: 37 GFAFVEFEDPRDAEDAVRALDGRRICGNRVRVELSRG 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|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 14/35 (40%), Positives = 22/35 (62%)

Query: 8  KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVAL 42
          KG+GFV  ++ EEA  A+  +NG  +G + L V+ 
Sbjct: 43 KGYGFVTMTNYEEAYSAIASLNGYRLGGRVLQVSF 77

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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 39.1 bits (91), Expect = 0.002
 Identities = 35/160 (21%), Positives = 63/160 (39%), Gaps = 41/160 (25%)

Query: 5   GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQ-------- 56
            RSKG  +V F    E+      + G+++  +P+ V  +Q +++R A  A+         
Sbjct: 128 RRSKGVAYVEFYD-VESVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNF 186

Query: 57  ---YMQRI-ANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAPQ 112
              Y+  +  N+  Q++ Q+F+P                 +G  +  Q+           
Sbjct: 187 LKLYVGNLHFNITEQELRQIFEP-----------------FGDIEDVQL----------H 219

Query: 113 MRPSGQTAQGFPNIPQFRSAPRASTGQTVIRGANMSARPI 152
             P    ++GF  I QF  A  A     V+ G  ++ RPI
Sbjct: 220 RDPETGRSKGFGFI-QFHDAEEAKEALEVMNGFELAGRPI 258

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|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 37.0 bits (85), Expect = 0.002
 Identities = 21/45 (46%), Positives = 25/45 (55%)

Query: 7  SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
          SK FGFV + +P  A  A+  MNG  IG K L V L + K D K 
Sbjct: 48 SKCFGFVSYDNPVSAQAAIQAMNGFQIGMKRLKVQLKRSKNDSKP 92

This subgroup corresponds to the RRM3 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It specifically binds to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contain three highly conserved RRMs. It binds to RNA via the first two RRMs, which are important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 92

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

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 13/29 (44%), Positives = 21/29 (72%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRII 33
          G+S G+GFV F++ E A +A+  +NG+ I
Sbjct: 38 GKSAGYGFVEFATHEAAEQALQSLNGKPI 66

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|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 14/38 (36%), Positives = 22/38 (57%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYV 40
          ++G+ K FGFVCF   E    A+  +NG  +  +P+ V
Sbjct: 37 KEGKPKSFGFVCFKHSESVPYAIALLNGIRLYGRPIKV 74

This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 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. RBM11 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. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 13/23 (56%), Positives = 15/23 (65%)

Query: 12 FVCFSSPEEATKAVTEMNGRIIG 34
          FV FS  +EA KAV  +NGR  G
Sbjct: 53 FVEFSDADEAIKAVRALNGRFFG 75

This subfamily corresponds to the RRM found in UHM domain of 45 kDa-splicing factor (SPF45 or RBM17), poly(U)-binding-splicing factor PUF60 (FIR or Hfp or RoBP1 or Siah-BP1), and similar proteins. SPF45 is an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. 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 RRMs and a C-terminal UHM domain. . Length = 85

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

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 5/37 (13%)

Query: 2  SEDGRSKGFGFVCFSSPEEATKAVTEMN-----GRII 33
           E  + +GF FV F  PE+A  A+  MN     GR I
Sbjct: 34 YETQKHRGFAFVEFEEPEDAAAAIDNMNESELFGRTI 70

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|241091 cd12647, RRM_UHM_SPF45, RNA recognition motif in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 12/23 (52%), Positives = 14/23 (60%)

Query: 12 FVCFSSPEEATKAVTEMNGRIIG 34
          FV F   E A KAV ++NGR  G
Sbjct: 55 FVEFERVESAIKAVVDLNGRFFG 77

This subgroup corresponds to the RRM of SPF45, also termed RNA-binding motif protein 17 (RBM17), an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. . Length = 96

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

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 4/36 (11%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTE----MNGRIIGSK 36
          GRS+GFGFV F   E   K + +    +NG++I  K
Sbjct: 37 GRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPK 72

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

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 3/36 (8%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTE---MNGRIIGSKP 37
          G+SKGFGFV F+  E+  K +++   ++GR    K 
Sbjct: 38 GQSKGFGFVRFADYEDQVKVLSQRHMIDGRWCDVKI 73

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

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

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 13/35 (37%), Positives = 20/35 (57%)

Query: 8  KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVAL 42
            F FV F S E A +A   ++G+++ + PLYV  
Sbjct: 33 SNFAFVEFESLESAIRAKDSVHGKVLNNNPLYVTY 67

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

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 15/37 (40%), Positives = 24/37 (64%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVAL 42
          R  G  +  FSSPE+A K V ++NG++  ++ L+V L
Sbjct: 44 RPLGIAYAEFSSPEQAEKVVKDLNGKVFKNRKLFVKL 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|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 12/37 (32%), Positives = 19/37 (51%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVA 41
            S+GF FV F    +A  A+  M+G+ +  + L V 
Sbjct: 37 RESRGFAFVRFYDKRDAEDAMDAMDGKELDGRELRVQ 73

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

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

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 15/36 (41%), Positives = 22/36 (61%)

Query: 9  GFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ 44
          GFGFV F  P +A  AV E+NG+ +  + + V  A+
Sbjct: 34 GFGFVEFEDPRDADDAVYELNGKELCGERVIVEHAR 69

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

 Score = 35.6 bits (83), Expect = 0.002
 Identities = 14/34 (41%), Positives = 19/34 (55%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPL 38
          G+SKG+ FV F SPE A      MN  ++  + L
Sbjct: 38 GKSKGYAFVEFESPEVAKIVAETMNNYLLFERLL 71

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

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 13/35 (37%), Positives = 21/35 (60%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYV 40
          + KGF FV +  PE A KA  E++G +   + L++
Sbjct: 42 KPKGFAFVTYMIPEHAVKAFAELDGTVFQGRLLHL 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 38.6 bits (90), Expect = 0.003
 Identities = 16/41 (39%), Positives = 27/41 (65%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR 45
           RS G+G+V F +P +A +A+  MN + +G KP+ +  +QR
Sbjct: 39 RRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQR 79

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

 Score = 35.6 bits (83), Expect = 0.003
 Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 1/41 (2%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRII-GSKPLYV 40
          M   G ++G+ FV +++ E A +AV +++   I   K L V
Sbjct: 35 MDFSGLNRGYAFVTYTNKEAAQRAVKQLHNYEIRPGKRLGV 75

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

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

 Score = 35.9 bits (83), Expect = 0.003
 Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 5/48 (10%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED 48
            E+G+S+G G V F   E   KA+  MN   +  + L V     KED
Sbjct: 34 KDEEGKSRGCGVVEFKDKESVQKALETMNRYELKGRKLVV-----KED 76

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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 35.8 bits (82), Expect = 0.003
 Identities = 15/44 (34%), Positives = 26/44 (59%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
          + KGFGFV  ++ +EA  A+  +NG  +G + L V+    K+ +
Sbjct: 41 KCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTSKQHK 84

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 35.8 bits (82), Expect = 0.003
 Identities = 15/44 (34%), Positives = 25/44 (56%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
          + KGFGFV  ++ +EA  A+  +NG  +G + L V+    K  +
Sbjct: 43 KCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNKTHK 86

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

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

 Score = 35.4 bits (82), Expect = 0.003
 Identities = 17/39 (43%), Positives = 21/39 (53%), Gaps = 1/39 (2%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
          GRS+GFGFV F S E A + V       +G K + V  A
Sbjct: 38 GRSRGFGFVTFDS-ESAVERVFSAGMLELGGKQVEVKRA 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|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 35.4 bits (82), Expect = 0.003
 Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 1/40 (2%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYV 40
          + E G    + FV +     A  A+  MNGR+I  + + V
Sbjct: 31 IREHGNDP-YAFVEYYDHRSAAAALQTMNGRLILGQEIKV 69

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|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 = 35.6 bits (83), Expect = 0.003
 Identities = 10/23 (43%), Positives = 13/23 (56%)

Query: 9  GFGFVCFSSPEEATKAVTEMNGR 31
          G  FV F+  E+A KA   + GR
Sbjct: 57 GKVFVEFADVEDAQKAQLALAGR 79

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

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 9/40 (22%)

Query: 5  GRSKGFGFVCFSSPEEATKAV----TEMNGRIIGSKPLYV 40
          G+SKG+ +V F + E   +A+      + GR     P++V
Sbjct: 37 GKSKGYAYVEFENEESVQEALKLDRELIKGR-----PMFV 71

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

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

 Score = 35.3 bits (82), Expect = 0.004
 Identities = 14/39 (35%), Positives = 23/39 (58%)

Query: 2  SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYV 40
           E G+ KG+GF+ + +P+ A  A+  MN   +G + L V
Sbjct: 36 PETGKHKGYGFIEYENPQSAQDAIASMNLFDLGGQQLRV 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|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 38.4 bits (89), Expect = 0.004
 Identities = 26/109 (23%), Positives = 45/109 (41%), Gaps = 8/109 (7%)

Query: 8   KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ---RKEDRKAHLASQYMQRIANM 64
           + + FV F   E+A KA+ E+NG+ +    + V LA+   +K   +    +    +    
Sbjct: 269 RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQA 328

Query: 65  RMQQMGQLFQPGSTG----GYFVPTLPQPQRFYGPTQMTQIRPQPRWAA 109
             Q +GQ++ P S       Y+      P   + P     IR + R  A
Sbjct: 329 ARQSLGQVYDPASRSLAYEDYYYHPPYAPSLHF-PRMPGPIRGRGRGGA 376

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 35.3 bits (81), Expect = 0.004
 Identities = 15/40 (37%), Positives = 25/40 (62%), Gaps = 6/40 (15%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMN------GRIIG 34
          M  DG+++G+ FV ++   EA +AV E+N      GR++G
Sbjct: 35 MDFDGKNRGYAFVMYTQKHEAKRAVRELNNYEIRPGRLLG 74

This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|240959 cd12515, RRM5_RBM12_like, RNA recognition motif 5 in RNA-binding protein RBM12, RBM12B and similar proteins

 Score = 35.1 bits (81), Expect = 0.004
 Identities = 14/37 (37%), Positives = 22/37 (59%)

Query: 2  SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPL 38
          +++G   G   V F +  EA  AV E+NGR IG++ +
Sbjct: 36 NDNGAPTGEATVAFDTHREAMAAVRELNGRPIGTRKV 72

This subfamily corresponds to the RRM5 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B show high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear. . Length = 75

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

 Score = 35.1 bits (81), Expect = 0.004
 Identities = 17/43 (39%), Positives = 25/43 (58%), Gaps = 3/43 (6%)

Query: 1  MSED---GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYV 40
          MS D    + KGF FV +  PE A  A+ +MNG ++G + + V
Sbjct: 32 MSWDPVTMKHKGFAFVEYEVPEAAQLALEQMNGVMLGGRNIKV 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|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins

 Score = 35.3 bits (82), Expect = 0.004
 Identities = 13/39 (33%), Positives = 20/39 (51%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ 44
          + + F FV F S EE  KA+  ++G     + L   LA+
Sbjct: 40 KRQDFAFVTFRSEEERQKALEILDGFKWKGRVLSARLAK 78

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	303
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
smart00517	64	PolyA C-terminal domain of Poly(A)-binding protein	99.96
PF00658	72	PABP: Poly-adenylate binding protein, unique domai	99.94
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	98.7
KOG0148|consensus	321		98.69
smart00361	70	RRM_1 RNA recognition motif.	98.63
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	98.42
KOG0111|consensus	298		98.39
KOG0125|consensus	376		98.38
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	98.35
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.35
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	98.25
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	98.25
KOG0108|consensus	435		98.24
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	98.2
KOG0123|consensus	369		98.16
KOG0145|consensus	360		98.14
KOG4207|consensus	256		98.13
KOG0144|consensus	510		98.13
smart00360	71	RRM RNA recognition motif.	98.1
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	98.09
KOG0123|consensus	369		98.09
KOG0117|consensus	506		98.06
KOG0126|consensus	219		98.04
KOG0226|consensus	290		98.03
KOG4208|consensus	214		98.02
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	98.0
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	97.96
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	97.95
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	97.91
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	97.89
smart00362	72	RRM_2 RNA recognition motif.	97.89
KOG0149|consensus	247		97.88
COG0724	306	RNA-binding proteins (RRM domain) [General functio	97.87
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	97.87
KOG0107|consensus	195		97.83
KOG0113|consensus	335		97.8
KOG0147|consensus	549		97.75
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	97.74
KOG0130|consensus	170		97.73
KOG0127|consensus	678		97.71
KOG0131|consensus	203		97.68
KOG4212|consensus	608		97.67
KOG0131|consensus	203		97.66
KOG0124|consensus	544		97.64
PLN03213	759	repressor of silencing 3; Provisional	97.62
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	97.55
KOG0146|consensus	371		97.55
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	97.5
PLN03120	260	nucleic acid binding protein; Provisional	97.43
KOG0943|consensus	3015		97.39
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	97.38
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	97.23
KOG0148|consensus	321		97.19
KOG0110|consensus	725		97.16
KOG0117|consensus	506		97.15
KOG0121|consensus	153		97.13
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	97.09
KOG0110|consensus	725		97.08
KOG0144|consensus	510		96.9
KOG0127|consensus	678		96.89
KOG4206|consensus	221		96.84
KOG0145|consensus	360		96.76
KOG0114|consensus	124		96.67
PLN03121	243	nucleic acid binding protein; Provisional	96.65
KOG0105|consensus	241		96.05
KOG0415|consensus	479		96.03
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	95.66
KOG0109|consensus	346		95.52
KOG4205|consensus	311		95.21
KOG4209|consensus	231		95.18
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	95.11
KOG2314|consensus	698		94.93
KOG4661|consensus	940		94.83
KOG0106|consensus	216		94.79
KOG4205|consensus	311		94.74
KOG0132|consensus	894		94.7
KOG0533|consensus	243		94.49
KOG0124|consensus	544		94.04
KOG0109|consensus	346		94.04
KOG1457|consensus	284		94.03
KOG0106|consensus	216		92.37
KOG1548|consensus	382		91.39
KOG1995|consensus	351		91.38
KOG0120|consensus	500		91.27
KOG4454|consensus	267		89.36
KOG0153|consensus	377		89.3
KOG4211|consensus	510		88.83
KOG0147|consensus	549		88.63
COG5175	480	MOT2 Transcriptional repressor [Transcription]	86.9
KOG1548|consensus	382		86.5
KOG0116|consensus	419		86.44
KOG2202|consensus	260		86.44
KOG4210|consensus	285		83.55
KOG4849|consensus	498		82.8
KOG4211|consensus	510		81.55
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	80.8

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

Probab=100.00  E-value=2.1e-39  Score=327.96  Aligned_cols=243  Identities=45%  Similarity=0.683  Sum_probs=144.1

Q ss_pred             CCCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCC
Q psy14476          1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIANMRMQQMGQLFQPGSTGG   80 (303)
Q Consensus         1 ~d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~~~~~~~~q~~~~~r~~~~~~~~~~~~~~~   80 (303)
                      +|.+|+|||||||+|++.++|.+|+++|||+.|+||+|+|.+|.++++|...+..+|.++....+  ...... +.  .+
T Consensus       319 ~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~~~~~~~~~~~~q~~~~~~--~~~~~~-p~--~~  393 (562)
T TIGR01628       319 LDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQFMQLQPRMR--QLPMGS-PM--GG  393 (562)
T ss_pred             ECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCcHHHHHHHHHHHHHhhhhcc--CCCCCC-CC--CC
Confidence            36789999999999999999999999999999999999999999999999999999877432211  111000 00  01


Q ss_pred             CCCCCCCCCCcccCCCCCCCCCCCC-cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCCCCcCCCCCCC
Q psy14476         81 YFVPTLPQPQRFYGPTQMTQIRPQP-RWAAAPQMRPSGQTAQGFPNIPQFRSAPRASTGQTVIRGANMSARPITGQSTMG  159 (303)
Q Consensus        81 ~f~~~lp~~~~~~~~~~~~~~rp~~-~~~~~~~~~p~~~~~~~~~~~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (303)
                      .|.     .+.|++++..+..++.| .|...+.+        +.+..++   ++..+.   +..       .++ ++   
T Consensus       394 ~~~-----~p~~~~~~~~~~~~~~p~~~~~~~~~--------~~~~~~~---~~~~p~---~~~-------~~~-~~---  443 (562)
T TIGR01628       394 AMG-----QPPYYGQGPQQQFNGQPLGWPRMSMM--------PTPMGPG---GPLRPN---GLA-------PMN-AV---  443 (562)
T ss_pred             ccc-----CCCccCCCCcccCCCCCCCCCCCCCC--------CCCCCCC---CCCCCC---CCC-------CCC-cC---
Confidence            110     11233322222222111 22210100        0000000   000000   000       000 00   


Q ss_pred             CCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCccccCCCCCccccccccccCCCCccchhHhhhcChHHHHHhhh
Q psy14476        160 PRGGGPMQAPGPASVSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGVQAVHVQGQEPLTSTMLAAAQPQEQKQMLG  239 (303)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~ltas~l~~~~~~~qk~~lG  239 (303)
                            +.+++........++.+.+ .|+...++.+.++.   + +.  ++...+..+++++++++|++++|++||++||
T Consensus       444 ------~~~~~~~~~~~~~~~~~~~-~~~p~~~~~~~~~~---~-~~--~~~~~~~~~~~~~~~~~la~~~p~~q~~~lg  510 (562)
T TIGR01628       444 ------RAPSRNAQNAAQKPPMQPV-MYPPNYQSLPLSQD---L-PQ--PQSTASQGGQNKKLAQVLASATPQMQKQVLG  510 (562)
T ss_pred             ------CCCCcccccccccccCCCc-CCCccccCCCCCcc---c-cc--ccCCccccccchhHHHHHhhCCHHHHHHHHH
Confidence                  0000000000000000111 22100000000000   0 10  1112333567789999999999999999999


Q ss_pred             ccchhhhhhhCCCCCCCchhhcccCChHHHHHhhCChHHHHHHHHHHHHHHH
Q psy14476        240 ERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQ  291 (303)
Q Consensus       240 e~ly~~v~~~~p~~A~KITGMlLe~~~~ell~ll~~~~~L~~kv~eA~~vl~  291 (303)
                      |+|||+|++++|++|+||||||||||++||||||||+|+|++||+||++||+
T Consensus       511 ~~~~~~~~~~~~~~~~~~tgm~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  562 (562)
T TIGR01628       511 ERLFPLVEAIEPALAAKITGMLLEMDNSELLHLLESPELLKSKVDEALEVLK  562 (562)
T ss_pred             HHhHHHHHhhChhhcCcceEEEecCCHHHHHHHhcCHHHHHHHHHHHHHHhC
Confidence            9999999999999999999999999999999999999999999999999994

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>smart00517 PolyA C-terminal domain of Poly(A)-binding protein

Probab=99.96  E-value=5.5e-30  Score=189.48  Aligned_cols=64  Identities=67%  Similarity=0.994  Sum_probs=62.2

Q ss_pred             ChHHHHHhhhccchhhhhhhCCCCCCCchhhcccCChHHHHHhhCChHHHHHHHHHHHHHHHHH
Q psy14476        230 QPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAH  293 (303)
Q Consensus       230 ~~~~qk~~lGe~ly~~v~~~~p~~A~KITGMlLe~~~~ell~ll~~~~~L~~kv~eA~~vl~~~  293 (303)
                      +|++||++|||+|||+|++++|++|+||||||||||++|||+||+|+++|++||+||++||++|
T Consensus         1 ~p~~qkq~LGE~Lyp~V~~~~p~~A~KITGMLLEmd~~ell~lle~~~~L~~kv~EA~~vl~~~   64 (64)
T smart00517        1 PPQEQKQALGERLYPKVQALEPELAGKITGMLLEMDNSELLHLLESPELLRSKVDEALEVLKSH   64 (64)
T ss_pred             CHHHHHHHHhHHHhHHHHhhCcccCCcCeeeeeCCCHHHHHHHhcCHHHHHHHHHHHHHHHHhC
Confidence            5889999999999999999999999999999999999999999999999999999999999864

Present also in Drosophila hyperplastics discs protein. Involved in homodimerisation (either directly or indirectly)

>PF00658 PABP: Poly-adenylate binding protein, unique domain; InterPro: IPR002004 The polyadenylate-binding protein (PABP) has a conserved C-terminal domain (PABC), which is also found in the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains (IPR000569 from INTERPRO) []

Probab=99.94  E-value=1.7e-28  Score=186.51  Aligned_cols=72  Identities=67%  Similarity=1.054  Sum_probs=70.1

Q ss_pred             CccchhHhhhcChHHHHHhhhccchhhhhhhCCCCCCCchhhcccCChHHHHHhhCChHHHHHHHHHHHHHH
Q psy14476        219 EPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVL  290 (303)
Q Consensus       219 ~~ltas~l~~~~~~~qk~~lGe~ly~~v~~~~p~~A~KITGMlLe~~~~ell~ll~~~~~L~~kv~eA~~vl  290 (303)
                      +++|++.|+++++++||++|||+||++|..++|++|+||||||||||++||++||+|++.|++||+||++||
T Consensus         1 ~~~~~~~la~~~~~~qk~~LGe~Ly~~V~~~~p~~A~KITGMLLe~~~~ell~ll~~~~~L~~kv~eA~~vL   72 (72)
T PF00658_consen    1 EPLTASALASASPEQQKQILGERLYPLVQAIYPELAGKITGMLLEMDNSELLHLLEDPELLREKVQEAIEVL   72 (72)
T ss_dssp             SSTSHHHHHTSCHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTTSCHHHHHHHHHTHHHHHHHHHHHHHHH
T ss_pred             CcchHHHHhcCCHHHHHHHHhccccHHHHHhCcchhHHHHHHHhcCCHHHHHHHhCCHHHHHHHHHHHHHhC
Confidence            467899999999999999999999999999999999999999999999999999999999999999999997

PABP recognises the 3' mRNA poly(A) tail and plays an essential role in eukaryotic translation initiation and mRNA stabilisation/degradation. PABC domains of PABP are peptide-binding domains that mediate PABP homo-oligomerisation and protein-protein interactions. In mammals, the PABC domain of PABP functions to recruit several different translation factors to the mRNA poly(A) tail [].; GO: 0003723 RNA binding; PDB: 3KUR_E 1JH4_A 2RQH_B 3KUI_A 3KUS_A 3KUJ_A 3KTR_A 2X04_A 3PTH_A 1JGN_A ....

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=98.70  E-value=2e-08  Score=85.94  Aligned_cols=44  Identities=41%  Similarity=0.730  Sum_probs=41.5

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .||++||||||+|++.++|++||+.||+..|+|+.|+|+++..+
T Consensus        71 ~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~~~  114 (144)
T PLN03134         71 ETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDR  114 (144)
T ss_pred             CCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCCcC
Confidence            47999999999999999999999999999999999999998754

>KOG0148|consensus

Probab=98.69  E-value=8.1e-09  Score=95.91  Aligned_cols=76  Identities=26%  Similarity=0.484  Sum_probs=58.1

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCC
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIANMRMQQMGQLFQPGSTGGYF   82 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~~~~~~~~q~~~~~r~~~~~~~~~~~~~~~~f   82 (303)
                      .|+||||||||.|...++|++||..|||..|++|.|+-+||.+|..+.......|.+-         .+..++- ..+.|
T Consensus        99 ~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp~e~n~~~ltfdeV---------~NQssp~-NtsVY  168 (321)
T KOG0148|consen   99 NTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKPSEMNGKPLTFDEV---------YNQSSPD-NTSVY  168 (321)
T ss_pred             cCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCccccCCCCccHHHH---------hccCCCC-CceEE
Confidence            3899999999999999999999999999999999999999999984443333333322         2222222 33678


Q ss_pred             CCCCCC
Q psy14476         83 VPTLPQ   88 (303)
Q Consensus        83 ~~~lp~   88 (303)
                      +++++.
T Consensus       169 ~G~I~~  174 (321)
T KOG0148|consen  169 VGNIAS  174 (321)
T ss_pred             eCCcCc
Confidence            888775

>smart00361 RRM_1 RNA recognition motif

Probab=98.63  E-value=5.1e-08  Score=72.91  Aligned_cols=37  Identities=22%  Similarity=0.547  Sum_probs=35.4

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCceecccceeee
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVA   41 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~   41 (303)
                      |++||||||.|.+.++|.+|++.|||+.++||.|.+.
T Consensus        34 ~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361       34 NHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             CCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            8999999999999999999999999999999999873

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

Probab=98.42  E-value=4.3e-07  Score=92.55  Aligned_cols=82  Identities=39%  Similarity=0.590  Sum_probs=65.9

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceec----ccceeeecccchHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCC
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIG----SKPLYVALAQRKEDRKAHLASQYMQRIANMRMQQMGQLFQPGS   77 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~----GR~L~V~~A~~k~~r~~~~~~~~~q~~~~~r~~~~~~~~~~~~   77 (303)
                      |.+|++||||||+|.+.++|.+|++.|||+.|.    |+.|+|.++..+.++...++..+.+.... +.    ....   
T Consensus       213 ~~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~-~~----~~~~---  284 (562)
T TIGR01628       213 DGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQE-RK----MKAQ---  284 (562)
T ss_pred             CCCCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEeecccChhhhHHHHHhhHHhhhhh-hh----cccC---
Confidence            678999999999999999999999999999999    99999999999999988888777654431 11    1111   


Q ss_pred             CCCCCCCCCCCCCc
Q psy14476         78 TGGYFVPTLPQPQR   91 (303)
Q Consensus        78 ~~~~f~~~lp~~~~   91 (303)
                      ...+||.||+....
T Consensus       285 ~~~l~V~nl~~~~~  298 (562)
T TIGR01628       285 GVNLYVKNLDDTVT  298 (562)
T ss_pred             CCEEEEeCCCCccC
Confidence            22689999987554

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0111|consensus

Probab=98.39  E-value=1.4e-07  Score=85.68  Aligned_cols=44  Identities=34%  Similarity=0.579  Sum_probs=42.1

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      +++|+||||||+|+..|+|..||..||+.+|.||.|+|++|.+.
T Consensus        47 esqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~AkP~   90 (298)
T KOG0111|consen   47 ESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAKPE   90 (298)
T ss_pred             hcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecCCc
Confidence            58999999999999999999999999999999999999999864

>KOG0125|consensus

Probab=98.38  E-value=2.2e-07  Score=88.32  Aligned_cols=42  Identities=33%  Similarity=0.629  Sum_probs=39.4

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .-|||||||+|++++||++|-++|||..|.||+|.|+.|..+
T Consensus       133 RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen  133 RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccchh
Confidence            358999999999999999999999999999999999999865

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=98.35  E-value=4e-07  Score=86.69  Aligned_cols=45  Identities=38%  Similarity=0.638  Sum_probs=42.0

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|+|||||||+|.+.++|++||+.|||..|.|++|+|.++.++.
T Consensus        40 ~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~~~   84 (352)
T TIGR01661        40 VTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARPSS   84 (352)
T ss_pred             CCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecccc
Confidence            479999999999999999999999999999999999999987653

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>PF13893 RRM_5: RNA recognition motif

Probab=98.35  E-value=7.6e-07  Score=63.25  Aligned_cols=36  Identities=47%  Similarity=0.820  Sum_probs=34.8

Q ss_pred             ccEEEEEeCCHHHHHHHHHHhCCceecccceeeecc
Q psy14476          8 KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA   43 (303)
Q Consensus         8 kGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A   43 (303)
                      +|++||+|.+.++|++|++.|||..++|++|+|.||
T Consensus        21 ~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen   21 RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            599999999999999999999999999999999986

(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 ....

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=98.25  E-value=8.4e-07  Score=86.14  Aligned_cols=43  Identities=33%  Similarity=0.553  Sum_probs=40.9

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      .+|+|||||||+|.++++|++||++||+..|.+++|+|.++.+
T Consensus       144 ~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a~p  186 (346)
T TIGR01659       144 KTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARP  186 (346)
T ss_pred             CCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecccc
Confidence            4799999999999999999999999999999999999999865

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).

>PF00076 RRM_1: RNA recognition motif

Probab=98.25  E-value=1.4e-06  Score=63.01  Aligned_cols=37  Identities=43%  Similarity=0.767  Sum_probs=34.8

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceeccccee
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLY   39 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~   39 (303)
                      .+++++|||||+|++.++|++|++.|||..+.|+.|+
T Consensus        34 ~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen   34 SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            5688999999999999999999999999999999875

(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 ....

>KOG0108|consensus

Probab=98.24  E-value=1e-06  Score=87.77  Aligned_cols=50  Identities=32%  Similarity=0.612  Sum_probs=45.7

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHHHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAH   52 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~~   52 (303)
                      +||++|||||++|.+.++|..|++.|||.++.||+|+|+|+.....+...
T Consensus        55 ~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~~~~~~~  104 (435)
T KOG0108|consen   55 ETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNRKNAERS  104 (435)
T ss_pred             cCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeecccccchhHHH
Confidence            58999999999999999999999999999999999999999876655443

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=98.20  E-value=1.7e-06  Score=89.08  Aligned_cols=82  Identities=22%  Similarity=0.390  Sum_probs=57.8

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHHHHHHHHHHHH------HHHHhhhhcCCCCCCCCCC
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR------IANMRMQQMGQLFQPGSTG   79 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~~~~~~~~q~------~~~~r~~~~~~~~~~~~~~   79 (303)
                      +.|+||||+|++.++|++|+++|||.+|+|+.|+|+||++++.....   .|..-      ....+...+.+.+++. +.
T Consensus       267 ~~rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~~~~~---~~~rg~gg~~~~~~~~~~~~g~~~sp~-s~  342 (578)
T TIGR01648       267 KIRDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKKSYV---RYTRGTGGRGKERQAARQSLGQVYDPA-SR  342 (578)
T ss_pred             eecCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCCccccc---ccccccCCCcccccccccccCcccCcc-cc
Confidence            46899999999999999999999999999999999999876432110   00000      0001123455666664 56


Q ss_pred             CCCCCCCCCCCc
Q psy14476         80 GYFVPTLPQPQR   91 (303)
Q Consensus        80 ~~f~~~lp~~~~   91 (303)
                      ++|+++++++..
T Consensus       343 ~~~~g~~~~~~~  354 (578)
T TIGR01648       343 SLAYEDYYYHPP  354 (578)
T ss_pred             cccccccccccc
Confidence            789999988654

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.

>KOG0123|consensus

Probab=98.16  E-value=1.6e-06  Score=84.83  Aligned_cols=73  Identities=15%  Similarity=-0.018  Sum_probs=64.7

Q ss_pred             hhHhhhcChHHHHHhhhccchhhhhhhCCCCCCCchhhcccCChHHHHHhhCChHHHHHHHHHHHHHHHHHHH
Q psy14476        223 STMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQA  295 (303)
Q Consensus       223 as~l~~~~~~~qk~~lGe~ly~~v~~~~p~~A~KITGMlLe~~~~ell~ll~~~~~L~~kv~eA~~vl~~~~~  295 (303)
                      ..++......+..+.+||....+|...+...+..++.+.++.+.++...|++-...+..+....+++.+.++.
T Consensus       279 d~~~~~e~L~~~f~~~GeI~s~kv~~~~~g~skG~gfV~fs~~eeA~~A~~~~n~~~i~~k~l~vav~qr~~~  351 (369)
T KOG0123|consen  279 DETLSDEKLRKIFSSFGEITSAKVMVDENGKSKGFGFVEFSSPEEAKKAMTEMNGRLIGGKPLYVAVAQRKED  351 (369)
T ss_pred             ccccchhHHHHHHhcccceeeEEEEeccCCCccceEEEEcCCHHHHHHHHHhhChhhhcCCchhhhHHhhhcc
Confidence            3566777888899999999999999999999999999999999999999999999888888888888886554

>KOG0145|consensus

Probab=98.14  E-value=1.8e-06  Score=80.17  Aligned_cols=45  Identities=36%  Similarity=0.665  Sum_probs=43.2

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      +|.|-|||||.|.+++||++||..|||..|..|.|+|+||++..+
T Consensus        79 tGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARPSs~  123 (360)
T KOG0145|consen   79 TGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARPSSD  123 (360)
T ss_pred             cccccccceeeecChHHHHHHHhhhcceeeccceEEEEeccCChh
Confidence            799999999999999999999999999999999999999998765

>KOG4207|consensus

Probab=98.13  E-value=1.6e-06  Score=78.28  Aligned_cols=41  Identities=32%  Similarity=0.632  Sum_probs=39.4

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      |+.++||+||-|.+..+|++|++.|||.+|+||.|.|.+|.
T Consensus        51 Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   51 TRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             cccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            78899999999999999999999999999999999999875

>KOG0144|consensus

Probab=98.13  E-value=3.2e-06  Score=83.06  Aligned_cols=54  Identities=35%  Similarity=0.542  Sum_probs=46.4

Q ss_pred             CCCCCCcccEEEEEeCCHHHHHHHHHHhCCce-e--cccceeeecccchHHHHHHHH
Q psy14476          1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRI-I--GSKPLYVALAQRKEDRKAHLA   54 (303)
Q Consensus         1 ~d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~-l--~GR~L~V~~A~~k~~r~~~~~   54 (303)
                      ||++|.||||+||+|++.|-|..||+.|||.. +  +..+|.|+||..+++|..+..
T Consensus       158 rd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk~~~~l  214 (510)
T KOG0144|consen  158 RDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDKDGKRL  214 (510)
T ss_pred             ecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCCchHHHH
Confidence            68899999999999999999999999999964 4  457999999998777665544

>smart00360 RRM RNA recognition motif

Probab=98.10  E-value=5.1e-06  Score=58.60  Aligned_cols=38  Identities=47%  Similarity=0.813  Sum_probs=35.5

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeee
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVA   41 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~   41 (303)
                      +++++|||||+|.+.++|.+|++.+++..+.|+.|.|.
T Consensus        34 ~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360       34 TGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            57899999999999999999999999999999998874

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=98.09  E-value=3.5e-06  Score=87.10  Aligned_cols=45  Identities=22%  Similarity=0.359  Sum_probs=41.9

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|++.++|.+||+.||+..|+|+.|+|+++..+.
T Consensus       241 ~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~pP  285 (612)
T TIGR01645       241 TGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPP  285 (612)
T ss_pred             CCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCCc
Confidence            368999999999999999999999999999999999999998653

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.

>KOG0123|consensus

Probab=98.09  E-value=1.4e-06  Score=85.23  Aligned_cols=59  Identities=71%  Similarity=1.102  Sum_probs=54.4

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHHHHHHHHHHHH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR   60 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~~~~~~~~q~   60 (303)
                      |+.|+|+|||||+|++.++|.+|+..+|+..+.+++|+|.+++++.+++.+++..+..+
T Consensus       305 ~~~g~skG~gfV~fs~~eeA~~A~~~~n~~~i~~k~l~vav~qr~~~r~~~~~~~~~~~  363 (369)
T KOG0123|consen  305 DENGKSKGFGFVEFSSPEEAKKAMTEMNGRLIGGKPLYVAVAQRKEDRRARLQAVFGAR  363 (369)
T ss_pred             ccCCCccceEEEEcCCHHHHHHHHHhhChhhhcCCchhhhHHhhhccchhhhhhhccee
Confidence            67899999999999999999999999999999999999999999999988887776543

>KOG0117|consensus

Probab=98.06  E-value=3.7e-06  Score=82.84  Aligned_cols=44  Identities=36%  Similarity=0.557  Sum_probs=39.7

Q ss_pred             CC-CCCCcccEEEEEeCCHHHHHHHHHHhCCceec-ccceeeeccc
Q psy14476          1 MS-EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIG-SKPLYVALAQ   44 (303)
Q Consensus         1 ~d-~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~-GR~L~V~~A~   44 (303)
                      || .+|.+||||||+|.+.++|++||+.||+++|. ||.|.|+.+.
T Consensus       117 mD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Sv  162 (506)
T KOG0117|consen  117 MDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSV  162 (506)
T ss_pred             ecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEee
Confidence            46 68999999999999999999999999999986 8999888654

>KOG0126|consensus

Probab=98.04  E-value=8.7e-07  Score=78.48  Aligned_cols=43  Identities=30%  Similarity=0.585  Sum_probs=40.2

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      .||+||||||+||++..+.--||..|||..|.||.|+|+....
T Consensus        72 ~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~~  114 (219)
T KOG0126|consen   72 KTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVSN  114 (219)
T ss_pred             CCCcccceEEEEecCccceEEEEeccCCceecceeEEeeeccc
Confidence            4999999999999999999999999999999999999997653

>KOG0226|consensus

Probab=98.03  E-value=4.6e-06  Score=77.22  Aligned_cols=54  Identities=35%  Similarity=0.708  Sum_probs=44.7

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHHHHHHHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQ   56 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~~~~~~   56 (303)
                      .||+|||||||.|.++.++..|+.+|||+.++.|+|+......++......+++
T Consensus       227 RTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~wkeRn~dvv~kk  280 (290)
T KOG0226|consen  227 RTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSEWKERNLDVVKKK  280 (290)
T ss_pred             cccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhhHHhhhhHHHhHH
Confidence            489999999999999999999999999999999999987666655333333333

>KOG4208|consensus

Probab=98.02  E-value=4.3e-06  Score=75.22  Aligned_cols=44  Identities=32%  Similarity=0.415  Sum_probs=41.0

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .||.|||||||+|++.|.|.-|.+.||++.|.++-|.|.+--+.
T Consensus        87 rTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmppe  130 (214)
T KOG4208|consen   87 RTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMPPE  130 (214)
T ss_pred             ccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeCch
Confidence            48999999999999999999999999999999999999877654

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=98.00  E-value=5.8e-06  Score=85.55  Aligned_cols=43  Identities=35%  Similarity=0.689  Sum_probs=39.9

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      .+|+|||||||+|++.++|++||+.|||..|+||.|+|.+...
T Consensus       144 ~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~~  186 (612)
T TIGR01645       144 ATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSN  186 (612)
T ss_pred             CCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccccc
Confidence            4899999999999999999999999999999999999986543

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.

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=97.96  E-value=6.6e-06  Score=79.94  Aligned_cols=44  Identities=36%  Similarity=0.577  Sum_probs=40.3

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecc--cceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGS--KPLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~G--R~L~V~~A~~k   46 (303)
                      .+|++||||||+|++.++|++||+.||+..|++  ++|.|.+|..+
T Consensus       230 ~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~  275 (346)
T TIGR01659       230 LTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEH  275 (346)
T ss_pred             CCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCcc
Confidence            389999999999999999999999999999876  68999998865

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).

>PF14259 RRM_6: RNA recognition motif (a

Probab=97.95  E-value=1.4e-05  Score=58.68  Aligned_cols=36  Identities=47%  Similarity=0.786  Sum_probs=33.7

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceeccccee
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLY   39 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~   39 (303)
                      +|+++|+|||+|.+.++|.+|++.+++..|+||.|+
T Consensus        35 ~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen   35 DGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             TSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             ccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            478999999999999999999999999999999875

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 ....

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=97.91  E-value=1.3e-05  Score=79.42  Aligned_cols=44  Identities=48%  Similarity=0.767  Sum_probs=41.1

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .+|++||||||+|.+.++|.+|++.|||..|.|++|.|.|+...
T Consensus       223 ~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~  266 (457)
T TIGR01622       223 ETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDS  266 (457)
T ss_pred             CCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccCC
Confidence            36799999999999999999999999999999999999998843

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.

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=97.89  E-value=1.5e-05  Score=82.14  Aligned_cols=44  Identities=34%  Similarity=0.521  Sum_probs=38.8

Q ss_pred             CCCCCCcccEEEEEeCCHHHHHHHHHHhCCceec-ccceeeeccc
Q psy14476          1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIG-SKPLYVALAQ   44 (303)
Q Consensus         1 ~d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~-GR~L~V~~A~   44 (303)
                      +|.+|+|||||||+|.+.++|++||+.||+.+|. ||.|.|+++.
T Consensus        92 ~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~  136 (578)
T TIGR01648        92 MDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISV  136 (578)
T ss_pred             ECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccccc
Confidence            4789999999999999999999999999999885 7777776553

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.

>smart00362 RRM_2 RNA recognition motif

Probab=97.89  E-value=2.1e-05  Score=55.72  Aligned_cols=37  Identities=51%  Similarity=0.890  Sum_probs=34.6

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCceecccceeee
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVA   41 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~   41 (303)
                      ++++|+|||+|.+.++|++|++.+++..+.|+.|.|.
T Consensus        36 ~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362       36 GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            6788999999999999999999999999999998874

>KOG0149|consensus

Probab=97.88  E-value=8.2e-06  Score=74.71  Aligned_cols=41  Identities=41%  Similarity=0.673  Sum_probs=36.4

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      .||||||||||+|.|.|.|.+|++. -.-.|+||+-.|++|.
T Consensus        49 ~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   49 NTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLAS   89 (247)
T ss_pred             CCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhh
Confidence            4899999999999999999999986 3467999999999774

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=97.87  E-value=1.8e-05  Score=69.37  Aligned_cols=43  Identities=49%  Similarity=0.774  Sum_probs=40.6

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      .+|++||||||+|.+.++|..|++.++|..|.||+|.|.++..
T Consensus       152 ~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         152 ETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             ccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            4899999999999999999999999999999999999999654

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=97.87  E-value=1.6e-05  Score=79.56  Aligned_cols=43  Identities=30%  Similarity=0.483  Sum_probs=40.7

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      .+|+++|||||+|.+.++|+.||+.|||..|.|+.|.|.+|..
T Consensus       332 ~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~  374 (509)
T TIGR01642       332 ATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACV  374 (509)
T ss_pred             CCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECcc
Confidence            4799999999999999999999999999999999999999864

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0107|consensus

Probab=97.83  E-value=1.1e-05  Score=71.22  Aligned_cols=41  Identities=32%  Similarity=0.562  Sum_probs=37.8

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      ...|||||+|+++.||+.|+..|||+.|+|..|.|.+...+
T Consensus        45 nPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~   85 (195)
T KOG0107|consen   45 NPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGR   85 (195)
T ss_pred             cCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCC
Confidence            35699999999999999999999999999999999988754

>KOG0113|consensus

Probab=97.80  E-value=2.2e-05  Score=74.09  Aligned_cols=43  Identities=21%  Similarity=0.474  Sum_probs=40.5

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      .||+|||||||+|+++.+...|.+..+|.+|+||.|.|++-..
T Consensus       138 vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvERg  180 (335)
T KOG0113|consen  138 VTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVERG  180 (335)
T ss_pred             ccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEeccc
Confidence            5899999999999999999999999999999999999998654

>KOG0147|consensus

Probab=97.75  E-value=2.2e-05  Score=78.99  Aligned_cols=44  Identities=39%  Similarity=0.724  Sum_probs=41.1

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      +||++||||||+|.+.++|.+|++.|||.+|.||.|+|+.-..+
T Consensus       315 ~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  315 ETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             ccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            49999999999999999999999999999999999999977654

>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=97.74  E-value=6.6e-05  Score=53.35  Aligned_cols=39  Identities=46%  Similarity=0.830  Sum_probs=35.5

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeec
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVAL   42 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~   42 (303)
                      .++++|++||+|.+.++|+.|++.+++..+.|+.+.|.+
T Consensus        36 ~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590          36 DTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            346789999999999999999999999999999999864

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).

>KOG0130|consensus

Probab=97.73  E-value=2e-05  Score=67.06  Aligned_cols=44  Identities=25%  Similarity=0.376  Sum_probs=41.6

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .||..|||++|+|++.++|++||..+||..|.|.+|.|+||.-+
T Consensus       109 RtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv~  152 (170)
T KOG0130|consen  109 RTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFVK  152 (170)
T ss_pred             ccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEec
Confidence            48999999999999999999999999999999999999999754

>KOG0127|consensus

Probab=97.71  E-value=3.5e-05  Score=77.80  Aligned_cols=46  Identities=37%  Similarity=0.596  Sum_probs=42.6

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .+|+-+|||||.|....+|.+|++.+||.+|+||+|.|+||..|+.
T Consensus       153 ~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~  198 (678)
T KOG0127|consen  153 KDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDT  198 (678)
T ss_pred             CCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeeccccc
Confidence            3578889999999999999999999999999999999999987754

>KOG0131|consensus

Probab=97.68  E-value=2.4e-05  Score=69.44  Aligned_cols=41  Identities=27%  Similarity=0.455  Sum_probs=38.8

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      +.+.+|||||+|.+.|+|+-||+-||..+|.||+|+|+.+.
T Consensus        47 ~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen   47 TQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             cccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            56789999999999999999999999999999999999876

>KOG4212|consensus

Probab=97.67  E-value=3.6e-05  Score=75.99  Aligned_cols=44  Identities=27%  Similarity=0.497  Sum_probs=41.3

Q ss_pred             CCCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         1 ~d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      +|++||+|||+.|+|+++|.++||++.||-+.+.||+|+|+-..
T Consensus        79 ~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   79 FDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             cccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            58999999999999999999999999999999999999998544

>KOG0131|consensus

Probab=97.66  E-value=3.8e-05  Score=68.15  Aligned_cols=48  Identities=33%  Similarity=0.682  Sum_probs=44.0

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK   50 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~   50 (303)
                      .||+++|||||.|++.|.+++||+.|||..++.|+|.|.++.++....
T Consensus       134 ~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~kg  181 (203)
T KOG0131|consen  134 DTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDTKG  181 (203)
T ss_pred             cCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCCCc
Confidence            479999999999999999999999999999999999999998765443

>KOG0124|consensus

Probab=97.64  E-value=3.4e-05  Score=74.71  Aligned_cols=42  Identities=36%  Similarity=0.706  Sum_probs=39.8

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      ||++|||+||+|+-+|.|.-|++.|||..++||.|+|.+-.+
T Consensus       151 T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsN  192 (544)
T KOG0124|consen  151 TGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSN  192 (544)
T ss_pred             cccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCC
Confidence            899999999999999999999999999999999999996554

>PLN03213 repressor of silencing 3; Provisional

Probab=97.62  E-value=8.9e-05  Score=74.23  Aligned_cols=43  Identities=23%  Similarity=0.383  Sum_probs=39.1

Q ss_pred             CCCCcccEEEEEeCCH--HHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSP--EEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~--e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      +||  ||||||+|.+.  .++++||..|||.++.||.|+|..|++.-
T Consensus        45 ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP~Y   89 (759)
T PLN03213         45 TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKEHY   89 (759)
T ss_pred             ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccHHH
Confidence            467  99999999987  78999999999999999999999998653

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=97.55  E-value=9.2e-05  Score=73.28  Aligned_cols=43  Identities=30%  Similarity=0.535  Sum_probs=39.0

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .+|++||||||+|.+.++|.+||. |+|..|.|++|.|.++...
T Consensus       126 ~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~~~~  168 (457)
T TIGR01622       126 NSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSSQAE  168 (457)
T ss_pred             CCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeecchh
Confidence            378999999999999999999996 8999999999999987543

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>KOG0146|consensus

Probab=97.55  E-value=0.00017  Score=67.56  Aligned_cols=57  Identities=35%  Similarity=0.489  Sum_probs=46.8

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCce-ec--ccceeeecccchHHHHHHHHHHHH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRI-IG--SKPLYVALAQRKEDRKAHLASQYM   58 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~-l~--GR~L~V~~A~~k~~r~~~~~~~~~   58 (303)
                      ..+|.||||+||.|.+..||..||..|+|.. +-  ...|.|+||...+||..+..++..
T Consensus        54 g~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~ADTdkER~lRRMQQma  113 (371)
T KOG0146|consen   54 GPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKFADTDKERTLRRMQQMA  113 (371)
T ss_pred             CCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEeccchHHHHHHHHHHHH
Confidence            3579999999999999999999999999865 33  467999999988887766555443

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=97.50  E-value=0.00012  Score=69.61  Aligned_cols=44  Identities=34%  Similarity=0.628  Sum_probs=39.5

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecc--cceeeecccchH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGS--KPLYVALAQRKE   47 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~G--R~L~V~~A~~k~   47 (303)
                      +|.+||||||+|++.++|++||+.|||..+.|  ++|.|.++..+.
T Consensus       127 ~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~~  172 (352)
T TIGR01661       127 TGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPS  172 (352)
T ss_pred             CCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCCC
Confidence            68899999999999999999999999999887  678899887654

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>PLN03120 nucleic acid binding protein; Provisional

Probab=97.43  E-value=0.00017  Score=67.42  Aligned_cols=39  Identities=21%  Similarity=0.407  Sum_probs=35.7

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      .++|||||+|.++++|+.||. |||..|.||.|.|.++..
T Consensus        41 ~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120         41 ERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            468999999999999999995 999999999999998753

>KOG0943|consensus

Probab=97.39  E-value=8e-05  Score=80.58  Aligned_cols=63  Identities=32%  Similarity=0.489  Sum_probs=59.9

Q ss_pred             HHHhhhccchhhhhhhCCCCCCCchhhcccCChHHHHHhhCChHHHHHHHHHHH--HHHHHHHHH
Q psy14476        234 QKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAV--AVLQAHQAK  296 (303)
Q Consensus       234 qk~~lGe~ly~~v~~~~p~~A~KITGMlLe~~~~ell~ll~~~~~L~~kv~eA~--~vl~~~~~~  296 (303)
                      .+|.|||+||+.++.+.|.+|.||||||||.....+|..|-+++.|+..|++|+  +++..|.++
T Consensus      2607 e~Q~la~l~wgqhe~~l~a~~s~~sGfL~dek~~g~llgi~ce~p~eafVdaa~ndd~i~~H~qe 2671 (3015)
T KOG0943|consen 2607 ERQALAELLWGQHEAMLPAFASKISGFLLDEKPAGLLLGIACEDPLEAFVDAAMNDDLIIAHGQE 2671 (3015)
T ss_pred             hhccchhhcchhhhhHHHHHHHhhhhhhhccchHHHHHHHhhcCcHHHHHHHhcchHHHHHHHHH
Confidence            589999999999999999999999999999999999999999999999999999  888888765

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=97.38  E-value=0.00019  Score=72.31  Aligned_cols=40  Identities=28%  Similarity=0.396  Sum_probs=37.3

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      +||||||+|.+.++|.+||+.|||..|.|++|+|.+++.+
T Consensus       312 ~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~  351 (481)
T TIGR01649       312 KKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQ  351 (481)
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccc
Confidence            4799999999999999999999999999999999998654

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=97.23  E-value=0.00036  Score=70.41  Aligned_cols=42  Identities=21%  Similarity=0.241  Sum_probs=37.5

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHh--CCceecccceeeecccchH
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEM--NGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~l--nG~~l~GR~L~V~~A~~k~   47 (303)
                      ++||||||+|++.++|++||+.+  ++..|.|++|+|.|+..++
T Consensus        36 ~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~~   79 (481)
T TIGR01649        36 PGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQE   79 (481)
T ss_pred             CCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCcc
Confidence            46899999999999999999974  7899999999999997653

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>KOG0148|consensus

Probab=97.19  E-value=0.00034  Score=65.58  Aligned_cols=42  Identities=26%  Similarity=0.539  Sum_probs=38.8

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      |-+||+||.|++.|.|.+||..||+.+|.|..++|.|.+...
T Consensus       198 k~qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~  239 (321)
T KOG0148|consen  198 KDQGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGD  239 (321)
T ss_pred             cccceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCC
Confidence            458999999999999999999999999999999999987654

>KOG0110|consensus

Probab=97.16  E-value=0.00038  Score=72.16  Aligned_cols=45  Identities=33%  Similarity=0.581  Sum_probs=42.0

Q ss_pred             CCCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         1 ~d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      ++.+|+||+||||.|.+.++|++||+.+|+..|+-..|.|.+|..
T Consensus         2 ~t~dGk~R~F~FiGf~~eeeA~~Ai~~fn~s~i~ts~i~Ve~~~~   46 (725)
T KOG0110|consen    2 RTKDGKFRRFGFIGFKSEEEAQKAIKYFNKSFINTSRITVEFCKS   46 (725)
T ss_pred             cCCCCceeeeeEeeeccHHHHHHHHHHhhccccccceEEEEehhh
Confidence            457899999999999999999999999999999999999998874

>KOG0117|consensus

Probab=97.15  E-value=0.00047  Score=68.35  Aligned_cols=47  Identities=32%  Similarity=0.617  Sum_probs=42.6

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHHHH
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAH   52 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~~   52 (303)
                      +.|-||||.|.+.++|-+|++++||++|+|..|.|.+|++..+++..
T Consensus       291 k~rDYaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~k~~  337 (506)
T KOG0117|consen  291 KPRDYAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKKKKE  337 (506)
T ss_pred             cccceeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhhccc
Confidence            56789999999999999999999999999999999999987765543

>KOG0121|consensus

Probab=97.13  E-value=0.00045  Score=58.39  Aligned_cols=42  Identities=21%  Similarity=0.388  Sum_probs=38.0

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      -...||+||+|-+.++|..|++-++|..|+.|+|.|+|...=
T Consensus        75 ktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~GF  116 (153)
T KOG0121|consen   75 KTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDAGF  116 (153)
T ss_pred             cCccceEEEEEecchhHHHHHHHhccCcccccceeeeccccc
Confidence            346799999999999999999999999999999999987543

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=97.09  E-value=0.00046  Score=69.19  Aligned_cols=39  Identities=28%  Similarity=0.388  Sum_probs=35.2

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      +++||||||+|.+.++|+.|| +|||..|.|+.|+|....
T Consensus       220 ~~~kg~afVeF~~~e~A~~Al-~l~g~~~~g~~l~v~r~~  258 (509)
T TIGR01642       220 NKEKNFAFLEFRTVEEATFAM-ALDSIIYSNVFLKIRRPH  258 (509)
T ss_pred             CCCCCEEEEEeCCHHHHhhhh-cCCCeEeeCceeEecCcc
Confidence            477999999999999999999 599999999999997543

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0110|consensus

Probab=97.08  E-value=0.00053  Score=71.08  Aligned_cols=40  Identities=35%  Similarity=0.687  Sum_probs=37.7

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      |.|||||+|.+.++|++|++.|+|..|+|+.|.|.++..+
T Consensus       559 SmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k  598 (725)
T KOG0110|consen  559 SMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENK  598 (725)
T ss_pred             ccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCc
Confidence            6799999999999999999999999999999999999833

>KOG0144|consensus

Probab=96.90  E-value=0.00084  Score=66.39  Aligned_cols=55  Identities=24%  Similarity=0.433  Sum_probs=43.6

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCce-ecc--cceeeecccchHHHHHHHHHHHH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRI-IGS--KPLYVALAQRKEDRKAHLASQYM   58 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~-l~G--R~L~V~~A~~k~~r~~~~~~~~~   58 (303)
                      ||.|||||||.|.+.+||++||..|+..+ |-|  .+|.|++|....+|..+..+.|.
T Consensus        72 t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~E~er~~~e~KLFv  129 (510)
T KOG0144|consen   72 TGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKYADGERERIVEERKLFV  129 (510)
T ss_pred             cCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecccchhhhccccchhhhh
Confidence            78999999999999999999999998765 444  68999999876666433344443

>KOG0127|consensus

Probab=96.89  E-value=0.00059  Score=69.16  Aligned_cols=45  Identities=27%  Similarity=0.505  Sum_probs=41.6

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      ++.+||||||+|.-.||++.|+.+.++..|.||.|+|+.|.++..
T Consensus        43 s~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R~r   87 (678)
T KOG0127|consen   43 SSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKRAR   87 (678)
T ss_pred             cccccCccceeeehHhHHHHHHHHhhcCcccceeccccccccccc
Confidence            567899999999999999999999999999999999999987654

>KOG4206|consensus

Probab=96.84  E-value=0.00092  Score=60.98  Aligned_cols=50  Identities=26%  Similarity=0.412  Sum_probs=45.4

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHHHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAH   52 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~~   52 (303)
                      .|.+.||=|||.|++.+.|..|+..|+|..+-||+++|.||+.+.+-..+
T Consensus        47 kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~s~sdii~~   96 (221)
T KOG4206|consen   47 KTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAKSDSDIIAQ   96 (221)
T ss_pred             CCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecccCccchhhc
Confidence            47899999999999999999999999999999999999999988765443

>KOG0145|consensus

Probab=96.76  E-value=0.0014  Score=61.42  Aligned_cols=43  Identities=33%  Similarity=0.588  Sum_probs=39.3

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceec--ccceeeecccch
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIG--SKPLYVALAQRK   46 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~--GR~L~V~~A~~k   46 (303)
                      ||.|||.|||.|+..+||+.||+.|||.+-.  ..+|.|+||...
T Consensus       165 tg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannP  209 (360)
T KOG0145|consen  165 TGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNP  209 (360)
T ss_pred             cceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCc
Confidence            7999999999999999999999999999854  578999999865

>KOG0114|consensus

Probab=96.67  E-value=0.0052  Score=50.37  Aligned_cols=44  Identities=23%  Similarity=0.357  Sum_probs=39.9

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      -..||-|||.|++..+|++|++.|+|..++++.|.|-+.++-+.
T Consensus        54 k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~~~   97 (124)
T KOG0114|consen   54 KETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPEDA   97 (124)
T ss_pred             cCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHHHH
Confidence            34689999999999999999999999999999999999886544

>PLN03121 nucleic acid binding protein; Provisional

Probab=96.65  E-value=0.0025  Score=59.03  Aligned_cols=40  Identities=18%  Similarity=0.215  Sum_probs=35.8

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      +++++|||||+|.++++++.|+ .|||..|.+++|.|..+.
T Consensus        40 D~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~   79 (243)
T PLN03121         40 SGEYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CCCcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCc
Confidence            4677899999999999999999 589999999999998654

>KOG0105|consensus

Probab=96.05  E-value=0.0035  Score=56.14  Aligned_cols=39  Identities=26%  Similarity=0.357  Sum_probs=36.4

Q ss_pred             ccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          8 KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         8 kGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      -.|+||+|+++.+|+.||..-||..++|..|+|.++..-
T Consensus        45 ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprgg   83 (241)
T KOG0105|consen   45 PPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGG   83 (241)
T ss_pred             CCeeEEEecCccchhhhhhcccccccCcceEEEEeccCC
Confidence            479999999999999999999999999999999998753

>KOG0415|consensus

Probab=96.03  E-value=0.0053  Score=59.66  Aligned_cols=45  Identities=22%  Similarity=0.406  Sum_probs=41.9

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .||.|--|+||+|++.+++++|..+|+...|+.|.|.|+|++.-.
T Consensus       276 ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQSVs  320 (479)
T KOG0415|consen  276 KTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQSVS  320 (479)
T ss_pred             cccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhhhhh
Confidence            489999999999999999999999999999999999999987643

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=95.66  E-value=0.018  Score=46.35  Aligned_cols=41  Identities=27%  Similarity=0.442  Sum_probs=36.0

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceec----ccceeeeccc
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIG----SKPLYVALAQ   44 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~----GR~L~V~~A~   44 (303)
                      ++.+.|||||.|.+++.+.+-.+.++|+.+.    .|.+.|.||+
T Consensus        41 ~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i~yAr   85 (97)
T PF04059_consen   41 NKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEISYAR   85 (97)
T ss_pred             CCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEEehhH
Confidence            5678999999999999999999999999886    5667788886

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG0109|consensus

Probab=95.52  E-value=0.0083  Score=56.97  Aligned_cols=41  Identities=24%  Similarity=0.434  Sum_probs=38.0

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .-|+|+||.|+-.++|..||+.||+.+|.|+++.|.....+
T Consensus       110 ivkdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen  110 IVKDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             eecceeEEEEeeccchHHHHhcccccccccceeeeeeeccc
Confidence            35899999999999999999999999999999999988765

>KOG4205|consensus

Probab=95.21  E-value=0.008  Score=57.84  Aligned_cols=46  Identities=30%  Similarity=0.363  Sum_probs=41.1

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR   49 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r   49 (303)
                      ++.++||||||.|++.+.+++++. ...+.|+++.+.|..|.+|+..
T Consensus       134 ~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk~~~  179 (311)
T KOG4205|consen  134 TTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPKEVM  179 (311)
T ss_pred             cccccccceeeEeccccccceecc-cceeeecCceeeEeeccchhhc
Confidence            478899999999999999999876 4889999999999999998754

>KOG4209|consensus

Probab=95.18  E-value=0.019  Score=53.11  Aligned_cols=40  Identities=35%  Similarity=0.519  Sum_probs=37.0

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      +|.+|||+||+|.+.+...+|+. |||..|.|+.+.|.+.+
T Consensus       139 ~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~r  178 (231)
T KOG4209|consen  139 RGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLKR  178 (231)
T ss_pred             CCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeeee
Confidence            46799999999999999999999 99999999999999754

>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=95.11  E-value=0.031  Score=44.11  Aligned_cols=40  Identities=23%  Similarity=0.331  Sum_probs=30.4

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      +.|-|+|.|.+.+.|++|.+.|+|..+.|++|.|.|....
T Consensus        38 ~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~~   77 (90)
T PF11608_consen   38 SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPKN   77 (90)
T ss_dssp             -TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--S
T ss_pred             eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCCc
Confidence            5688999999999999999999999999999999998543

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG2314|consensus

Probab=94.93  E-value=0.03  Score=57.36  Aligned_cols=41  Identities=37%  Similarity=0.681  Sum_probs=35.9

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecc-cceeeec
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGS-KPLYVAL   42 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~G-R~L~V~~   42 (303)
                      |+.|.++||.|++|.+..+|+.||+.|||+.|+- +++.|..
T Consensus        99 ~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~v~~  140 (698)
T KOG2314|consen   99 DEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFFVRL  140 (698)
T ss_pred             CccCCeeeEEEEEecChhhHHHHHHhcccceecccceEEeeh
Confidence            6788899999999999999999999999999984 4555554

>KOG4661|consensus

Probab=94.83  E-value=0.021  Score=58.56  Aligned_cols=39  Identities=26%  Similarity=0.457  Sum_probs=36.3

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      -|+||||++++.++|.++|+.|+..+|.||.|.|..++.
T Consensus       446 aRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  446 ARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             cceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            378999999999999999999999999999999998764

>KOG0106|consensus

Probab=94.79  E-value=0.012  Score=53.80  Aligned_cols=39  Identities=38%  Similarity=0.697  Sum_probs=36.2

Q ss_pred             ccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          8 KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         8 kGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .||+||+|++..+|+.||..+|+++|+|..+.|.++...
T Consensus        35 ~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen   35 NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             cccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            589999999999999999999999999998999998853

>KOG4205|consensus

Probab=94.74  E-value=0.0084  Score=57.69  Aligned_cols=45  Identities=31%  Similarity=0.596  Sum_probs=39.3

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR   49 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r   49 (303)
                      +|+||||+||+|++.+..++++.. .-++|+||.|.+..|.++++.
T Consensus        44 t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av~r~~~   88 (311)
T KOG4205|consen   44 TGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAVSREDQ   88 (311)
T ss_pred             CCCcccccceecCCCcchheeecc-cccccCCccccceeccCcccc
Confidence            799999999999999999988864 667899999999999887754

>KOG0132|consensus

Probab=94.70  E-value=0.027  Score=59.42  Aligned_cols=45  Identities=20%  Similarity=0.356  Sum_probs=41.3

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHH
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK   50 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~   50 (303)
                      .+||||||+.....+|.+|+.+|+...+.++.|+|.||..+.-+.
T Consensus       455 ~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~ks  499 (894)
T KOG0132|consen  455 PPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGPKS  499 (894)
T ss_pred             cCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCcch
Confidence            468999999999999999999999999999999999999776555

>KOG0533|consensus

Probab=94.49  E-value=0.045  Score=50.97  Aligned_cols=45  Identities=27%  Similarity=0.496  Sum_probs=41.4

Q ss_pred             CCCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         1 ~d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      +|++|+|.|.|-|.|...++|..||+.++|..++|++|++....+
T Consensus       117 y~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~  161 (243)
T KOG0533|consen  117 YDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISS  161 (243)
T ss_pred             cCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecC
Confidence            478999999999999999999999999999999999999886653

>KOG0124|consensus

Probab=94.04  E-value=0.035  Score=54.30  Aligned_cols=43  Identities=23%  Similarity=0.380  Sum_probs=38.7

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .+.+|||||++|.+..+-+.||..||-..|+|.-|+|..+...
T Consensus       248 ~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vTP  290 (544)
T KOG0124|consen  248 GRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTP  290 (544)
T ss_pred             CCCccceeeEEeccccchHHHhhhcchhhcccceEecccccCC
Confidence            4569999999999999999999999999999999999977543

>KOG0109|consensus

Probab=94.04  E-value=0.032  Score=53.12  Aligned_cols=41  Identities=22%  Similarity=0.388  Sum_probs=38.2

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .-|-||||..++...+..||..|+|.+|+|..|+|.-++.|
T Consensus        34 IvKNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen   34 IVKNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             eecccceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            35789999999999999999999999999999999988877

>KOG1457|consensus

Probab=94.03  E-value=0.062  Score=49.55  Aligned_cols=40  Identities=28%  Similarity=0.378  Sum_probs=35.6

Q ss_pred             ccEEEEEeCCHHHHHHHHHHhCCceec---ccceeeecccchH
Q psy14476          8 KGFGFVCFSSPEEATKAVTEMNGRIIG---SKPLYVALAQRKE   47 (303)
Q Consensus         8 kGfgFV~F~s~e~A~~Ai~~lnG~~l~---GR~L~V~~A~~k~   47 (303)
                      +-+|||+|.+..+|.+|+..|||..|+   +..|.+++|+...
T Consensus        77 ~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiElAKSNt  119 (284)
T KOG1457|consen   77 KPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIELAKSNT  119 (284)
T ss_pred             cceEEEEecchHHHHHHHHHhcCeeeccccCceeEeeehhcCc
Confidence            469999999999999999999999987   6789999987653

>KOG0106|consensus

Probab=92.37  E-value=0.06  Score=49.30  Aligned_cols=38  Identities=26%  Similarity=0.558  Sum_probs=34.4

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      .++|+||+|++.+++++|++.|++..+.++.|.|...-
T Consensus       132 ~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~~  169 (216)
T KOG0106|consen  132 RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKNS  169 (216)
T ss_pred             hccccceeehhhhhhhhcchhccchhhcCceeeecccC
Confidence            37999999999999999999999999999999994443

>KOG1548|consensus

Probab=91.39  E-value=0.18  Score=48.99  Aligned_cols=44  Identities=23%  Similarity=0.361  Sum_probs=41.8

Q ss_pred             CCCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         1 ~d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      +|+.|+.||=|.++|...|+.+-|+.-|++..|.|+.|+|..|+
T Consensus       176 rd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~~rVerAk  219 (382)
T KOG1548|consen  176 RDNQGKLKGDALCCYIKRESVELAIKILDEDELRGKKLRVERAK  219 (382)
T ss_pred             ecCCCCccCceEEEeecccHHHHHHHHhCcccccCcEEEEehhh
Confidence            46789999999999999999999999999999999999999886

>KOG1995|consensus

Probab=91.38  E-value=0.13  Score=50.11  Aligned_cols=46  Identities=28%  Similarity=0.448  Sum_probs=42.8

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      +|+++||=|.|+|+++..|+.||.-++++.+++-+|+|.+|..+..
T Consensus       111 eT~~~KGeatvS~~D~~~akaai~~~agkdf~gn~ikvs~a~~r~~  156 (351)
T KOG1995|consen  111 ETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGNTIKVSLAERRTG  156 (351)
T ss_pred             cccCcCCceeeeecChhhhhhhhhhhccccccCCCchhhhhhhccC
Confidence            6899999999999999999999999999999999999999987653

>KOG0120|consensus

Probab=91.27  E-value=0.093  Score=53.48  Aligned_cols=44  Identities=34%  Similarity=0.552  Sum_probs=40.5

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .+|.||||+|.+|.++...+.|+..|||..+.++.|.|..|...
T Consensus       326 ~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g  369 (500)
T KOG0120|consen  326 ATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVG  369 (500)
T ss_pred             ccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhcc
Confidence            36899999999999999999999999999999999999987643

>KOG4454|consensus

Probab=89.36  E-value=0.23  Score=45.81  Aligned_cols=43  Identities=21%  Similarity=0.224  Sum_probs=37.6

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      |.+++-| |+||.|.++....-|++.|||..+.++.|.|.+-..
T Consensus        44 ~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~G   86 (267)
T KOG4454|consen   44 GQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRCG   86 (267)
T ss_pred             CccCCCc-eeeeecccccchhhhhhhcccchhccchhhcccccC
Confidence            3456777 999999999999999999999999999998887553

>KOG0153|consensus

Probab=89.30  E-value=0.35  Score=47.10  Aligned_cols=38  Identities=32%  Similarity=0.431  Sum_probs=33.1

Q ss_pred             ccEEEEEeCCHHHHHHHHHHh-CCceecccceeeecccc
Q psy14476          8 KGFGFVCFSSPEEATKAVTEM-NGRIIGSKPLYVALAQR   45 (303)
Q Consensus         8 kGfgFV~F~s~e~A~~Ai~~l-nG~~l~GR~L~V~~A~~   45 (303)
                      +|+|||.|.+.+.|+.|.++. |-..|+|++|+|.|..+
T Consensus       264 ~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  264 KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            679999999999999988754 44568999999999987

>KOG4211|consensus

Probab=88.83  E-value=0.4  Score=48.54  Aligned_cols=50  Identities=34%  Similarity=0.446  Sum_probs=41.2

Q ss_pred             CCCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHHH
Q psy14476          1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA   51 (303)
Q Consensus         1 ~d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~   51 (303)
                      +|..|++-|=+||+|++.|.|++|+.. |...|..|-|.|..+...+.++.
T Consensus       138 ~d~rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~Ss~~e~~~~  187 (510)
T KOG4211|consen  138 MDQRGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRSSRAEVKRA  187 (510)
T ss_pred             ccCCCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehhHHHHHHhh
Confidence            466789999999999999999999986 77788888888887776555443

>KOG0147|consensus

Probab=88.63  E-value=0.46  Score=48.65  Aligned_cols=39  Identities=26%  Similarity=0.333  Sum_probs=35.7

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      .|-||-||.|.+.+.|..|+++|||..|.||.|...|-.
T Consensus       488 ns~g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~~  526 (549)
T KOG0147|consen  488 NSAGCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKYLP  526 (549)
T ss_pred             CCCceEEEecCcHHHHHHHHHHHhhhhhccceeEEEEee
Confidence            455999999999999999999999999999999988753

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=86.90  E-value=0.62  Score=45.44  Aligned_cols=35  Identities=20%  Similarity=0.563  Sum_probs=33.2

Q ss_pred             EEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476         12 FVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus        12 FV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      ||+|.+.|||.++|.+.+|..++||.|+..|...|
T Consensus       169 YITy~~kedAarcIa~vDgs~~DGr~lkatYGTTK  203 (480)
T COG5175         169 YITYSTKEDAARCIAEVDGSLLDGRVLKATYGTTK  203 (480)
T ss_pred             EEEecchHHHHHHHHHhccccccCceEeeecCchH
Confidence            99999999999999999999999999999988765

>KOG1548|consensus

Probab=86.50  E-value=1.1  Score=43.83  Aligned_cols=38  Identities=26%  Similarity=0.441  Sum_probs=33.6

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecc
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA   43 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A   43 (303)
                      ...|.+-|.|.+.++|+.+|+.|+|+.|+||.|.-...
T Consensus       312 hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~  349 (382)
T KOG1548|consen  312 HPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIW  349 (382)
T ss_pred             CCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEe
Confidence            45688999999999999999999999999999875543

>KOG0116|consensus

Probab=86.44  E-value=0.51  Score=47.31  Aligned_cols=37  Identities=30%  Similarity=0.487  Sum_probs=32.9

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeec
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVAL   42 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~   42 (303)
                      +++.+||||+|.+.+++..||.+ +-..|++++|+|.-
T Consensus       327 ~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Vee  363 (419)
T KOG0116|consen  327 GKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEE  363 (419)
T ss_pred             CCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEe
Confidence            56669999999999999999987 67889999999984

>KOG2202|consensus

Probab=86.44  E-value=0.44  Score=44.63  Aligned_cols=40  Identities=28%  Similarity=0.415  Sum_probs=35.6

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      -+|=.||.|...|+|.+|++.||+..+.|++|...+.---
T Consensus       109 l~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT  148 (260)
T KOG2202|consen  109 LVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVT  148 (260)
T ss_pred             hhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcC
Confidence            3678899999999999999999999999999998876543

>KOG4210|consensus

Probab=83.55  E-value=0.37  Score=45.91  Aligned_cols=46  Identities=33%  Similarity=0.569  Sum_probs=40.6

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      +++|.++||+||+|.+..++..++.. ....+.++++.+.+..++.+
T Consensus       221 ~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  266 (285)
T KOG4210|consen  221 EESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRPK  266 (285)
T ss_pred             CCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCcc
Confidence            46899999999999999999999887 78899999999998876643

>KOG4849|consensus

Probab=82.80  E-value=41  Score=33.36  Aligned_cols=41  Identities=17%  Similarity=0.315  Sum_probs=35.1

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA   43 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A   43 (303)
                      .+|.||||++|...+....++-++-|--++|.|..-.|--+
T Consensus       119 ~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~  159 (498)
T KOG4849|consen  119 TNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSY  159 (498)
T ss_pred             cCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeecc
Confidence            37999999999999999999999999999999987555543

>KOG4211|consensus

Probab=81.55  E-value=1.3  Score=45.03  Aligned_cols=41  Identities=29%  Similarity=0.472  Sum_probs=33.7

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      ++||..|=|||+|.+.|++++|+++ |...+..|-|.|-.+.
T Consensus        44 ~~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~RYIEVf~~~   84 (510)
T KOG4211|consen   44 RNGRPSGEAYVEFTSEEDVEKALKK-DRESMGHRYIEVFTAG   84 (510)
T ss_pred             cCCCcCcceEEEeechHHHHHHHHh-hHHHhCCceEEEEccC
Confidence            4699999999999999999999985 6666777777766553

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=80.80  E-value=1.3  Score=33.31  Aligned_cols=34  Identities=35%  Similarity=0.473  Sum_probs=20.9

Q ss_pred             cEEEEEeCCHHHHHHHHHHhCCceecccceeeecc
Q psy14476          9 GFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA   43 (303)
Q Consensus         9 GfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A   43 (303)
                      -|.||+-.. +.++.+++.|++..+.||+++|..|
T Consensus        41 ~~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   41 NFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             S-EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             eEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            588998754 5888999999999999999999865

; PDB: 2G0C_A 3MOJ_B.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	303
1g9l_A	144	Solution Structure Of The Pabc Domain Of Human Poly		2e-25
2rqg_B	83	Structure Of Gspt1ERF3A-Pabc Length = 83		1e-24
3pth_A	82	The Pabc1 Mlle Domain Bound To The Variant Pam2 Mot		1e-24
1jgn_A	98	Solution Structure Of The C-Terminal Pabc Domain Of		2e-24
3kus_A	88	Crystal Structure Of The Mlle Domain Of Poly(A)-Bin		3e-24
3kur_A	79	Crystal Structure Of The Mlle Domain Of Poly(A)-Bin		5e-24
2x04_A	80	Crystal Structure Of The Pabc-Tnrc6c Complex Length		3e-23
4ive_A	98	Crystal Structure Of A Polyadenylate-binding Protei		3e-20
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		9e-20
2dyd_A	85	Solution Structure Of The Pabc Domain From Triticum		2e-10
1nmr_A	85	Solution Structure Of C-Terminal Domain From Trypan		1e-09
3ntw_A	65	Structure Of The Mlle Domain Of Edd In Complex With		8e-07
1i2t_A	61	X-Ray Structure Of The Human Hyperplastic Discs Pro		2e-06
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		2e-05
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		8e-05
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		2e-04
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		2e-04
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		4e-04

>pdb|1G9L|A Chain A, Solution Structure Of The Pabc Domain Of Human Poly(A) Binding Protein Length = 144

Iteration: 1
 Score =  112 bits (281), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 54/67 (80%), Positives = 62/67 (92%)
Query: 219 EPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNES 278
           EPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ES
Sbjct: 51  EPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPES 110
Query: 279 LKSKVEE 285
           L+SKV+E
Sbjct: 111 LRSKVDE 117

>pdb|2RQG|B Chain B, Structure Of Gspt1ERF3A-Pabc Length = 83

Iteration: 1
 Score =  110 bits (274), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 54/67 (80%), Positives = 62/67 (92%)
Query: 219 EPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNES 278
           EPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ES
Sbjct: 3   EPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPES 62
Query: 279 LKSKVEE 285
           L+SKV+E
Sbjct: 63  LRSKVDE 69

>pdb|3PTH|A Chain A, The Pabc1 Mlle Domain Bound To The Variant Pam2 Motif Of Larp4b Length = 82

Iteration: 1
 Score =  109 bits (273), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 54/67 (80%), Positives = 62/67 (92%)
Query: 219 EPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNES 278
           EPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ES
Sbjct: 4   EPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPES 63
Query: 279 LKSKVEE 285
           L+SKV+E
Sbjct: 64  LRSKVDE 70

>pdb|1JGN|A Chain A, Solution Structure Of The C-Terminal Pabc Domain Of Human Poly(A)-Binding Protein In Complex With The Peptide From Paip2 Length = 98

Iteration: 1
 Score =  109 bits (273), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 53/66 (80%), Positives = 61/66 (92%)
Query: 220 PLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESL 279
           PLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ESL
Sbjct: 6   PLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESL 65
Query: 280 KSKVEE 285
           +SKV+E
Sbjct: 66  RSKVDE 71

>pdb|3KUS|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding Protein In Complex With The Binding Region Of Paip2 Length = 88

Iteration: 1
 Score =  108 bits (270), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 53/66 (80%), Positives = 61/66 (92%)
Query: 220 PLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESL 279
           PLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ESL
Sbjct: 6   PLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESL 65
Query: 280 KSKVEE 285
           +SKV+E
Sbjct: 66  RSKVDE 71

>pdb|3KUR|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding Protein Length = 79

Iteration: 1
 Score =  108 bits (269), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 53/66 (80%), Positives = 61/66 (92%)
Query: 220 PLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESL 279
           PLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ESL
Sbjct: 6   PLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESL 65
Query: 280 KSKVEE 285
           +SKV+E
Sbjct: 66  RSKVDE 71

>pdb|2X04|A Chain A, Crystal Structure Of The Pabc-Tnrc6c Complex Length = 80

Iteration: 1
 Score =  105 bits (263), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 52/65 (80%), Positives = 60/65 (92%)
Query: 221 LTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLK 280
           LT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ESL+
Sbjct: 6   LTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLR 65
Query: 281 SKVEE 285
           SKV+E
Sbjct: 66  SKVDE 70

>pdb|4IVE|A Chain A, Crystal Structure Of A Polyadenylate-binding Protein 3 (pabpc3) From Homo Sapiens At 2.30 A Resolution Length = 98

Iteration: 1
 Score = 95.9 bits (237), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 48/67 (71%), Positives = 56/67 (83%)
Query: 219 EPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNES 278
           E LT++ LA+A PQ+QKQ LGERLFPLIQ  +P LAGKITG LLEIDN+ELLY LE  ES
Sbjct: 5   ETLTASRLASAPPQKQKQXLGERLFPLIQAXHPTLAGKITGXLLEIDNSELLYXLESPES 64
Query: 279 LKSKVEE 285
           L+SKV+E
Sbjct: 65  LRSKVDE 71

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 94.0 bits (232), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 43/51 (84%), Positives = 48/51 (94%)
Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
          M E GRSKGFGFVCFSSPEEATKAVTEMNGRI+ +KPLYVALAQRKE+R++
Sbjct: 48 MMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQS 98

>pdb|2DYD|A Chain A, Solution Structure Of The Pabc Domain From Triticum Aevestium Poly(A)-Binding Protein Length = 85

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 29/63 (46%), Positives = 47/63 (74%)
Query: 223 STMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSK 282
           ++ LA + P+ Q+ MLGE L+PL+ ++  + A K+TGMLLE+D  E+L++LE  ++LK+K
Sbjct: 11  ASALANSPPETQRMMLGENLYPLVDQLEHDQAAKVTGMLLEMDQTEVLHLLESPDALKAK 70
Query: 283 VEE 285
           V E
Sbjct: 71  VAE 73

>pdb|1NMR|A Chain A, Solution Structure Of C-Terminal Domain From Trypanosoma Cruzi Poly(A)-Binding Protein Length = 85

Iteration: 1
 Score = 60.1 bits (144), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 31/63 (49%), Positives = 44/63 (69%)
Query: 223 STMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSK 282
           ST+LA   P++QK +LGERL+  I  + P  A K+TGMLLE+DN E+L +L+    L +K
Sbjct: 12  STVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILNLLDTPGLLDAK 71
Query: 283 VEE 285
           V+E
Sbjct: 72  VQE 74

>pdb|3NTW|A Chain A, Structure Of The Mlle Domain Of Edd In Complex With A Pam2 Peptide From Paip1 Length = 65

Iteration: 1
 Score = 50.8 bits (120), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 28/52 (53%), Positives = 38/52 (73%)
Query: 234 QKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEE 285
            +Q LGERL+P +Q M P  A KITGMLLE+  A+LL +L   +SL+++VEE
Sbjct: 6   HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVEE 57

>pdb|1I2T|A Chain A, X-Ray Structure Of The Human Hyperplastic Discs Protein: An Ortholog Of The C-Terminal Domain Of Poly(A)-Binding Protein Length = 61

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/52 (51%), Positives = 38/52 (73%)
Query: 234 QKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEE 285
            +Q LGERL+P +Q M P  A KITGMLLE+  A+LL +L   +SL+++V+E
Sbjct: 1   HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDE 52

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 47/78 (60%), Gaps = 5/78 (6%)
Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           + ++  SKG+GFV F + E A +A+ +MNG ++  + ++V   + +++R+A L ++  + 
Sbjct: 38  VCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAR-AKE 96
Query: 61  IANMRMQQMGQLFQPGST 78
             N+ ++  G    PGST
Sbjct: 97  FTNVYIKNFG----PGST 110

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 20/47 (42%), Positives = 29/47 (61%)
Query: 2   SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED 48
           SE GRSKG+GF+ FS  E A KA+ ++NG  +  +P+ V     + D
Sbjct: 62  SETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 17/56 (30%), Positives = 37/56 (66%)
Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQ 56
           + ++  SKG+GFV F + E A +A+ +MNG ++  + ++V   + +++R+A L ++
Sbjct: 136 VCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAR 191

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 17/56 (30%), Positives = 37/56 (66%)
Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQ 56
           + ++  SKG+GFV F + E A +A+ +MNG ++  + ++V   + +++R+A L ++
Sbjct: 131 VCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAR 186

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 18/49 (36%), Positives = 34/49 (69%), Gaps = 1/49 (2%)
Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
          E+G SKG+GFV F + E A +A+ +MNG ++  + ++V   + +++R+A
Sbjct: 47 ENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREA 94

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	303
1ifw_A	92	Polyadenylate-binding protein, cytoplasmic and nuc	2e-35
1nmr_A	85	Poly(A)-binding protein; all helical domain, pepti	1e-34
2dyd_A	85	Poly(A)-binding protein; alpha helical protein, RN	2e-32
1i2t_A	61	HYD protein; four alpha-helical domain, ligase; 1.	1e-30
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-29
3kuj_A	88	Polyadenylate-binding protein 1; protein-protein c	5e-29
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-26
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-15
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-10
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-26
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-25
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-23
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-23
1x5o_A	114	RNA binding motif, single-stranded interacting pro	4e-22
1g9l_A	144	Polyadenylate-binding protein 1; all-helical domai	6e-22
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-21
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	5e-21
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-20
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-09
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-20
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	8e-20
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-19
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	2e-19
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-19
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	5e-10
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-19
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-13
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-19
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-07
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	5e-19
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	8e-19
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	5e-18
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-18
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-11
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	9e-18
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	6e-09
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-17
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-13
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-17
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-17
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-17
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-17
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-12
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	6e-17
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	6e-10
1x5p_A	97	Negative elongation factor E; structure genomics,	6e-17
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-16
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-16
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-16
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-16
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-16
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-16
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	3e-16
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	6e-16
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-11
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-15
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-11
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-14
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-14
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	7e-14
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	7e-14
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-13
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-13
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-09
1x4e_A	85	RNA binding motif, single-stranded interacting pro	5e-13
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	5e-13
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	6e-13
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	6e-13
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	9e-13
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	1e-12
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-12
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-12
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-12
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-12
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-12
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-12
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-12
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-12
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	3e-12
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	5e-12
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	6e-12
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-11
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	1e-11
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-11
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-11
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	3e-11
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	3e-11
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	3e-11
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-11
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	3e-11
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	4e-11
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	6e-11
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	8e-11
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	8e-11
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	9e-11
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-10
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-10
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-10
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-10
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-10
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-10
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-10
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-10
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-10
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	4e-10
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-10
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	6e-10
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	7e-10
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	9e-10
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	9e-10
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	9e-10
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	1e-09
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-09
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-09
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-09
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	4e-09
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	6e-09
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	6e-09
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	6e-09
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	6e-09
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	8e-09
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	8e-09
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-08
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-08
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	1e-08
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-08
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	5e-07
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-08
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-08
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	3e-08
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	3e-08
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-08
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	4e-08
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	4e-08
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	5e-08
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	6e-08
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	6e-08
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-06
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	8e-08
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	9e-08
2div_A	99	TRNA selenocysteine associated protein; structural	1e-07
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-07
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	1e-07
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-07
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-07
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	1e-07
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-07
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	3e-07
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	3e-07
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-07
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-07
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-07
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	4e-07
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	5e-07
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	5e-07
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-07
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	5e-07
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-07
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	6e-07
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	7e-07
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-06
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	1e-06
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-06
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-06
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-06
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-06
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-06
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	3e-06
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	3e-06
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	3e-06
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	5e-06
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	5e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	6e-06
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	6e-06
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-05
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-05
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-05
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	3e-05
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	4e-04
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	4e-05
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	4e-05
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	7e-05
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	7e-05
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	9e-05
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	9e-05
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	2e-04
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-04
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	4e-04
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	8e-04
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	9e-04

>1ifw_A Polyadenylate-binding protein, cytoplasmic and nuclear; all-helical domain, RNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.144.1.1 Length = 92

 Score =  122 bits (307), Expect = 2e-35
 Identities = 25/88 (28%), Positives = 45/88 (51%), Gaps = 2/88 (2%)

Query: 218 QEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMY--PELAGKITGMLLEIDNAELLYMLEH 275
             P  +        Q+Q+Q LGE+L+  +       E AGKITGM+L++   E+  +LE 
Sbjct: 4   GSPRNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLLES 63

Query: 276 NESLKSKVEEAVAVLQAHQAKQAAVKKE 303
           +E  +   +EA A  ++ + +Q    ++
Sbjct: 64  DELFEQHYKEASAAYESFKKEQEQQTEQ 91

>1nmr_A Poly(A)-binding protein; all helical domain, peptide binding protein; NMR {Trypanosoma cruzi} SCOP: a.144.1.1 Length = 85

 Score =  119 bits (301), Expect = 1e-34
 Identities = 36/84 (42%), Positives = 51/84 (60%)

Query: 212 AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 271
              +  Q    ST+LA   P++QK +LGERL+  I  + P  A K+TGMLLE+DN E+L 
Sbjct: 1   GSSLASQGQNLSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILN 60

Query: 272 MLEHNESLKSKVEEAVAVLQAHQA 295
           +L+    L +KV+EA+ VL  H  
Sbjct: 61  LLDTPGLLDAKVQEALEVLNRHMN 84

>2dyd_A Poly(A)-binding protein; alpha helical protein, RNA binding protein; NMR {Triticum aestivum} Length = 85

 Score =  114 bits (287), Expect = 2e-32
 Identities = 33/82 (40%), Positives = 55/82 (67%)

Query: 215 VQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLE 274
           +       ++ LA + P+ Q+ MLGE L+PL+ ++  + A K+TGMLLE+D  E+L++LE
Sbjct: 3   LGSPIGALASALANSPPETQRMMLGENLYPLVDQLEHDQAAKVTGMLLEMDQTEVLHLLE 62

Query: 275 HNESLKSKVEEAVAVLQAHQAK 296
             ++LK+KV EA+ VL++ Q  
Sbjct: 63  SPDALKAKVAEAMEVLRSAQQH 84

>1i2t_A HYD protein; four alpha-helical domain, ligase; 1.04A {Homo sapiens} SCOP: a.144.1.1 PDB: 3ntw_A Length = 61

 Score =  109 bits (273), Expect = 1e-30
 Identities = 30/60 (50%), Positives = 44/60 (73%)

Query: 234 QKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAH 293
            +Q LGERL+P +Q M P  A KITGMLLE+  A+LL +L   +SL+++V+EA+ ++ AH
Sbjct: 1   HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELIIAH 60

>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 =  106 bits (267), Expect = 3e-29
 Identities = 44/55 (80%), Positives = 50/55 (90%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLAS 55
           M E GRSKGFGFVCFSSPEEATKAVTEMNGRI+ +KPLYVALAQRKE+R++  +S
Sbjct: 48  MMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQSGPSS 102

>3kuj_A Polyadenylate-binding protein 1; protein-protein complex, methylation, mRNA processing, mRNA nucleus, phosphoprotein, RNA-binding, spliceosome; 1.40A {Homo sapiens} PDB: 3ktr_A 3kui_A 3ktp_A 3kus_A* 3kut_A 3pkn_A 2rqg_B 2rqh_B 3kur_A 3pth_A 2x04_A Length = 88

 Score =  105 bits (263), Expect = 5e-29
 Identities = 66/83 (79%), Positives = 75/83 (90%)

Query: 217 GQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHN 276
              PLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  
Sbjct: 3   LGSPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESP 62

Query: 277 ESLKSKVEEAVAVLQAHQAKQAA 299
           ESL+SKV+EAVAVLQAHQAK+AA
Sbjct: 63  ESLRSKVDEAVAVLQAHQAKEAA 85

>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 =  104 bits (262), Expect = 1e-26
 Identities = 14/62 (22%), Positives = 29/62 (46%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIA 62
           +DG+ KGF  + + + E A +A  + +G  +G   L V+        ++ LA+    +  
Sbjct: 221 QDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQAT 280

Query: 63  NM 64
            +
Sbjct: 281 AL 282

>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 = 74.6 bits (184), Expect = 1e-15
 Identities = 16/54 (29%), Positives = 29/54 (53%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQ 56
             G+SKG+GF  +   + A +A +++ G+ +G + LYV      +   A L S+
Sbjct: 132 RTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSR 185

>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 = 58.1 bits (141), Expect = 5e-10
 Identities = 10/42 (23%), Positives = 17/42 (40%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
           + KG  FV   + E+A  A+   +   +  + L V L    
Sbjct: 54 DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTD 95

>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 = 99.3 bits (248), Expect = 2e-26
 Identities = 16/65 (24%), Positives = 33/65 (50%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
             +DG+S+G G V F    EA +A++  NG+++  +P++V + +R   +      +  Q+
Sbjct: 49  EDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQ 108

Query: 61  IANMR 65
                
Sbjct: 109 SGPSS 113

>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 = 97.0 bits (242), Expect = 2e-25
 Identities = 22/53 (41%), Positives = 29/53 (54%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLAS 55
           +   SK FGFV + +P  A  A+  MNG  IG K L V L + K D K+  +S
Sbjct: 62  QTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSGPSS 114

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 92.0 bits (229), Expect = 1e-23
 Identities = 21/55 (38%), Positives = 33/55 (60%), Gaps = 1/55 (1%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRI-IGSKPLYVALAQRKEDRKAHLASQ 56
           + G SKG+GFV F+   E  +A+TE  G + +GSKP+ +++A  K  R   + S 
Sbjct: 46  QTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASRVKPVESG 100

>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 = 92.1 bits (229), Expect = 2e-23
 Identities = 14/56 (25%), Positives = 23/56 (41%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQ 56
               GRS G   V F    +A KA+ +  G  +  +P+ + L   + D + H    
Sbjct: 69  YDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHHH 124

>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 = 88.1 bits (219), Expect = 4e-22
 Identities = 13/55 (23%), Positives = 22/55 (40%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLAS 55
               G S+G GF    S E+    +   NG+ I + P   A  +    + +  +S
Sbjct: 59  RDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSGPSS 113

>1g9l_A Polyadenylate-binding protein 1; all-helical domain, RNA binding protein; NMR {Homo sapiens} SCOP: a.144.1.1 PDB: 1jgn_A 1jh4_A Length = 144

 Score = 88.7 bits (219), Expect = 6e-22
 Identities = 81/141 (57%), Positives = 92/141 (65%), Gaps = 10/141 (7%)

Query: 159 GPRGGGPMQAPGPASVSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGVQAVHVQGQ 218
           GP G      P                +Y        PQ  +           AVHVQGQ
Sbjct: 1   GPLGSAAAATPAV----------RTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQ 50

Query: 219 EPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNES 278
           EPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ES
Sbjct: 51  EPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPES 110

Query: 279 LKSKVEEAVAVLQAHQAKQAA 299
           L+SKV+EAVAVLQAHQAK+AA
Sbjct: 111 LRSKVDEAVAVLQAHQAKEAA 131

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 87.2 bits (216), Expect = 4e-21
 Identities = 14/54 (25%), Positives = 23/54 (42%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQ 56
             GRS G   V F    +A KA+ +  G  +  +P+ + L   + D + H    
Sbjct: 124 RSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHHH 177

>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 = 84.6 bits (210), Expect = 5e-21
 Identities = 16/51 (31%), Positives = 27/51 (52%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLAS 55
            S GFGFV +  PE+A KA+ ++ G  +    L V +++R     +  +S
Sbjct: 47 LLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATKPASGPSS 97

>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 = 88.5 bits (220), Expect = 1e-20
 Identities = 12/46 (26%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
             E   +    F+ F + + A +A+ +MN  ++G++ + V+LA +K
Sbjct: 247 QKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK 291

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 70.0 bits (172), Expect = 5e-14
 Identities = 12/55 (21%), Positives = 23/55 (41%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQY 57
               S+ F ++  +S E+A   V ++NG  I    L   ++   E  K   ++  
Sbjct: 154 RFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATL 208

>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 = 56.1 bits (136), Expect = 3e-09
 Identities = 6/45 (13%), Positives = 17/45 (37%), Gaps = 1/45 (2%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR 45
                ++  F  + F+  + A  A+T+ +  +     + V+    
Sbjct: 74  ADSLKKNFRFARIEFARYDGALAAITKTHKVVGQ-NEIIVSHLTE 117

>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 = 83.5 bits (207), Expect = 2e-20
 Identities = 17/59 (28%), Positives = 38/59 (64%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQ 59
          + ++  SKG+GFV F + E A +A+ +MNG ++  + ++V   + +++R+A L ++  +
Sbjct: 38 VCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKE 96

>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 = 81.6 bits (202), Expect = 8e-20
 Identities = 12/54 (22%), Positives = 26/54 (48%)

Query: 7  SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           K + F+ F   + A KA+ EMNG+ +  + + +  A+  + ++    +Q    
Sbjct: 44 LKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAA 97

>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 = 80.7 bits (200), Expect = 2e-19
 Identities = 15/53 (28%), Positives = 23/53 (43%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHL 53
          +S   + +G  FV F     AT A+  M G     KP+ +  A+   D  A +
Sbjct: 44 VSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 96

>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 = 80.8 bits (200), Expect = 2e-19
 Identities = 13/44 (29%), Positives = 20/44 (45%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ 44
               GRS G   V F    +A KA+ + NG  +  +P+ + L  
Sbjct: 63  YDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 106

>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 = 84.7 bits (210), Expect = 2e-19
 Identities = 17/103 (16%), Positives = 35/103 (33%), Gaps = 4/103 (3%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRII----GSKPLYVALAQRKEDRKAHLASQYM 58
           + GR+ G GFV F++   A KA+              +P+ V   ++ +D          
Sbjct: 132 DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQ 191

Query: 59  QRIANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQI 101
           +     + ++    F    T  +   +  +        Q  Q+
Sbjct: 192 KTQQYHKEREQPPRFAQPGTFEFEYASRWKALDEMEKQQREQV 234

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 58.2 bits (141), Expect = 5e-10
 Identities = 15/40 (37%), Positives = 22/40 (55%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR 45
          R +GFGF+   S   A  A  E++G I+ S+PL +  A  
Sbjct: 56 RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH 95

>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 = 82.3 bits (204), Expect = 3e-19
 Identities = 14/46 (30%), Positives = 24/46 (52%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
           +S+DG+SKG  ++ F S  +A K + E  G  I  + + +     K
Sbjct: 129 VSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 65.7 bits (161), Expect = 3e-13
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
            G ++ FG+V F S E+  KA+ E+ G  +    + +   + ++ +K 
Sbjct: 49 RTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDSKKV 96

>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 = 84.2 bits (207), Expect = 4e-19
 Identities = 27/169 (15%), Positives = 45/169 (26%), Gaps = 2/169 (1%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           +S   + +G  FV F     AT A+  M G     KP+ +  A+   D  A +   +++R
Sbjct: 45  VSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVER 104

Query: 61  IANMRMQQMGQLFQPGSTGGY--FVPTLPQPQRFYGPTQMTQIRPQPRWAAAPQMRPSGQ 118
                 ++      P +         T            M  +   PR       +P   
Sbjct: 105 DRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYM 164

Query: 119 TAQGFPNIPQFRSAPRASTGQTVIRGANMSARPITGQSTMGPRGGGPMQ 167
              G    P               +       P    S   P     + 
Sbjct: 165 PPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLT 213

>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 = 51.4 bits (122), Expect = 1e-07
 Identities = 8/40 (20%), Positives = 18/40 (45%), Gaps = 1/40 (2%)

Query: 7   SKGFGFVCFSSPEEATKAVTEMNG-RIIGSKPLYVALAQR 45
                FV F +  +A  A   + G +I  +  + ++ A++
Sbjct: 243 RHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 282

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 80.1 bits (198), Expect = 5e-19
 Identities = 18/42 (42%), Positives = 25/42 (59%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ 44
           +   SK FGFV F +P+ A  A+  MNG  +G+K L V L +
Sbjct: 77  QTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118

>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 = 80.3 bits (198), Expect = 8e-19
 Identities = 15/51 (29%), Positives = 28/51 (54%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
           + ++GR KG  F+   + + A KA+ E NG ++  KP+ V  A+    ++ 
Sbjct: 85  LMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARPKQD 135

>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 = 76.5 bits (189), Expect = 5e-18
 Identities = 16/53 (30%), Positives = 34/53 (64%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLAS 55
          + G SKG+ F+ F+S + +  A+  MNG+ + ++P+ V+ A +K+ + +  +S
Sbjct: 43 DTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGSGPSS 95

>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 = 78.3 bits (194), Expect = 6e-18
 Identities = 15/43 (34%), Positives = 27/43 (62%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR 45
           + G S+G+GFV F+S ++A  A+  M G+ +  +PL +  A +
Sbjct: 124 QTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166

>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 = 58.7 bits (143), Expect = 9e-11
 Identities = 8/45 (17%), Positives = 21/45 (46%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
           ++  + FV +    +A  A+  +NG+ I +  + +  A + +  
Sbjct: 38 NKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQS 82

>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 = 78.0 bits (193), Expect = 9e-18
 Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 3/46 (6%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRII---GSKPLYVALA 43
              DG S+G  FV F++   A  A+  M+        S P+ V  A
Sbjct: 129 RGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 53.4 bits (129), Expect = 6e-09
 Identities = 9/47 (19%), Positives = 19/47 (40%)

Query: 4  DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
            +SKG  FV F + + A +A   ++   +     +    +  +  K
Sbjct: 43 PPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEK 89

>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 = 77.2 bits (191), Expect = 2e-17
 Identities = 18/43 (41%), Positives = 26/43 (60%), Gaps = 2/43 (4%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRII--GSKPLYVALA 43
             GR +G  FV ++  EEA +A++ +N  I   GS+PL V LA
Sbjct: 126 LTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 66.4 bits (163), Expect = 1e-13
 Identities = 14/47 (29%), Positives = 27/47 (57%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
          + G S G+ FV F+S  ++ +A+  +NG  + +K L V+ A+   + 
Sbjct: 40 KTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGES 86

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 74.9 bits (185), Expect = 2e-17
 Identities = 17/51 (33%), Positives = 26/51 (50%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
            E+G+SKG G V F SPE A +A   MNG  +  + + V + +      +
Sbjct: 41 KMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNASGPSS 91

>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 = 74.5 bits (184), Expect = 2e-17
 Identities = 16/45 (35%), Positives = 28/45 (62%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE 47
          + G S+G+GFV F+S ++A  A+  M G+ +  +PL +  A + E
Sbjct: 38 QTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKLE 82

>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 = 74.2 bits (183), Expect = 4e-17
 Identities = 15/42 (35%), Positives = 24/42 (57%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ 44
           +G+ K FGFVCF  PE  + A+  +NG  +  +P+ V+   
Sbjct: 52 REGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS 93

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 77.4 bits (191), Expect = 5e-17
 Identities = 13/44 (29%), Positives = 22/44 (50%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
             G+ KG+GF+ +   + +  AV+ MN   +G + L V  A   
Sbjct: 162 TTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 64.3 bits (157), Expect = 2e-12
 Identities = 13/55 (23%), Positives = 24/55 (43%)

Query: 5   GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQ 59
            + KGF FV +  PE A  A+ +MN  ++G + + V         +  +     +
Sbjct: 67  MKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEE 121

>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 = 76.9 bits (190), Expect = 6e-17
 Identities = 17/75 (22%), Positives = 38/75 (50%), Gaps = 4/75 (5%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           + ++  SKG+GFV F + E A +A+ +MNG ++  + ++V   + +++R+A L ++    
Sbjct: 136 VCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARA--- 192

Query: 61  IANMRMQQMGQLFQP 75
                   +      
Sbjct: 193 -KEFYPYDVPDYAGS 206

>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 = 56.9 bits (138), Expect = 6e-10
 Identities = 15/42 (35%), Positives = 24/42 (57%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
           RS G+ +V F  P +A +A+  MN  +I  KP+ +  +QR 
Sbjct: 54 RRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRD 95

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 73.5 bits (181), Expect = 6e-17
 Identities = 14/51 (27%), Positives = 25/51 (49%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLAS 55
             +   FV +   E A +AV E+NG  + S  L V +A+++    +  +S
Sbjct: 46 DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDSGPSS 96

>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 = 73.1 bits (180), Expect = 1e-16
 Identities = 18/50 (36%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRII---GSKPLYVALAQRKEDR 49
            DG SKG  FV FSS  EA  A+  ++G       S  L V  A   ++ 
Sbjct: 51  PDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKES 100

>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 = 73.1 bits (180), Expect = 1e-16
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
             G ++ FG+V F S E+  KA+ E+ G  +    + +   + ++  + 
Sbjct: 53  RTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDGTRG 100

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 73.1 bits (180), Expect = 1e-16
 Identities = 15/43 (34%), Positives = 23/43 (53%)

Query: 8   KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
            GF FV F   E A KA+ E++G+   ++PL V  ++    R 
Sbjct: 65  NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRY 107

>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 = 73.1 bits (180), Expect = 1e-16
 Identities = 14/47 (29%), Positives = 25/47 (53%)

Query: 5   GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
           GR +G  F+ F + E A +A+  +NG  +  K L +   + K+ R +
Sbjct: 64  GRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQRSS 110

>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 = 73.1 bits (180), Expect = 2e-16
 Identities = 14/57 (24%), Positives = 26/57 (45%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQ 59
             +S+GF F+ F +P +A  A  +MNG+ +  K + V  A++   +          
Sbjct: 43 RTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPAS 99

>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 = 75.9 bits (186), Expect = 2e-16
 Identities = 18/120 (15%), Positives = 37/120 (30%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIA 62
            +G+SKGF  V   S   + K +  +  R +  +   V    ++   +  + S+   +  
Sbjct: 107 ANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSG 166

Query: 63  NMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAPQMRPSGQTAQG 122
            M  +         S   +      + +         +          P   P+GQT   
Sbjct: 167 QMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPGGPPPPFPAGQTHHH 226

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 71.9 bits (177), Expect = 3e-16
 Identities = 13/46 (28%), Positives = 28/46 (60%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
          + + + FV FS+ E+A +A+  +NG+++   P+ V LA+  +   +
Sbjct: 49 KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSS 94

>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 = 73.9 bits (182), Expect = 6e-16
 Identities = 14/46 (30%), Positives = 20/46 (43%)

Query: 2   SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE 47
           S  G SKG+ F  +       +A+  +NG  +G K L V  A    
Sbjct: 150 SATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA 195

>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 = 60.4 bits (147), Expect = 3e-11
 Identities = 11/49 (22%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
          +  + K F F+ F S +E T+A+   +G I   + L +      +    
Sbjct: 46 QINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPG 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 = 70.7 bits (174), Expect = 4e-15
 Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 2/43 (4%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRII--GSKPLYVALA 43
             G S+G GF+ F    EA +A+  +NG+     ++P+ V  A
Sbjct: 125 VTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 60.3 bits (147), Expect = 2e-11
 Identities = 15/45 (33%), Positives = 27/45 (60%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
          G+S G+GFV +  P++A KA+  +NG  + +K + V+ A+     
Sbjct: 41 GQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSAS 85

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 68.1 bits (167), Expect = 1e-14
 Identities = 13/46 (28%), Positives = 26/46 (56%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
           +  +  SKGFGFV F +  +A +A  +++G ++  + + V  A  +
Sbjct: 62  IFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107

>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 = 67.6 bits (166), Expect = 1e-14
 Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 2/56 (3%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQ 56
              G SKG+GFV F +  +  K V   +      K L +  A RK++   +    
Sbjct: 43 TDRTGVSKGYGFVSFYNDVDVQKIV--ESQINFHGKKLKLGPAIRKQNLSTYHVQP 96

>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 = 65.4 bits (160), Expect = 7e-14
 Identities = 13/51 (25%), Positives = 27/51 (52%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
          +  +  SKGFGFV F +  +A +A  +++G ++  + + V  A  +    +
Sbjct: 48 IFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNS 98

>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 = 64.9 bits (159), Expect = 7e-14
 Identities = 16/44 (36%), Positives = 26/44 (59%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
            G+SKG+GFV F +  +A  A+ +M G+ +G + +    A RK
Sbjct: 43 ATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86

>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 = 64.7 bits (158), Expect = 2e-13
 Identities = 16/56 (28%), Positives = 28/56 (50%)

Query: 5   GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           G+SKG+GFV F +  +A  A+ +M G+ +G + +    A RK            ++
Sbjct: 54  GKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQ 109

>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 = 65.3 bits (160), Expect = 4e-13
 Identities = 14/42 (33%), Positives = 20/42 (47%)

Query: 2   SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
           S  G SKG+ F  +       +A+  +NG  +G K L V  A
Sbjct: 130 SATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 55.3 bits (134), Expect = 1e-09
 Identities = 11/48 (22%), Positives = 20/48 (41%), Gaps = 1/48 (2%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAH 52
           + K F F+ F S +E T+A+   +G I   + L +      +     
Sbjct: 48 NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGA 94

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 62.5 bits (153), Expect = 5e-13
 Identities = 13/40 (32%), Positives = 20/40 (50%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ 44
           + KG+GFV F SP  A KAVT +    + ++    +   
Sbjct: 44 NKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS 83

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 63.6 bits (155), Expect = 5e-13
 Identities = 8/51 (15%), Positives = 19/51 (37%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHL 53
             +  G   V F+S   A + V  ++   +    ++  L  + + R  + 
Sbjct: 43 RTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIKGQQRMKYY 93

>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 = 62.7 bits (153), Expect = 6e-13
 Identities = 13/49 (26%), Positives = 23/49 (46%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
          +DG+SKG  ++ F S  +A K + E  G  I  + + +     K   + 
Sbjct: 48 QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTRG 96

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 63.8 bits (155), Expect = 6e-13
 Identities = 9/51 (17%), Positives = 20/51 (39%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
           +     + G  ++ F++ E A   V    G      PL +  ++  + + A
Sbjct: 65  VDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVA 115

>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 = 62.3 bits (152), Expect = 9e-13
 Identities = 17/47 (36%), Positives = 24/47 (51%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE 47
           +E G   G   V F S +EAT AV ++N R IGS+ + + L     
Sbjct: 50 YNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPS 96

>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 = 62.3 bits (152), Expect = 1e-12
 Identities = 17/49 (34%), Positives = 29/49 (59%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
          E  RS+GFGFV F + ++A  A+  MNG+ +  + + V  A +  D ++
Sbjct: 49 ETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRS 97

>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 = 62.3 bits (152), Expect = 1e-12
 Identities = 18/47 (38%), Positives = 24/47 (51%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
          E G SKGFGFV F+S E+A  A   M    I    + +  A+ K + 
Sbjct: 49 ETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEG 95

>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 = 61.4 bits (150), Expect = 1e-12
 Identities = 14/48 (29%), Positives = 22/48 (45%)

Query: 2  SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
               SKG+ +V F +P+EA KA+  M+G  I  + +          R
Sbjct: 41 MHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAPWPR 88

>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 = 61.8 bits (151), Expect = 1e-12
 Identities = 17/47 (36%), Positives = 28/47 (59%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
          + GRSKG+GF+ FS  E A +A+ ++NG  +  +P+ V     + D 
Sbjct: 42 DTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLDG 88

>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 = 61.9 bits (151), Expect = 2e-12
 Identities = 14/47 (29%), Positives = 27/47 (57%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
          ++G+SKG+ F+ F+S E+A +A+   N R I  + + + L   +   
Sbjct: 48 QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSP 94

>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 = 61.4 bits (150), Expect = 2e-12
 Identities = 11/47 (23%), Positives = 20/47 (42%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
           +G+SKGF  V   S   + K +  +  R +  +   V  + + E  
Sbjct: 40 ANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKLEHH 86

>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 = 61.5 bits (150), Expect = 2e-12
 Identities = 16/48 (33%), Positives = 26/48 (54%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
             + KGF FV F  PE A KA  E++G++   + L+V  +  K++  
Sbjct: 45 LTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEAS 92

>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 = 61.5 bits (150), Expect = 2e-12
 Identities = 14/49 (28%), Positives = 25/49 (51%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
          E  + +GF FV F   E+A  A+  MN   +  + + V LA+    +++
Sbjct: 49 ETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKES 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 = 61.6 bits (150), Expect = 3e-12
 Identities = 8/68 (11%), Positives = 27/68 (39%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           +     ++G  +V +    +A  AV  ++G  + ++ L V         +     +  ++
Sbjct: 40  VGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQ 99

Query: 61  IANMRMQQ 68
           +  ++ + 
Sbjct: 100 LKLLKEKY 107

>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 = 61.3 bits (149), Expect = 3e-12
 Identities = 15/48 (31%), Positives = 22/48 (45%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
           E G+ KG   V +  P  A  AV   +G+      L V+LA++K    
Sbjct: 60  ETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMN 107

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 60.9 bits (148), Expect = 5e-12
 Identities = 15/47 (31%), Positives = 22/47 (46%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
          E G+ KG   V F  P  A  A+   +G+     P+ V+ A R+ D 
Sbjct: 52 ETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADF 98

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 60.0 bits (146), Expect = 6e-12
 Identities = 12/45 (26%), Positives = 24/45 (53%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
          G+ KG  +V + +  +A++AV +M+G  I    + VA++      
Sbjct: 55 GKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPSS 99

>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 = 59.6 bits (145), Expect = 1e-11
 Identities = 19/46 (41%), Positives = 28/46 (60%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED 48
           E GRSKG+GF+ FS  E A KA+ ++NG  +  +P+ V     + D
Sbjct: 63  ETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108

>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 = 59.2 bits (144), Expect = 1e-11
 Identities = 15/49 (30%), Positives = 24/49 (48%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
          + GRSKG+ F+ F   E +  AV  +NG  +GS+ L    +   +    
Sbjct: 39 QTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDISGV 87

>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 = 59.2 bits (144), Expect = 1e-11
 Identities = 12/46 (26%), Positives = 19/46 (41%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
          + KGFGF+   +   A  A  E++   +  K L V  A       +
Sbjct: 49 KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTS 94

>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 = 60.1 bits (146), Expect = 2e-11
 Identities = 19/48 (39%), Positives = 26/48 (54%)

Query: 5   GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAH 52
            +S+G+GFV F S   A +A+  +NG  I +K L VALA     R   
Sbjct: 81  RQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGI 128

>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 = 59.9 bits (145), Expect = 3e-11
 Identities = 14/50 (28%), Positives = 24/50 (48%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAH 52
               S+GF FV F    +A  A+  M+G ++  + L V +A+      +H
Sbjct: 107 YTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSH 156

>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 = 58.1 bits (141), Expect = 3e-11
 Identities = 16/43 (37%), Positives = 24/43 (55%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
           +E G   G   V F S +EAT AV ++N R IGS+ + ++  
Sbjct: 50 YNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP 92

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 58.0 bits (141), Expect = 3e-11
 Identities = 14/48 (29%), Positives = 23/48 (47%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
            G+SKGF F+ F   E+A +A+  ++G       L V  A+   +  
Sbjct: 52 TTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNSG 99

>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 = 58.0 bits (141), Expect = 3e-11
 Identities = 12/47 (25%), Positives = 19/47 (40%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
               +GF FV F    +A  A   M+G  +  + L V +A+     
Sbjct: 50 HTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRD 96

>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 = 58.0 bits (141), Expect = 3e-11
 Identities = 12/43 (27%), Positives = 22/43 (51%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR 45
          +  RS+GF FV F + ++A +A    NG  +  + + V+    
Sbjct: 52 QSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPSS 94

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 58.0 bits (141), Expect = 4e-11
 Identities = 15/48 (31%), Positives = 26/48 (54%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
          E G+ KG+GF  +   E A  A+  +NGR    + L V  A  +++++
Sbjct: 45 ETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKE 92

>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 = 57.2 bits (139), Expect = 6e-11
 Identities = 8/41 (19%), Positives = 19/41 (46%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
          +  +SKG  F+ F   + A      +N + +  + +  ++A
Sbjct: 53 DTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93

>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 = 58.7 bits (142), Expect = 8e-11
 Identities = 12/47 (25%), Positives = 22/47 (46%)

Query: 5   GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
           G SKG+  V + + ++A  A   +NG  I  + + V     K  ++ 
Sbjct: 111 GFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRV 157

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 57.8 bits (140), Expect = 8e-11
 Identities = 14/50 (28%), Positives = 24/50 (48%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAH 52
               S+GF FV F    +A  A+  M+G ++  + L V +A+      +H
Sbjct: 84  YTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSH 133

>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 = 56.4 bits (137), Expect = 9e-11
 Identities = 14/42 (33%), Positives = 22/42 (52%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ 44
          E  + +GF FV F   E+A  A+  MN   +  + + V LA+
Sbjct: 44 ETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK 85

>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 = 56.9 bits (138), Expect = 1e-10
 Identities = 12/48 (25%), Positives = 22/48 (45%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
             G SKG+  V + + ++A  A   +NG  I  + + V     K  ++
Sbjct: 63  RTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR 110

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 56.6 bits (137), Expect = 2e-10
 Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 6/52 (11%)

Query: 5   GRSKGFGFVCFSSPEEATKAVTEMN------GRIIGSKPLYVALAQRKEDRK 50
             SKG  F  F + E A K +   +      G  +  + L V LA  +++  
Sbjct: 54  EHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAA 105

>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 = 56.1 bits (136), Expect = 2e-10
 Identities = 15/49 (30%), Positives = 24/49 (48%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
             G+ +G+GFV F S E+A  A+  M+   +  KP+ V  A       +
Sbjct: 52  VTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLS 100

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 55.5 bits (134), Expect = 2e-10
 Identities = 12/36 (33%), Positives = 21/36 (58%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSK 36
            EDG++KG+ F+ ++SP  A  AV   +G  +  +
Sbjct: 40 PEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 75

>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 = 56.2 bits (136), Expect = 2e-10
 Identities = 13/52 (25%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 5   GRSKGFGFVCFSSPEEATKAVTEM-NGRIIGSKPLYVALAQRKEDRKAHLAS 55
           G  +GFGFV F + ++A KA   + +   +  + L +  A  +   ++  +S
Sbjct: 55  GAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSS 106

>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 = 55.8 bits (135), Expect = 2e-10
 Identities = 13/41 (31%), Positives = 19/41 (46%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
          E G+ KG   V F  P  A  A+   +G+     P+ V+ A
Sbjct: 58 ETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 56.9 bits (137), Expect = 3e-10
 Identities = 11/48 (22%), Positives = 24/48 (50%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
            +G+SKG+  V  +S     K +  + G+++  + + V  A R+   +
Sbjct: 94  ANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQ 141

>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 = 56.3 bits (136), Expect = 3e-10
 Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 3/50 (6%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAH 52
           +  RS+GF FV F + ++A +A    NG  +  + + V  +     ++ H
Sbjct: 83  QSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSIT---KRPH 129

>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 = 55.4 bits (134), Expect = 4e-10
 Identities = 14/50 (28%), Positives = 22/50 (44%)

Query: 6   RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLAS 55
             KG+ FV FS+ E A  A+  +NG  I    +     +   D  +  +S
Sbjct: 59  PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGPSS 108

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 55.1 bits (133), Expect = 4e-10
 Identities = 17/54 (31%), Positives = 22/54 (40%), Gaps = 6/54 (11%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVA-----LAQRKEDRKA 51
               KG  FV F S E A K V E  G+      L +       A++ E+RK 
Sbjct: 47 LHKAFKGSIFVVFDSIESAKKFV-ETPGQKYKETDLLILFKDDYFAKKNEERKQ 99

>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 = 55.5 bits (134), Expect = 6e-10
 Identities = 12/50 (24%), Positives = 23/50 (46%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAH 52
             G  KG+  V + + +EA  A+  +NG+ +  +P+ V     +   K  
Sbjct: 59  RTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGK 108

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 55.6 bits (134), Expect = 7e-10
 Identities = 14/41 (34%), Positives = 21/41 (51%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
           E  + +GF FV F   E+A  A+  MN   +  + + V LA
Sbjct: 100 ETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 53.8 bits (130), Expect = 9e-10
 Identities = 10/48 (20%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRI-IGSKPLYVALAQRKEDRKA 51
              G+ FV +     A +A+  ++G++ +  K + V  +  K+ R +
Sbjct: 41 LLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLRSS 88

>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 = 54.2 bits (131), Expect = 9e-10
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
           S   R KGFG+  F   +    A+  +N   +G+K + V +A + +D+
Sbjct: 50 PSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDK 97

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 54.3 bits (131), Expect = 9e-10
 Identities = 12/34 (35%), Positives = 21/34 (61%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSK 36
          EDG++KG+ F+ ++SP  A  AV   +G  +  +
Sbjct: 56 EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 89

>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 = 53.8 bits (130), Expect = 1e-09
 Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 1/46 (2%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED 48
              R KGFG+  F   +    A+  +N   +G++ + V +A + +D
Sbjct: 56  NPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVADQAQD 100

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 53.8 bits (130), Expect = 1e-09
 Identities = 11/44 (25%), Positives = 22/44 (50%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
             G  KG+  V + + +EA  A+  +NG+ +  +P+ V     +
Sbjct: 60  RTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVR 103

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 12/48 (25%), Positives = 26/48 (54%), Gaps = 1/48 (2%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
          +  + KGF +V F   +   +A+   +G ++G + L V +A+ ++  K
Sbjct: 51 DTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQDK 97

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 53.1 bits (128), Expect = 2e-09
 Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 4/45 (8%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGR----IIGSKPLYVALAQR 45
           +++GF FV  SS  +A++ +  +        I  K + V  A+ 
Sbjct: 50 QQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS 94

>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 = 52.2 bits (126), Expect = 4e-09
 Identities = 12/47 (25%), Positives = 22/47 (46%), Gaps = 1/47 (2%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
          E  + KGFGFV     E  ++A+ +++      + + V  A  K+  
Sbjct: 38 ETKKPKGFGFVEMQE-ESVSEAIAKLDNTDFMGRTIRVTEANPKKSL 83

>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 = 51.4 bits (124), Expect = 6e-09
 Identities = 10/44 (22%), Positives = 22/44 (50%)

Query: 8  KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
          K + FV      +A  A+ ++NG+ +  K + V L+ + + +  
Sbjct: 43 KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQKKSG 86

>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 = 51.9 bits (125), Expect = 6e-09
 Identities = 14/43 (32%), Positives = 19/43 (44%)

Query: 8  KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
            + FV F    +A  A+  MNGR I  K + V  A     +K
Sbjct: 55 DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQK 97

>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 = 52.3 bits (126), Expect = 6e-09
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
              RSKG  +V F   +    A+  + G+ +   P+ V  +Q +++R +
Sbjct: 62  NSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKNRLS 109

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 51.7 bits (124), Expect = 6e-09
 Identities = 10/47 (21%), Positives = 21/47 (44%)

Query: 4  DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
                   V +SS ++A +A+ ++NG  + +  L VA    +   +
Sbjct: 50 TDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEMAAQ 96

>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 = 51.7 bits (124), Expect = 8e-09
 Identities = 13/51 (25%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
              GR+ G G V F SP++  +A+ + N  ++  + + V+ A  ++   A
Sbjct: 49 KDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATERQWVAA 98

>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 = 51.0 bits (123), Expect = 8e-09
 Identities = 8/43 (18%), Positives = 16/43 (37%)

Query: 8  KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
          K +GFV       A  A+  ++   +    + V  ++ K    
Sbjct: 42 KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKAS 84

>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 = 51.7 bits (124), Expect = 1e-08
 Identities = 8/60 (13%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           +  +G+  G   V F + ++A K+   ++ + +  +  +V +   ++ R+         +
Sbjct: 50  VDNNGQGLGQALVQFKNEDDARKSE-RLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGK 108

>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 = 53.4 bits (128), Expect = 1e-08
 Identities = 14/97 (14%), Positives = 33/97 (34%), Gaps = 3/97 (3%)

Query: 6   RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIANMR 65
             K    V  +   +A  A++ +NG  +  KP+ + L++ +  +      Q  Q +    
Sbjct: 39  NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPR-EGQEDQGLTKDY 97

Query: 66  MQQMGQLFQPGSTGGYFVPTLPQPQRFYG--PTQMTQ 100
                  F+   +  +     P         P  +++
Sbjct: 98  GNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSE 134

>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 = 51.4 bits (123), Expect = 4e-08
 Identities = 7/42 (16%), Positives = 20/42 (47%), Gaps = 1/42 (2%)

Query: 6   RSKGFGFVCFSSPEEATKAVTEMNG-RIIGSKPLYVALAQRK 46
           + +    +   S EEA +A+ +++   +  +  L V+ ++  
Sbjct: 156 KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 197

>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 = 51.2 bits (123), Expect = 1e-08
 Identities = 11/52 (21%), Positives = 22/52 (42%), Gaps = 3/52 (5%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRII---GSKPLYVALAQRKEDRKA 51
             G  KG  F+ +   E A KA + ++ +      ++P+ V  A  +    +
Sbjct: 50  FTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRGGS 101

>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 = 50.9 bits (122), Expect = 1e-08
 Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
          +   GRS G  FV F+S E A KA+ + +   IG + + +  + R E R +
Sbjct: 50 VDFQGRSTGEAFVQFASQEIAEKAL-KKHKERIGHRYIEIFKSSRAEVRTS 99

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 52.7 bits (127), Expect = 1e-08
 Identities = 13/54 (24%), Positives = 21/54 (38%), Gaps = 1/54 (1%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQ 56
             G+ +GF FV F   +   K V       +      V  A  K++  +  +SQ
Sbjct: 141 GSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKALSKQEMASASSSQ 193

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 48.1 bits (115), Expect = 5e-07
 Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 5   GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRI 61
            RS+GFGFV +++ EE   A+       +  + +    A  +ED +   A   +++I
Sbjct: 52  KRSRGFGFVTYATVEEVDAAM-NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKI 107

>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 = 49.9 bits (120), Expect = 2e-08
 Identities = 9/43 (20%), Positives = 19/43 (44%)

Query: 8  KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
          K + FV     E+A +A+  ++      K ++V L+  +    
Sbjct: 44 KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTA 86

>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 = 52.8 bits (126), Expect = 2e-08
 Identities = 8/47 (17%), Positives = 16/47 (34%), Gaps = 4/47 (8%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRII----GSKPLYVALA 43
            S        G + + S  +A + +  +N   +    G  P  + L 
Sbjct: 158 FSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC 204

>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 = 46.2 bits (109), Expect = 3e-06
 Identities = 6/87 (6%), Positives = 20/87 (22%)

Query: 7   SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIANMRM 66
             G   V  +      +A+T +N   +  + + V ++++                +    
Sbjct: 41  KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDF 100

Query: 67  QQMGQLFQPGSTGGYFVPTLPQPQRFY 93
            +                        +
Sbjct: 101 SESRNNRFSTPEQAAKNRIQHPSNVLH 127

>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 = 50.6 bits (121), Expect = 3e-08
 Identities = 10/51 (19%), Positives = 24/51 (47%), Gaps = 1/51 (1%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
              +G++ G GFV F +  +   A+   + + +G++ + V    +K   + 
Sbjct: 60  YGPNGKATGEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVHPITKKGMLEK 109

>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 = 51.3 bits (123), Expect = 3e-08
 Identities = 17/80 (21%), Positives = 31/80 (38%), Gaps = 7/80 (8%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQ-RI 61
               + GF FV + S  +A  A+  +NG  +  + +        ++ +     QY + R 
Sbjct: 76  MKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGR-----QYGRGRS 130

Query: 62  ANMRMQQMGQLFQPGSTGGY 81
                 +  Q +  G  GGY
Sbjct: 131 GGQVRDEYRQDYDAGR-GGY 149

>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 = 49.6 bits (119), Expect = 4e-08
 Identities = 11/46 (23%), Positives = 14/46 (30%)

Query: 4   DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
                 F FV F  P +A  AV   +G       L V   +     
Sbjct: 57  RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGT 102

>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 = 49.0 bits (118), Expect = 4e-08
 Identities = 8/42 (19%), Positives = 18/42 (42%), Gaps = 1/42 (2%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ 44
            G  KGF ++ FS  E    ++  ++  +   + + V   +
Sbjct: 43 FSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR 83

>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 = 49.3 bits (118), Expect = 4e-08
 Identities = 10/51 (19%), Positives = 21/51 (41%), Gaps = 1/51 (1%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
          +  DGR  G   V F++ E+A  A+   +   +  + + + L        +
Sbjct: 48 IGPDGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELFLNSTAGTSGS 97

>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 = 50.2 bits (120), Expect = 5e-08
 Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRI 61
            DGR  G   V F++ EEA  A+   +   +  + + + L           +SQ MQ +
Sbjct: 81  PDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGASNGAYSSQVMQGM 138

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 49.5 bits (118), Expect = 6e-08
 Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 11/70 (15%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
              DGR  G  FV F+  E A  A+   +  ++G + + +  +   E          +Q+
Sbjct: 61  TYPDGRPTGDAFVLFACEEYAQNAL-RKHKDLLGKRYIELFRSTAAE----------VQQ 109

Query: 61  IANMRMQQMG 70
           + N      G
Sbjct: 110 VLNRFSSASG 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 = 50.2 bits (121), Expect = 6e-08
 Identities = 9/44 (20%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
           + G+S+GFGFV + S +   +   +        + + +  A+ +
Sbjct: 124 DTGQSRGFGFVTYDSADAVDRVC-QNKFIDFKDRKIEIKRAEPR 166

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 47.1 bits (113), Expect = 1e-06
 Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 2/45 (4%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
          GRS+GFGF+ F  P    + V   +  I+  K +    A  ++++
Sbjct: 42 GRSRGFGFLSFEKPSSVDEVVKTQH--ILDGKVIDPKRAIPRDEQ 84

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 48.6 bits (116), Expect = 8e-08
 Identities = 12/46 (26%), Positives = 22/46 (47%), Gaps = 1/46 (2%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRII-GSKPLYVALAQRKE 47
            G++KGF FV   S  +A K +   +G+ +     L++   +  E
Sbjct: 49 ATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDVE 94

>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 = 48.6 bits (116), Expect = 9e-08
 Identities = 12/44 (27%), Positives = 17/44 (38%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
             G G V F   E+ T AV +++     S     A  + K D 
Sbjct: 48 YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG 91

>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 = 48.1 bits (115), Expect = 1e-07
 Identities = 9/38 (23%), Positives = 16/38 (42%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVAL 42
          G   G+ FV F+    A K + ++NG+ +         
Sbjct: 49 GIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRF 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 = 48.1 bits (115), Expect = 1e-07
 Identities = 12/47 (25%), Positives = 22/47 (46%), Gaps = 1/47 (2%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE 47
           +  G   G+ FV FS+ EE  +A+ + N   +G + + V   +   
Sbjct: 43 RNAHGNKTGYIFVDFSNEEEVKQAL-KCNREYMGGRYIEVFREKSGP 88

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 2/47 (4%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
          G SKGFGFV F+  E   K +++ +  +I  +     L   K+ + +
Sbjct: 54 GHSKGFGFVRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQDS 98

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 47.9 bits (114), Expect = 1e-07
 Identities = 12/44 (27%), Positives = 24/44 (54%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
            +   F+ +     A +AV+ + G  +G+  L VALA+++ D+
Sbjct: 54 GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRDK 97

>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 = 48.0 bits (115), Expect = 1e-07
 Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
           R +GFGF+ F   +   +AV  M+   I  K + V  A+ ++ + +
Sbjct: 49 QRPRGFGFITFEDEQSVDQAV-NMHFHDIMGKKVEVKRAEPRDSKSS 94

>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 = 48.1 bits (115), Expect = 1e-07
 Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 5   GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAH 52
           G+S+G+GFV  +    A +A  + N  I G +   V LA      ++ 
Sbjct: 56  GKSRGYGFVTMADRAAAERACKDPNPIIDG-RKANVNLAYLGAKPRSL 102

>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 = 47.8 bits (114), Expect = 2e-07
 Identities = 8/45 (17%), Positives = 17/45 (37%), Gaps = 1/45 (2%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE 47
             G  KG+ ++ F+       AV  M+  +   + + V   +   
Sbjct: 73  FSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTNM 116

>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 = 47.5 bits (113), Expect = 3e-07
 Identities = 13/46 (28%), Positives = 18/46 (39%)

Query: 4  DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
          D    G G V F   E+ T AV +++     S     A  + K D 
Sbjct: 47 DVYRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG 92

>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 = 47.5 bits (113), Expect = 3e-07
 Identities = 8/41 (19%), Positives = 18/41 (43%)

Query: 6   RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
                 +V +   E+A +A+  +N  ++  + L  +L   K
Sbjct: 61  GPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTK 101

>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 = 47.4 bits (113), Expect = 3e-07
 Identities = 13/44 (29%), Positives = 23/44 (52%)

Query: 7   SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
            KG+ FV +S+   A  AV   NGR++  + L + +A   +  +
Sbjct: 61  HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDR 104

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 46.8 bits (112), Expect = 3e-07
 Identities = 8/44 (18%), Positives = 18/44 (40%)

Query: 7  SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
             FGF+ F +P+    A+   +  +   K L + ++      +
Sbjct: 44 KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNARPQ 87

>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 = 46.9 bits (112), Expect = 3e-07
 Identities = 10/43 (23%), Positives = 19/43 (44%), Gaps = 2/43 (4%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIG--SKPLYVALAQRK 46
          +   F ++ + S + A  A  +M G  +G   + L V  A+  
Sbjct: 51 KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG 93

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 46.5 bits (111), Expect = 4e-07
 Identities = 14/44 (31%), Positives = 21/44 (47%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
             GF FV F  P +A  AV  ++G++I    + V L+     R
Sbjct: 35 NPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRR 78

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 45.5 bits (109), Expect = 5e-07
 Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 4/33 (12%)

Query: 5  GRSKGFGFVCFSSPEEATKAVT----EMNGRII 33
           R +GFGFV F S +   K       E+N +++
Sbjct: 38 NRHRGFGFVTFESEDIVEKVCEIHFHEINNKMV 70

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 46.7 bits (111), Expect = 5e-07
 Identities = 9/47 (19%), Positives = 15/47 (31%), Gaps = 5/47 (10%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
                 G G + F S E   +A+  +N        + V     + D 
Sbjct: 62  NTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITV-----ERDD 103

>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 = 46.8 bits (111), Expect = 5e-07
 Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE 47
           +  +G+  G  FV F+S E A KA+   +   IG + + V  + ++E
Sbjct: 77  VDPEGKITGEAFVQFASQELAEKAL-GKHKERIGHRYIEVFKSSQEE 122

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 45.6 bits (109), Expect = 5e-07
 Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 4/36 (11%)

Query: 5  GRSKGFGFVCFSSPEEATKAVT----EMNGRIIGSK 36
           RS+GFGFV F       K +     E++ + I  K
Sbjct: 39 KRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPK 74

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 46.1 bits (110), Expect = 6e-07
 Identities = 6/34 (17%), Positives = 13/34 (38%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPL 38
             KG  F+ + + E+A   +  +       + L
Sbjct: 60 YPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNL 93

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 47.2 bits (112), Expect = 6e-07
 Identities = 14/41 (34%), Positives = 21/41 (51%)

Query: 6   RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
              GF FV F  P +A  AV E++GR +    + V L+  +
Sbjct: 108 NPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE 148

>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 = 46.3 bits (110), Expect = 7e-07
 Identities = 11/41 (26%), Positives = 13/41 (31%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
                 V F  P EA KA   +        PLY+  A   
Sbjct: 44 EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG 84

>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 = 45.6 bits (108), Expect = 1e-06
 Identities = 10/56 (17%), Positives = 21/56 (37%), Gaps = 2/56 (3%)

Query: 5   GRSKGFGFVCFSSPEEATKAVTEMNGR--IIGSKPLYVALAQRKEDRKAHLASQYM 58
            +++GF FV + S   A  A  ++      +    + V  A+ + D    +     
Sbjct: 49  MKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVS 104

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 44.9 bits (107), Expect = 1e-06
 Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 4/36 (11%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEM----NGRIIGSK 36
          GRS+GFGF+ F       K + +     +GR+I  K
Sbjct: 50 GRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPK 85

>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 = 44.7 bits (106), Expect = 1e-06
 Identities = 11/44 (25%), Positives = 16/44 (36%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
             R+K   FV   + E+A  A+   +      K L V L    
Sbjct: 35 YVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD 78

>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 = 46.9 bits (111), Expect = 2e-06
 Identities = 13/93 (13%), Positives = 31/93 (33%), Gaps = 9/93 (9%)

Query: 6   RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIANMR 65
             K    V  +   +A  A++ +NG  +  KP+ + L++ +  +                
Sbjct: 70  NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPR---------EGQE 120

Query: 66  MQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQM 98
            Q + + +       +  P     Q  + P+  
Sbjct: 121 DQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSAT 153

>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 = 46.1 bits (109), Expect = 4e-06
 Identities = 7/42 (16%), Positives = 20/42 (47%), Gaps = 1/42 (2%)

Query: 6   RSKGFGFVCFSSPEEATKAVTEMNG-RIIGSKPLYVALAQRK 46
           + +    +   S EEA +A+ +++   +  +  L V+ ++  
Sbjct: 187 KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 228

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 8/47 (17%), Positives = 17/47 (36%), Gaps = 1/47 (2%)

Query: 5   GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
            +S+GFGFV F  P      +       +  + +       +  + +
Sbjct: 55  NQSRGFGFVKFKDPNCVGTVL-ASRPHTLDGRNIDPKPCTPRGMQPS 100

>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 = 44.2 bits (105), Expect = 2e-06
 Identities = 8/36 (22%), Positives = 17/36 (47%)

Query: 8  KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
            FGF+ F +P+    A+   +  +   K L + ++
Sbjct: 57 NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVS 92

>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 = 43.6 bits (104), Expect = 3e-06
 Identities = 6/33 (18%), Positives = 11/33 (33%), Gaps = 4/33 (12%)

Query: 5  GRSKGFGFVCFSSPEEATKAVT----EMNGRII 33
           + +GF F+ F   E   K +      +     
Sbjct: 38 NKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKC 70

>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 = 44.5 bits (105), Expect = 3e-06
 Identities = 11/51 (21%), Positives = 22/51 (43%), Gaps = 1/51 (1%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
            + +GR  G  FV   S ++   A+ + +   +G + + V  + R E    
Sbjct: 54  YTREGRQSGEAFVELESEDDVKLAL-KKDRESMGHRYIEVFKSHRTEMDWV 103

>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 = 44.1 bits (104), Expect = 3e-06
 Identities = 12/40 (30%), Positives = 19/40 (47%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVAL 42
                 G  +V F   E+A KAV ++N R    +P++  L
Sbjct: 63  LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102

>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 = 43.8 bits (104), Expect = 5e-06
 Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 9/49 (18%)

Query: 5   GRSKGFGFVCFSSPEEATKAVT----EMNGRIIGSKPLYVALAQRKEDR 49
            RS+GFGFV F       K +     E++ + I  K     +A  +  +
Sbjct: 64  KRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPK-----VAFPRRAQ 107

>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 = 43.7 bits (103), Expect = 5e-06
 Identities = 9/51 (17%), Positives = 23/51 (45%), Gaps = 1/51 (1%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
          ++ DG+ +G   +   S ++  KA+ E +   +G + + V     ++    
Sbjct: 48 LNRDGKRRGDALIEMESEQDVQKAL-EKHRMYMGQRYVEVYEINNEDVDAL 97

>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 = 45.2 bits (106), Expect = 6e-06
 Identities = 12/50 (24%), Positives = 16/50 (32%), Gaps = 1/50 (2%)

Query: 2   SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
           +     KG  FV F S E A K V     +      L +        +K 
Sbjct: 144 TLHKAFKGSIFVVFDSIESAKKFVETPGQKYKE-TDLLILFKDDYFAKKN 192

>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 = 43.4 bits (103), Expect = 6e-06
 Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 9/51 (17%)

Query: 5   GRSKGFGFVCFSSPEEATKAVT----EMNGRIIGSKPLYVALAQRKEDRKA 51
            RS+GFGFV FSS  E   A+      ++GR++  K      A  +E+  +
Sbjct: 66  KRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKR-----AVAREESGS 111

>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 = 42.6 bits (100), Expect = 1e-05
 Identities = 9/45 (20%), Positives = 21/45 (46%), Gaps = 5/45 (11%)

Query: 6   RSKGFGFVCFSSPEEATKAVTEMNGRIIG-----SKPLYVALAQR 45
            +K + F  + + EE+ +A   +NG+ +         LY+   ++
Sbjct: 61  PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEK 105

>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 = 43.1 bits (101), Expect = 1e-05
 Identities = 11/51 (21%), Positives = 22/51 (43%), Gaps = 1/51 (1%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
            + +GR  G  FV   S ++   A+ + +   +G + + V  + R E    
Sbjct: 81  YTREGRQSGEAFVELGSEDDVKMAL-KKDRESMGHRYIEVFKSHRTEMDWV 130

>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 = 41.8 bits (99), Expect = 2e-05
 Identities = 10/45 (22%), Positives = 20/45 (44%), Gaps = 2/45 (4%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
            + F FV F+  + A     E    II    ++++ A+ K ++ 
Sbjct: 46 PFRAFAFVTFADDKVAQSLCGEDL--IIKGISVHISNAEPKHNKL 88

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 44.8 bits (105), Expect = 3e-05
 Identities = 26/151 (17%), Positives = 38/151 (25%), Gaps = 5/151 (3%)

Query: 87  PQPQRFYG----PTQMTQIRPQPRWAAAPQMRPSGQTAQGFPNIPQFRSAPRASTGQTVI 142
           PQ Q  YG    P Q       P+  AA  M            +P        +  Q  +
Sbjct: 10  PQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQL 69

Query: 143 RGANMSARPITGQSTMGPRGGGPMQAPGPASVSAAGRQTGGYNKYPVRNPGT-QPQAQIG 201
                 A        +         A     V           + P+  P   QP A +G
Sbjct: 70  HQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMG 129

Query: 202 GIQPAAAGVQAVHVQGQEPLTSTMLAAAQPQ 232
                   +  + +  + P   T L    P 
Sbjct: 130 QNMRPMNQLYPIDLLTELPPPITDLTLPPPP 160

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 41.0 bits (95), Expect = 4e-04
 Identities = 27/185 (14%), Positives = 49/185 (26%), Gaps = 5/185 (2%)

Query: 55  SQYMQRIANMRMQQMGQLFQPGSTGGYFVPTLPQPQRFYGPTQMTQIRPQPRWAAAPQMR 114
           S + +R+      Q GQ   P      F+P  PQ     G +      P     A P M 
Sbjct: 2   SHHKKRVYPQAQLQYGQNATPLQQPAQFMP--PQDPAAAGMSYGQMGMPPQ--GAVPSMG 57

Query: 115 PSGQTAQGFPNIPQFRSAPRASTGQTVIRGANMSARPITGQSTMGPRGGGPMQAPG-PAS 173
                      + Q       S     +    +       Q  +  + G P+Q    P +
Sbjct: 58  QQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMA 117

Query: 174 VSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGVQAVHVQGQEPLTSTMLAAAQPQE 233
             A G+ +    +         P   +  + P    +         P    ++ +     
Sbjct: 118 APAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSNA 177

Query: 234 QKQML 238
               +
Sbjct: 178 SPDYI 182

>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 = 40.3 bits (95), Expect = 4e-05
 Identities = 8/36 (22%), Positives = 17/36 (47%), Gaps = 1/36 (2%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEM-NGRIIGSKPLYV 40
          + +   F+ F++ + A  A  +  N  I+  + L V
Sbjct: 46 QRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV 81

>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 = 41.2 bits (97), Expect = 4e-05
 Identities = 12/45 (26%), Positives = 17/45 (37%)

Query: 4   DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED 48
           D    G   V F  PEEA   +  ++GR  G + +         D
Sbjct: 60  DRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTD 104

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 40.6 bits (95), Expect = 7e-05
 Identities = 10/53 (18%), Positives = 22/53 (41%), Gaps = 2/53 (3%)

Query: 6   RSKGFGFVCFSSPEEATKAVT--EMNGRIIGSKPLYVALAQRKEDRKAHLASQ 56
           + K   F+  ++ E A   V        ++  +P+Y+  +  KE +     +Q
Sbjct: 50  KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQ 102

>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 = 39.9 bits (94), Expect = 7e-05
 Identities = 9/45 (20%), Positives = 18/45 (40%), Gaps = 2/45 (4%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
             + F FV F+  + A          II    ++++ A+ K + 
Sbjct: 39 KPFRAFAFVTFADDQIAQSLC--GEDLIIKGISVHISNAEPKHNS 81

>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 = 39.7 bits (93), Expect = 9e-05
 Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 1/36 (2%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYV 40
           + K F F+ F S +E T+A+   +G I   + L +
Sbjct: 50 NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKI 84

>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 = 40.3 bits (94), Expect = 9e-05
 Identities = 10/53 (18%), Positives = 22/53 (41%), Gaps = 2/53 (3%)

Query: 6   RSKGFGFVCFSSPEEATKAVT--EMNGRIIGSKPLYVALAQRKEDRKAHLASQ 56
           + K   F+  ++ E A   V        ++  +P+Y+  +  KE +     +Q
Sbjct: 65  KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQ 117

>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 = 2e-04
 Identities = 9/40 (22%), Positives = 17/40 (42%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVAL 42
           +    G  FV F+S  +  KA+  + GR   ++ +    
Sbjct: 54 VEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKY 93

>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 = 39.0 bits (91), Expect = 2e-04
 Identities = 9/44 (20%), Positives = 19/44 (43%), Gaps = 2/44 (4%)

Query: 6  RSKGFGFVCFSSPEEATKAVT--EMNGRIIGSKPLYVALAQRKE 47
          + K   F+  ++ E A   V         + ++P+Y+  +  KE
Sbjct: 49 KGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE 92

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 37.8 bits (88), Expect = 4e-04
 Identities = 9/44 (20%), Positives = 13/44 (29%), Gaps = 2/44 (4%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGR--IIGSKPLYVALAQRKE 47
            K    V F     A  AV         I   P +V  +  ++
Sbjct: 55 PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQK 98

>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 = 37.4 bits (87), Expect = 8e-04
 Identities = 12/30 (40%), Positives = 14/30 (46%)

Query: 2  SEDGRSKGFGFVCFSSPEEATKAVTEMNGR 31
           ED       FV FS   E  KA+  +NGR
Sbjct: 65 EEDAEIIVKIFVEFSIASETHKAIQALNGR 94

>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 = 37.3 bits (87), Expect = 9e-04
 Identities = 8/23 (34%), Positives = 11/23 (47%)

Query: 9  GFGFVCFSSPEEATKAVTEMNGR 31
          G  +V   S   A  AV  ++GR
Sbjct: 56 GNVYVKCPSIAAAIAAVNALHGR 78

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	303
1g9l_A	144	Polyadenylate-binding protein 1; all-helical domai	99.98
3kuj_A	88	Polyadenylate-binding protein 1; protein-protein c	99.97
1nmr_A	85	Poly(A)-binding protein; all helical domain, pepti	99.97
1ifw_A	92	Polyadenylate-binding protein, cytoplasmic and nuc	99.97
2dyd_A	85	Poly(A)-binding protein; alpha helical protein, RN	99.97
1i2t_A	61	HYD protein; four alpha-helical domain, ligase; 1.	99.95
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.07
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.04
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.0
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	98.93
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	98.93
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.91
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	98.91
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	98.9
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.89
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	98.89
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	98.89
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	98.89
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	98.88
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	98.87
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	98.87
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	98.87
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	98.87
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	98.86
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	98.86
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	98.84
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	98.84
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	98.84
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	98.83
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	98.83
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	98.83
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	98.83
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	98.83
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	98.82
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	98.82
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	98.82
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	98.82
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	98.82
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	98.81
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	98.81
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	98.81
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	98.8
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	98.8
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	98.8
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	98.79
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	98.79
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	98.79
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	98.79
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	98.79
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	98.79
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	98.78
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	98.78
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	98.78
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	98.77
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	98.77
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	98.77
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	98.77
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	98.77
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	98.77
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	98.76
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	98.76
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	98.76
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	98.76
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	98.76
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	98.76
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	98.76
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	98.75
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	98.75
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	98.75
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	98.75
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	98.75
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	98.74
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	98.74
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	98.73
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	98.73
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	98.73
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	98.73
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	98.73
2dis_A	109	Unnamed protein product; structural genomics, RRM	98.72
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	98.72
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	98.72
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	98.72
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	98.72
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	98.72
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	98.71
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	98.71
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	98.71
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	98.17
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	98.71
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	98.71
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	98.7
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	98.7
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.7
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	98.7
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	98.7
2div_A	99	TRNA selenocysteine associated protein; structural	98.7
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	98.69
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	98.69
1x5o_A	114	RNA binding motif, single-stranded interacting pro	98.68
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	98.68
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	98.68
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	98.68
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	98.67
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	98.66
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	98.66
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.66
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	98.65
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	98.65
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	98.65
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	98.64
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	98.63
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	98.63
1x5p_A	97	Negative elongation factor E; structure genomics,	98.62
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	98.62
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	98.61
1x4e_A	85	RNA binding motif, single-stranded interacting pro	98.61
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	98.6
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	98.6
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	98.6
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	98.6
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	98.59
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	98.57
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	98.57
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	98.55
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	98.55
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	98.54
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	98.54
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	98.54
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	98.54
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	98.54
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	98.52
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	98.51
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	98.51
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	98.5
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	98.49
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	98.49
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	98.49
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	98.49
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	98.48
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	98.48
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	98.48
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	98.47
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.46
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	98.46
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	98.45
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	98.44
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.43
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.43
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	98.43
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	98.43
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.42
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	98.41
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	98.4
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	98.4
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	98.4
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	98.4
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	98.39
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	98.38
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	98.37
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	98.35
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	98.34
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	98.33
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	98.32
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	98.31
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.31
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	98.27
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	98.26
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	98.23
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	98.22
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	98.19
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	98.18
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	98.18
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	98.14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	98.13
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	98.13
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	98.12
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	98.11
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	98.1
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	98.07
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	98.06
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	98.03
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	98.01
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	98.01
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	97.97
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	97.85
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	97.82
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	97.82
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	97.77
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	97.73
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	97.67
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	97.6
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	97.45
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	97.15
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	96.42
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	96.18
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.03
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	92.97
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	92.82
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	90.0

>1g9l_A Polyadenylate-binding protein 1; all-helical domain, RNA binding protein; NMR {Homo sapiens} SCOP: a.144.1.1 PDB: 1jgn_A 1jh4_A

Probab=99.98  E-value=4.9e-33  Score=234.58  Aligned_cols=87  Identities=84%  Similarity=1.114  Sum_probs=81.9

Q ss_pred             ccccCCCCccchhHhhhcChHHHHHhhhccchhhhhhhCCCCCCCchhhcccCChHHHHHhhCChHHHHHHHHHHHHHHH
Q psy14476        212 AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQ  291 (303)
Q Consensus       212 ~~~~~~~~~ltas~l~~~~~~~qk~~lGe~ly~~v~~~~p~~A~KITGMlLe~~~~ell~ll~~~~~L~~kv~eA~~vl~  291 (303)
                      +.++.+++++|+++|+++++++||++|||+|||+|+.++|++|+||||||||||++|||+||+|+|+|++||+||++||+
T Consensus        44 ~~~~~~~~pl~as~La~a~p~eQkq~LGE~LyplV~~~~p~~A~KITGMLLEmd~~ElL~LLes~e~L~~kV~EA~~vL~  123 (144)
T 1g9l_A           44 AVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQ  123 (144)
T ss_dssp             SCCCCSCCCCSHHHHTTCTTTTTTTTTTSSSHHHHHHHTTSCCSSHHHHTTTSSSHHHHHHHHCTTHHHHHHHHHHHHHH
T ss_pred             CCCCCCcchhhHHHHHcCCHHHHHHHHHHHHHHHHHHhCccccchhhhhhccCCHHHHHHHHcCHHHHHHHHHHHHHHHH
Confidence            34556788999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHH
Q psy14476        292 AHQAKQA  298 (303)
Q Consensus       292 ~~~~~~~  298 (303)
                      +|++++.
T Consensus       124 ~~~~~~~  130 (144)
T 1g9l_A          124 AHQAKEA  130 (144)
T ss_dssp             TTSSSTT
T ss_pred             HHHhccc
Confidence            9986554

>3kuj_A Polyadenylate-binding protein 1; protein-protein complex, methylation, mRNA processing, mRNA nucleus, phosphoprotein, RNA-binding, spliceosome; 1.40A {Homo sapiens} PDB: 3ktr_A 3kui_A 3ktp_A 3kus_A* 3kut_A 3pkn_A 2rqg_B 2rqh_B 3kur_A 3pth_A 2x04_A

Probab=99.97  E-value=3.8e-33  Score=217.63  Aligned_cols=84  Identities=80%  Similarity=1.048  Sum_probs=76.1

Q ss_pred             CccchhHhhhcChHHHHHhhhccchhhhhhhCCCCCCCchhhcccCChHHHHHhhCChHHHHHHHHHHHHHHHHHHHHHH
Q psy14476        219 EPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQAKQA  298 (303)
Q Consensus       219 ~~ltas~l~~~~~~~qk~~lGe~ly~~v~~~~p~~A~KITGMlLe~~~~ell~ll~~~~~L~~kv~eA~~vl~~~~~~~~  298 (303)
                      +++|+++|+++++++||++|||+|||+|++++|++|+||||||||||++|||+||+|+++|++||+||++||++|+.++.
T Consensus         5 ~~l~~s~la~a~p~~Qkq~LGE~Lyp~V~~~~p~~A~KITGMLLEmd~~Ell~lle~~e~L~~kV~EA~~vL~~~~~~~~   84 (88)
T 3kuj_A            5 SPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEA   84 (88)
T ss_dssp             -CCCHHHHHTSCHHHHHHHHHHHHHHHHHHHCTTTHHHHHHHHTTSCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             ccchHHHHHcCCHHHHHHHHHHHhHHHHHhhCCCccchhhhHhhcCCHHHHHHHHcCHHHHHHHHHHHHHHHHHHHhhhc
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             hhhc
Q psy14476        299 AVKK  302 (303)
Q Consensus       299 ~~~~  302 (303)
                      .+++
T Consensus        85 ~~~~   88 (88)
T 3kuj_A           85 AQKA   88 (88)
T ss_dssp             ----
T ss_pred             cCCC
Confidence            6653

>1nmr_A Poly(A)-binding protein; all helical domain, peptide binding protein; NMR {Trypanosoma cruzi} SCOP: a.144.1.1

Probab=99.97  E-value=1e-33  Score=219.16  Aligned_cols=80  Identities=45%  Similarity=0.662  Sum_probs=76.8

Q ss_pred             cCCCCccchhHhhhcChHHHHHhhhccchhhhhhhCCCCCCCchhhcccCChHHHHHhhCChHHHHHHHHHHHHHHHHHH
Q psy14476        215 VQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQ  294 (303)
Q Consensus       215 ~~~~~~ltas~l~~~~~~~qk~~lGe~ly~~v~~~~p~~A~KITGMlLe~~~~ell~ll~~~~~L~~kv~eA~~vl~~~~  294 (303)
                      +++++|+|+++|+++++++||++|||+|||+|+.++|++||||||||||||++|||+||+|+|+|++||+||++||++|+
T Consensus         4 ~~~~~~l~~s~La~a~p~~Qkq~LGE~LyplV~~~~p~~AgKITGMLLEmd~~ElL~Lle~~e~L~~kV~EA~~vL~~~~   83 (85)
T 1nmr_A            4 LASQGQNLSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILNLLDTPGLLDAKVQEALEVLNRHM   83 (85)
T ss_dssp             CCCCCCTTHHHHTTCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHCSCTHHHHHHTTCCTHHHHHHHHHHHHHHTTCCC
T ss_pred             ccCCCccCHHHHHcCChHHHHHHHHHHHHHHHHHhCccccchhhHhHhcCCHHHHHHHHcCHHHHHHHHHHHHHHHHHhh
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999998764

>1ifw_A Polyadenylate-binding protein, cytoplasmic and nuclear; all-helical domain, RNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.144.1.1

Probab=99.97  E-value=4.3e-33  Score=218.62  Aligned_cols=81  Identities=31%  Similarity=0.452  Sum_probs=76.8

Q ss_pred             CccchhHhhhcChHHHHHhhhccchhhhhh--hCCCCCCCchhhcccCChHHHHHhhCChHHHHHHHHHHHHHHHHHHHH
Q psy14476        219 EPLTSTMLAAAQPQEQKQMLGERLFPLIQR--MYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQAK  296 (303)
Q Consensus       219 ~~ltas~l~~~~~~~qk~~lGe~ly~~v~~--~~p~~A~KITGMlLe~~~~ell~ll~~~~~L~~kv~eA~~vl~~~~~~  296 (303)
                      .|+++++|+++++++||++|||+|||+|..  ++|++||||||||||||++|||+||+|+|+|++||+||++||++|++.
T Consensus         5 ~p~~a~~la~~~p~~Qkq~LGE~LyplV~~~~~~pelAgKITGMLLEmd~~ElL~LLes~e~L~~kV~EA~~vL~~~~~~   84 (92)
T 1ifw_A            5 SPRNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLLESDELFEQHYKEASAAYESFKKE   84 (92)
T ss_dssp             CSSCCSSCCSCSCHHHHHHHHHHHHHHHGGGCCCHHHHHHHHHHHTTSCHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CccchHHHhcCChHHHHHHHHHHHHHHHHHhhcCccccchhhHhHhcCCHHHHHHHHcCHHHHHHHHHHHHHHHHHHHHh
Confidence            467899999999999999999999999999  999999999999999999999999999999999999999999999975


Q ss_pred             HHh
Q psy14476        297 QAA  299 (303)
Q Consensus       297 ~~~  299 (303)
                      +..
T Consensus        85 ~~~   87 (92)
T 1ifw_A           85 QEQ   87 (92)
T ss_dssp             CTT
T ss_pred             hhh
Confidence            443

>2dyd_A Poly(A)-binding protein; alpha helical protein, RNA binding protein; NMR {Triticum aestivum}

Probab=99.97  E-value=1.3e-32  Score=213.02  Aligned_cols=75  Identities=44%  Similarity=0.721  Sum_probs=72.6

Q ss_pred             cchhHhhhcChHHHHHhhhccchhhhhhhCCCCCCCchhhcccCChHHHHHhhCChHHHHHHHHHHHHHHHHHHH
Q psy14476        221 LTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQA  295 (303)
Q Consensus       221 ltas~l~~~~~~~qk~~lGe~ly~~v~~~~p~~A~KITGMlLe~~~~ell~ll~~~~~L~~kv~eA~~vl~~~~~  295 (303)
                      +++++|+++++++||++|||+|||+|++++|++||||||||||||++|||+||+|+|+|++||+||++||++|++
T Consensus         9 ~~as~La~~~p~~Qkq~LGE~LyplV~~~~p~~AgKITGMLLEmd~~Ell~Lles~e~L~~kv~EA~~vL~~~~~   83 (85)
T 2dyd_A            9 ALASALANSPPETQRMMLGENLYPLVDQLEHDQAAKVTGMLLEMDQTEVLHLLESPDALKAKVAEAMEVLRSAQQ   83 (85)
T ss_dssp             TSCHHHHCCCHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHCHHHHHHHTTCSHHHHHHHHHHHHHHTSCSS
T ss_pred             hhHHHHHcCCHHHHHHHHHHHHHHHHHHhCccccchhhhhhhcCCHHHHHHHHcCHHHHHHHHHHHHHHHHHHhh
Confidence            488999999999999999999999999999999999999999999999999999999999999999999998764

>1i2t_A HYD protein; four alpha-helical domain, ligase; 1.04A {Homo sapiens} SCOP: a.144.1.1 PDB: 3ntw_A

Probab=99.95  E-value=6.1e-29  Score=181.56  Aligned_cols=60  Identities=50%  Similarity=0.855  Sum_probs=59.0

Q ss_pred             HHHhhhccchhhhhhhCCCCCCCchhhcccCChHHHHHhhCChHHHHHHHHHHHHHHHHH
Q psy14476        234 QKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAH  293 (303)
Q Consensus       234 qk~~lGe~ly~~v~~~~p~~A~KITGMlLe~~~~ell~ll~~~~~L~~kv~eA~~vl~~~  293 (303)
                      ||++|||+|||+|++++|++|+||||||||||++|||+||+|+|+|++||+||++||++|
T Consensus         1 qkq~LGe~Lyp~V~~~~p~~A~KITGMLLE~d~~ell~ll~~~e~L~~kv~EA~~vl~~~   60 (61)
T 1i2t_A            1 HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELIIAH   60 (61)
T ss_dssp             CHHHHHHHHHHHHHHHCGGGHHHHHHHHTTSCHHHHHHHHHCHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhCcccccchhhhhccCCHHHHHHHHcCHHHHHHHHHHHHHHHHHc
Confidence            699999999999999999999999999999999999999999999999999999999987

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.07  E-value=1.8e-10  Score=92.23  Aligned_cols=49  Identities=16%  Similarity=0.219  Sum_probs=44.9

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA   51 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~   51 (303)
                      .||+|||||||+|++.++|++||+.|||..|+||.|+|.++..++.++.
T Consensus        43 ~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~~~~~~~~   91 (110)
T 3s8s_A           43 RTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIKGQQRMK   91 (110)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSTTHHHHH
T ss_pred             CCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCcHHHH
Confidence            3699999999999999999999999999999999999999987766544

>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=99.04  E-value=9.8e-11  Score=93.89  Aligned_cols=48  Identities=33%  Similarity=0.713  Sum_probs=42.1

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHHH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA   51 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~   51 (303)
                      .++|||||||+|.+.++|++||+.|||..|+||.|+|.++.++.++..
T Consensus        41 ~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~~~~~   88 (115)
T 4f25_A           41 ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREA   88 (115)
T ss_dssp             TTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCCCC---
T ss_pred             CCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCcccccc
Confidence            356899999999999999999999999999999999999998776544

>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=99.00  E-value=3.1e-10  Score=89.04  Aligned_cols=43  Identities=33%  Similarity=0.596  Sum_probs=41.1

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      .+|++||||||+|.+.++|++||+.|||..|+||+|+|+||++
T Consensus        56 ~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           56 VAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             SSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             CCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            4799999999999999999999999999999999999999975

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=98.93  E-value=6.9e-10  Score=86.75  Aligned_cols=46  Identities=26%  Similarity=0.447  Sum_probs=42.6

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecc-cceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGS-KPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~G-R~L~V~~A~~k~~   48 (303)
                      .||+|||||||+|.+.++|++||+.|||..|+| |.|+|.+|.+++.
T Consensus        49 ~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l~V~~a~~~~~   95 (100)
T 3ns6_A           49 ATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDVER   95 (100)
T ss_dssp             TTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEESHHHHH
T ss_pred             CCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEEEEEECchhhh
Confidence            369999999999999999999999999999999 9999999987643

>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=98.93  E-value=4.1e-10  Score=86.03  Aligned_cols=46  Identities=24%  Similarity=0.346  Sum_probs=38.9

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .+|+|||||||+|.+.++|++||+.|||..|+||.|+|.++.++..
T Consensus        40 ~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~~~~~   85 (90)
T 3p5t_L           40 ANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKLEH   85 (90)
T ss_dssp             TTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-----
T ss_pred             CCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECCCCcc
Confidence            4899999999999999999999999999999999999999987643

>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=98.91  E-value=1.2e-09  Score=81.46  Aligned_cols=45  Identities=36%  Similarity=0.733  Sum_probs=42.6

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|+++|||||+|.+.++|++|++.|||..|+|++|+|.++.+++
T Consensus        38 ~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   82 (83)
T 3md1_A           38 QTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKLE   82 (83)
T ss_dssp             TTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcCC
Confidence            579999999999999999999999999999999999999998764

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=98.91  E-value=8.6e-10  Score=90.93  Aligned_cols=49  Identities=18%  Similarity=0.375  Sum_probs=45.2

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA   51 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~   51 (303)
                      .+|++||||||+|.+.++|++||+.|||..|.||+|+|+||..+.++..
T Consensus        67 ~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~a~~~~~~~~  115 (127)
T 2a3j_A           67 LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVA  115 (127)
T ss_dssp             CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEECCCCCHHHH
T ss_pred             cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEEccCcchhcc
Confidence            4789999999999999999999999999999999999999998876543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=98.90  E-value=7.7e-10  Score=86.65  Aligned_cols=43  Identities=26%  Similarity=0.417  Sum_probs=40.0

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCc----eecccceeeecccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGR----IIGSKPLYVALAQR   45 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~----~l~GR~L~V~~A~~   45 (303)
                      .||+|||||||+|.+.++|++||+.|||.    .|+||+|+|+||+.
T Consensus        48 ~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           48 QTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS   94 (95)
T ss_dssp             SSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEEEEECCC
T ss_pred             CCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEEEEEccC
Confidence            47999999999999999999999999997    59999999999974

>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=98.89  E-value=1.3e-09  Score=86.48  Aligned_cols=42  Identities=29%  Similarity=0.425  Sum_probs=39.8

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecc
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA   43 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A   43 (303)
                      |.+|+|||||||+|.+.++|.+|++.|||+.++||+|+|.|+
T Consensus        62 ~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~v~~s  103 (104)
T 1jmt_A           62 NLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             SSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             CCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEEc
Confidence            556899999999999999999999999999999999999986

>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=98.89  E-value=1.5e-09  Score=81.58  Aligned_cols=44  Identities=36%  Similarity=0.684  Sum_probs=40.7

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .+|++||||||+|.+.++|++|++.|||..++|+.|+|.++.++
T Consensus        43 ~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~k   86 (87)
T 3bs9_A           43 ATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK   86 (87)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC--
T ss_pred             CCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecCCC
Confidence            48999999999999999999999999999999999999999875

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.89  E-value=9.5e-10  Score=84.31  Aligned_cols=46  Identities=33%  Similarity=0.671  Sum_probs=43.0

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .+|+++|||||+|.+.++|++|++.|||..|+|++|+|.++.++..
T Consensus        43 ~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   88 (96)
T 1x5t_A           43 DTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDS   88 (96)
T ss_dssp             TTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCCC
T ss_pred             CCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEecccCC
Confidence            5899999999999999999999999999999999999999987643

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=98.89  E-value=8.5e-10  Score=85.01  Aligned_cols=45  Identities=27%  Similarity=0.380  Sum_probs=40.7

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhC-CceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMN-GRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~ln-G~~l~GR~L~V~~A~~k~   47 (303)
                      .||++||||||+|.+.++|++|++.++ +..|+||+|+|.+|.++.
T Consensus        39 ~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~~~~   84 (91)
T 2lxi_A           39 SSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSDPKP   84 (91)
T ss_dssp             SSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCCSCC
T ss_pred             CCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcCCCC
Confidence            479999999999999999999999874 567999999999998764

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.88  E-value=9.3e-10  Score=85.41  Aligned_cols=46  Identities=39%  Similarity=0.555  Sum_probs=43.2

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .+|++||||||+|.+.++|++||+.|||..|+|+.|+|.+++++.+
T Consensus        49 ~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   94 (102)
T 2fc8_A           49 ETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGE   94 (102)
T ss_dssp             SSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCCCS
T ss_pred             CCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCCCC
Confidence            4789999999999999999999999999999999999999987654

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.87  E-value=8.8e-10  Score=85.40  Aligned_cols=46  Identities=26%  Similarity=0.503  Sum_probs=43.3

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      |.+|++||||||+|.+.++|++|++.|||..|+|+.|+|.++.++.
T Consensus        52 ~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   97 (100)
T 2do4_A           52 NRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGP   97 (100)
T ss_dssp             CTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCCCS
T ss_pred             CCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            5689999999999999999999999999999999999999998764

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=98.87  E-value=2.6e-09  Score=90.69  Aligned_cols=47  Identities=23%  Similarity=0.394  Sum_probs=43.8

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR   49 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r   49 (303)
                      .+|++||||||+|.+.++|++||+.|||..|+||.|+|.+|.++...
T Consensus        94 ~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~a~~~~~~  140 (156)
T 3n9u_C           94 ANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLS  140 (156)
T ss_dssp             TTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEECCHHHHH
T ss_pred             CCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEEcCCCcch
Confidence            48999999999999999999999999999999999999999876543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.87  E-value=1.3e-09  Score=82.97  Aligned_cols=45  Identities=27%  Similarity=0.408  Sum_probs=42.2

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      |.+|++||||||+|.+.++|++|++ |||..|+||.|.|.++.++.
T Consensus        44 ~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a~~~~   88 (91)
T 2dgw_A           44 NAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREKSGP   88 (91)
T ss_dssp             CTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEESSCC
T ss_pred             CCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEECCcCC
Confidence            5789999999999999999999999 99999999999999998763

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.87  E-value=1.3e-09  Score=86.25  Aligned_cols=46  Identities=33%  Similarity=0.471  Sum_probs=43.1

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .+|++||||||+|.+.++|++||+.|||..|+|+.|+|.++.++..
T Consensus        60 ~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           60 ETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP  105 (113)
T ss_dssp             TTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCCC
T ss_pred             CCCCeeeEEEEEECCHHHHHHHHHHcCCCccCCCEEEEEECCCCCC
Confidence            5799999999999999999999999999999999999999987643

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.86  E-value=1.9e-09  Score=83.56  Aligned_cols=46  Identities=30%  Similarity=0.560  Sum_probs=43.0

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      |.+|++||||||+|.+.++|++||+.||+..|+|+.|+|.++.++.
T Consensus        47 ~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   92 (101)
T 2fc9_A           47 NQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRG   92 (101)
T ss_dssp             CSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSCC
T ss_pred             CCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCCC
Confidence            4689999999999999999999999999999999999999998763

>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=98.86  E-value=1.7e-09  Score=83.41  Aligned_cols=45  Identities=36%  Similarity=0.578  Sum_probs=42.6

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      +|++||||||+|.+.++|++|++.|||..|+|++|+|.++.++..
T Consensus        46 ~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   90 (99)
T 1whw_A           46 TKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKE   90 (99)
T ss_dssp             TCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCST
T ss_pred             CCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCcc
Confidence            899999999999999999999999999999999999999987643

>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=98.84  E-value=2.7e-09  Score=82.90  Aligned_cols=49  Identities=31%  Similarity=0.590  Sum_probs=45.0

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA   51 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~   51 (303)
                      .+|++||||||+|.+.++|++|++.|||..|+|+.|+|.++.++..+..
T Consensus        45 ~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~   93 (104)
T 1p1t_A           45 ETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKEE   93 (104)
T ss_dssp             TTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCTTHHHH
T ss_pred             CCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCCccchhh
Confidence            4789999999999999999999999999999999999999998766543

>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=98.84  E-value=2.9e-09  Score=81.94  Aligned_cols=47  Identities=32%  Similarity=0.551  Sum_probs=43.6

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR   49 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r   49 (303)
                      .+|++||||||+|.+.++|++|++.|||..|+|+.|+|.++.++...
T Consensus        39 ~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~   85 (96)
T 2x1f_A           39 QTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDIS   85 (96)
T ss_dssp             TTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSSGG
T ss_pred             CCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCCCCCC
Confidence            47899999999999999999999999999999999999999987543

>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=98.84  E-value=3e-09  Score=81.92  Aligned_cols=44  Identities=39%  Similarity=0.560  Sum_probs=41.6

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .+|++||||||+|.+.++|++||+.|||..|+||.|+|.++..+
T Consensus        52 ~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (98)
T 2cqp_A           52 EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGP   95 (98)
T ss_dssp             SSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEESSCS
T ss_pred             CCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEcCCC
Confidence            57899999999999999999999999999999999999998754

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=98.83  E-value=2.6e-09  Score=83.47  Aligned_cols=39  Identities=18%  Similarity=0.403  Sum_probs=37.5

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      .|||||||+|.+.++|++||+.||+.+|.||+|+|++|.
T Consensus        41 ~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A           41 LNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             CCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            489999999999999999999999999999999999994

>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=98.83  E-value=2.6e-09  Score=85.29  Aligned_cols=49  Identities=16%  Similarity=0.363  Sum_probs=44.3

Q ss_pred             CCCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHH
Q psy14476          1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK   50 (303)
Q Consensus         1 ~d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~   50 (303)
                      +|.+|++||||||+|.+.++|++||+. |+..|+||.|+|.++.+++.+.
T Consensus        50 ~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~a~~~~~~~   98 (114)
T 2cpy_A           50 VDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVVTLEDMRE   98 (114)
T ss_dssp             CCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEEECHHHHHH
T ss_pred             ECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEECCHHHHHH
Confidence            467899999999999999999999987 9999999999999998776543

>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=98.83  E-value=1.9e-09  Score=84.95  Aligned_cols=46  Identities=26%  Similarity=0.343  Sum_probs=43.1

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .+|++||||||+|.+.++|++||+.|||..|+|+.|+|.++.++..
T Consensus        63 ~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  108 (110)
T 1oo0_B           63 RTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGP  108 (110)
T ss_dssp             TTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEESSC
T ss_pred             CCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEcccCCC
Confidence            4799999999999999999999999999999999999999987654

>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=98.83  E-value=3.2e-09  Score=84.32  Aligned_cols=44  Identities=18%  Similarity=0.323  Sum_probs=40.6

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      ++++||||||+|.+.++|++||+.|||..|+||+|+|.+|.++.
T Consensus        59 ~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           59 SQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKY  102 (111)
T ss_dssp             SSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEESCCCCS
T ss_pred             cCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEEEEEeccccc
Confidence            34677999999999999999999999999999999999998763

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.83  E-value=4.1e-09  Score=84.56  Aligned_cols=45  Identities=27%  Similarity=0.395  Sum_probs=41.3

Q ss_pred             CCCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         1 ~d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      +|.+|++||||||+|.+.++|++|| .+|+..|+||.|.|..+..+
T Consensus        49 ~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~~   93 (109)
T 2dnn_A           49 KDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATER   93 (109)
T ss_dssp             CCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCHH
T ss_pred             ECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCcc
Confidence            4677999999999999999999999 68999999999999988754

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.82  E-value=1.3e-09  Score=84.92  Aligned_cols=46  Identities=41%  Similarity=0.718  Sum_probs=43.1

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCce-ecccceeeecccchH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRI-IGSKPLYVALAQRKE   47 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~-l~GR~L~V~~A~~k~   47 (303)
                      |.+|++||||||+|.+.++|++||+.|||.. |+|++|+|.++.++.
T Consensus        45 ~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~a~~~~   91 (104)
T 2dhg_A           45 DQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKA   91 (104)
T ss_dssp             CTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCBCCCCC
T ss_pred             CCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEEccCCC
Confidence            5689999999999999999999999999999 999999999998764

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.82  E-value=1.6e-09  Score=84.32  Aligned_cols=45  Identities=89%  Similarity=1.370  Sum_probs=42.6

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      +|+++|||||+|.+.++|++||+.|||..|+|+.|+|.++.++.+
T Consensus        51 ~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   95 (103)
T 2d9p_A           51 GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEE   95 (103)
T ss_dssp             SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECSSCCC
T ss_pred             CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeccccc
Confidence            789999999999999999999999999999999999999987654

>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=98.82  E-value=3.1e-09  Score=85.34  Aligned_cols=45  Identities=31%  Similarity=0.660  Sum_probs=42.6

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      |.+|+++|||||+|.+.++|++||+.|||..|+|+.|+|.++.++
T Consensus        42 ~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   86 (116)
T 2fy1_A           42 DRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKP   86 (116)
T ss_dssp             STTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCCS
T ss_pred             CCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            568999999999999999999999999999999999999999865

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.82  E-value=3.4e-09  Score=81.01  Aligned_cols=45  Identities=36%  Similarity=0.692  Sum_probs=42.3

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|++|++.|||..|+|++|+|.++.++.
T Consensus        42 ~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   86 (95)
T 2dnz_A           42 DTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERL   86 (95)
T ss_dssp             SSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESSCCC
T ss_pred             CCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccccc
Confidence            369999999999999999999999999999999999999998764

>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=98.82  E-value=1.7e-09  Score=84.36  Aligned_cols=48  Identities=35%  Similarity=0.499  Sum_probs=43.9

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecc---cceeeecccchHHH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGS---KPLYVALAQRKEDR   49 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~G---R~L~V~~A~~k~~r   49 (303)
                      |.+|++||||||+|.+.++|++||+.|||..|.|   ++|+|.+|..+.++
T Consensus        50 ~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~~a~~~~~~  100 (105)
T 2dnh_A           50 GPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKES  100 (105)
T ss_dssp             CSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEEESCSSCCC
T ss_pred             CCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEEECccCccc
Confidence            5689999999999999999999999999999998   99999999876543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=98.81  E-value=3.2e-09  Score=82.14  Aligned_cols=42  Identities=31%  Similarity=0.535  Sum_probs=40.0

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      ++|++||||||+|.+.++|++|++.|||..|+|+.|+|.+|+
T Consensus        58 ~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~A~   99 (99)
T 2la6_A           58 ETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFAT   99 (99)
T ss_dssp             TTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             CCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEecC
Confidence            579999999999999999999999999999999999999874

>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=98.81  E-value=2.1e-09  Score=83.68  Aligned_cols=44  Identities=25%  Similarity=0.504  Sum_probs=41.4

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|++|| .|||..|+|+.|+|.++.++.
T Consensus        56 ~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~~a~~~~   99 (100)
T 2j76_E           56 NPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVADQAQ   99 (100)
T ss_dssp             TTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCEECCCSC
T ss_pred             cCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEEeccCCC
Confidence            48999999999999999999999 899999999999999998764

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.81  E-value=3.3e-09  Score=82.29  Aligned_cols=45  Identities=31%  Similarity=0.486  Sum_probs=42.3

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|++||+.|||..|+|+.|+|.++.++.
T Consensus        49 ~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   93 (102)
T 2cqb_A           49 ETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMR   93 (102)
T ss_dssp             SSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeCCCCC
Confidence            478999999999999999999999999999999999999998764

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=98.80  E-value=5e-09  Score=83.43  Aligned_cols=42  Identities=26%  Similarity=0.326  Sum_probs=40.0

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      +++|||||||+|.+.++|.+|++.|||+.++||.|+|.++..
T Consensus        52 ~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i~v~~a~~   93 (105)
T 2pe8_A           52 PDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNL   93 (105)
T ss_dssp             CTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             CCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcCH
Confidence            478999999999999999999999999999999999999974

>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=98.80  E-value=3.5e-09  Score=80.97  Aligned_cols=44  Identities=34%  Similarity=0.706  Sum_probs=41.3

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      |.+|++||||||+|.+.++|++|++.|||..|+|++|+|.+++.
T Consensus        51 ~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   94 (95)
T 2ywk_A           51 DREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPSS   94 (95)
T ss_dssp             CTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcCC
Confidence            55689999999999999999999999999999999999999864

>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=98.80  E-value=2.5e-09  Score=85.01  Aligned_cols=46  Identities=43%  Similarity=0.634  Sum_probs=42.9

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .+|++||||||+|.+.++|++||+.||+..|+|+.|+|.++.++..
T Consensus        62 ~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~  107 (115)
T 2cpz_A           62 QTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND  107 (115)
T ss_dssp             SSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSCC
T ss_pred             CCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCc
Confidence            3799999999999999999999999999999999999999987643

>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=98.79  E-value=4.5e-09  Score=78.58  Aligned_cols=42  Identities=33%  Similarity=0.536  Sum_probs=40.0

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      .+|+++|||||+|.+.++|++|++.|||..|+|++|+|.+|+
T Consensus        44 ~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~ak   85 (85)
T 3mdf_A           44 ETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   85 (85)
T ss_dssp             TTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            578999999999999999999999999999999999999984

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=98.79  E-value=2.6e-09  Score=83.44  Aligned_cols=45  Identities=24%  Similarity=0.399  Sum_probs=42.2

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|+++|||||+|.+.++|++|++.|||..|+|+.|+|.+|.++.
T Consensus        60 ~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~  104 (106)
T 1p27_B           60 RTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG  104 (106)
T ss_dssp             TTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEESEESS
T ss_pred             CCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEeecCCC
Confidence            468999999999999999999999999999999999999998764

>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=98.79  E-value=3.7e-09  Score=85.46  Aligned_cols=46  Identities=22%  Similarity=0.372  Sum_probs=42.8

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      +.+|++||||||+|.+.++|++||+ |||..|+||.|.|.++.+++.
T Consensus        61 ~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~~~~~  106 (124)
T 1wel_A           61 GPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITKKGM  106 (124)
T ss_dssp             CTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEECHHHH
T ss_pred             CCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECCHHHH
Confidence            4689999999999999999999999 999999999999999987654

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.79  E-value=1.6e-09  Score=84.01  Aligned_cols=45  Identities=22%  Similarity=0.454  Sum_probs=41.8

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .+|++||||||+|.+.++|++||+ |||..|+|+.|+|.++.++..
T Consensus        53 ~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a~~~~~   97 (101)
T 1fj7_A           53 RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDG   97 (101)
T ss_dssp             EEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCSCCCC
T ss_pred             CCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcCCCCC
Confidence            368999999999999999999998 999999999999999987654

>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=98.79  E-value=4.6e-09  Score=82.11  Aligned_cols=43  Identities=30%  Similarity=0.482  Sum_probs=41.0

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      |.+|+++|||||+|.+.++|++||+.|||..|+|+.|+|.++.
T Consensus        64 ~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           64 DRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             CTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            5689999999999999999999999999999999999999985

>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=98.79  E-value=3.8e-09  Score=83.38  Aligned_cols=45  Identities=18%  Similarity=0.333  Sum_probs=41.8

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      |.+|++||||||+|.+.++|++||+ +|+..|+||.|+|.++.+++
T Consensus        49 ~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~a~~~~   93 (107)
T 2lmi_A           49 NRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEVYEINNED   93 (107)
T ss_dssp             CTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCCEECCHHH
T ss_pred             CCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEEEECCHHH
Confidence            5669999999999999999999999 99999999999999998754

>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=98.78  E-value=6.1e-09  Score=79.59  Aligned_cols=43  Identities=37%  Similarity=0.525  Sum_probs=40.2

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      .+|++||||||+|.+.++|++||+.||+..|+||.|+|.++..
T Consensus        52 ~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~s   94 (95)
T 2ek1_A           52 EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPSS   94 (95)
T ss_dssp             TTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC-
T ss_pred             CCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEeccC
Confidence            5789999999999999999999999999999999999998863

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.78  E-value=5.3e-09  Score=81.36  Aligned_cols=45  Identities=31%  Similarity=0.482  Sum_probs=42.4

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|++||+.|||..|+|+.|+|.++.++.
T Consensus        52 ~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   96 (103)
T 2cq0_A           52 TTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPST   96 (103)
T ss_dssp             SSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCC
T ss_pred             CCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEECCCCC
Confidence            478999999999999999999999999999999999999998764

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=98.78  E-value=2.1e-09  Score=84.60  Aligned_cols=44  Identities=32%  Similarity=0.543  Sum_probs=41.5

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceeccc-ceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSK-PLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR-~L~V~~A~~k   46 (303)
                      ++|++||||||+|.+.++|++||+.|||..|+|| +|+|.+|...
T Consensus        56 ~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l~V~~a~~~  100 (105)
T 2nlw_A           56 EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDF  100 (105)
T ss_dssp             BTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEEEEECSCCC
T ss_pred             CCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceEEEEEcchH
Confidence            5799999999999999999999999999999999 9999999754

>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=98.77  E-value=3.2e-09  Score=84.24  Aligned_cols=45  Identities=40%  Similarity=0.722  Sum_probs=42.6

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|++|++.|||..|+|+.|+|.++.++.
T Consensus        63 ~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~k~  107 (108)
T 2jrs_A           63 ETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERT  107 (108)
T ss_dssp             TTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEECSCSSC
T ss_pred             CCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcccCC
Confidence            478999999999999999999999999999999999999998774

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=98.77  E-value=4.4e-09  Score=84.72  Aligned_cols=45  Identities=24%  Similarity=0.410  Sum_probs=41.6

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      |.+|++||||||+|.+.++|++||+ ||+..|+||.|+|.++.+++
T Consensus        55 ~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~~~~   99 (118)
T 2db1_A           55 TREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVFKSHRTE   99 (118)
T ss_dssp             CSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEEEECHHH
T ss_pred             CCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEEECCHHH
Confidence            5669999999999999999999999 99999999999999997654

>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=98.77  E-value=1.9e-09  Score=82.74  Aligned_cols=47  Identities=28%  Similarity=0.372  Sum_probs=43.2

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK   50 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~   50 (303)
                      +|++||||||+|.+.++|++|++.|||..|+|+.|+|.++.++.+..
T Consensus        47 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~   93 (97)
T 1nu4_A           47 SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDII   93 (97)
T ss_dssp             HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSCCTHH
T ss_pred             CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEEccCCCccc
Confidence            46789999999999999999999999999999999999999876554

>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=98.77  E-value=3.1e-09  Score=84.19  Aligned_cols=44  Identities=30%  Similarity=0.451  Sum_probs=41.9

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      +|++||||||+|.+.++|++||+.|||..|+|+.|+|.++.++.
T Consensus        63 ~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~  106 (115)
T 2cpx_A           63 TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKK  106 (115)
T ss_dssp             CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCS
T ss_pred             CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEccCCC
Confidence            68999999999999999999999999999999999999998764

>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=98.77  E-value=4.6e-09  Score=81.84  Aligned_cols=44  Identities=34%  Similarity=0.495  Sum_probs=42.0

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      +|++||||||+|.+.++|++||+.|||..|+|++|+|.++.++.
T Consensus        53 ~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   96 (105)
T 1x5u_A           53 TGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHN   96 (105)
T ss_dssp             SCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTS
T ss_pred             CCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCC
Confidence            79999999999999999999999999999999999999998764

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=98.77  E-value=6.2e-09  Score=83.87  Aligned_cols=45  Identities=27%  Similarity=0.434  Sum_probs=42.3

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      |.+|++||||||+|.+.++|++|++.|||..|+|++|+|.+|..+
T Consensus        70 ~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  114 (124)
T 2kt5_A           70 DRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ  114 (124)
T ss_dssp             CSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEECCT
T ss_pred             CCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCC
Confidence            568999999999999999999999999999999999999999754

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.76  E-value=6.5e-09  Score=79.26  Aligned_cols=42  Identities=19%  Similarity=0.385  Sum_probs=39.7

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      .+|++||||||+|.+.++|++|++.|||..|+|++|+|.+|+
T Consensus        53 ~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~ak   94 (94)
T 2e5h_A           53 DTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIAI   94 (94)
T ss_dssp             SSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             CCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEecC
Confidence            368999999999999999999999999999999999999984

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.76  E-value=4.2e-09  Score=81.69  Aligned_cols=45  Identities=36%  Similarity=0.654  Sum_probs=42.3

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|++||+.||+..|+|+.|+|.++.++.
T Consensus        49 ~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   93 (102)
T 1x5s_A           49 ETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSS   93 (102)
T ss_dssp             SSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCC
T ss_pred             CCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            478999999999999999999999999999999999999998764

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=98.76  E-value=4.3e-09  Score=79.97  Aligned_cols=45  Identities=38%  Similarity=0.601  Sum_probs=42.1

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      ++|++||||||+|.+.++|++|++.|||..|+|+.|+|.++.++.
T Consensus        43 ~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   87 (92)
T 2dgv_A           43 ENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNAS   87 (92)
T ss_dssp             SSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSCCS
T ss_pred             cCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCC
Confidence            378999999999999999999999999999999999999998654

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.76  E-value=7.1e-09  Score=79.05  Aligned_cols=43  Identities=28%  Similarity=0.489  Sum_probs=40.6

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      .+|++||||||+|.+.++|++|++.|||..|+|++|+|.+++.
T Consensus        52 ~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   94 (95)
T 2cqc_A           52 QSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPSS   94 (95)
T ss_dssp             SSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCSC
T ss_pred             CCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecCC
Confidence            4689999999999999999999999999999999999999874

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.76  E-value=4.5e-09  Score=80.61  Aligned_cols=45  Identities=29%  Similarity=0.508  Sum_probs=42.2

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|++|++.|||..|+|+.|+|.++.++.
T Consensus        48 ~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   92 (96)
T 1fjc_A           48 QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG   92 (96)
T ss_dssp             ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSC
T ss_pred             CCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            478999999999999999999999999999999999999998764

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=98.76  E-value=7e-09  Score=82.22  Aligned_cols=45  Identities=36%  Similarity=0.666  Sum_probs=42.3

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|++||+.|||..|+|+.|+|.++.++.
T Consensus        52 ~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   96 (115)
T 2dgo_A           52 ATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKP   96 (115)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCC
T ss_pred             CCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccCCC
Confidence            489999999999999999999999999999999999999998763

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.76  E-value=6.8e-09  Score=82.04  Aligned_cols=45  Identities=33%  Similarity=0.666  Sum_probs=42.0

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      |.+|++||||||+|.+.++|++||+.|||..|+|+.|+|.++...
T Consensus        50 ~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   94 (114)
T 2do0_A           50 DKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERA   94 (114)
T ss_dssp             CTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCC
T ss_pred             CCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEcccC
Confidence            567999999999999999999999999999999999999998753

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=98.75  E-value=2.8e-09  Score=87.12  Aligned_cols=44  Identities=23%  Similarity=0.394  Sum_probs=41.4

Q ss_pred             CC-CCCcccEEEEEeCCHHHHHHHHHHhCCc----eecccceeeecccch
Q psy14476          2 SE-DGRSKGFGFVCFSSPEEATKAVTEMNGR----IIGSKPLYVALAQRK   46 (303)
Q Consensus         2 d~-tGkSkGfgFV~F~s~e~A~~Ai~~lnG~----~l~GR~L~V~~A~~k   46 (303)
                      |. +|++||||||+|.+. +|.+||+.|||.    .|+||.|+|+++.++
T Consensus        60 d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~l~V~~a~~~  108 (131)
T 2m2b_A           60 DKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKTINVEFAKGS  108 (131)
T ss_dssp             CSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCCCCCEECCCS
T ss_pred             cCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEEEEEEECCCC
Confidence            44 899999999999999 999999999999    999999999999875

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.75  E-value=7.1e-09  Score=80.91  Aligned_cols=45  Identities=27%  Similarity=0.473  Sum_probs=42.4

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHh-CCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEM-NGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~l-nG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|++||+.| |+..|+|+.|+|.++.++.
T Consensus        53 ~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~~a~~~~   98 (107)
T 2cph_A           53 GTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEV   98 (107)
T ss_dssp             SSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCC
T ss_pred             CCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEEEeCCCCC
Confidence            38999999999999999999999999 9999999999999998764

>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=98.75  E-value=4.2e-09  Score=87.80  Aligned_cols=45  Identities=24%  Similarity=0.417  Sum_probs=41.9

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      |.+|+|||||||+|++.++|++||+ ||+..|+||.|+|.++.+++
T Consensus        82 d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~~a~~~e  126 (136)
T 2hgl_A           82 TREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVFKSHRTE  126 (136)
T ss_dssp             CSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEEECCHHH
T ss_pred             CCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEEECChHH
Confidence            5669999999999999999999999 99999999999999997664

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=98.75  E-value=5.9e-09  Score=91.46  Aligned_cols=50  Identities=34%  Similarity=0.714  Sum_probs=45.1

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHHHHH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHL   53 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~~~   53 (303)
                      ++.+||||||+|.+.++|++||+.|||..|+||+|.|.+|.+++++..+.
T Consensus       139 ~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~~~~~~~~  188 (213)
T 4f02_A          139 ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL  188 (213)
T ss_dssp             TTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCHHHHHHHH
T ss_pred             CCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCCcccchhh
Confidence            35689999999999999999999999999999999999999987765543

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.75  E-value=5.2e-09  Score=80.57  Aligned_cols=44  Identities=34%  Similarity=0.579  Sum_probs=41.1

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      ||++||||||+|.+.++|++|++.|||..|+|+.|+|.++.++.
T Consensus        46 t~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   89 (98)
T 2cpf_A           46 VLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERAT   89 (98)
T ss_dssp             CEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSCSS
T ss_pred             CcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEccCCC
Confidence            45999999999999999999999999999999999999998753

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=98.74  E-value=3.6e-09  Score=79.02  Aligned_cols=39  Identities=33%  Similarity=0.629  Sum_probs=37.0

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceeccc-ceeee
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSK-PLYVA   41 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR-~L~V~   41 (303)
                      ++|++||||||+|.+.++|++|++.|||..|+|| +|+|+
T Consensus        42 ~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V~   81 (81)
T 2krb_A           42 EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVN   81 (81)
T ss_dssp             BTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCCC
T ss_pred             CCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEeC
Confidence            5899999999999999999999999999999999 99884

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.74  E-value=7.7e-09  Score=79.85  Aligned_cols=45  Identities=31%  Similarity=0.499  Sum_probs=41.6

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .+|++||||||+|.+.++|++||+ ||+..|+|+.|+|.++.++..
T Consensus        47 ~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a~~~~~   91 (99)
T 2dgs_A           47 EKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRAEPRDS   91 (99)
T ss_dssp             TTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEECCCCCC
T ss_pred             CCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEECCCCcc
Confidence            478999999999999999999998 999999999999999987643

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.73  E-value=7.4e-09  Score=80.66  Aligned_cols=44  Identities=25%  Similarity=0.568  Sum_probs=41.1

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|++|+ .|||..|+|+.|+|.++.++.
T Consensus        51 ~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~   94 (103)
T 2dng_A           51 DTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRK   94 (103)
T ss_dssp             SSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEECCCCC
T ss_pred             CCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEecCCC
Confidence            36999999999999999999999 899999999999999998764

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=98.73  E-value=4.1e-09  Score=86.33  Aligned_cols=46  Identities=41%  Similarity=0.553  Sum_probs=42.7

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .+|++||||||+|.+.++|++||+.|||..|+|+.|+|.++..+..
T Consensus        79 ~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  124 (139)
T 1u6f_A           79 ETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQ  124 (139)
T ss_dssp             TTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCCC
T ss_pred             CCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            3689999999999999999999999999999999999999987643

>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=98.73  E-value=5.1e-09  Score=85.91  Aligned_cols=45  Identities=29%  Similarity=0.522  Sum_probs=42.4

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|++||+.|||..|+|++|+|.++.++.
T Consensus        83 ~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a~~~~  127 (129)
T 2kxn_B           83 QSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKR  127 (129)
T ss_dssp             SSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCCSSSS
T ss_pred             CCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            478999999999999999999999999999999999999998764

>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=98.73  E-value=6.5e-09  Score=81.58  Aligned_cols=45  Identities=36%  Similarity=0.448  Sum_probs=41.7

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      |.+|++||||||+|.+.++|++||+. |+..|+||.|.|.++.+++
T Consensus        51 ~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~~~~~~   95 (104)
T 1wg5_A           51 DFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKSSRAE   95 (104)
T ss_dssp             CSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEECTTT
T ss_pred             CCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEECCHHH
Confidence            67899999999999999999999998 9999999999999987653

>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=98.73  E-value=1e-08  Score=92.86  Aligned_cols=57  Identities=25%  Similarity=0.402  Sum_probs=52.5

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHHHHHHHHHH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYM   58 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~~~~~~~~   58 (303)
                      |.+|+++|||||+|.+.++|.+|++.|||..|+|++|.|.|+.++..++..+.++..
T Consensus       220 ~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~a  276 (284)
T 3smz_A          220 GQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIA  276 (284)
T ss_dssp             CSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSSCHHHHHHHHHH
T ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCcccchhhhhhH
Confidence            568999999999999999999999999999999999999999999988887766654

>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=98.72  E-value=6.8e-09  Score=81.41  Aligned_cols=46  Identities=22%  Similarity=0.303  Sum_probs=41.6

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhC--CceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMN--GRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~ln--G~~l~GR~L~V~~A~~k~~   48 (303)
                      .+|++||||||+|.+.++|++|++.||  +..|+|+.|+|.+|.++.+
T Consensus        47 ~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V~~a~~~~~   94 (109)
T 2dis_A           47 DKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEID   94 (109)
T ss_dssp             TTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCS
T ss_pred             CCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEEEEcCCCCC
Confidence            368999999999999999999999996  5899999999999987643

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=98.72  E-value=6.6e-09  Score=82.76  Aligned_cols=42  Identities=43%  Similarity=0.682  Sum_probs=39.5

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      .+|++||||||+|.+.++|++||+.|||..|+|+.|+|.+++
T Consensus        77 ~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~ak  118 (118)
T 2khc_A           77 QTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK  118 (118)
T ss_dssp             SSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEEC-
T ss_pred             CCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            478999999999999999999999999999999999999874

>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=98.72  E-value=4.2e-09  Score=82.96  Aligned_cols=44  Identities=23%  Similarity=0.259  Sum_probs=40.7

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      |.+|++||||||+|.+.++|++|| ++|+..|+||.|.|.++...
T Consensus        49 d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~~~~~   92 (102)
T 1wez_A           49 GPDGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELFLNSTA   92 (102)
T ss_dssp             SSSSCEEEEEEEECSSSHHHHHHH-TTSSCCSSSSCCEEEEECCC
T ss_pred             CCCCCEeeEEEEEECCHHHHHHHH-HhCCCeECCcEEEEEECCCC
Confidence            678999999999999999999999 57999999999999988754

>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=98.72  E-value=6.5e-09  Score=85.78  Aligned_cols=47  Identities=32%  Similarity=0.569  Sum_probs=42.8

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR   49 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r   49 (303)
                      .+|++||||||+|.+.++|.+||+.|||..|+|++|+|.+|+.+..+
T Consensus        87 ~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~~~  133 (143)
T 3egn_A           87 KEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARPK  133 (143)
T ss_dssp             EETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEECEEEECCCSCC-
T ss_pred             cCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCCc
Confidence            47999999999999999999999999999999999999999865443

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.72  E-value=5.7e-09  Score=81.17  Aligned_cols=44  Identities=27%  Similarity=0.464  Sum_probs=41.5

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .+|++||||||+|.+.++|++||+.|||..|+|+.|.|.++..+
T Consensus        50 ~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~   93 (103)
T 2dnm_A           50 HTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYG   93 (103)
T ss_dssp             SSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEECSSC
T ss_pred             CCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEECCcC
Confidence            36899999999999999999999999999999999999999865

>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=98.72  E-value=6.9e-09  Score=81.49  Aligned_cols=46  Identities=28%  Similarity=0.465  Sum_probs=42.7

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhC------CceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMN------GRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~ln------G~~l~GR~L~V~~A~~k~~   48 (303)
                      .+|++||||||+|.+.++|++||+.||      +..|+|+.|+|.++.++..
T Consensus        52 ~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~l~v~~a~~~~~  103 (111)
T 1x4h_A           52 DTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE  103 (111)
T ss_dssp             SSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCCC
T ss_pred             CCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEEEEEEECCCCcc
Confidence            468999999999999999999999999      9999999999999987643

>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=98.71  E-value=6.3e-09  Score=82.52  Aligned_cols=45  Identities=27%  Similarity=0.467  Sum_probs=41.7

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR   49 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r   49 (303)
                      +|++||||||+|.+.++|++|| .|||..|+|+.|+|.++..+..+
T Consensus        63 ~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~~  107 (114)
T 2cq4_A           63 SRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKNR  107 (114)
T ss_dssp             SSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHHHHHH
T ss_pred             CCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCCCccC
Confidence            5899999999999999999999 99999999999999999876544

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=98.71  E-value=1e-08  Score=82.63  Aligned_cols=43  Identities=19%  Similarity=0.164  Sum_probs=39.2

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      +++||||||+|.+.++|++||+.|||..|+||.|+|.++..+.
T Consensus        64 ~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~p  106 (111)
T 2jvr_A           64 RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNPP  106 (111)
T ss_dssp             CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC--
T ss_pred             CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCCC
Confidence            4689999999999999999999999999999999999998653

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.71  E-value=1e-08  Score=81.08  Aligned_cols=45  Identities=27%  Similarity=0.220  Sum_probs=40.9

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      |.+|+|||||||+|.+.++|++||+ +||..|+|+.|.|.++....
T Consensus        46 d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~~~~   90 (103)
T 1s79_A           46 TLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKDDYF   90 (103)
T ss_dssp             CCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHHHHH
T ss_pred             CCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEchHHH
Confidence            5569999999999999999999999 89999999999999877543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=98.17  E-value=1.5e-09  Score=86.48  Aligned_cols=47  Identities=32%  Similarity=0.541  Sum_probs=43.6

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR   49 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r   49 (303)
                      .+|++||||||+|.+.++|++||+.|||..|+|++|+|.++.++..+
T Consensus        52 ~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           52 ETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADF   98 (116)
Confidence            47899999999999999999999999999999999999999877544

>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=98.71  E-value=4.3e-09  Score=79.02  Aligned_cols=42  Identities=31%  Similarity=0.495  Sum_probs=39.4

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      +++|||||+|.+.++|++|++.|||..|+|+.|+|.++.+..
T Consensus        45 ~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   86 (88)
T 4a8x_A           45 LSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAPW   86 (88)
T ss_dssp             EECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECCCC
T ss_pred             CCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECCCCC
Confidence            489999999999999999999999999999999999997653

>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=98.71  E-value=6.9e-09  Score=78.64  Aligned_cols=44  Identities=25%  Similarity=0.449  Sum_probs=38.5

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.+ |.+|+..|||..++|++|+|.+|..+.
T Consensus        38 ~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~~   81 (90)
T 2ki2_A           38 ETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPKK   81 (90)
T ss_dssp             SSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC----
T ss_pred             CCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            36999999999999999 999999999999999999999998754

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.70  E-value=6.9e-09  Score=80.08  Aligned_cols=44  Identities=25%  Similarity=0.385  Sum_probs=40.9

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      ++++||||||+|.+.++|++|++.|||..|+|+.|+|.++.++.
T Consensus        52 ~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   95 (97)
T 2e5j_A           52 WQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQR   95 (97)
T ss_dssp             EETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCCC
T ss_pred             cCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCC
Confidence            35789999999999999999999999999999999999998764

>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=98.70  E-value=1.1e-08  Score=85.43  Aligned_cols=45  Identities=29%  Similarity=0.527  Sum_probs=42.4

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|++||+.|||..|+|++|+|.+|.++.
T Consensus       107 ~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  151 (158)
T 2kn4_A          107 YTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  151 (158)
T ss_dssp             SCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSS
T ss_pred             CCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            489999999999999999999999999999999999999998754

>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=98.70  E-value=1.1e-08  Score=83.35  Aligned_cols=43  Identities=28%  Similarity=0.350  Sum_probs=40.4

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      ++++++||+||+|.+.++|.+|++.|||+.++||.|+|.++..
T Consensus        66 ~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~GR~i~v~~~~~  108 (118)
T 3ue2_A           66 EDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  108 (118)
T ss_dssp             TTCEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECH
T ss_pred             cCCcceEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcCh
Confidence            4678999999999999999999999999999999999999864

>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=98.70  E-value=7.1e-09  Score=80.90  Aligned_cols=43  Identities=30%  Similarity=0.554  Sum_probs=40.7

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      |++||||||+|.+.++|++|| .||+..|+|+.|+|.++.++..
T Consensus        54 g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~   96 (104)
T 1wi8_A           54 ERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQD   96 (104)
T ss_dssp             TSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEECCCCCC
T ss_pred             CCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEEccCCCC
Confidence            899999999999999999999 9999999999999999987653

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=98.70  E-value=9.1e-09  Score=75.35  Aligned_cols=40  Identities=30%  Similarity=0.428  Sum_probs=37.7

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA   43 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A   43 (303)
                      .+|++||||||+|.+.++|++|++ |||..|+|++|.|.+|
T Consensus        36 ~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A           36 TTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             SSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            379999999999999999999997 9999999999999986

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.70  E-value=1.2e-08  Score=78.70  Aligned_cols=44  Identities=23%  Similarity=0.379  Sum_probs=41.3

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccc----eeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKP----LYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~----L~V~~A~~k   46 (303)
                      .+|++||||||+|.+.++|++|++.|||..|+|+.    |+|.||...
T Consensus        47 ~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~v~~a~~~   94 (99)
T 2div_A           47 LTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYS   94 (99)
T ss_dssp             SSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECCEEETTCC
T ss_pred             CCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEEEeecCCC
Confidence            47999999999999999999999999999999999    999999754

>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=98.69  E-value=8.7e-09  Score=80.39  Aligned_cols=45  Identities=24%  Similarity=0.369  Sum_probs=41.7

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCcee---cccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRII---GSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l---~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|++||+.|||..+   .|++|+|.++..+.
T Consensus        50 ~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v~~a~~~~   97 (106)
T 2dgp_A           50 FTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSES   97 (106)
T ss_dssp             SSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECCCCS
T ss_pred             CCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEEEECCccc
Confidence            3699999999999999999999999999998   89999999998764

>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=98.69  E-value=1.5e-08  Score=78.22  Aligned_cols=40  Identities=28%  Similarity=0.288  Sum_probs=38.0

Q ss_pred             ccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          8 KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         8 kGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      ||||||+|.+.++|++||+.|||..|+||+|+|.+|+++.
T Consensus        52 rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~   91 (96)
T 2dgx_A           52 QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATGAS   91 (96)
T ss_dssp             TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCSS
T ss_pred             CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            8999999999999999999999999999999999998653

>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=98.68  E-value=1.3e-08  Score=80.58  Aligned_cols=45  Identities=27%  Similarity=0.559  Sum_probs=41.3

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCcee--------cccceeeecccch
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRII--------GSKPLYVALAQRK   46 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l--------~GR~L~V~~A~~k   46 (303)
                      |.+|++||||||+|.+.++|++|++.|||..|        .+++|.|.||.++
T Consensus        60 ~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~~l~v~~a~p~  112 (114)
T 1x5o_A           60 DSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSGPS  112 (114)
T ss_dssp             CSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSCBEEEECCCS
T ss_pred             CCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCCceeEEccCCC
Confidence            55899999999999999999999999999999        5788999999865

>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=98.68  E-value=1.3e-08  Score=76.73  Aligned_cols=43  Identities=19%  Similarity=0.427  Sum_probs=40.4

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .+|+++|||||+|.+.++|++|+ .|||..|+|+.|+|.+++.+
T Consensus        43 ~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~~   85 (89)
T 3ucg_A           43 FSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRTN   85 (89)
T ss_dssp             SSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTTT
T ss_pred             CCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccCC
Confidence            47999999999999999999999 99999999999999998754

>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=98.68  E-value=1.8e-08  Score=80.08  Aligned_cols=42  Identities=21%  Similarity=0.250  Sum_probs=39.4

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      ++++||+||+|.+.++|.+|++.|||+.++||.|.|.++...
T Consensus        56 ~~~~G~~fV~f~~~~~A~~Ai~~lnG~~f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           56 VPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPD   97 (105)
T ss_dssp             CTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECHH
T ss_pred             cCCcEEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEeCHH
Confidence            478999999999999999999999999999999999998654

>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=98.68  E-value=1.4e-08  Score=81.81  Aligned_cols=46  Identities=24%  Similarity=0.385  Sum_probs=42.6

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .+|+++|||||+|.+.++|++||+.|||..|+|+.|+|.+|..+..
T Consensus        59 ~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  104 (126)
T 3ex7_B           59 RTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP  104 (126)
T ss_dssp             TTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEESEESSS
T ss_pred             CCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCC
Confidence            3899999999999999999999999999999999999999986543

>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=98.67  E-value=2.5e-08  Score=77.47  Aligned_cols=43  Identities=30%  Similarity=0.562  Sum_probs=40.0

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      +.++|||||+|.+.++|++||+.|||..|+|+.|+|.++.++.
T Consensus        52 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   94 (103)
T 2cq3_A           52 RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV   94 (103)
T ss_dssp             TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSC
T ss_pred             CCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcccCC
Confidence            3489999999999999999999999999999999999998753

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.66  E-value=1.1e-08  Score=83.89  Aligned_cols=47  Identities=26%  Similarity=0.384  Sum_probs=42.5

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR   49 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r   49 (303)
                      |.+|++||||||+|.+.++|++||+. |++.|+||.|.|..+.+++..
T Consensus        62 d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V~~a~~~e~~  108 (123)
T 2dha_A           62 YPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIELFRSTAAEVQ  108 (123)
T ss_dssp             CTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECCEEECHHHHH
T ss_pred             CCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEEEECCHHHHH
Confidence            67899999999999999999999986 999999999999998765433

>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=98.66  E-value=1.9e-08  Score=79.05  Aligned_cols=45  Identities=24%  Similarity=0.319  Sum_probs=41.4

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .++++||||||+|.+.++|++||+.||+..|+|+.|+|.++..+.
T Consensus        56 ~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~  100 (109)
T 1x4a_A           56 NRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGR  100 (109)
T ss_dssp             CSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             ECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcccCC
Confidence            356789999999999999999999999999999999999998653

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=98.66  E-value=1.6e-08  Score=78.38  Aligned_cols=41  Identities=15%  Similarity=0.296  Sum_probs=38.9

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      ++||||||+|.+.++|++|++.|||..|+|+.|+|.||+++
T Consensus        61 ~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           61 PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER  101 (101)
T ss_dssp             TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCCC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccCC
Confidence            57999999999999999999999999999999999999864

>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=98.65  E-value=4.5e-08  Score=77.49  Aligned_cols=45  Identities=18%  Similarity=0.299  Sum_probs=41.4

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      +++++|||||+|.+.++|.+|++.|||..|+|+.|.|.++.++..
T Consensus        43 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   87 (115)
T 3lqv_A           43 TPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRA   87 (115)
T ss_dssp             STTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCHHHH
T ss_pred             CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCChh
Confidence            477899999999999999999999999999999999999986543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.65  E-value=1.7e-08  Score=79.89  Aligned_cols=43  Identities=30%  Similarity=0.597  Sum_probs=40.2

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .+++||||||+|.+.++|++|++.|||..|+|+.|+|.++.++
T Consensus        65 ~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  107 (109)
T 2err_A           65 ERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR  107 (109)
T ss_dssp             TTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEECCCS
T ss_pred             CCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            3568999999999999999999999999999999999999875

>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=98.65  E-value=2.8e-08  Score=77.19  Aligned_cols=45  Identities=29%  Similarity=0.361  Sum_probs=40.9

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .+.+||||||+|.+.++|++|++.|||..|+|+.|+|.++..+..
T Consensus        51 ~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   95 (103)
T 2cqi_A           51 HTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSS   95 (103)
T ss_dssp             CCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTTC
T ss_pred             CCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECCCCcc
Confidence            345799999999999999999999999999999999999987643

>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=98.64  E-value=1.5e-08  Score=91.09  Aligned_cols=46  Identities=22%  Similarity=0.278  Sum_probs=43.1

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .+|+|||||||+|.+.++|++||+.||++.|+||.|+|.+|.++..
T Consensus       107 ~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~a~~~~~  152 (229)
T 3q2s_C          107 ANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFL  152 (229)
T ss_dssp             TTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEECCHHHH
T ss_pred             CCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEECCCCcc
Confidence            4899999999999999999999999999999999999999987643

>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=98.63  E-value=1.9e-08  Score=84.12  Aligned_cols=45  Identities=20%  Similarity=0.269  Sum_probs=42.1

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|++||+.||+..|+|+.|+|.||..+.
T Consensus        76 ~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  120 (156)
T 1h2v_Z           76 MKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK  120 (156)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCCC
T ss_pred             CCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            368999999999999999999999999999999999999998654

>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=98.63  E-value=2.2e-08  Score=84.78  Aligned_cols=48  Identities=25%  Similarity=0.367  Sum_probs=42.9

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK   50 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~   50 (303)
                      .+|+++|||||+|.+.++|.+||+.|||..|.|++|.|.|+..+..+.
T Consensus       109 ~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~~  156 (165)
T 1rk8_A          109 RTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR  156 (165)
T ss_dssp             TTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC---
T ss_pred             CCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCCCC
Confidence            479999999999999999999999999999999999999999776543

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.62  E-value=2.9e-08  Score=76.53  Aligned_cols=43  Identities=30%  Similarity=0.482  Sum_probs=40.1

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      +++||||||+|.+.++|++||+.|||..|+|++|+|.++.++.
T Consensus        46 ~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~   88 (97)
T 1x5p_A           46 DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP   88 (97)
T ss_dssp             ETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCC
T ss_pred             cCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCC
Confidence            3689999999999999999999999999999999999998753

>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=98.62  E-value=1.2e-08  Score=84.11  Aligned_cols=46  Identities=30%  Similarity=0.426  Sum_probs=41.3

Q ss_pred             CCCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         1 ~d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      +|.+|++||||||+|.+.++|++||+. ++..|+||.|+|.++.+++
T Consensus        77 ~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V~~a~~~e  122 (126)
T 2hgm_A           77 VDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIEVFKSSQEE  122 (126)
T ss_dssp             CCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCCEEECHHH
T ss_pred             ECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEEEECCHHH
Confidence            366799999999999999999999985 7899999999999987654

>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=98.61  E-value=2.4e-08  Score=75.78  Aligned_cols=41  Identities=27%  Similarity=0.316  Sum_probs=38.6

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      ++||||||+|.+.++|++|++.|||..++|++|+|.++..+
T Consensus        38 ~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   78 (88)
T 1wg1_A           38 RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCC
Confidence            68999999999999999999999999999999999998653

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.61  E-value=1.2e-08  Score=76.49  Aligned_cols=42  Identities=31%  Similarity=0.456  Sum_probs=39.6

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      .+|++||||||+|.+.++|++|++.|||..|+|+.|+|.++.
T Consensus        42 ~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A           42 TTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             SSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCCC
T ss_pred             CCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCCC
Confidence            479999999999999999999999999999999999998865

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=98.60  E-value=3.4e-08  Score=79.24  Aligned_cols=43  Identities=19%  Similarity=0.411  Sum_probs=40.3

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .+|++||||||+|.+.++|++|| +|||..|+|+.|+|.+++..
T Consensus        73 ~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~  115 (124)
T 2jwn_A           73 FSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTN  115 (124)
T ss_dssp             TTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSCC
T ss_pred             CCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCCC
Confidence            47999999999999999999999 89999999999999998753

>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=98.60  E-value=1.7e-08  Score=77.00  Aligned_cols=43  Identities=21%  Similarity=0.316  Sum_probs=39.6

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCC-ceecccceeeecccchHH
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNG-RIIGSKPLYVALAQRKED   48 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG-~~l~GR~L~V~~A~~k~~   48 (303)
                      ++||||||+|.+.++|++|++.||| ..|+|+.|+|.++.++..
T Consensus        42 ~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~~~   85 (93)
T 2cqh_A           42 LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL   85 (93)
T ss_dssp             EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCccc
Confidence            3689999999999999999999999 999999999999987643

>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=98.60  E-value=3e-08  Score=78.86  Aligned_cols=42  Identities=24%  Similarity=0.447  Sum_probs=39.5

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+||||||+|.+.++|.+|++.|||..|+||+|.|.++.++.
T Consensus        62 ~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           62 HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTT  103 (112)
T ss_dssp             CTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCC
T ss_pred             CCCEEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCC
Confidence            489999999999999999999999999999999999998753

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=98.60  E-value=3.5e-08  Score=76.39  Aligned_cols=41  Identities=32%  Similarity=0.585  Sum_probs=39.2

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      +||||||+|.+.++|++|++.|||..++|+.|+|.++.++.
T Consensus        36 ~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   76 (101)
T 2hvz_A           36 PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMP   76 (101)
T ss_dssp             SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCC
Confidence            79999999999999999999999999999999999998764

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.59  E-value=1.7e-08  Score=78.68  Aligned_cols=45  Identities=18%  Similarity=0.351  Sum_probs=41.8

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .+|++||||||+|.+.++|++||+. |+..|+|+.|+|.++.++.+
T Consensus        53 ~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~a~~~~~   97 (105)
T 2dh8_A           53 TTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPCTPRGM   97 (105)
T ss_dssp             SSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCCSCCSSC
T ss_pred             CCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEccCCCC
Confidence            4789999999999999999999999 99999999999999987653

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.57  E-value=2.7e-08  Score=79.03  Aligned_cols=45  Identities=33%  Similarity=0.467  Sum_probs=41.7

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .+|++||||||+|.+.++|++||+. |+..|+|+.|+|.++.++.+
T Consensus        64 ~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~~~~  108 (116)
T 1x4b_A           64 ASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREE  108 (116)
T ss_dssp             TTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSSCCC
T ss_pred             CCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCCCcc
Confidence            4799999999999999999999998 99999999999999987753

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.57  E-value=3.9e-08  Score=78.08  Aligned_cols=43  Identities=33%  Similarity=0.535  Sum_probs=40.0

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .+|++||||||+|.+.++|++||+.+|+ .|+|+.|+|.++..+
T Consensus        54 ~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~a~~~   96 (116)
T 2cqd_A           54 QTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLG   96 (116)
T ss_dssp             SSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTTT
T ss_pred             CCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEEcccC
Confidence            4799999999999999999999999998 899999999999654

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.55  E-value=2.7e-08  Score=72.92  Aligned_cols=40  Identities=30%  Similarity=0.464  Sum_probs=38.0

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA   43 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A   43 (303)
                      .+|++||||||+|.+.++|++|++.++ ..++|+.|.|.+|
T Consensus        37 ~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A           37 LTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            478999999999999999999999999 9999999999987

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=98.55  E-value=2.8e-08  Score=82.01  Aligned_cols=45  Identities=29%  Similarity=0.527  Sum_probs=42.1

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|++||+.|||..|+|++|+|.+++++.
T Consensus        84 ~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~  128 (135)
T 2lea_A           84 YTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  128 (135)
T ss_dssp             SSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCC
T ss_pred             CCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            378999999999999999999999999999999999999998653

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=98.54  E-value=3.1e-08  Score=78.53  Aligned_cols=45  Identities=27%  Similarity=0.398  Sum_probs=40.7

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .+|++||||||+|.+.++|++||+.+ +..|+|+.|+|.++..+..
T Consensus        62 ~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~a~~~~~  106 (109)
T 2rs2_A           62 LTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKVAFPRRA  106 (109)
T ss_dssp             TTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEECCCCCC
T ss_pred             CCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEEccCCCC
Confidence            36999999999999999999999986 5999999999999987653

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=98.54  E-value=8.9e-08  Score=82.52  Aligned_cols=73  Identities=21%  Similarity=0.335  Sum_probs=54.0

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCC
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIANMRMQQMGQLFQPGSTGGYFV   83 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~~~~~~~~q~~~~~r~~~~~~~~~~~~~~~~f~   83 (303)
                      +|+++|||||+|.+.++|++|++.|||..|+|+.|+|.++..+............      ..       .  ....+||
T Consensus        66 ~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~------~~-------~--~~~~l~v  130 (216)
T 2qfj_A           66 TMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAE------EA-------R--AFNRIYV  130 (216)
T ss_dssp             C-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSCCGGGHHHHHHHHH------HH-------T--TSCEEEE
T ss_pred             CCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCCccccchhhhhhhc------cc-------C--CCcEEEE
Confidence            7899999999999999999999999999999999999999877654332211100      00       0  1237899


Q ss_pred             CCCCCCCc
Q psy14476         84 PTLPQPQR   91 (303)
Q Consensus        84 ~~lp~~~~   91 (303)
                      .||+....
T Consensus       131 ~nlp~~~t  138 (216)
T 2qfj_A          131 ASVHQDLS  138 (216)
T ss_dssp             ECCCTTCC
T ss_pred             eCCCCcCC
Confidence            99998654

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=98.54  E-value=3.5e-08  Score=78.41  Aligned_cols=42  Identities=21%  Similarity=0.252  Sum_probs=38.2

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCce--ecccceeeecccchH
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRI--IGSKPLYVALAQRKE   47 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~--l~GR~L~V~~A~~k~   47 (303)
                      ++||||||+|++.++|.+||+.|++..  |.||+|+|.|++.++
T Consensus        55 ~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k~   98 (100)
T 3r27_A           55 PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQK   98 (100)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSCSC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEeccccc
Confidence            468999999999999999999999875  789999999998763

>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=98.54  E-value=1.6e-08  Score=84.68  Aligned_cols=47  Identities=23%  Similarity=0.272  Sum_probs=42.9

Q ss_pred             CCCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         1 ~d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      +|.+|++||||||+|++.++|++|| ++|+..|+||.|.|.++..++.
T Consensus        79 ~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~~  125 (139)
T 2hgn_A           79 IGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGA  125 (139)
T ss_dssp             CSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSCC
T ss_pred             ECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCCC
Confidence            3667999999999999999999999 7899999999999999987654

>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=98.52  E-value=5.8e-08  Score=74.95  Aligned_cols=41  Identities=29%  Similarity=0.431  Sum_probs=38.7

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      ++||||||+|.+.++|++|++.|||..|+|++|+|.++.++
T Consensus        49 ~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   89 (99)
T 2cpj_A           49 KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS   89 (99)
T ss_dssp             TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCC
Confidence            45899999999999999999999999999999999999865

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.51  E-value=8.6e-08  Score=73.99  Aligned_cols=42  Identities=31%  Similarity=0.665  Sum_probs=39.1

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+||||||+|.+.++|++||+.|||..|+|+.|+|.+++++.
T Consensus        49 ~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   90 (99)
T 2cpd_A           49 KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD   90 (99)
T ss_dssp             ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             EeCCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCCC
Confidence            368999999999999999999999999999999999998754

>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=98.51  E-value=7.2e-08  Score=72.47  Aligned_cols=40  Identities=25%  Similarity=0.489  Sum_probs=36.8

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA   43 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A   43 (303)
                      .+|++||||||+|.+.++|++|++ +++..|+|+.|.|.+|
T Consensus        48 ~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A           48 NTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             TTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEEC
T ss_pred             CCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEeC
Confidence            479999999999999999999996 4889999999999876

>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=98.50  E-value=1e-07  Score=73.95  Aligned_cols=40  Identities=20%  Similarity=0.430  Sum_probs=38.0

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      +||||||+|.+.++|++|++.|||..++|+.|+|.+++.+
T Consensus        56 ~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (97)
T 2xnq_A           56 KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN   95 (97)
T ss_dssp             CSSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCC
T ss_pred             eCCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCC
Confidence            4899999999999999999999999999999999999865

>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=98.49  E-value=8.4e-08  Score=76.32  Aligned_cols=41  Identities=27%  Similarity=0.242  Sum_probs=38.4

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      ++||||||+|.+.++|++||+.|||..|+|++|+|.||...
T Consensus        44 ~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   84 (111)
T 1whx_A           44 EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            47899999999999999999999999999999999999753

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=98.49  E-value=9e-08  Score=75.88  Aligned_cols=42  Identities=36%  Similarity=0.640  Sum_probs=38.4

Q ss_pred             ccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHH
Q psy14476          8 KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR   49 (303)
Q Consensus         8 kGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r   49 (303)
                      ||||||+|.+.++|++|++.|||..|+|+.|+|.++..+..+
T Consensus        65 kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~r  106 (108)
T 2jvo_A           65 NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKR  106 (108)
T ss_dssp             TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCCC--
T ss_pred             CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCCCCC
Confidence            799999999999999999999999999999999999876544

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.49  E-value=8.4e-08  Score=76.84  Aligned_cols=41  Identities=22%  Similarity=0.464  Sum_probs=37.2

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhC--CceecccceeeecccchH
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMN--GRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~ln--G~~l~GR~L~V~~A~~k~   47 (303)
                      .||||||+|++.++|++||+.|+  +..|+||+|+|+||..+.
T Consensus        51 ~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~~   93 (105)
T 1sjq_A           51 GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKE   93 (105)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSSS
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCCC
Confidence            48999999999999999999886  478999999999998764

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=98.49  E-value=6.5e-08  Score=74.51  Aligned_cols=42  Identities=19%  Similarity=0.380  Sum_probs=39.0

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      +||||||+|.+.++|++|++.|||..+.|++|+|.++..+..
T Consensus        44 ~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   85 (96)
T 2kvi_A           44 KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNAR   85 (96)
T ss_dssp             ETTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCCC
T ss_pred             eCCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCCC
Confidence            589999999999999999999999999999999999986544

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.48  E-value=6.4e-08  Score=76.46  Aligned_cols=39  Identities=13%  Similarity=0.214  Sum_probs=37.5

Q ss_pred             cEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          9 GFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         9 GfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      |||||.|.+.++|++|++.|||..|.||+|+|+||+.+.
T Consensus        47 G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~~s   85 (96)
T 2diu_A           47 CSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKNR   85 (96)
T ss_dssp             TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCCSC
T ss_pred             CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCCCc
Confidence            999999999999999999999999999999999998764

>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=98.48  E-value=9.3e-08  Score=74.20  Aligned_cols=43  Identities=33%  Similarity=0.524  Sum_probs=39.4

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|++||+  +++.|+|+.|.|.++..++
T Consensus        52 ~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~a~~~~   94 (103)
T 2cqg_A           52 KTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLPNSKQ   94 (103)
T ss_dssp             SSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEECCCTTC
T ss_pred             CCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEecCCCC
Confidence            479999999999999999999998  5789999999999998764

>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=98.48  E-value=5.9e-08  Score=70.82  Aligned_cols=40  Identities=20%  Similarity=0.398  Sum_probs=37.1

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA   43 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A   43 (303)
                      .+|++||||||+|.+.++|++|++. ++..++|+.|.|.+|
T Consensus        36 ~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A           36 KTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            4689999999999999999999985 999999999999875

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.47  E-value=1.2e-07  Score=71.88  Aligned_cols=40  Identities=20%  Similarity=0.353  Sum_probs=38.0

Q ss_pred             ccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          8 KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         8 kGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      ||||||+|.+.++|++|++.||+..|+|+.|+|.++.++.
T Consensus        42 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   81 (90)
T 2dnq_A           42 KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKS   81 (90)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCC
Confidence            7999999999999999999999999999999999998764

>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=98.46  E-value=5.5e-08  Score=78.72  Aligned_cols=42  Identities=19%  Similarity=0.233  Sum_probs=37.5

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhC--CceecccceeeecccchH
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMN--GRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~ln--G~~l~GR~L~V~~A~~k~   47 (303)
                      ++||||||+|++.++|++||+.||  +..|+||+|+|.+|+++.
T Consensus        60 ~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~~~  103 (112)
T 1x4f_A           60 RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYK  103 (112)
T ss_dssp             TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCS
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECcccc
Confidence            579999999999999999999886  456999999999998654

>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=98.46  E-value=1.3e-07  Score=70.69  Aligned_cols=38  Identities=21%  Similarity=0.335  Sum_probs=36.2

Q ss_pred             cccEEEEEeCCHHHHHHHHHHh-CCceecccceeeeccc
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEM-NGRIIGSKPLYVALAQ   44 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~l-nG~~l~GR~L~V~~A~   44 (303)
                      +||||||+|.+.++|++|++.| ||..++|++|+|.||+
T Consensus        47 ~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A           47 RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             GGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            5899999999999999999999 9999999999999984

>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=98.45  E-value=1.2e-07  Score=77.00  Aligned_cols=40  Identities=23%  Similarity=0.527  Sum_probs=37.0

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCcee-----cccceeeecccch
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNGRII-----GSKPLYVALAQRK   46 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG~~l-----~GR~L~V~~A~~k   46 (303)
                      +||||||+|.+.++|++|+++|||++|     .|++|+|+|+...
T Consensus        62 ~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~a~~~  106 (114)
T 2cq2_A           62 NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKV  106 (114)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEEESCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEecccC
Confidence            489999999999999999999999998     7999999999754

>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=98.44  E-value=1.8e-07  Score=73.58  Aligned_cols=40  Identities=30%  Similarity=0.489  Sum_probs=38.2

Q ss_pred             ccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          8 KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         8 kGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      ||||||+|.+.++|++||+.|||..|+|+.|+|.|+.++.
T Consensus        61 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  100 (109)
T 1x4g_A           61 KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP  100 (109)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCC
Confidence            8999999999999999999999999999999999998764

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=98.43  E-value=1.5e-07  Score=76.23  Aligned_cols=39  Identities=26%  Similarity=0.281  Sum_probs=37.3

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      +|||+||+|.+.++|.+|++.|||+.++||.|+|.++..
T Consensus        54 ~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i~v~~~~~   92 (114)
T 3s6e_A           54 AQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPL   92 (114)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHTTCEETTEECEEEEECH
T ss_pred             CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEEcH
Confidence            699999999999999999999999999999999999864

>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=98.43  E-value=8.6e-08  Score=76.12  Aligned_cols=41  Identities=24%  Similarity=0.327  Sum_probs=36.7

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCc--eecccceeeecccch
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGR--IIGSKPLYVALAQRK   46 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~--~l~GR~L~V~~A~~k   46 (303)
                      +.||||||+|++.++|++||+.||+.  .|+||+|+|.+|+.+
T Consensus        50 ~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~   92 (102)
T 1x4d_A           50 NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKY   92 (102)
T ss_dssp             SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCCC
Confidence            35799999999999999999999864  599999999999864

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=98.43  E-value=4.1e-08  Score=76.09  Aligned_cols=45  Identities=33%  Similarity=0.468  Sum_probs=41.0

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      |.+|++||||||+|.+.++|++|++  ++..++|+.|.|.++.++..
T Consensus        44 ~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~~~~~   88 (102)
T 2xs2_A           44 DRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAIRKQN   88 (102)
T ss_dssp             CTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEEECC-
T ss_pred             CCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECCcCcc
Confidence            5589999999999999999999998  99999999999999987754

>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=98.43  E-value=1.6e-07  Score=72.19  Aligned_cols=40  Identities=25%  Similarity=0.458  Sum_probs=38.1

Q ss_pred             ccEEEEEeCCHHHHHHHHHHhCCceec--ccceeeecccchH
Q psy14476          8 KGFGFVCFSSPEEATKAVTEMNGRIIG--SKPLYVALAQRKE   47 (303)
Q Consensus         8 kGfgFV~F~s~e~A~~Ai~~lnG~~l~--GR~L~V~~A~~k~   47 (303)
                      ||||||+|.+.++|++|++.|||..|+  |+.|+|.+++++.
T Consensus        53 ~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~~   94 (97)
T 1why_A           53 DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCCC
Confidence            899999999999999999999999999  9999999998764

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=98.42  E-value=2.6e-07  Score=75.83  Aligned_cols=46  Identities=17%  Similarity=0.400  Sum_probs=41.8

Q ss_pred             CCCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         1 ~d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      +|.+|+++|||||+|.+.++|.+|++.|||..+.|+.|+|.++..+
T Consensus        34 ~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A           34 IDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             ECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            3667899999999999999999999999999999999999998764

>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=98.41  E-value=2.2e-07  Score=73.35  Aligned_cols=41  Identities=22%  Similarity=0.373  Sum_probs=36.9

Q ss_pred             cccEEEEEeCCHHHHHHHHHHh--CCceecccceeeecccchH
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEM--NGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~l--nG~~l~GR~L~V~~A~~k~   47 (303)
                      .||||||+|++.++|++||+.|  ++..|.||+|+|.|+..+.
T Consensus        50 ~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~   92 (101)
T 2cq1_A           50 GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE   92 (101)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSS
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCccc
Confidence            3899999999999999999977  5778999999999998654

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.40  E-value=2.5e-07  Score=70.42  Aligned_cols=40  Identities=23%  Similarity=0.402  Sum_probs=37.7

Q ss_pred             ccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          8 KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         8 kGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      ++||||+|.+.++|++|++.|||..|+|+.|+|.++.++.
T Consensus        44 ~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   83 (92)
T 2dgt_A           44 KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRL   83 (92)
T ss_dssp             SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCC
Confidence            6799999999999999999999999999999999998753

>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=98.40  E-value=1.6e-07  Score=73.08  Aligned_cols=42  Identities=26%  Similarity=0.517  Sum_probs=38.8

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .||||||+|.+.++|++||+.||+..|+|+.|+|.++.++..
T Consensus        44 ~~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   85 (103)
T 2dgu_A           44 LKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQ   85 (103)
T ss_dssp             CSSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCC
T ss_pred             ECCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCcc
Confidence            478999999999999999999999999999999999987643

>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=98.40  E-value=1.4e-07  Score=74.35  Aligned_cols=40  Identities=33%  Similarity=0.556  Sum_probs=37.8

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      +||||||+|.+.++|++|++.|||..|+|+.|+|.++..+
T Consensus        61 ~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~  100 (110)
T 1wf1_A           61 HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEP  100 (110)
T ss_dssp             ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCC
T ss_pred             eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            5899999999999999999999999999999999999743

>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=98.40  E-value=1.4e-07  Score=85.31  Aligned_cols=46  Identities=28%  Similarity=0.416  Sum_probs=42.9

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .+|++||||||+|.+.++|++||+.|||..|.|+.|+|.|+..+.+
T Consensus        47 ~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   92 (282)
T 3pgw_A           47 RSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSD   92 (282)
T ss_pred             CCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEEeccCcc
Confidence            3789999999999999999999999999999999999999987654

>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=98.39  E-value=2.5e-07  Score=76.01  Aligned_cols=43  Identities=35%  Similarity=0.662  Sum_probs=41.2

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      +|++||||||+|.+.++|++|++.|||..+.|++|.|.++.++
T Consensus        40 ~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~   82 (167)
T 1fxl_A           40 TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPS   82 (167)
T ss_dssp             TCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCCC
Confidence            8999999999999999999999999999999999999999865

>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=98.38  E-value=1.5e-07  Score=74.74  Aligned_cols=41  Identities=20%  Similarity=0.206  Sum_probs=36.7

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCc--eecccceeeecccchH
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNGR--IIGSKPLYVALAQRKE   47 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG~--~l~GR~L~V~~A~~k~   47 (303)
                      +||||||+|++.++|++|++.|++.  .|+||+|+|.|+..+.
T Consensus        50 ~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~~   92 (104)
T 1wex_A           50 FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKR   92 (104)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSS
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCcc
Confidence            4899999999999999999998764  5999999999998654

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.37  E-value=3e-07  Score=69.69  Aligned_cols=40  Identities=25%  Similarity=0.527  Sum_probs=37.5

Q ss_pred             ccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          8 KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         8 kGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      +|||||+|.+.++|++||+.|||..|+|+.|+|.++.++.
T Consensus        43 ~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   82 (90)
T 2dnp_A           43 KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQ   82 (90)
T ss_dssp             SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCC
Confidence            6799999999999999999999999999999999998653

>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=98.35  E-value=3.3e-07  Score=75.71  Aligned_cols=44  Identities=32%  Similarity=0.514  Sum_probs=41.5

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .+|+++|||||+|.+.++|++|++.|||..+.|++|.|.++.++
T Consensus        40 ~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~   83 (168)
T 1b7f_A           40 KTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPG   83 (168)
T ss_dssp             TTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCCC
Confidence            47899999999999999999999999999999999999999765

>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=98.34  E-value=2.7e-07  Score=79.59  Aligned_cols=41  Identities=15%  Similarity=0.229  Sum_probs=38.0

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecc--cceeeecccch
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGS--KPLYVALAQRK   46 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~G--R~L~V~~A~~k   46 (303)
                      +++|||||+|++.++|++|++.|||..|.|  ++|+|.|++.+
T Consensus        82 ~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~  124 (164)
T 1sjr_A           82 NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT  124 (164)
T ss_dssp             SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSS
T ss_pred             CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCC
Confidence            468999999999999999999999999966  99999999875

>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=98.33  E-value=3.8e-07  Score=68.18  Aligned_cols=36  Identities=31%  Similarity=0.533  Sum_probs=33.9

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeec
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVAL   42 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~   42 (303)
                      ++||||||+|.+.++|++|+ .|||..|+||.|+|.+
T Consensus        51 ~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~r   86 (87)
T 2hzc_A           51 QDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRR   86 (87)
T ss_dssp             SSSSEEEEEESSHHHHHHHG-GGTTCEETTEECEEEC
T ss_pred             CCCcEEEEEcCCHHHHHHHH-hcCCCEECCeEEEEeC
Confidence            55899999999999999999 9999999999999974

>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=98.32  E-value=3.7e-07  Score=71.80  Aligned_cols=39  Identities=26%  Similarity=0.324  Sum_probs=37.1

Q ss_pred             cEEEEEeCCHHHHHHHHHHhCCceecc-----cceeeecccchH
Q psy14476          9 GFGFVCFSSPEEATKAVTEMNGRIIGS-----KPLYVALAQRKE   47 (303)
Q Consensus         9 GfgFV~F~s~e~A~~Ai~~lnG~~l~G-----R~L~V~~A~~k~   47 (303)
                      |||||+|.+.++|++||+.|||..|+|     +.|+|.+|.++.
T Consensus        51 g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~~~~   94 (108)
T 1x4c_A           51 GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRS   94 (108)
T ss_dssp             TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEESSCCS
T ss_pred             CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeCCCCC
Confidence            999999999999999999999999999     999999998754

>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=98.31  E-value=2.9e-07  Score=76.95  Aligned_cols=44  Identities=25%  Similarity=0.491  Sum_probs=40.5

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|++|+ +|||..|.|+.|+|.++..+.
T Consensus        49 ~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~~~~~~~   92 (175)
T 1fje_B           49 RTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRD   92 (175)
T ss_dssp             EEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEECCCCSS
T ss_pred             CCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEecCCCcc
Confidence            36889999999999999999999 599999999999999998763

>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=98.31  E-value=3.3e-07  Score=74.84  Aligned_cols=41  Identities=22%  Similarity=0.477  Sum_probs=37.2

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCC--ceecccceeeecccchH
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNG--RIIGSKPLYVALAQRKE   47 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG--~~l~GR~L~V~~A~~k~   47 (303)
                      .||||||+|++.++|++||+.|++  ..|+||+|+|.||..++
T Consensus        66 ~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k~  108 (119)
T 2ad9_A           66 GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKE  108 (119)
T ss_dssp             GGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSSS
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCCC
Confidence            489999999999999999999884  68999999999998764

>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=98.27  E-value=5.2e-07  Score=88.45  Aligned_cols=45  Identities=16%  Similarity=0.490  Sum_probs=42.3

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|+++|||||+|.+.++|.+||+.|||..|+|+.|.|.++..+.
T Consensus       139 ~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~~~~  183 (437)
T 3pgw_S          139 RSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRT  183 (437)
T ss_pred             CCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            489999999999999999999999999999999999999998653

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=98.26  E-value=6.2e-07  Score=74.46  Aligned_cols=41  Identities=17%  Similarity=0.355  Sum_probs=37.8

Q ss_pred             CcccE-EEEEeCCHHHHHHHHHHhCCceecc--cceeeecccch
Q psy14476          6 RSKGF-GFVCFSSPEEATKAVTEMNGRIIGS--KPLYVALAQRK   46 (303)
Q Consensus         6 kSkGf-gFV~F~s~e~A~~Ai~~lnG~~l~G--R~L~V~~A~~k   46 (303)
                      ++||| |||+|.+.++|++|++.|||..|.|  ++|+|.|++.+
T Consensus        63 ~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~  106 (130)
T 3zzy_A           63 KNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT  106 (130)
T ss_dssp             ETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCS
T ss_pred             CCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCC
Confidence            35788 9999999999999999999999998  99999999865

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.23  E-value=8.8e-07  Score=69.99  Aligned_cols=41  Identities=22%  Similarity=0.332  Sum_probs=35.9

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      +++||||||+|.+.++|++||+.+++  +.+++|+|.|+..+.
T Consensus        51 ~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           51 SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQP   91 (100)
T ss_dssp             SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCC
T ss_pred             cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCC
Confidence            57899999999999999999998544  689999999998653

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=98.22  E-value=1.2e-06  Score=73.12  Aligned_cols=46  Identities=20%  Similarity=0.125  Sum_probs=38.0

Q ss_pred             CCCCcccEEEEEeCC----HHH----HHHHHH--HhCCceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSS----PEE----ATKAVT--EMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s----~e~----A~~Ai~--~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      +||+|||||||+|.+    +++    |.+||.  .|||..|+||+|+|.+-.....
T Consensus        43 ~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~I~Gr~irV~ln~~g~~   98 (136)
T 2j8a_A           43 NSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCFIMGFKFEVILNKHSIL   98 (136)
T ss_dssp             TTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEEETTEEEEEEECCTTHH
T ss_pred             CCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCeecCcEEEEEECcccHH
Confidence            489999999999996    444    889998  7899999999999998765433

>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=98.19  E-value=1.1e-06  Score=77.36  Aligned_cols=40  Identities=15%  Similarity=0.284  Sum_probs=37.6

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      +||||||+|.+.++|++||+.|||..|.||+|+|.+++.+
T Consensus        41 ~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~   80 (205)
T 3tyt_A           41 KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQP   80 (205)
T ss_dssp             STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCS
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCC
Confidence            5899999999999999999999999999999999998743

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=98.18  E-value=1.9e-06  Score=75.31  Aligned_cols=65  Identities=28%  Similarity=0.498  Sum_probs=53.4

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCC
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIANMRMQQMGQLFQPGSTGGYF   82 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~~~~~~~~q~~~~~r~~~~~~~~~~~~~~~~f   82 (303)
                      .+|+++|||||+|.+.++|++||+.+|+..+.||.|+|.++.........                        ....+|
T Consensus        52 ~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~~~~~~~~~------------------------~~~~l~  107 (213)
T 4f02_A           52 ITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKS------------------------GVGNIF  107 (213)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCTHHHHH------------------------CTTEEE
T ss_pred             CCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccccccccccccc------------------------ccccce
Confidence            47999999999999999999999999999999999999998865432110                        123689


Q ss_pred             CCCCCCCCc
Q psy14476         83 VPTLPQPQR   91 (303)
Q Consensus        83 ~~~lp~~~~   91 (303)
                      |.||++...
T Consensus       108 v~nl~~~~t  116 (213)
T 4f02_A          108 IKNLDKSID  116 (213)
T ss_dssp             EESCCTTCC
T ss_pred             ECCcccccH
Confidence            999998654

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.18  E-value=1.6e-06  Score=66.18  Aligned_cols=41  Identities=24%  Similarity=0.272  Sum_probs=37.5

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      ..|.|||+|.+.++|++||+.|||..|+||+|+|.+|.+++
T Consensus        53 ~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   93 (96)
T 2e44_A           53 ETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEM   93 (96)
T ss_dssp             SSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCccc
Confidence            34559999999999999999999999999999999998763

>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=98.14  E-value=2.1e-06  Score=77.60  Aligned_cols=44  Identities=30%  Similarity=0.649  Sum_probs=41.8

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .+|+++|||||+|.+.++|.+|++.|||..++|+.|.|.++.++
T Consensus       132 ~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~  175 (284)
T 3smz_A          132 RTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAG  175 (284)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGG
T ss_pred             CCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            48999999999999999999999999999999999999999865

>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=98.13  E-value=1.6e-06  Score=78.58  Aligned_cols=71  Identities=18%  Similarity=0.209  Sum_probs=48.9

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCC
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIANMRMQQMGQLFQPGSTGGY   81 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~~~~~~~~q~~~~~r~~~~~~~~~~~~~~~~   81 (303)
                      |.+|+++|||||+|.+.++|.+|++.|||..|.|+.|.|.++.++......         .        .. .. ....+
T Consensus       153 ~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~---------~--------~~-~~-~~~~l  213 (292)
T 2ghp_A          153 LRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRT---------D--------SA-TL-EGREI  213 (292)
T ss_dssp             ------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC---------------------------CC-TTTEE
T ss_pred             CCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcccccc---------c--------cc-CC-CCceE
Confidence            456889999999999999999999999999999999999999876543221         0        00 11 13478


Q ss_pred             CCCCCCCC-Cc
Q psy14476         82 FVPTLPQP-QR   91 (303)
Q Consensus        82 f~~~lp~~-~~   91 (303)
                      ||.|||.. ..
T Consensus       214 ~v~nlp~~~~t  224 (292)
T 2ghp_A          214 MIRNLSTELLD  224 (292)
T ss_dssp             EEEEECTTTCC
T ss_pred             EEECCCcccCC
Confidence            99999987 44

>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=98.13  E-value=2.1e-06  Score=72.72  Aligned_cols=68  Identities=22%  Similarity=0.350  Sum_probs=50.2

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCC
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIANMRMQQMGQLFQPGSTGGYF   82 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~~~~~~~~q~~~~~r~~~~~~~~~~~~~~~~f   82 (303)
                      .+|++||||||+|.+.++|++|++. ++..|+|+.|.|.++..+......                  .. .. ....+|
T Consensus        50 ~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~~~~~~~~~~~------------------~~-~~-~~~~l~  108 (196)
T 1l3k_A           50 NTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRP------------------GA-HL-TVKKIF  108 (196)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCC-------------------------------CCSEEE
T ss_pred             CCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeecccCccccccc------------------cc-CC-CcceEE
Confidence            4789999999999999999999986 999999999999999876433210                  00 01 124789


Q ss_pred             CCCCCCCCc
Q psy14476         83 VPTLPQPQR   91 (303)
Q Consensus        83 ~~~lp~~~~   91 (303)
                      |.|||....
T Consensus       109 V~nLp~~~t  117 (196)
T 1l3k_A          109 VGGIKEDTE  117 (196)
T ss_dssp             EECCTTTCC
T ss_pred             EeCCCCCCC
Confidence            999998654

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=98.12  E-value=1.2e-06  Score=74.40  Aligned_cols=42  Identities=26%  Similarity=0.423  Sum_probs=39.1

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      ++++||||||+|.+.++|++|+ .|||..|+|+.|+|.++..+
T Consensus        47 ~~~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i~v~~~~~~   88 (198)
T 2yh0_A           47 INQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDY   88 (198)
T ss_dssp             EETTTTEEEEEESCSHHHHHHG-GGTTEEETTEEEEEECCCCC
T ss_pred             ecCCCCEEEEEeCCHHHHHHHH-HhcCCEEcCceEEEeCCCCC
Confidence            4688999999999999999999 89999999999999998764

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.11  E-value=1.6e-06  Score=66.28  Aligned_cols=37  Identities=19%  Similarity=0.275  Sum_probs=34.8

Q ss_pred             EEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476         10 FGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus        10 fgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      ||||+|.+.++|++||+ |||..|+|+.|.|.++..+.
T Consensus        47 ~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~~   83 (94)
T 2e5g_A           47 FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKE   83 (94)
T ss_dssp             EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCSC
T ss_pred             EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcCC
Confidence            99999999999999999 99999999999999987653

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.10  E-value=2e-06  Score=70.60  Aligned_cols=38  Identities=32%  Similarity=0.301  Sum_probs=35.6

Q ss_pred             cE-EEEEeCCHHHHHHHHHHhCCceecc--cceeeecccch
Q psy14476          9 GF-GFVCFSSPEEATKAVTEMNGRIIGS--KPLYVALAQRK   46 (303)
Q Consensus         9 Gf-gFV~F~s~e~A~~Ai~~lnG~~l~G--R~L~V~~A~~k   46 (303)
                      || |||+|++.++|.+|++.|||..|.|  ++|+|.+|+.+
T Consensus        62 Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~  102 (124)
T 2e5i_A           62 GIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPT  102 (124)
T ss_dssp             SEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCS
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCC
Confidence            87 9999999999999999999999988  68999999866

>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=98.07  E-value=2.3e-06  Score=70.95  Aligned_cols=42  Identities=26%  Similarity=0.423  Sum_probs=38.3

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      ++++||||||+|.+.++|++|+ .|||..+.|++|+|.++...
T Consensus        47 ~~~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~v~~~~~~   88 (172)
T 2g4b_A           47 INQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDY   88 (172)
T ss_dssp             EETTTTEEEEEESSHHHHHHHG-GGTTCEETTEECEEECCSSC
T ss_pred             ecCCCCEEEEEeCCHHHHHHHH-HhCCcEecCceeeecCCccc
Confidence            3678999999999999999999 89999999999999987643

>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=98.06  E-value=3.2e-06  Score=67.38  Aligned_cols=35  Identities=29%  Similarity=0.282  Sum_probs=31.2

Q ss_pred             cEEEEEeCCHHHHHHHHHHhCCceecccceeeecc
Q psy14476          9 GFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA   43 (303)
Q Consensus         9 GfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A   43 (303)
                      |||||+|.+.++|++||+.|||..|+|+.|+|.+.
T Consensus        52 g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i   86 (115)
T 3beg_B           52 GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   86 (115)
T ss_dssp             SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBC
T ss_pred             CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEE
Confidence            99999999999999999999999999999444433

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.03  E-value=3e-06  Score=67.29  Aligned_cols=39  Identities=13%  Similarity=0.145  Sum_probs=33.5

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      |++||||||+|.+.++|++||+.|+  .++|+.|.|..+..
T Consensus        49 g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~~~~~~   87 (114)
T 2dnl_A           49 FPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLCVSSPT   87 (114)
T ss_dssp             SCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEEECCSS
T ss_pred             CCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEeccCCC
Confidence            8999999999999999999999984  47888887776553

>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=98.01  E-value=2.4e-06  Score=77.10  Aligned_cols=46  Identities=28%  Similarity=0.507  Sum_probs=40.1

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhC-Cceec---ccceeeecccchH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMN-GRIIG---SKPLYVALAQRKE   47 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~ln-G~~l~---GR~L~V~~A~~k~   47 (303)
                      |.+|+++|||||+|.+.++|.+|++.|| +..+.   +|+|.|.++...+
T Consensus       131 ~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          131 DDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             ETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCEE
T ss_pred             CCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeeccccC
Confidence            5789999999999999999999999995 55555   9999999998653

>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=98.01  E-value=4.9e-06  Score=68.56  Aligned_cols=43  Identities=30%  Similarity=0.577  Sum_probs=39.0

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|++|++.  +..++|+.|.|.++..+.
T Consensus        40 ~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~~~~   82 (167)
T 2cjk_A           40 ATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAIPRD   82 (167)
T ss_dssp             TTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECCCHH
T ss_pred             CCCCccceEEEEEccHHHHHHHHhc--ccccCCeEcccccccchh
Confidence            4799999999999999999999984  789999999999998754

>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=97.97  E-value=6e-06  Score=62.97  Aligned_cols=40  Identities=20%  Similarity=0.365  Sum_probs=29.7

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCcee--cccceeeecccchHHH
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRII--GSKPLYVALAQRKEDR   49 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l--~GR~L~V~~A~~k~~r   49 (303)
                      +|||||||+|++.++|++    +++..+  .|+.|.|.+|.++.++
T Consensus        46 ~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~~k~~~   87 (89)
T 3d2w_A           46 PFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAEPKHNK   87 (89)
T ss_dssp             SCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC-----
T ss_pred             CCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcCCCCcC
Confidence            389999999999999983    566654  5999999999987653

>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=97.85  E-value=1.1e-05  Score=72.65  Aligned_cols=40  Identities=38%  Similarity=0.674  Sum_probs=37.8

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      +++||||||.|.+.++|++|+..|||..|.|+.|+|.++.
T Consensus        55 ~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~   94 (261)
T 3sde_A           55 NRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFAT   94 (261)
T ss_dssp             ETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             eCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeecc
Confidence            4679999999999999999999999999999999999986

>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=97.82  E-value=1.2e-05  Score=70.95  Aligned_cols=39  Identities=23%  Similarity=0.436  Sum_probs=37.1

Q ss_pred             ccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          8 KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         8 kGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      ||||||+|.+.++|++|++.|||..|.|+.|+|.++..+
T Consensus        72 ~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  110 (229)
T 2adc_A           72 KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ  110 (229)
T ss_dssp             SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCc
Confidence            899999999999999999999999999999999998754

>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=97.82  E-value=1.4e-05  Score=66.13  Aligned_cols=41  Identities=24%  Similarity=0.349  Sum_probs=36.3

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceec---ccceeeecccch
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIG---SKPLYVALAQRK   46 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~---GR~L~V~~A~~k   46 (303)
                      ++||||||+|.+.++|++|++.|||..+.   ++.+.|.++..+
T Consensus        45 ~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~~~~~~~   88 (175)
T 3nmr_A           45 QSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSE   88 (175)
T ss_dssp             EEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECGGG
T ss_pred             CcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEEcccccc
Confidence            89999999999999999999999998876   677888877644

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=97.77  E-value=1e-05  Score=69.02  Aligned_cols=39  Identities=23%  Similarity=0.436  Sum_probs=37.2

Q ss_pred             ccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          8 KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         8 kGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      +|||||+|.+.++|++|++.|||..|.|+.|+|.++..+
T Consensus        41 ~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~   79 (198)
T 1qm9_A           41 KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   79 (198)
T ss_dssp             SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCC
Confidence            799999999999999999999999999999999998764

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.73  E-value=1.6e-05  Score=62.11  Aligned_cols=37  Identities=19%  Similarity=0.305  Sum_probs=34.2

Q ss_pred             cEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          9 GFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         9 GfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      +.+||+|.+.++|.+||+ |||..++||.|+|.++.+.
T Consensus        50 d~~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~lkt~d   86 (91)
T 2dnr_A           50 DKMWVTFLEGSSALNVLS-LNGKELLNRTITIALKSPS   86 (91)
T ss_dssp             SSEEEEESSHHHHHHGGG-GTTCEETTEEEEEEECCCS
T ss_pred             CCEEEEECChHHHHHHHh-cCCeEeCCeEEEEEeCCCC
Confidence            458999999999999998 9999999999999998764

>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=97.67  E-value=3.1e-05  Score=73.93  Aligned_cols=39  Identities=23%  Similarity=0.569  Sum_probs=34.4

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCceec---cc--ceeeecccc
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNGRIIG---SK--PLYVALAQR   45 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG~~l~---GR--~L~V~~A~~   45 (303)
                      +||||||+|++.++|++||+.|||+.+.   |+  +|+|+|+..
T Consensus        55 ~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~~~~~   98 (345)
T 3tht_A           55 NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEK   98 (345)
T ss_dssp             TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEECSS
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEEEeec
Confidence            6899999999999999999999999883   44  789998853

>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=97.60  E-value=1.3e-05  Score=60.13  Aligned_cols=40  Identities=25%  Similarity=0.324  Sum_probs=31.8

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+||||||+|.+.++|++|+..  ...+.|++|.|.++.++.
T Consensus        40 ~~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~~~~   79 (88)
T 1wf0_A           40 PFRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             SCCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCCCCC
T ss_pred             CCCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecCCCC
Confidence            3799999999999999865322  344589999999998764

>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=97.45  E-value=0.0001  Score=66.59  Aligned_cols=36  Identities=19%  Similarity=0.312  Sum_probs=33.9

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCceecccceeeecc
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA   43 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A   43 (303)
                      ++|||||+|.+.++|.+|++ +||..|.|+.|+|.++
T Consensus        80 ~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~~~  115 (292)
T 2ghp_A           80 NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL  115 (292)
T ss_dssp             SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEEEC
Confidence            68999999999999999994 8999999999999975

>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=97.15  E-value=0.00023  Score=55.93  Aligned_cols=33  Identities=12%  Similarity=0.265  Sum_probs=31.0

Q ss_pred             EEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476         11 GFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus        11 gFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      +||+|.+.++|.+||+ |||..++||.|+|.+-.
T Consensus        61 ~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           61 MLVTFADSHSALSVLD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             EEEECSCSHHHHHHHH-GGGSEETTEEEEEECCC
T ss_pred             EEEEEcChHHHHHHHh-cCCeeeCCeEEEEeccC
Confidence            9999999999999998 99999999999998643

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=96.42  E-value=0.0018  Score=58.66  Aligned_cols=28  Identities=32%  Similarity=0.411  Sum_probs=26.2

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCcee
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRII   33 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l   33 (303)
                      .+||||||+|.+.++|+.|++.|+|..|
T Consensus       177 ~~kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          177 ESKNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             GGGTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             CCCCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            3699999999999999999999999887

>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=96.18  E-value=0.0014  Score=53.76  Aligned_cols=41  Identities=15%  Similarity=0.010  Sum_probs=37.9

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHh-CCceecccceeeecccch
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEM-NGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~l-nG~~l~GR~L~V~~A~~k   46 (303)
                      .+.+|+++|+|.+.++|++|+++| ||..++| .|.|+++..+
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~   51 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKT   51 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTE
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCc
Confidence            467999999999999999999999 9999999 9999998764

>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=96.03  E-value=0.0028  Score=52.12  Aligned_cols=28  Identities=14%  Similarity=-0.022  Sum_probs=24.9

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCce
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEMNGRI   32 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~lnG~~   32 (303)
                      .+++|||||+|.+.++|++|++.+++..
T Consensus        10 ~~~~G~~fV~f~~~~~A~~al~~~~~~~   37 (158)
T 2kn4_A           10 KTLKGETTTEAVDAATAEKVFKQYANDN   37 (158)
T ss_dssp             SSCEEEEEEECSSHHHHHHHHHHHHHHH
T ss_pred             ccccchhHHHHHHHHhHHHHHHhhcccC
Confidence            4799999999999999999999887643

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=92.97  E-value=0.11  Score=42.16  Aligned_cols=40  Identities=15%  Similarity=0.238  Sum_probs=33.8

Q ss_pred             EEEEEeCC-HHHHHHHHHHhC--CceecccceeeecccchHHH
Q psy14476         10 FGFVCFSS-PEEATKAVTEMN--GRIIGSKPLYVALAQRKEDR   49 (303)
Q Consensus        10 fgFV~F~s-~e~A~~Ai~~ln--G~~l~GR~L~V~~A~~k~~r   49 (303)
                      +|||.|.+ .++|..|++.||  +.+|+|..+.+......++.
T Consensus        57 tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL~GeeE~   99 (121)
T 1owx_A           57 EGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEGEVEK   99 (121)
T ss_dssp             EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECCHHHHH
T ss_pred             EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEECCCHHHH
Confidence            69999999 899999999995  78899998888877755443

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=92.82  E-value=0.13  Score=41.41  Aligned_cols=35  Identities=17%  Similarity=0.183  Sum_probs=32.2

Q ss_pred             cEEEEEeCCHHHHHHHHHHhCCceecccceeeecc
Q psy14476          9 GFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA   43 (303)
Q Consensus         9 GfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A   43 (303)
                      |=|+|+|.|...|-+|.=.|||.+|+||+|+|.-.
T Consensus        63 ~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gTv   97 (117)
T 2l9w_A           63 NGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGTI   97 (117)
T ss_dssp             TEEEEECSCHHHHHHHHHHHSSEEETTEEEEEECH
T ss_pred             CceEEEEccchhhHHHHhhcCCeeecCeEEEecCH
Confidence            45999999999999999999999999999999854

>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=90.00  E-value=0.24  Score=39.33  Aligned_cols=37  Identities=22%  Similarity=0.142  Sum_probs=34.0

Q ss_pred             cEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          9 GFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         9 GfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      .-..|.|.++++|.+|-..|++..+.|+.|+|-+++.
T Consensus        47 RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~   83 (104)
T 1wey_A           47 KRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             TEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             eEEEEEeCChHHHHHHHHHhccceecCceeEEEecCC
Confidence            3467999999999999999999999999999999983

---

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	303
d1nmra_	85	a.144.1.1 (A:) poly(A) binding protein {Protozoan	2e-39
d1g9la_	144	a.144.1.1 (A:) poly(A) binding protein {Human (Hom	2e-38
d1ifwa_	92	a.144.1.1 (A:) poly(A) binding protein {Baker's ye	6e-33
d1i2ta_	61	a.144.1.1 (A:) hyperplastic discs protein {Human (	2e-32
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-11
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	2e-11
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	5e-11
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-10
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-10
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-09
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-09
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-09
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	6e-09
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-09
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-08
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-08
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-08
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-08
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	3e-08
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	4e-08
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	5e-08
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-08
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	5e-08
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	8e-08
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-07
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-07
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-07
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-07
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-07
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-07
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-07
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	5e-07
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	6e-07
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	6e-07
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	7e-07
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	7e-07
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-06
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-06
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-06
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-06
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-06
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	3e-06
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	3e-06
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	4e-06
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	5e-06
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	7e-06
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	8e-06
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	8e-06
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	1e-05
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	1e-05
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-05
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-05
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-05
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	4e-05
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	4e-05
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	4e-05
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-05
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	6e-05
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-05
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 6e-05
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	7e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	8e-05
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	8e-05
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	1e-04
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-04
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-04
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	2e-04
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	2e-04
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	2e-04
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	4e-04
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	5e-04
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	8e-04
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	0.001
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.002
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	0.002
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	0.003

>d1nmra_ a.144.1.1 (A:) poly(A) binding protein {Protozoan (Trypanosoma cruzi) [TaxId: 5693]} Length = 85

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Protozoan (Trypanosoma cruzi) [TaxId: 5693]

 Score =  131 bits (330), Expect = 2e-39
 Identities = 38/83 (45%), Positives = 54/83 (65%), Gaps = 2/83 (2%)

Query: 212 AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 271
           ++  QGQ    ST+LA   P++QK +LGERL+  I  + P  A K+TGMLLE+DN E+L 
Sbjct: 3   SLASQGQN--LSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILN 60

Query: 272 MLEHNESLKSKVEEAVAVLQAHQ 294
           +L+    L +KV+EA+ VL  H 
Sbjct: 61  LLDTPGLLDAKVQEALEVLNRHM 83

>d1g9la_ a.144.1.1 (A:) poly(A) binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 144

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  130 bits (329), Expect = 2e-38
 Identities = 87/145 (60%), Positives = 97/145 (66%), Gaps = 10/145 (6%)

Query: 159 GPRGGGPMQAPGPASVSAAGRQTGGYNKYPVRNPGTQPQAQIGGIQPAAAGVQAVHVQGQ 218
           GP G      P   +V       G      VRNP     AQ            AVHVQGQ
Sbjct: 1   GPLGSAAAATPAVRTVPQYKYAAG------VRNPQQHLNAQ----PQVTMQQPAVHVQGQ 50

Query: 219 EPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNES 278
           EPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE  ES
Sbjct: 51  EPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPES 110

Query: 279 LKSKVEEAVAVLQAHQAKQAAVKKE 303
           L+SKV+EAVAVLQAHQAK+AA K  
Sbjct: 111 LRSKVDEAVAVLQAHQAKEAAQKAV 135

>d1ifwa_ a.144.1.1 (A:) poly(A) binding protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 92

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  114 bits (288), Expect = 6e-33
 Identities = 25/86 (29%), Positives = 45/86 (52%), Gaps = 2/86 (2%)

Query: 220 PLTSTMLAAAQPQEQKQMLGERLFPLIQRMY--PELAGKITGMLLEIDNAELLYMLEHNE 277
           P  +        Q+Q+Q LGE+L+  +       E AGKITGM+L++   E+  +LE +E
Sbjct: 6   PRNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLLESDE 65

Query: 278 SLKSKVEEAVAVLQAHQAKQAAVKKE 303
             +   +EA A  ++ + +Q    ++
Sbjct: 66  LFEQHYKEASAAYESFKKEQEQQTEQ 91

>d1i2ta_ a.144.1.1 (A:) hyperplastic discs protein {Human (Homo sapiens) [TaxId: 9606]} Length = 61

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: hyperplastic discs protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  112 bits (282), Expect = 2e-32
 Identities = 30/60 (50%), Positives = 44/60 (73%)

Query: 234 QKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAH 293
            +Q LGERL+P +Q M P  A KITGMLLE+  A+LL +L   +SL+++V+EA+ ++ AH
Sbjct: 1   HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELIIAH 60

>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 = 58.4 bits (141), Expect = 1e-11
 Identities = 12/47 (25%), Positives = 18/47 (38%)

Query: 4  DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
          D    G   V F  PEEA   +  ++GR  G + +         D +
Sbjct: 53 DRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTDYQ 99

>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 = 57.0 bits (137), Expect = 2e-11
 Identities = 15/53 (28%), Positives = 23/53 (43%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHL 53
          +S   + +G  FV F     AT A+  M G     KP+ +  A+   D  A +
Sbjct: 39 VSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 91

>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 = 56.9 bits (137), Expect = 5e-11
 Identities = 7/68 (10%), Positives = 26/68 (38%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQR 60
           +     ++G  +V +    +A  A   ++G  + ++ L V         +     +  ++
Sbjct: 39  VGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQ 98

Query: 61  IANMRMQQ 68
           +  ++ + 
Sbjct: 99  LKLLKEKY 106

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.5 bits (133), Expect = 1e-10
 Identities = 21/50 (42%), Positives = 26/50 (52%)

Query: 1   MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
             +   SK FGFV + +P  A  A+  MNG  IG K L V L + K D K
Sbjct: 53  DKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSK 102

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.0 bits (129), Expect = 3e-10
 Identities = 14/44 (31%), Positives = 26/44 (59%)

Query: 8  KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
          +GFGFV F + ++A  A+  MNG+ +  + + V  A +  D ++
Sbjct: 47 RGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRS 90

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.0 bits (124), Expect = 1e-09
 Identities = 15/47 (31%), Positives = 25/47 (53%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE 47
           +    S GFGFV +  PE+A KA+ ++ G  +    L V +++R  
Sbjct: 36 KAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERAT 82

>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 = 52.2 bits (125), Expect = 1e-09
 Identities = 12/47 (25%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEM-NGRIIGSKPLYVALAQRKEDRK 50
          G  +GFGFV F + ++A KA   + +   +  + L +  A  +   +
Sbjct: 48 GAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 94

>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 = 51.5 bits (123), Expect = 2e-09
 Identities = 15/45 (33%), Positives = 24/45 (53%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR 45
               RS G+ +V F  P +A +A+  MN  +I  KP+ +  +QR
Sbjct: 35 DMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR 79

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.9 bits (128), Expect = 2e-09
 Identities = 11/49 (22%), Positives = 18/49 (36%), Gaps = 1/49 (2%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
             G+ +GF FV F   +   K V       +      V  A  K++  +
Sbjct: 134 GSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKALSKQEMAS 181

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.1 bits (119), Expect = 6e-09
 Identities = 14/44 (31%), Positives = 29/44 (65%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
           SKG+ F+ F+S + +  A+  MNG+ + ++P+ V+ A +K+ +
Sbjct: 39 NSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSK 82

>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 = 50.3 bits (120), Expect = 8e-09
 Identities = 13/42 (30%), Positives = 21/42 (50%)

Query: 9  GFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
          GF FV + +   A  AV   +GR+I  + L + LA   +  +
Sbjct: 51 GFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVNR 92

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 2e-08
 Identities = 15/49 (30%), Positives = 32/49 (65%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
          + ++  SKG+GFV F + E A +A+ +MNG ++  + ++V   + +++R
Sbjct: 41 VCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKER 89

>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 = 48.9 bits (116), Expect = 2e-08
 Identities = 10/52 (19%), Positives = 20/52 (38%), Gaps = 2/52 (3%)

Query: 7  SKGFGFVCFSSPEEATKAVTEMNGR--IIGSKPLYVALAQRKEDRKAHLASQ 56
          ++GF FV + S   A  A  ++      +    + V  A+ + D    +   
Sbjct: 44 NRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 95

>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 = 48.4 bits (115), Expect = 3e-08
 Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 1/46 (2%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ-RKEDRK 50
           + GF FV + S  +A  A+  +NG  +  + +        KE R+
Sbjct: 47 TACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQ 92

>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 = 48.1 bits (114), Expect = 3e-08
 Identities = 12/41 (29%), Positives = 18/41 (43%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
           SKG+ F  +       +A+  +NG  +G K L V  A   
Sbjct: 41 LSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG 81

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.1 bits (114), Expect = 3e-08
 Identities = 13/45 (28%), Positives = 27/45 (60%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
           + + + FV FS+ E+A +A+  +NG+++   P+ V LA+  +  
Sbjct: 41 KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKD 85

>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 = 47.7 bits (113), Expect = 4e-08
 Identities = 17/43 (39%), Positives = 24/43 (55%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
           +E G   G   V F S +EAT AV ++N R IGS+ + + L 
Sbjct: 44 YNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG 86

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.7 bits (113), Expect = 5e-08
 Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 2/43 (4%)

Query: 7  SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
          SKGFGFV F+  E   K +++ +  +I  +     L   K+ +
Sbjct: 49 SKGFGFVRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQ 89

>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 = 48.1 bits (114), Expect = 5e-08
 Identities = 9/48 (18%), Positives = 18/48 (37%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
            +    G  FV F+S  +  KA+  + GR   ++ +           +
Sbjct: 53  VEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHR 100

>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 = 47.6 bits (113), Expect = 5e-08
 Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 2/45 (4%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRII--GSKPLYVALA 43
              GR +G  FV ++  EEA +A++ +N  I   GS+PL V LA
Sbjct: 41 DKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 85

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 8e-08
 Identities = 12/42 (28%), Positives = 22/42 (52%)

Query: 9  GFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
          G+GF  +   E A  A+  +NGR    + L V  A  +++++
Sbjct: 51 GYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKE 92

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.6 bits (110), Expect = 1e-07
 Identities = 17/50 (34%), Positives = 27/50 (54%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
           S   + KGF FV F  PE A KA  E++G++   + L+V  +  K++  
Sbjct: 43 DSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEAS 92

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 46.6 bits (110), Expect = 1e-07
 Identities = 14/50 (28%), Positives = 25/50 (50%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
          +S+DG+SKG  ++ F S  +A K + E  G  I  + + +     K   +
Sbjct: 46 VSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTR 95

>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 = 46.1 bits (109), Expect = 1e-07
 Identities = 9/35 (25%), Positives = 16/35 (45%)

Query: 10 FGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ 44
             V F    +A KA+ + NG  +  +P+ + L  
Sbjct: 43 TADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 77

>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 = 46.3 bits (109), Expect = 2e-07
 Identities = 11/47 (23%), Positives = 18/47 (38%)

Query: 8  KGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLA 54
               + FS+P  A  A   ++      K + +  AQ      +HLA
Sbjct: 46 FKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLHIGSSHLA 92

>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 = 45.8 bits (108), Expect = 2e-07
 Identities = 15/50 (30%), Positives = 23/50 (46%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
          ++E   +  + FV F    +A  A+  MNGR I  K + V  A     +K
Sbjct: 41 ITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQK 90

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 45.5 bits (107), Expect = 2e-07
 Identities = 12/46 (26%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
            E   +    F+ F + + A +A+ +MN  ++G++ + V+LA +K
Sbjct: 41 QKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK 85

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (108), Expect = 3e-07
 Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 5   GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
            RS+GFGFV FSS  E   A+       I  + +    A  +E+ 
Sbjct: 59  KRSRGFGFVTFSSMAEVDAAM-AARPHSIDGRVVEPKRAVAREES 102

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.2 bits (106), Expect = 5e-07
 Identities = 15/47 (31%), Positives = 22/47 (46%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
          E G+ KG   V +  P  A  AV   +G+      L V+LA++K   
Sbjct: 53 ETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 99

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.6 bits (105), Expect = 6e-07
 Identities = 10/37 (27%), Positives = 15/37 (40%)

Query: 10 FGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
          FGF+   +   A  A  E++   +  K L V  A   
Sbjct: 46 FGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS 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 = 44.7 bits (105), Expect = 6e-07
 Identities = 13/44 (29%), Positives = 22/44 (50%)

Query: 7  SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
           +GF FV F   E+A  A+  MN   +  + + V LA+    ++
Sbjct: 46 HRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKE 89

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.7 bits (105), Expect = 7e-07
 Identities = 13/48 (27%), Positives = 26/48 (54%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED 48
          +  +  SKGFGFV F +  +A +A  +++G ++  + + V  A  +  
Sbjct: 44 IFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVM 91

>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 = 44.3 bits (104), Expect = 7e-07
 Identities = 13/42 (30%), Positives = 21/42 (50%)

Query: 7  SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED 48
          SKGF F+ F   E+A +A+  ++G       L V  A+   +
Sbjct: 49 SKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTN 90

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 43.4 bits (102), Expect = 1e-06
 Identities = 14/44 (31%), Positives = 26/44 (59%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ 44
            + G S G+ FV F+S  ++ +A+  +NG  + +K L V+ A+
Sbjct: 37 DYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR 80

>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 = 43.5 bits (102), Expect = 2e-06
 Identities = 15/47 (31%), Positives = 23/47 (48%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE 47
              G+ +G+GFV F S E+A  A+  M+   +  KP+ V  A    
Sbjct: 44 DRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHN 90

>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 = 43.2 bits (101), Expect = 2e-06
 Identities = 15/44 (34%), Positives = 27/44 (61%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ 44
              G+S G+GFV +  P++A KA+  +NG  + +K + V+ A+
Sbjct: 37 DKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR 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 = 42.7 bits (100), Expect = 2e-06
 Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 2/45 (4%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIG--SKPLYVALA 43
              G S+G GF+ F    EA +A+  +NG+     ++P+ V  A
Sbjct: 41 DQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 85

>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 = 42.7 bits (100), Expect = 2e-06
 Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 1/43 (2%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
               RS+GFGFV F       K +   +   + SK +   +A
Sbjct: 35 DPLTKRSRGFGFVTFMDQAGVDKVL-AQSRHELDSKTIDPKVA 76

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.0 bits (101), Expect = 3e-06
 Identities = 13/44 (29%), Positives = 19/44 (43%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
            KG+ FV FS+ E A  A+  +NG  I    +     +   D 
Sbjct: 52 PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDM 95

>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 = 42.3 bits (99), Expect = 3e-06
 Identities = 13/42 (30%), Positives = 22/42 (52%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
             +   FV +   E A +AV E+NG  + S  L V +A+++
Sbjct: 36 DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ 77

>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 = 42.4 bits (99), Expect = 4e-06
 Identities = 12/51 (23%), Positives = 16/51 (31%), Gaps = 2/51 (3%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
          +        F FV F  P +A  AV   +G       L V     +  R  
Sbjct: 46 LKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP--RSGRGT 94

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.6 bits (97), Expect = 5e-06
 Identities = 10/46 (21%), Positives = 22/46 (47%), Gaps = 1/46 (2%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRI-IGSKPLYVALAQRKEDR 49
              G+ FV +     A +A+  ++G++ +  K + V  +  K+ R
Sbjct: 34 LLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR 79

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.9 bits (98), Expect = 7e-06
 Identities = 12/44 (27%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 6   RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
           RSKG  +V F   +    A+  + G+ +   P+ V  +Q +++R
Sbjct: 58  RSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKNR 100

>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 = 41.9 bits (98), Expect = 8e-06
 Identities = 6/44 (13%), Positives = 17/44 (38%), Gaps = 2/44 (4%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRII--GSKPLYVALAQRKE 47
           ++    + ++ P  A  A   ++G+ I      L +  ++   
Sbjct: 43 NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS 86

>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 = 41.2 bits (96), Expect = 8e-06
 Identities = 9/42 (21%), Positives = 17/42 (40%), Gaps = 2/42 (4%)

Query: 9  GFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRK 50
           F FV F+  + A          II    ++++ A+ K +  
Sbjct: 43 AFAFVTFADDQIAQSLC--GEDLIIKGISVHISNAEPKHNSN 82

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.4 bits (96), Expect = 1e-05
 Identities = 8/50 (16%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAH 52
           +G+  G   V F + ++A K+   ++ + +  +  +V +   ++ R+  
Sbjct: 45 NNGQGLGQALVQFKNEDDARKSE-RLHRKKLNGREAFVHVVTLEDMREIE 93

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.9 bits (95), Expect = 1e-05
 Identities = 6/42 (14%), Positives = 16/42 (38%)

Query: 10 FGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
           G V +   E+   A+ +++     S     +  +   +R +
Sbjct: 52 MGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPERSS 93

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.9 bits (95), Expect = 2e-05
 Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 1/51 (1%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
            + G+S+G+GFV  +    A +A  + N  I G +   V LA      ++
Sbjct: 45 DRQTGKSRGYGFVTMADRAAAERACKDPNPIIDG-RKANVNLAYLGAKPRS 94

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.4 bits (94), Expect = 2e-05
 Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 1/39 (2%)

Query: 5  GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
           RS+GFGFV +++ EE   A+       +  + +    A
Sbjct: 45 KRSRGFGFVTYATVEEVDAAM-NARPHKVDGRVVEPKRA 82

>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 = 39.7 bits (92), Expect = 3e-05
 Identities = 11/40 (27%), Positives = 19/40 (47%)

Query: 7  SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
          SKG+  V + + ++A  A   +NG  I  + + V     K
Sbjct: 48 SKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK 87

>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 = 39.3 bits (91), Expect = 4e-05
 Identities = 11/34 (32%), Positives = 19/34 (55%)

Query: 7  SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYV 40
          S+GF FV F + ++A +A    NG  +  + + V
Sbjct: 50 SRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 83

>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 = 38.9 bits (90), Expect = 4e-05
 Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 1/43 (2%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
               R +GFGFV F S +   K   E++   I +K +    A
Sbjct: 34 DKTTNRHRGFGFVTFESEDIVEKVC-EIHFHEINNKMVECKKA 75

>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 = 39.8 bits (92), Expect = 4e-05
 Identities = 11/39 (28%), Positives = 17/39 (43%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ 44
           S+G GF    S E+    +   NG+ I + P   A  +
Sbjct: 57 TSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE 95

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.8 bits (90), Expect = 5e-05
 Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 1/41 (2%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
            GRS+GFGFV F   E   K + +     +  K +    A
Sbjct: 36 ITGRSRGFGFVLFKESESVDKVM-DQKEHKLNGKVIDPKRA 75

>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 = 39.1 bits (90), Expect = 6e-05
 Identities = 8/40 (20%), Positives = 17/40 (42%), Gaps = 2/40 (5%)

Query: 10 FGFVCFSSPEEATKAVTEM--NGRIIGSKPLYVALAQRKE 47
            F+  ++ E A   V         + ++P+Y+  +  KE
Sbjct: 46 QAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE 85

>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 = 39.4 bits (91), Expect = 6e-05
 Identities = 7/43 (16%), Positives = 14/43 (32%), Gaps = 2/43 (4%)

Query: 10 FGFVCFSSPEEATKAVTEM--NGRIIGSKPLYVALAQRKEDRK 50
             V F + + A + VT        I  +  +   +  K   +
Sbjct: 53 QALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITR 95

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.2 bits (91), Expect = 6e-05
 Identities = 12/40 (30%), Positives = 19/40 (47%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVAL 42
                 G  +V F   E+A KAV ++N R    +P++  L
Sbjct: 63  LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.0 bits (90), Expect = 7e-05
 Identities = 12/43 (27%), Positives = 22/43 (51%)

Query: 7   SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
            +G  F+ F + E A +A+  +NG  +  K L +   + K+ R
Sbjct: 59  MRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQR 101

>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 = 38.6 bits (89), Expect = 8e-05
 Identities = 10/40 (25%), Positives = 15/40 (37%)

Query: 7  SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
          +K   FV   + E+A  A+   +      K L V L    
Sbjct: 39 NKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD 78

>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 = 38.6 bits (89), Expect = 8e-05
 Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 6/49 (12%)

Query: 7  SKGFGFVCFSSPEEATKAVTEMN------GRIIGSKPLYVALAQRKEDR 49
          SKG  F  F + E A K +   +      G  +  + L V LA  +++ 
Sbjct: 49 SKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEA 97

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.0 bits (88), Expect = 1e-04
 Identities = 10/48 (20%), Positives = 18/48 (37%), Gaps = 2/48 (4%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKP-LYVALAQRKE 47
                +  +  + + S  +A KA+   +GRI G    + V     K 
Sbjct: 32 KHVMSNTGNWMHIRYQSKLQARKAL-SKDGRIFGESIMIGVKPCIDKN 78

>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 = 37.6 bits (87), Expect = 1e-04
 Identities = 9/37 (24%), Positives = 15/37 (40%), Gaps = 1/37 (2%)

Query: 7  SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA 43
           +GF F+ F   E   K + E     +G     + +A
Sbjct: 40 RRGFCFITFKEEEPVKKIM-EKKYHNVGLSKCEIKVA 75

>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 = 37.5 bits (86), Expect = 2e-04
 Identities = 10/39 (25%), Positives = 19/39 (48%)

Query: 6  RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ 44
           S+ F ++  +S E+A   V ++NG  I    L   ++ 
Sbjct: 41 TSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN 79

>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 = 37.6 bits (86), Expect = 2e-04
 Identities = 10/46 (21%), Positives = 21/46 (45%), Gaps = 1/46 (2%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK 46
              G ++ FG+V F S E+  KA+  + G  +    + +   + +
Sbjct: 47 DVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGR 91

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.9 bits (87), Expect = 2e-04
 Identities = 10/49 (20%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 3   EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
            +G++ G GFV F +  +   A+   + + +G++ + V    +K   + 
Sbjct: 55  PNGKATGEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVHPITKKGMLEK 102

>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 = 37.4 bits (86), Expect = 2e-04
 Identities = 8/40 (20%), Positives = 18/40 (45%), Gaps = 5/40 (12%)

Query: 10 FGFVCFSSPEEATKAVTEMNGRIIG-----SKPLYVALAQ 44
          + F  + + EE+ +A   +NG+ +         LY+   +
Sbjct: 58 YSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVE 97

>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 = 37.6 bits (86), Expect = 4e-04
 Identities = 17/40 (42%), Positives = 22/40 (55%)

Query: 10  FGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR 49
           +GFV F S   A +A+  +NG  I +K L VALA     R
Sbjct: 86  YGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQR 125

>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 = 36.7 bits (84), Expect = 5e-04
 Identities = 11/68 (16%), Positives = 28/68 (41%)

Query: 10  FGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIANMRMQQM 69
              V  +   +A  A++ +NG  +  KP+ + L++ +  +      +      +     +
Sbjct: 42  NALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPL 101

Query: 70  GQLFQPGS 77
            +  +PGS
Sbjct: 102 HRFKKPGS 109

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.9 bits (82), Expect = 8e-04
 Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 1/40 (2%)

Query: 1  MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYV 40
            +  + K F F+ F S +E T+A+   +G I   + L +
Sbjct: 41 AVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKI 79

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.7 bits (79), Expect = 0.001
 Identities = 10/27 (37%), Positives = 14/27 (51%)

Query: 12 FVCFSSPEEATKAVTEMNGRIIGSKPL 38
          FV F SP  A KAVT +    + ++  
Sbjct: 44 FVDFDSPSAAQKAVTALKASGVQAQMA 70

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.2 bits (80), Expect = 0.002
 Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 3  EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA 51
            GRS G  FV F+S E A KA+   +   IG + + +  + R E R +
Sbjct: 52 FQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSSRAEVRTS 99

>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 = 34.1 bits (77), Expect = 0.002
 Identities = 7/37 (18%), Positives = 18/37 (48%), Gaps = 1/37 (2%)

Query: 10 FGFVCFSSPEEATKAVTEMNG-RIIGSKPLYVALAQR 45
            FV F++  ++  A   + G +I  +  + +  A++
Sbjct: 47 IAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAKK 83

>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 = 34.3 bits (78), Expect = 0.003
 Identities = 10/39 (25%), Positives = 18/39 (46%), Gaps = 2/39 (5%)

Query: 10 FGFVCFSSPEEATKAVTEMNGRIIG--SKPLYVALAQRK 46
          F ++ + S + A  A  +M G  +G   + L V  A+  
Sbjct: 55 FAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG 93

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	303
d1g9la_	144	poly(A) binding protein {Human (Homo sapiens) [Tax	100.0
d1nmra_	85	poly(A) binding protein {Protozoan (Trypanosoma cr	99.96
d1ifwa_	92	poly(A) binding protein {Baker's yeast (Saccharomy	99.96
d1i2ta_	61	hyperplastic discs protein {Human (Homo sapiens) [	99.94
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.06
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.04
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.02
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.0
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	98.99
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	98.99
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.95
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	98.94
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	98.93
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	98.93
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	98.92
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	98.92
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	98.92
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	98.92
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	98.91
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	98.91
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	98.9
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.9
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	98.9
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	98.88
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.87
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	98.86
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	98.86
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	98.86
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	98.85
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.85
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	98.84
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.83
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	98.81
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	98.81
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	98.8
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	98.79
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	98.78
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	98.78
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	98.76
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.75
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	98.75
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	98.74
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	98.73
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	98.72
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	98.72
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	98.71
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	98.71
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	98.71
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	98.71
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	98.7
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	98.69
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	98.69
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.68
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	98.68
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	98.68
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	98.67
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	98.66
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	98.65
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.64
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	98.64
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.64
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	98.63
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.62
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	98.6
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	98.59
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	98.58
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.57
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.57
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	98.56
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	98.55
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	98.5
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	98.49
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	98.48
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	98.48
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.43
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	98.38
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.35
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	98.28
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.28
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	98.28
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	98.24
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	98.21
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.2
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.17
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.14
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	98.13
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.11
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	97.95
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	97.72
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	96.45
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	87.28
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	81.04

>d1g9la_ a.144.1.1 (A:) poly(A) binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=4.1e-36  Score=251.54  Aligned_cols=119  Identities=71%  Similarity=0.941  Sum_probs=99.0

Q ss_pred             CCCCCCCCCC--CCCCCCCCccccCCCCCccccccccccCCCCccchhHhhhcChHHHHHhhhccchhhhhhhCCCCCCC
Q psy14476        179 RQTGGYNKYP--VRNPGTQPQAQIGGIQPAAAGVQAVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGK  256 (303)
Q Consensus       179 r~~~~~~~~~--~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~ltas~l~~~~~~~qk~~lGe~ly~~v~~~~p~~A~K  256 (303)
                      |..++| ||.  +||++.....+    +....++++.++.++++||+++|+++++++||++|||+||++|++++|++|+|
T Consensus        14 ~~~P~~-ky~~~~rnp~~~~~~~----p~~~~~~p~~~~~~q~pltas~la~a~p~eQkq~LGE~Lyp~I~~~~p~~A~K   88 (144)
T d1g9la_          14 RTVPQY-KYAAGVRNPQQHLNAQ----PQVTMQQPAVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGK   88 (144)
T ss_dssp             SSCCCC-CCCCTTSCCCCCCCCC----SCCCCSSCSCCCCSCCCCSHHHHTTCTTTTTTTTTTSSSHHHHHHHTTSCCSS
T ss_pred             CCCCCC-CCCCCCCCCCCCCCCC----CCCCCCCCCCCCCCCCcccHHHHhhCCHHHHHHHHHHHHHHHHHHhChhhccc
Confidence            334567 885  67764322111    11111345667788999999999999999999999999999999999999999


Q ss_pred             chhhcccCChHHHHHhhCChHHHHHHHHHHHHHHHHHHHHHHhhhc
Q psy14476        257 ITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQAKQAAVKK  302 (303)
Q Consensus       257 ITGMlLe~~~~ell~ll~~~~~L~~kv~eA~~vl~~~~~~~~~~~~  302 (303)
                      |||||||||++|||+||+|+++|++||+||++||++|+.+++++++
T Consensus        89 ITGMLLEmd~~ell~lL~~~~~L~~kV~EA~~vL~~~~~~~~~~~~  134 (144)
T d1g9la_          89 ITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEAAQKA  134 (144)
T ss_dssp             HHHHTTTSSSHHHHHHHHCTTHHHHHHHHHHHHHHTTSSSTTCCCC
T ss_pred             hhhhhhcCCHHHHHHHHcCHHHHHHHHHHHHHHHHHHhccHHHHHh
Confidence            9999999999999999999999999999999999999988877665

>d1nmra_ a.144.1.1 (A:) poly(A) binding protein {Protozoan (Trypanosoma cruzi) [TaxId: 5693]}

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Protozoan (Trypanosoma cruzi) [TaxId: 5693]

Probab=99.96  E-value=1.8e-31  Score=204.83  Aligned_cols=73  Identities=48%  Similarity=0.722  Sum_probs=71.3

Q ss_pred             chhHhhhcChHHHHHhhhccchhhhhhhCCCCCCCchhhcccCChHHHHHhhCChHHHHHHHHHHHHHHHHHH
Q psy14476        222 TSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQ  294 (303)
Q Consensus       222 tas~l~~~~~~~qk~~lGe~ly~~v~~~~p~~A~KITGMlLe~~~~ell~ll~~~~~L~~kv~eA~~vl~~~~  294 (303)
                      ++++|++++|++||++|||+|||+|++++|++|+||||||||||++||++||+|++.|++||+||++||++|+
T Consensus        11 ~a~~la~~~p~eqK~~LGE~Lyp~V~~~~p~~AgKITGMLLEm~~~ell~lL~~~~~L~~kV~EA~~vL~~h~   83 (85)
T d1nmra_          11 LSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILNLLDTPGLLDAKVQEALEVLNRHM   83 (85)
T ss_dssp             THHHHTTCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHCSCTHHHHHHTTCCTHHHHHHHHHHHHHHTTCCC
T ss_pred             HHHHHhhCCHHHHHHHHHHHHHHHHHHHCcccccchhHHhhCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHhc
Confidence            7899999999999999999999999999999999999999999999999999999999999999999998875

>d1ifwa_ a.144.1.1 (A:) poly(A) binding protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.96  E-value=1.5e-30  Score=202.54  Aligned_cols=83  Identities=30%  Similarity=0.440  Sum_probs=77.5

Q ss_pred             ccchhHhhhcChHHHHHhhhccchhhhhhh--CCCCCCCchhhcccCChHHHHHhhCChHHHHHHHHHHHHHHHHHHHHH
Q psy14476        220 PLTSTMLAAAQPQEQKQMLGERLFPLIQRM--YPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAHQAKQ  297 (303)
Q Consensus       220 ~ltas~l~~~~~~~qk~~lGe~ly~~v~~~--~p~~A~KITGMlLe~~~~ell~ll~~~~~L~~kv~eA~~vl~~~~~~~  297 (303)
                      |.++++++.+++++||++|||+||++|+++  +|++|+||||||||||++||++||+|+++|++||+||++||++|++++
T Consensus         6 p~~~~~~~~~~~~~qk~~LGe~Lyp~V~~~~~~pe~A~KITGMLLEm~~~ell~lL~~~~~L~~kV~EA~~vL~~~~~~~   85 (92)
T d1ifwa_           6 PRNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLLESDELFEQHYKEASAAYESFKKEQ   85 (92)
T ss_dssp             SSCCSSCCSCSCHHHHHHHHHHHHHHHGGGCCCHHHHHHHHHHHTTSCHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCChHHHhhcCHHHHHHHHHHHHHHHHHHhccCccccccchhhhcCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHhcc
Confidence            357788999999999999999999999998  689999999999999999999999999999999999999999999988


Q ss_pred             Hhhhc
Q psy14476        298 AAVKK  302 (303)
Q Consensus       298 ~~~~~  302 (303)
                      ++..+
T Consensus        86 ~~~~~   90 (92)
T d1ifwa_          86 EQQTE   90 (92)
T ss_dssp             TTSCC
T ss_pred             ccccc
Confidence            76654

>d1i2ta_ a.144.1.1 (A:) hyperplastic discs protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: hyperplastic discs protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.94  E-value=5.5e-29  Score=179.84  Aligned_cols=60  Identities=50%  Similarity=0.855  Sum_probs=59.1

Q ss_pred             HHHhhhccchhhhhhhCCCCCCCchhhcccCChHHHHHhhCChHHHHHHHHHHHHHHHHH
Q psy14476        234 QKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAH  293 (303)
Q Consensus       234 qk~~lGe~ly~~v~~~~p~~A~KITGMlLe~~~~ell~ll~~~~~L~~kv~eA~~vl~~~  293 (303)
                      ||++|||+|||+|++++|++|+||||||||||++||++||+|+++|++||+||++||++|
T Consensus         1 qk~~LGE~Ly~~V~~~~p~~A~KITGMLLEm~~~ell~lL~~~~~L~~kV~EA~~vL~~h   60 (61)
T d1i2ta_           1 HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELIIAH   60 (61)
T ss_dssp             CHHHHHHHHHHHHHHHCGGGHHHHHHHHTTSCHHHHHHHHHCHHHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHhHHHHHHHChhhhcchhHHHhcCCHHHHHHHHCCHHHHHHHHHHHHHHHHHc
Confidence            799999999999999999999999999999999999999999999999999999999987

>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=99.06  E-value=3.8e-11  Score=89.30  Aligned_cols=46  Identities=33%  Similarity=0.671  Sum_probs=43.2

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      ++|++||||||+|.+.++|++|++.|||..|+||+|+|++|.+++.
T Consensus        36 ~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~~   81 (83)
T d1x5ta1          36 DTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDS   81 (83)
T ss_dssp             TTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCCC
T ss_pred             cccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCCc
Confidence            4799999999999999999999999999999999999999987754

>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=99.04  E-value=1.1e-10  Score=86.13  Aligned_cols=44  Identities=30%  Similarity=0.470  Sum_probs=41.8

Q ss_pred             CCCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         1 ~d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      +|.+|++||||||+|.+.++|++|++.|||..++||+|+|++|.
T Consensus        34 ~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_          34 YDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             CSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            46799999999999999999999999999999999999999985

>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=99.02  E-value=4.9e-11  Score=92.54  Aligned_cols=47  Identities=43%  Similarity=0.619  Sum_probs=44.3

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR   49 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r   49 (303)
                      .+|++||||||+|.+.++|++||+.|||..|.||+|+|.||+++.++
T Consensus        55 ~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~~k~~~  101 (102)
T d2cpza1          55 QTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDS  101 (102)
T ss_dssp             SSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSCCC
T ss_pred             ccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeCCCCCC
Confidence            57999999999999999999999999999999999999999988654

>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=99.00  E-value=1.5e-10  Score=88.47  Aligned_cols=45  Identities=27%  Similarity=0.473  Sum_probs=42.1

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHh-CCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEM-NGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~l-nG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|.+||+.| ||..|+||+|+|+||..+.
T Consensus        46 ~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~A~~~~   91 (94)
T d2cpha1          46 GTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEV   91 (94)
T ss_dssp             SSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCC
T ss_pred             cCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEEcCCCC
Confidence            57999999999999999999999998 8999999999999998753

>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=98.99  E-value=1.2e-10  Score=88.06  Aligned_cols=45  Identities=31%  Similarity=0.482  Sum_probs=42.7

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|.+||+.|||..|+|+.|+|.||+++.
T Consensus        45 ~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~akp~~   89 (90)
T d2cq0a1          45 TTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPST   89 (90)
T ss_dssp             SSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCC
T ss_pred             cccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeeeCCC
Confidence            479999999999999999999999999999999999999999874

>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=98.99  E-value=1.6e-10  Score=87.09  Aligned_cols=44  Identities=27%  Similarity=0.370  Sum_probs=42.0

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .+|++||||||+|.+.++|++|++.|||..|+||.|+|+||..|
T Consensus        44 ~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~~k   87 (88)
T d1rk8a_          44 RTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK   87 (88)
T ss_dssp             TTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEEC
T ss_pred             cccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEecCC
Confidence            47999999999999999999999999999999999999999875

>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=98.95  E-value=2.7e-10  Score=84.12  Aligned_cols=44  Identities=23%  Similarity=0.310  Sum_probs=37.0

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      +.+|++||||||+|.+.++|++|++.|||..++||+|+|.++++
T Consensus        37 ~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1          37 LRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             ------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            35789999999999999999999999999999999999999875

>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=98.94  E-value=3e-10  Score=84.01  Aligned_cols=43  Identities=33%  Similarity=0.534  Sum_probs=41.1

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      .+|++||||||+|.+.++|++||+.|||..|+|++|+|.||++
T Consensus        39 ~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1          39 KTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             TTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             ccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            4789999999999999999999999999999999999999975

>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=98.93  E-value=2.9e-10  Score=84.08  Aligned_cols=43  Identities=35%  Similarity=0.596  Sum_probs=40.7

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      .+|++||||||+|.+.++|.+|++.|||..|.||+|+|.||++
T Consensus        37 ~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1          37 ITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             cccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            4799999999999999999999999999999999999999964

>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=98.93  E-value=1.6e-10  Score=87.08  Aligned_cols=47  Identities=36%  Similarity=0.658  Sum_probs=43.7

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      +.+|++||||||+|.+.++|++||+.|||..|+|++|+|.+|.++.+
T Consensus        41 ~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~~~~   87 (90)
T d1x5sa1          41 RETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSD   87 (90)
T ss_dssp             SSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCC
T ss_pred             cccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCC
Confidence            35799999999999999999999999999999999999999987754

>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=98.92  E-value=2.1e-10  Score=86.54  Aligned_cols=45  Identities=31%  Similarity=0.486  Sum_probs=42.3

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|++||+.|||..|+|++|+|++|+++.
T Consensus        42 ~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p~~   86 (89)
T d2cqba1          42 ETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMR   86 (89)
T ss_dssp             SSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             ccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            369999999999999999999999999999999999999998764

>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=98.92  E-value=3.2e-10  Score=86.34  Aligned_cols=45  Identities=33%  Similarity=0.470  Sum_probs=42.6

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|++|++.|||..|+|+.|+|.+|.+++
T Consensus        46 ~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~~~   90 (93)
T d1x5ua1          46 VTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHN   90 (93)
T ss_dssp             SSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTS
T ss_pred             cccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCC
Confidence            479999999999999999999999999999999999999998764

>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=98.92  E-value=2.3e-10  Score=87.92  Aligned_cols=47  Identities=30%  Similarity=0.448  Sum_probs=44.0

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR   49 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r   49 (303)
                      .+|+++|||||+|.+.++|++||+.|||..|.|++|+|+||+++++|
T Consensus        55 ~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak~k~~r  101 (102)
T d2cpxa1          55 MTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQR  101 (102)
T ss_dssp             ECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCSCC
T ss_pred             ccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCCCcccC
Confidence            37899999999999999999999999999999999999999987654

>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=98.92  E-value=4.9e-10  Score=86.64  Aligned_cols=47  Identities=32%  Similarity=0.606  Sum_probs=43.4

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR   49 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r   49 (303)
                      .+|++||||||+|.+.++|++|++.|||..|.|++|+|.+|..+..+
T Consensus        45 ~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~~~~~   91 (104)
T d1p1ta_          45 ETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNK   91 (104)
T ss_dssp             TTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCTTHH
T ss_pred             ceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCc
Confidence            47999999999999999999999999999999999999999876544

>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=98.91  E-value=5.4e-10  Score=85.51  Aligned_cols=45  Identities=33%  Similarity=0.487  Sum_probs=42.4

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|+++|||||+|.+.++|++||+.|||..|+||+|+|.+|+++.
T Consensus        53 ~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~a~~~~   97 (101)
T d2cpea1          53 ETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP   97 (101)
T ss_dssp             TTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCC
T ss_pred             ccccccceeeEEecCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            468999999999999999999999999999999999999998764

>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=98.91  E-value=1.5e-10  Score=87.30  Aligned_cols=46  Identities=33%  Similarity=0.718  Sum_probs=42.3

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR   49 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r   49 (303)
                      .+.+||||||+|.+.++|++||+.|||..|+|++|+|.+|+++++|
T Consensus        44 ~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~~R   89 (89)
T d1cvja2          44 ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKER   89 (89)
T ss_dssp             TTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTTTC
T ss_pred             cCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence            3568999999999999999999999999999999999999988654

>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=98.90  E-value=6.4e-10  Score=82.04  Aligned_cols=43  Identities=35%  Similarity=0.640  Sum_probs=40.9

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      .+|++||||||+|.+.++|++|++.|||..|+|++|+|+||++
T Consensus        39 ~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1          39 ITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            4689999999999999999999999999999999999999975

>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=98.90  E-value=4.1e-10  Score=86.41  Aligned_cols=45  Identities=36%  Similarity=0.537  Sum_probs=42.7

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|++||+.|||..|+||+|+|.+|..+.
T Consensus        45 ~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~~~~   89 (99)
T d1whwa_          45 LTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKK   89 (99)
T ss_dssp             TTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCS
T ss_pred             cccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            579999999999999999999999999999999999999998764

>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=98.90  E-value=6.5e-10  Score=82.94  Aligned_cols=42  Identities=40%  Similarity=0.605  Sum_probs=40.1

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecc
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA   43 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A   43 (303)
                      |++|+++|||||+|.+.++|++||++||++.|.||+|+|.+|
T Consensus        45 ~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1          45 NEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            578999999999999999999999999999999999999875

>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=98.88  E-value=3.1e-10  Score=86.27  Aligned_cols=44  Identities=23%  Similarity=0.435  Sum_probs=40.7

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      +.+|++||||||+|.+.++|++||+ |||..|+||.|+|++|+.|
T Consensus        48 ~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak~k   91 (91)
T d1fjeb1          48 VRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGR   91 (91)
T ss_dssp             EEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCCS
T ss_pred             cCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecCCC
Confidence            3579999999999999999999995 9999999999999999865

>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=98.87  E-value=5.3e-10  Score=83.26  Aligned_cols=42  Identities=36%  Similarity=0.630  Sum_probs=39.2

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      ++|||||||+|.+.++|.+|++.|||..|+||+|.|.+|.++
T Consensus        40 ~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~~   81 (85)
T d2cpfa1          40 LLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERA   81 (85)
T ss_dssp             EEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSCS
T ss_pred             cccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            368999999999999999999999999999999999999754

>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=98.86  E-value=9.4e-10  Score=85.84  Aligned_cols=43  Identities=28%  Similarity=0.392  Sum_probs=40.5

Q ss_pred             CCCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecc
Q psy14476          1 MSEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA   43 (303)
Q Consensus         1 ~d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A   43 (303)
                      +|.+|++||||||+|.+.++|.+|++.|||+.++||+|+|.|.
T Consensus        61 ~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          61 DNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             CSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             cCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            3678999999999999999999999999999999999999875

>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=98.86  E-value=5.4e-10  Score=85.05  Aligned_cols=45  Identities=20%  Similarity=0.269  Sum_probs=41.8

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|.+|++.|||..|+||+|+|+|+....
T Consensus        44 ~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~~~~   88 (93)
T d1h2vz_          44 MKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK   88 (93)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCCC
T ss_pred             ccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            478999999999999999999999999999999999999997543

>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=98.86  E-value=5.3e-10  Score=86.70  Aligned_cols=46  Identities=26%  Similarity=0.461  Sum_probs=41.4

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDR   49 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r   49 (303)
                      .+|+|||||||+|.+.++|.+|++ |||..|+|+.|.|.++..+..|
T Consensus        55 ~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~~~nr  100 (101)
T d2cq4a1          55 NSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAEKNR  100 (101)
T ss_dssp             CSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHHHHHH
T ss_pred             CCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCCCCCC
Confidence            479999999999999999999995 9999999999999998765443

>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=98.85  E-value=4.6e-10  Score=91.07  Aligned_cols=45  Identities=42%  Similarity=0.558  Sum_probs=42.1

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .||++||||||+|.+.++|.+||+.|||..|+||.|+|.+|..+.
T Consensus        79 ~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~~~  123 (139)
T d1u6fa1          79 ETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGH  123 (139)
T ss_dssp             TTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCC
T ss_pred             ccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            478999999999999999999999999999999999999998653

>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=98.85  E-value=8.2e-10  Score=82.76  Aligned_cols=43  Identities=28%  Similarity=0.540  Sum_probs=38.3

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      ++|++||||||+|.+.++|++|++ |||..|+||.|+|++|.+|
T Consensus        43 ~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~a~~k   85 (86)
T d2ghpa3          43 EHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLADKK   85 (86)
T ss_dssp             ---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEECCCC
T ss_pred             CccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEEcCCC
Confidence            579999999999999999999995 9999999999999999875

>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=98.84  E-value=3.6e-10  Score=85.55  Aligned_cols=48  Identities=29%  Similarity=0.381  Sum_probs=44.3

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHHH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA   51 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~   51 (303)
                      ++++||||||+|.+.++|.+|++.|||..++|++|+|.||+.+.+...
T Consensus        42 ~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~ak~~~~~~~   89 (91)
T d1nu4a_          42 SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIA   89 (91)
T ss_dssp             HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSCCTHHH
T ss_pred             eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeCCCchhhc
Confidence            567899999999999999999999999999999999999998877654

>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=98.83  E-value=8.9e-10  Score=82.48  Aligned_cols=44  Identities=30%  Similarity=0.463  Sum_probs=41.7

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .||++||||||+|.+.++|.+|++.|||..|+||+|+|.+|...
T Consensus        38 ~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_          38 ATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             SSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             cccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            47999999999999999999999999999999999999999754

>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=98.81  E-value=1.6e-09  Score=80.85  Aligned_cols=41  Identities=39%  Similarity=0.622  Sum_probs=38.7

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecc--cceeeecc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGS--KPLYVALA   43 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~G--R~L~V~~A   43 (303)
                      .+|++||||||+|.+.++|.+||+.|||..+.|  |+|+|.||
T Consensus        43 ~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2          43 LTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             ccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            479999999999999999999999999999986  89999987

>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=98.81  E-value=2.6e-09  Score=83.49  Aligned_cols=44  Identities=16%  Similarity=0.267  Sum_probs=41.0

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .++++||||||+|.+.++|.+||+.|||+.|+||.|.|.++..+
T Consensus        41 ~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~   84 (114)
T d2f9da1          41 NTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNAN   84 (114)
T ss_dssp             CSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHH
T ss_pred             ccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            36789999999999999999999999999999999999998754

>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=98.80  E-value=2.3e-09  Score=81.37  Aligned_cols=43  Identities=30%  Similarity=0.562  Sum_probs=40.3

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      +.+||||||+|.+.++|.+||+.|||..|+||.|+|.+|++|.
T Consensus        48 ~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~r~   90 (93)
T d2cq3a1          48 RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV   90 (93)
T ss_dssp             TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSC
T ss_pred             cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCcCC
Confidence            4589999999999999999999999999999999999998764

>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=98.79  E-value=6.9e-10  Score=82.19  Aligned_cols=46  Identities=22%  Similarity=0.311  Sum_probs=41.3

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCc-eecccceeeecccchHHH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGR-IIGSKPLYVALAQRKEDR   49 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~-~l~GR~L~V~~A~~k~~r   49 (303)
                      .+++||||||+|.+.++|++|++.|||. .|+|++|+|.||.++..|
T Consensus        33 ~~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~r   79 (80)
T d2cqha1          33 VLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR   79 (80)
T ss_dssp             EEEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCC
T ss_pred             EecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCcC
Confidence            4568999999999999999999999996 699999999999987543

>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=98.78  E-value=1.7e-09  Score=82.56  Aligned_cols=46  Identities=28%  Similarity=0.498  Sum_probs=42.9

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .+|++||||||+|.+.++|++|++.|||..|+||+|+|.|+.+|..
T Consensus        48 ~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~~   93 (96)
T d1fjca_          48 QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCCC
Confidence            3689999999999999999999999999999999999999998753

>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=98.78  E-value=1.7e-09  Score=83.39  Aligned_cols=44  Identities=27%  Similarity=0.487  Sum_probs=41.1

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      |.+++++|||||+|.+.++|++||+.|||..|.||++.|.++++
T Consensus        53 ~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          53 DSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP   96 (101)
T ss_dssp             CSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSC
T ss_pred             ccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCCC
Confidence            56899999999999999999999999999999999999988764

>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=98.76  E-value=2.7e-09  Score=80.97  Aligned_cols=46  Identities=28%  Similarity=0.465  Sum_probs=41.5

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhC------CceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMN------GRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~ln------G~~l~GR~L~V~~A~~k~~   48 (303)
                      .++++||||||+|.+.++|.+||+.||      |..|+||.|+|++|.+|++
T Consensus        45 ~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l~v~~a~~k~~   96 (98)
T d1x4ha1          45 DTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE   96 (98)
T ss_dssp             SSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCCC
T ss_pred             ccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEEEEEECCCCCc
Confidence            478899999999999999999999886      6789999999999988754

>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=98.75  E-value=3.4e-09  Score=81.58  Aligned_cols=45  Identities=16%  Similarity=0.403  Sum_probs=41.1

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      +.+|+++|||||+|.+.++|++||+ ||++.|+||.|.|.++..++
T Consensus        44 ~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~~~~   88 (103)
T d2cpya1          44 DNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVTLED   88 (103)
T ss_dssp             CTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEECHHH
T ss_pred             CCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECCHHH
Confidence            5689999999999999999999995 89999999999999986543

>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=98.75  E-value=3.3e-09  Score=79.16  Aligned_cols=41  Identities=34%  Similarity=0.591  Sum_probs=38.0

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecc--cceeeecc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGS--KPLYVALA   43 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~G--R~L~V~~A   43 (303)
                      .+|++||||||+|.+.++|++|++.|||..+.|  ++|+|+||
T Consensus        43 ~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2          43 VTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             ccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            479999999999999999999999999999997  56999986

>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=98.74  E-value=2.9e-09  Score=77.89  Aligned_cols=43  Identities=23%  Similarity=0.318  Sum_probs=40.4

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      ++++||||||+|.+.++|++|++.|||..+.||+|+|.++..+
T Consensus        29 ~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1          29 VDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             ecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            4689999999999999999999999999999999999999754

>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=98.73  E-value=3e-09  Score=79.33  Aligned_cols=43  Identities=30%  Similarity=0.641  Sum_probs=40.6

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      +++||||||+|.+.++|.+|+..|||..|+||.|+|.||++++
T Consensus        41 ~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~   83 (86)
T d2cpda1          41 KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD   83 (86)
T ss_dssp             EECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             ccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCC
Confidence            5789999999999999999999999999999999999998764

>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=98.72  E-value=3.8e-09  Score=81.23  Aligned_cols=40  Identities=35%  Similarity=0.558  Sum_probs=38.0

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      +||||||+|++.++|++||+.|||+.|+|++|+|+++..+
T Consensus        49 ~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   88 (98)
T d1wf2a_          49 HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEP   88 (98)
T ss_dssp             ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSC
T ss_pred             eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            6899999999999999999999999999999999999754

>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=98.72  E-value=4.7e-09  Score=77.28  Aligned_cols=42  Identities=31%  Similarity=0.498  Sum_probs=39.4

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .+.+|||||+|.+.++|.+|+++|||..|+|++|+|.||+++
T Consensus        36 ~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1          36 DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             ETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             ccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            467899999999999999999999999999999999999865

>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=98.71  E-value=4.8e-09  Score=76.57  Aligned_cols=40  Identities=33%  Similarity=0.498  Sum_probs=37.1

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA   43 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A   43 (303)
                      .+|++||||||+|.+.++|++||+ +++..|+||.|.|..|
T Consensus        36 ~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_          36 ITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             TTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            479999999999999999999997 7999999999999865

>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=98.71  E-value=2.7e-09  Score=78.59  Aligned_cols=40  Identities=30%  Similarity=0.450  Sum_probs=37.5

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA   43 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A   43 (303)
                      .||+|||||||+|.+.++|++|++ +|++.|+||.|.|..|
T Consensus        37 ~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_          37 LTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            469999999999999999999997 6999999999999986

>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=98.71  E-value=2.9e-09  Score=82.77  Aligned_cols=45  Identities=33%  Similarity=0.462  Sum_probs=41.4

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .++++||||||+|.+.++|++|++ ++++.|+||.|.|.+|.+|++
T Consensus        57 ~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~ke~  101 (103)
T d1x4ba1          57 ASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAREE  101 (103)
T ss_dssp             TTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSSCCC
T ss_pred             cCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcccCC
Confidence            468999999999999999999995 799999999999999998865

>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=98.71  E-value=5.7e-09  Score=75.37  Aligned_cols=40  Identities=30%  Similarity=0.428  Sum_probs=37.6

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA   43 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A   43 (303)
                      .+|+++|||||+|.+.++|++|++ +||+.|+||+|.|.+|
T Consensus        36 ~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_          36 TTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             TCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             cccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            478999999999999999999996 9999999999999876

>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=98.70  E-value=4.1e-09  Score=80.20  Aligned_cols=46  Identities=22%  Similarity=0.299  Sum_probs=40.3

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCC--ceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNG--RIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG--~~l~GR~L~V~~A~~k~~   48 (303)
                      .+|++||||||+|.+.++|.+|++.|++  ..++|++|+|+||.++.+
T Consensus        40 ~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~A~p~~~   87 (96)
T d2disa1          40 DKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEID   87 (96)
T ss_dssp             TTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCS
T ss_pred             ccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEEcCCCCC
Confidence            4689999999999999999999999964  456799999999987654

>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=98.69  E-value=3.9e-09  Score=79.45  Aligned_cols=43  Identities=26%  Similarity=0.280  Sum_probs=40.2

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      ++++||||||+|.+.++|++||+.||+..|+||+|+|.++..+
T Consensus        36 ~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~   78 (88)
T d1wg1a_          36 VDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             EEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             eeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            4678999999999999999999999999999999999999754

>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=98.69  E-value=6.4e-09  Score=76.97  Aligned_cols=38  Identities=32%  Similarity=0.580  Sum_probs=36.3

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceee
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYV   40 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V   40 (303)
                      .+|++||||||+|.+.++|++|++.|||..|+||+|+|
T Consensus        46 ~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1          46 QSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             SSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             cccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            36999999999999999999999999999999999987

>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=98.68  E-value=7.3e-09  Score=78.72  Aligned_cols=43  Identities=26%  Similarity=0.323  Sum_probs=40.2

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      ++.+||||||+|.+.++|++||+.|||+.|+|++|+|.||+..
T Consensus        49 ~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~~   91 (95)
T d1x4aa1          49 RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG   91 (95)
T ss_dssp             SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             cccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccCC
Confidence            5678999999999999999999999999999999999999753

>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=98.68  E-value=5.2e-09  Score=78.79  Aligned_cols=43  Identities=30%  Similarity=0.383  Sum_probs=39.6

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      ..+|||||+|.+.++|++|++.|||..|.|+.|+|.||.++..
T Consensus        46 ~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~~   88 (90)
T d2cqia1          46 SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSS   88 (90)
T ss_dssp             SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTTC
T ss_pred             ccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCC
Confidence            4589999999999999999999999999999999999987643

>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=98.68  E-value=6.2e-09  Score=80.45  Aligned_cols=43  Identities=33%  Similarity=0.535  Sum_probs=39.2

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .||+|||||||+|.+.++|++||+.+|+ .|+||+|+|++|..+
T Consensus        47 ~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~~~   89 (103)
T d2cqda1          47 QTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLG   89 (103)
T ss_dssp             SSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTTT
T ss_pred             cccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcCCC
Confidence            4799999999999999999999999876 799999999998754

>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=98.67  E-value=3.6e-09  Score=80.18  Aligned_cols=44  Identities=32%  Similarity=0.523  Sum_probs=39.4

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .+|+|||||||+|.+.++|++||+.  .+.|+||.|.|.+|.+++.
T Consensus        45 ~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a~~k~~   88 (90)
T d2cqga1          45 KTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLPNSKQS   88 (90)
T ss_dssp             SSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECCCTTCC
T ss_pred             CCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeCCCCCC
Confidence            3799999999999999999999985  5589999999999988753

>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=98.66  E-value=6.1e-09  Score=80.16  Aligned_cols=44  Identities=27%  Similarity=0.508  Sum_probs=39.7

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      .+|++||||||+|.+.++|++|+ +||+..|+||.|+|.+|.++.
T Consensus        52 ~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~a~~~~   95 (104)
T d1wi8a_          52 NPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQ   95 (104)
T ss_dssp             CTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEECCCCC
T ss_pred             cCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEECCCCC
Confidence            47899999999999999998776 599999999999999998754

>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=98.65  E-value=4e-09  Score=81.34  Aligned_cols=45  Identities=22%  Similarity=0.252  Sum_probs=41.2

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      |.+|+++|||||+|.+.++|++|++ ||++.|+||.|+|.++.++.
T Consensus        49 ~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~~~~   93 (102)
T d1weza_          49 GPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAG   93 (102)
T ss_dssp             SSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECCCC
T ss_pred             ecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcCCCC
Confidence            5689999999999999999999986 89999999999999987653

>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=98.64  E-value=1.2e-08  Score=74.46  Aligned_cols=40  Identities=25%  Similarity=0.411  Sum_probs=37.1

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA   43 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A   43 (303)
                      .+++++|||||+|.+.+++++|++ +||+.|+||.|+|+.|
T Consensus        39 ~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2          39 GSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            478999999999999999999985 7999999999999976

>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=98.64  E-value=1.3e-08  Score=77.86  Aligned_cols=40  Identities=30%  Similarity=0.495  Sum_probs=38.1

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .||||||+|.+.++|.+||..|||..|+|++|+|.|++++
T Consensus        53 ~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~   92 (96)
T d1x4ga1          53 EKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   92 (96)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             cceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            4899999999999999999999999999999999999865

>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=98.64  E-value=1.3e-08  Score=75.85  Aligned_cols=41  Identities=27%  Similarity=0.435  Sum_probs=38.0

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      .+|++||||||+|.+.++|++||+ ++++.|+||.|+|..|.
T Consensus        43 ~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1          43 NTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             cCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            369999999999999999999997 59999999999999875

>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=98.63  E-value=1.2e-08  Score=76.26  Aligned_cols=43  Identities=16%  Similarity=0.302  Sum_probs=38.9

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCcee-cccceeeecccch
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRII-GSKPLYVALAQRK   46 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l-~GR~L~V~~A~~k   46 (303)
                      .+++||||||+|++.++|.+|+..|||..| +||+|+|+|++.+
T Consensus        44 ~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~~   87 (88)
T d2adca2          44 FQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST   87 (88)
T ss_dssp             CSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             eecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCCC
Confidence            457799999999999999999999999988 5899999998753

>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=98.62  E-value=1.3e-08  Score=75.93  Aligned_cols=42  Identities=29%  Similarity=0.286  Sum_probs=38.7

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      |.+|++||||||+|.+.++|++||+ +++..+.||.|.|.+..
T Consensus        41 ~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2          41 TLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             CTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             eccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            5789999999999999999999996 69999999999998753

>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=98.60  E-value=9.2e-09  Score=80.03  Aligned_cols=42  Identities=21%  Similarity=0.080  Sum_probs=39.3

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      -+++|||||+|.+.++|.+|++.|||..|+|++|+|.||+.+
T Consensus        43 ~k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   84 (104)
T d1weya_          43 FKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTL   84 (104)
T ss_dssp             ETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCS
T ss_pred             ecCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecccC
Confidence            368999999999999999999999999999999999999754

>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=98.59  E-value=1.5e-08  Score=78.22  Aligned_cols=45  Identities=36%  Similarity=0.429  Sum_probs=41.1

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      +.+++++|||||+|.++++|++|++ +|+..|+||.|+|.++.+++
T Consensus        51 ~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~~~~   95 (104)
T d1wg5a_          51 DFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSSRAE   95 (104)
T ss_dssp             CSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEECTTT
T ss_pred             CCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECCHHH
Confidence            5689999999999999999999995 89999999999999988664

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.58  E-value=1.6e-08  Score=77.75  Aligned_cols=44  Identities=25%  Similarity=0.455  Sum_probs=40.5

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      +++++||+||+|++.++|.+|+..|||+.++||+|.|.++..+.
T Consensus        53 ~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          53 DRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTT   96 (99)
T ss_dssp             TTCTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCC
T ss_pred             CCCCccEEEEEECCHHHHHHHHHHhCCcEECCEEEEEEEeCCcC
Confidence            45778999999999999999999999999999999999987653

>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=98.57  E-value=1.9e-08  Score=77.72  Aligned_cols=42  Identities=26%  Similarity=0.224  Sum_probs=39.0

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          5 GRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         5 GkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      .++||||||+|.+.++|.+||+.|||..|.||+|+|+||...
T Consensus        43 ~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~   84 (111)
T d1whxa_          43 PEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             CSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             eccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            467999999999999999999999999999999999998654

>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=98.57  E-value=1.9e-08  Score=78.72  Aligned_cols=49  Identities=20%  Similarity=0.340  Sum_probs=43.4

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHHH
Q psy14476          2 SEDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKA   51 (303)
Q Consensus         2 d~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~   51 (303)
                      +.+|+++|||||+|.+.++|++|++ |||..|+||.|.|..+.+++..+.
T Consensus        54 ~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~~~~~~~~~  102 (112)
T d1wela1          54 GPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITKKGMLEK  102 (112)
T ss_dssp             CTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEECHHHHHHH
T ss_pred             CcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEcChHHHHHH
Confidence            4689999999999999999999995 899999999999999987765433

>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=98.56  E-value=1.9e-08  Score=75.19  Aligned_cols=41  Identities=29%  Similarity=0.431  Sum_probs=38.7

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccch
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k   46 (303)
                      +.||||||+|++.++|++|++.|||..|+|+.|+|+||..+
T Consensus        42 ~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~   82 (86)
T d2cpja1          42 KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS   82 (86)
T ss_dssp             TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             cccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCc
Confidence            56899999999999999999999999999999999999765

>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=98.55  E-value=3.6e-08  Score=74.14  Aligned_cols=36  Identities=17%  Similarity=0.355  Sum_probs=33.6

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeee
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVA   41 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~   41 (303)
                      .++|||||+|++.++|.+||+.|||..|+||+|+|+
T Consensus        54 ~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lkvS   89 (89)
T d2cpia1          54 GPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKAS   89 (89)
T ss_dssp             CCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CcceEEEEecccchhHHHHHHHhCCCEECCEEEEEC
Confidence            456999999999999999999999999999999985

>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=98.50  E-value=1.8e-08  Score=72.45  Aligned_cols=37  Identities=35%  Similarity=0.556  Sum_probs=34.8

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceeccccee
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLY   39 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~   39 (303)
                      .+++++|||||+|.+.++|++|++.|||+.|+||.|+
T Consensus        35 ~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1          35 TTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             SSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             ccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            4789999999999999999999999999999999875

>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=98.49  E-value=2.3e-08  Score=76.64  Aligned_cols=43  Identities=14%  Similarity=0.216  Sum_probs=39.3

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .++|||||+|.+.++|++||+.|||..|.|+.|+|.+++.+.+
T Consensus        48 ~~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~~   90 (98)
T d1wg4a_          48 QKDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPE   90 (98)
T ss_dssp             ETTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEECC
T ss_pred             cccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCCC
Confidence            4689999999999999999999999999999999999876543

>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=98.48  E-value=2.4e-08  Score=73.12  Aligned_cols=40  Identities=20%  Similarity=0.398  Sum_probs=36.6

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA   43 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A   43 (303)
                      .+|++||||||+|.+.++|++||+. +++.|+||.|.|..|
T Consensus        36 ~t~~~rG~~FV~f~~~~~a~~al~~-~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1          36 KTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             TTCCTTCCEEEEESSSHHHHHHTTC-SSCCBTTBCCEEECC
T ss_pred             cccccccEEEEEECCHHHHHHHHhh-CCCEECCEEeEEEEC
Confidence            4799999999999999999999964 888999999999876

>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=98.48  E-value=5e-08  Score=75.16  Aligned_cols=39  Identities=23%  Similarity=0.424  Sum_probs=36.9

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      +||||||+|++.++|++|++.|||..|+||.|+|.|+..
T Consensus        39 ~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~   77 (109)
T d2adca1          39 KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH   77 (109)
T ss_dssp             TSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             ccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            489999999999999999999999999999999999863

>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=98.43  E-value=3.9e-08  Score=73.49  Aligned_cols=43  Identities=28%  Similarity=0.261  Sum_probs=38.8

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHH
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKED   48 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~   48 (303)
                      .++|||||+|.+.++|++||+.|||..|+|+.|+|.++..+.+
T Consensus        33 ~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~~   75 (87)
T d3begb1          33 YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVD   75 (87)
T ss_dssp             CTTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEEC
T ss_pred             cccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCcC
Confidence            3569999999999999999999999999999999999876543

>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=98.38  E-value=1.2e-07  Score=69.99  Aligned_cols=39  Identities=18%  Similarity=0.366  Sum_probs=35.7

Q ss_pred             cccEEEEEeCCHHHHHHHHHHhCCceec-ccceeeecccc
Q psy14476          7 SKGFGFVCFSSPEEATKAVTEMNGRIIG-SKPLYVALAQR   45 (303)
Q Consensus         7 SkGfgFV~F~s~e~A~~Ai~~lnG~~l~-GR~L~V~~A~~   45 (303)
                      +||||||+|.+.++|.+|++.|||..|. |++|+|+||+.
T Consensus        44 ~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~akk   83 (83)
T d2b0ga1          44 RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAKK   83 (83)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECCC
T ss_pred             cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEecC
Confidence            5799999999999999999999999885 79999999863

>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=98.35  E-value=1.5e-08  Score=76.01  Aligned_cols=41  Identities=27%  Similarity=0.472  Sum_probs=36.9

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      .++++||||||+|.+.++|++|++ |||..|.||.|+|.+++
T Consensus        43 ~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~r~k   83 (90)
T d1u2fa_          43 QINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRRPH   83 (90)
T ss_dssp             CEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCBCTT
T ss_pred             ccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEECCCC
Confidence            467899999999999999999985 99999999999997543

>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=98.28  E-value=2e-07  Score=72.11  Aligned_cols=41  Identities=15%  Similarity=0.259  Sum_probs=37.0

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCcee--cccceeeecccch
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRII--GSKPLYVALAQRK   46 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l--~GR~L~V~~A~~k   46 (303)
                      ++||||||+|.+.++|.+||+.|||..|  .++.|+|.|++.+
T Consensus        43 ~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~   85 (108)
T d2adba1          43 NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT   85 (108)
T ss_dssp             TTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSC
T ss_pred             CCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCc
Confidence            5799999999999999999999999998  4788999988764

>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=98.28  E-value=2.2e-07  Score=71.04  Aligned_cols=42  Identities=19%  Similarity=0.234  Sum_probs=38.0

Q ss_pred             CcccEEEEEeCCHHHHHHHHH--HhCCceecccceeeecccchH
Q psy14476          6 RSKGFGFVCFSSPEEATKAVT--EMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~--~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      ++||||||+|++.++|.+||+  ++++..|+||+|+|.||+++.
T Consensus        53 ~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~~~   96 (99)
T d1x4fa1          53 RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYK   96 (99)
T ss_dssp             TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCS
T ss_pred             ecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCCcc
Confidence            568999999999999999998  578889999999999998664

>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=98.28  E-value=8e-08  Score=71.85  Aligned_cols=42  Identities=21%  Similarity=0.273  Sum_probs=37.9

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~   47 (303)
                      ..++||||||+|.+.++|++|+.  +++.|+||+|+|++|.+|.
T Consensus        38 ~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~   79 (88)
T d1wf0a_          38 PKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             CSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCC
T ss_pred             eeccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCC
Confidence            45789999999999999999985  7899999999999998764

>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=98.24  E-value=4e-07  Score=69.10  Aligned_cols=41  Identities=24%  Similarity=0.475  Sum_probs=37.1

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecc--cceeeecccch
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGS--KPLYVALAQRK   46 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~G--R~L~V~~A~~k   46 (303)
                      +.||||||+|.+.++|.+|++.||+..|.|  ++|+|+||+.+
T Consensus        51 ~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~   93 (97)
T d1whya_          51 KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             SSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             ccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCC
Confidence            468999999999999999999999999986  58999999864

>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=98.21  E-value=6.3e-07  Score=66.61  Aligned_cols=42  Identities=21%  Similarity=0.385  Sum_probs=37.3

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHh--CCceecccceeeecccchH
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEM--NGRIIGSKPLYVALAQRKE   47 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~l--nG~~l~GR~L~V~~A~~k~   47 (303)
                      +++|||||+|.+.++|++|++.+  ++..+.||+|+|.|+..++
T Consensus        42 ~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~~~   85 (88)
T d2cq1a1          42 KGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE   85 (88)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSS
T ss_pred             ccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCCCC
Confidence            56899999999999999999865  5778999999999998653

>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=98.20  E-value=7.1e-07  Score=64.76  Aligned_cols=37  Identities=19%  Similarity=0.328  Sum_probs=33.5

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecc
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALA   43 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A   43 (303)
                      ..+|||||+|++.++|++|++ +|++.|+|++|.|..+
T Consensus        38 ~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2          38 KNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             SSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             ccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            456899999999999999995 8999999999999865

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.17  E-value=7.9e-07  Score=68.45  Aligned_cols=40  Identities=23%  Similarity=0.286  Sum_probs=37.5

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccc
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQR   45 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~   45 (303)
                      .++||+||.|.+.++|.+|+..|||+.++||.|.|.++..
T Consensus        56 ~~~g~vfV~f~~~e~A~~A~~~l~Gr~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          56 PGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDP   95 (104)
T ss_dssp             TTCCEEEEEESCHHHHHHHHHHHSSCCSSSSCCEEEEECH
T ss_pred             CCceEEEEEECCHHHHHHHHHHHCCCEECCeEEEEEEcCH
Confidence            4569999999999999999999999999999999999864

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.14  E-value=9.6e-07  Score=65.43  Aligned_cols=43  Identities=23%  Similarity=0.308  Sum_probs=37.5

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHHhCCceecccc-eeeecccchH
Q psy14476          4 DGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKP-LYVALAQRKE   47 (303)
Q Consensus         4 tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~-L~V~~A~~k~   47 (303)
                      .+++|||+||+|++.++|++|++ +||..|+|+. |.|..+..|.
T Consensus        35 ~~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~k~   78 (81)
T d1wwha1          35 MSNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCIDKN   78 (81)
T ss_dssp             ECSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCCHH
T ss_pred             ecCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCChh
Confidence            36789999999999999999995 8999999985 5688887764

>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=98.13  E-value=9.2e-07  Score=67.86  Aligned_cols=41  Identities=20%  Similarity=0.166  Sum_probs=36.8

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHh--CCceecccceeeecccch
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEM--NGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~l--nG~~l~GR~L~V~~A~~k   46 (303)
                      ++||||||+|++.++|.+||+.|  ++..+.|++|+|.|+..+
T Consensus        49 ~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~   91 (104)
T d1wexa_          49 PFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSS
T ss_pred             ecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCC
Confidence            57899999999999999999987  566789999999999764

>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=98.11  E-value=1.1e-06  Score=65.92  Aligned_cols=41  Identities=24%  Similarity=0.319  Sum_probs=36.7

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHh--CCceecccceeeecccch
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEM--NGRIIGSKPLYVALAQRK   46 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~l--nG~~l~GR~L~V~~A~~k   46 (303)
                      ++++||||+|++.++|.+|++.|  ++..+.||+|+|+||++.
T Consensus        43 ~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~~   85 (89)
T d1x4da1          43 NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKY   85 (89)
T ss_dssp             SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCC
T ss_pred             ccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCCc
Confidence            46789999999999999999965  688999999999999754

>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=97.95  E-value=6.5e-06  Score=64.05  Aligned_cols=56  Identities=13%  Similarity=0.131  Sum_probs=46.2

Q ss_pred             CcccEEEEEeCCH-HHHHHHHHHhCCceecccceeeecccchHHHHHHHHHHHHHHH
Q psy14476          6 RSKGFGFVCFSSP-EEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRI   61 (303)
Q Consensus         6 kSkGfgFV~F~s~-e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~~~~~~~~q~~   61 (303)
                      +.||||||.|.+. ++|.+|+..+|+..+.++.+.|.++..+.+...+...+..+..
T Consensus        45 ~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~~~~~e~~~~~k~~~~~  101 (113)
T d1owxa_          45 RGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEGEVEKEALKKIIEDQ  101 (113)
T ss_dssp             TTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECCHHHHHHHHHHHHHHH
T ss_pred             cCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeeccchhhHHHHHHHHHHH
Confidence            4589999999985 7899999999999999999999999887777666666555443

>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=97.72  E-value=1.3e-05  Score=61.15  Aligned_cols=29  Identities=24%  Similarity=0.504  Sum_probs=26.7

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHhCCceec
Q psy14476          6 RSKGFGFVCFSSPEEATKAVTEMNGRIIG   34 (303)
Q Consensus         6 kSkGfgFV~F~s~e~A~~Ai~~lnG~~l~   34 (303)
                      ++||||||.|.+.++|.+|++.|||+.|.
T Consensus        54 ~~k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          54 PNKPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             TTCSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             cCccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            46899999999999999999999999874

>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=96.45  E-value=0.0012  Score=53.39  Aligned_cols=68  Identities=22%  Similarity=0.347  Sum_probs=49.3

Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceecccceeeecccchHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCC
Q psy14476          3 EDGRSKGFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQRKEDRKAHLASQYMQRIANMRMQQMGQLFQPGSTGGYF   82 (303)
Q Consensus         3 ~tGkSkGfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~~k~~r~~~~~~~~~q~~~~~r~~~~~~~~~~~~~~~~f   82 (303)
                      .+|++||||||+|.+.++|.+|+.. ++..+..+.+.+.....+.....                  ... .. ...++|
T Consensus        43 ~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~~~~~~~~~------------------~~~-~~-~~~~i~  101 (183)
T d1u1qa_          43 NTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQR------------------PGA-HL-TVKKIF  101 (183)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCCTTGGGS------------------TTT-TC-CCSEEE
T ss_pred             cCCCccCceecccCCHHHHHHHHHh-cCCcccccchhhhhhhhcccccc------------------ccc-cc-ccceeE
Confidence            3789999999999999999999975 77788888888887665532211                  000 11 133689


Q ss_pred             CCCCCCCCc
Q psy14476         83 VPTLPQPQR   91 (303)
Q Consensus        83 ~~~lp~~~~   91 (303)
                      |.+||+...
T Consensus       102 V~~lp~~~t  110 (183)
T d1u1qa_         102 VGGIKEDTE  110 (183)
T ss_dssp             EECCCTTCC
T ss_pred             EccCCCcCC
Confidence            999998654

>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=87.28  E-value=0.37  Score=33.94  Aligned_cols=35  Identities=31%  Similarity=0.368  Sum_probs=32.7

Q ss_pred             EEEEEeCCHHHHHHHHHHhCCceecccceeeeccc
Q psy14476         10 FGFVCFSSPEEATKAVTEMNGRIIGSKPLYVALAQ   44 (303)
Q Consensus        10 fgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~A~   44 (303)
                      .|-|...+..+|..||..|+.++|++|+|.|.++.
T Consensus        37 ~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          37 KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            47899999999999999999999999999999875

>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=81.04  E-value=0.5  Score=34.88  Aligned_cols=33  Identities=15%  Similarity=0.301  Sum_probs=29.1

Q ss_pred             cEEEEEeCCHHHHHHHHHHhCCceecccceeeec
Q psy14476          9 GFGFVCFSSPEEATKAVTEMNGRIIGSKPLYVAL   42 (303)
Q Consensus         9 GfgFV~F~s~e~A~~Ai~~lnG~~l~GR~L~V~~   42 (303)
                      +--+|+|.+-+.|-+|+. ++|.+++||.|.|..
T Consensus        59 d~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~   91 (95)
T d1ufwa_          59 GQMLVTFADSHSALSVLD-VDGMKVKGRAVKISG   91 (95)
T ss_dssp             TEEEEECSCSHHHHHHHH-GGGSEETTEEEEEEC
T ss_pred             CeEEEEECCcHHHHHHhc-cCCeEEcceEEEEec
Confidence            346899999999999986 699999999999874