Citrus Sinensis ID: 016231

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390---
Protein Sequence
MMDKKKSEDNNISAPSSIFTTLFGGIPNESTVASSLFSDSNPFKRQHRESQSAENESIFNPMNSDSLDSNNSELKKIKKTRQEKPNPDLPDAEGAATKTLSLSNKSTKLIYPRSILGFEPNGTIENEIKKEHSSNVGSESYLNRQKQNSNFSVEGKKRSENKKTKKRKRDDVEKDYVEKKYGVIAKEEEGKKVGVGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRV
Secondary Structure (PSIPRED)
cccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccHHHHHHccccccccHHHHHHHccccccccccccccHHHHHHccccHHHHHHHHHHHccHHHHHccccccccccccccccccHHHHHccccccccccccccccEEEEcccccccHHHHHHHHHHcccEEEEEEEEcccccccccccccEEccccccccccEEEEEEEccHHHHHHHHHccccccccEEEEEccccccccccccccccccccccEEEEccccccccHHHHHHHHHHcccccccEEEEEEEccccccccccEEEEEEcccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccHHHHHHHHcccccccHHHHHHcccccccccccccccccccccccccccccccccccHHHHHHccccccccccccccccccEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHccccccHHcccccccHcccccHHHcccEEEEEcccccccHHHHHHHHHHcccEEEEEEEEEccccccccccEEEEEEEcccccccEEEEEEEccHHHHHHHHHHcccEEcccEEEEccccccccccccccccccccccEEEEEcccccccHHHHHHHHHccccccccEEEEEEEEccccccccEEEEEEEcccc
Coil and Loop (DISEMBL)
mmdkkksednnisapssifttlfggipnestvasslfsdsnpfkrqhresqsaenesifnpmnsdsldsnnSELKKIKKTrqekpnpdlpdaegaatktlslsnkstkliyprsilgfepngtieneikkehssnvgsesylnrqkqnsnfsvegkkrsenkktkkrkrddVEKDYVEKKYGVIakeeegkkvgvgekrkkadneTEDMLVHrkeegfddegKLLRTIFVgnlplkvkKKTLIKEFIKfgeidsvrirsvpiidtkiprkGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGgnhirldracpprkklkgedaplydikktvfvgnlpfdvkdEEIYQLFCGLNDLESSVEAVRVIrhphmrvgKGIAYVLFKTRV
Flexible Loop (DISEMBL)
mmdkkksednnisapSSIFTTLFGGIPNESTVASSLFSDSNPFKRQHRESQSaenesifnpmnsdsldsnNSELKKIKKtrqekpnpdlpdaegaatktlslsnkstkliyprsiLGFEPNGTIENEIKKEHssnvgsesylnrqkqnsnfsvegkkrsenkktkkrkrddvekdyvekkygviakeeegkkvgvgekrkkadnetedmlvhrkeegfddegkllrtifvgnlplkvkkkTLIKEFikfgeidsvrirsvpiidtkiprkGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLkgedaplydikktvFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRvirhphmrvgkgiayvlfktrv
Low Complexity Region (SEG)
MMDKKKSEDNNISAPSSIFTTLFGGIPNESTVASSLFSDSNPFKRQHRESQSAENESIFNPMnsdsldsnnsELKKIKKTRQEKPNPDLPDAEGAATKTLSLSNKSTKLIYPRSILGFEPNGTIENEIKKEHSSNVGSESYLNRQKQNSNFSVegkkrsenkktkkrkrddvekdYVEKKYGVIAkeeegkkvgvgekrkkADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRV
Disordered region (IsUnstruct)
*****************IFTTLFGGI**********************************************************************************LIYPRSILGF******************************************************************************************************EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFK***
Disordered Region (DISOPRED)
***********************************************************************************************************************************************************************************************************************************IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVP***************QINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIR************************VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRV
Disordered Region (DISEMBL)
***********ISAPSSIFTTLFGGIPNESTVASSLFSD*****************SIFNPMNSDSLDSNNSELKKIKKTRQEKPNPDLPDAEGAATKTLSLSNKSTKLIYPRSILGFEPNGTIENEIKKEHSSNVGSESYLNR****************************EKDYVEKKYGVIAKEEEGKKVGVGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRV
Disordered Region (DISPRO)
*****************I**TLFG*IPNE****SS***********************************************************AATKTLSLS***********************************************************************************************************************KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRAC***************IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MMDKKKSEDNNISAPSSIFTTLFGGIPNESTVASSLFSDSNPFKRQHRESQSAENESIFNPMNSDSLDSNNSELKKIKKTRQEKPNPDLPDAEGAATKTLSLSNKSTKLIYPRSILGFEPNGTIENEIKKEHSSNVGSESYLNRQKQNSNFSVEGKKRSENKKTKKRKRDDVEKDYVEKKYGVIAKEEEGKKVGVGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRV
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	393	2.2.26 [Sep-21-2011]
Q5AHI7	454	Nucleolar protein 12 OS=C	N/A	no	0.389	0.337	0.394	4e-25
O13741	438	Nucleolar protein 12 OS=S	yes	no	0.379	0.340	0.372	2e-23
Q8C5L7	375	RNA-binding protein 34 OS	no	no	0.376	0.394	0.389	1e-22
P42696	430	RNA-binding protein 34 OS	yes	no	0.458	0.418	0.364	1e-22
Q5M9F1	428	RNA-binding protein 34 OS	yes	no	0.376	0.345	0.389	1e-22
Q6C2Q7	509	Nucleolar protein 12 OS=Y	yes	no	0.381	0.294	0.384	2e-22
Q75BJ7	426	Nucleolar protein 12 OS=A	yes	no	0.386	0.356	0.329	4e-21
Q6BTS9	462	Nucleolar protein 12 OS=D	yes	no	0.389	0.331	0.374	2e-20
Q6FUS6	396	Nucleolar protein 12 OS=C	yes	no	0.394	0.391	0.372	2e-18
Q08208	459	Nucleolar protein 12 OS=S	yes	no	0.396	0.339	0.318	9e-18

>sp|Q5AHI7|NOP12_CANAL Nucleolar protein 12 OS=Candida albicans (strain SC5314 / ATCC MYA-2876) GN=NOP12 PE=3 SV=1

 Score =  116 bits (290), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 67/170 (39%), Positives = 100/170 (58%), Gaps = 17/170 (10%)

Query: 226 RTIFVGNLPLKVKKKTLIKE-----FIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINE 280
           RT+FVGN+P  V    +I +     F  +G+IDS+R RS+   D  +PRK A  +K +++
Sbjct: 159 RTVFVGNVPADVITSKIIAKNFKNLFKHYGKIDSIRYRSISF-DEHLPRKVAFAKKNLHK 217

Query: 281 NADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVF 340
           + DSV+AYIV+K + ++ AA   N  V   +H+R+D    P        AP  D K+T+F
Sbjct: 218 SRDSVNAYIVYKEKPASIAAKELNATVFEDHHLRVDHVSHP--------AP-KDNKRTIF 268

Query: 341 VGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFK 390
           VGNL F+ K+E +++ F     L+  VE+VR+IR     +GKG A V FK
Sbjct: 269 VGNLDFEEKEETLWKYFNS--KLDQDVESVRIIRDSKTNLGKGFALVQFK 316

Involved in pre-25S rRNA processing.
Candida albicans (strain SC5314 / ATCC MYA-2876) (taxid: 237561)

>sp|O13741|NOP12_SCHPO Nucleolar protein 12 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=nop12 PE=1 SV=1

 Score =  110 bits (276), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 64/172 (37%), Positives = 97/172 (56%), Gaps = 23/172 (13%)

Query: 226 RTIFVGNLPLKV-----KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINE 280
           +T+FV NLP +V       K L K F +FG +DS+R RS+   +  IPRK A  +K+ + 
Sbjct: 164 KTVFVNNLPARVVTNKGDYKDLTKHFRQFGAVDSIRFRSLAFSEA-IPRKVAFFEKKFHS 222

Query: 281 NADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVF 340
             D+V+AYIVF+   S  +AL+ N  +    H+R+D    P  +         D K+ VF
Sbjct: 223 ERDTVNAYIVFRDSSSARSALSLNGTMFMDRHLRVDSVSHPMPQ---------DTKRCVF 273

Query: 341 VGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFK 390
           VGNL F+ ++E +++ F  CG      S++ VR++R P   +GKG AY+ FK
Sbjct: 274 VGNLAFEAEEEPLWRYFGDCG------SIDYVRIVRDPKTNLGKGFAYIQFK 319

Involved in pre-25S rRNA processing.

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

>sp|Q8C5L7|RBM34_MOUSE RNA-binding protein 34 OS=Mus musculus GN=Rbm34 PE=1 SV=1

 Score =  108 bits (269), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 65/167 (38%), Positives = 98/167 (58%), Gaps = 19/167 (11%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           RT+FVGNLP+   KK L   F ++G+++SVR RSV   +  + +K A ++++ + +  S+
Sbjct: 189 RTVFVGNLPVTCNKKKLKSFFKEYGQVESVRFRSVMPAEGTLTKKLAAIKRKFHPDQKSI 248

Query: 286 HAYIVFKSEQSTEAALAFNMAVIG-GNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNL 344
           +AY+VFK E +   AL  N A I  G  IR+D        L  E A     K++VFVGNL
Sbjct: 249 NAYVVFKDESAAAKALQRNGAQIAEGFRIRVD--------LASETAS--RDKRSVFVGNL 298

Query: 345 PFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLF 389
           P+ ++D  + + F  CG      S+ AVR++R+P   VG+G  YVLF
Sbjct: 299 PYKIEDSALEEHFLDCG------SIVAVRIVRNPLTGVGRGFGYVLF 339

Mus musculus (taxid: 10090)

>sp|P42696|RBM34_HUMAN RNA-binding protein 34 OS=Homo sapiens GN=RBM34 PE=1 SV=2

 Score =  108 bits (269), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 74/203 (36%), Positives = 114/203 (56%), Gaps = 23/203 (11%)

Query: 194 GVGEKRKKADNETEDMLV-HRKEEGFDDEGKLL---RTIFVGNLPLKVKKKTLIKEFIKF 249
           GV    +K  ++TED +V  RK+   + E + L   RT+FVGNLP+   KK L   F ++
Sbjct: 149 GVKVADRKILDDTEDTVVSQRKKIQINQEEERLKNERTVFVGNLPVTCNKKKLKSFFKEY 208

Query: 250 GEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIG 309
           G+I+SVR RS+   +  + +K A ++++I+ +  +++AY+VFK E +   AL  N A I 
Sbjct: 209 GQIESVRFRSLIPAEGTLSKKLAAIKRKIHPDQKNINAYVVFKEESAATQALKRNGAQIA 268

Query: 310 -GNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESS 366
            G  IR+D A     +           K++VFVGNLP+ V++  I + F  CG      S
Sbjct: 269 DGFRIRVDLASETSSR----------DKRSVFVGNLPYKVEESAIEKHFLDCG------S 312

Query: 367 VEAVRVIRHPHMRVGKGIAYVLF 389
           + AVR++R     +GKG  YVLF
Sbjct: 313 IMAVRIVRDKMTGIGKGFGYVLF 335

Homo sapiens (taxid: 9606)

>sp|Q5M9F1|RBM34_RAT RNA-binding protein 34 OS=Rattus norvegicus GN=Rbm34 PE=2 SV=1

 Score =  107 bits (268), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 65/167 (38%), Positives = 98/167 (58%), Gaps = 19/167 (11%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           RT+FVGNLP+   KK L   F ++G+++SVR RSV   +  + +K A ++++ + +  S+
Sbjct: 183 RTVFVGNLPVTCNKKKLKSFFKEYGQVESVRFRSVMPAEGTLSKKLAAIKRKFHPDQKSI 242

Query: 286 HAYIVFKSEQSTEAALAFNMAVIG-GNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNL 344
           +AY+VFK E++   AL  N A I  G  IR+D        L  E A     K++VFVGNL
Sbjct: 243 NAYVVFKEERAAAKALQRNGAQIAEGFRIRVD--------LASETA--SRDKRSVFVGNL 292

Query: 345 PFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLF 389
           P+ V +  + + F  CG      S+ AVR++R+P   VG+G  YVLF
Sbjct: 293 PYRVDESALEEHFLDCG------SIVAVRIVRNPLTGVGRGFGYVLF 333

Rattus norvegicus (taxid: 10116)

>sp|Q6C2Q7|NOP12_YARLI Nucleolar protein 12 OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=NOP12 PE=3 SV=1

 Score =  107 bits (267), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 65/169 (38%), Positives = 91/169 (53%), Gaps = 19/169 (11%)

Query: 227 TIFVGNLPLKV-KKKTLIKEF----IKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINEN 281
           TIFVGN+  +V   KT+   F       G + SVR RS+      +PRK A + +Q +  
Sbjct: 169 TIFVGNVSSEVITDKTVYNNFKALFAAIGTVASVRFRSISFSKL-LPRKVAFISQQFHSK 227

Query: 282 ADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFV 341
            D+V+AYIVFK+ +S + AL  N +V  G H+R+D    P            D K+ VFV
Sbjct: 228 RDTVNAYIVFKNVKSVKGALTLNGSVFKGFHMRVDSVAHP---------GAQDHKRCVFV 278

Query: 342 GNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFK 390
           G L F+ ++E +++ F    D    VE VR++R P   VGKG AYV FK
Sbjct: 279 GALDFEEQEESLWEAFSSCGD----VEYVRIVRDPKTNVGKGFAYVQFK 323

Involved in pre-25S rRNA processing.

Yarrowia lipolytica (strain CLIB 122 / E 150) (taxid: 284591)

>sp|Q75BJ7|NOP12_ASHGO Nucleolar protein 12 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=NOP12 PE=3 SV=1

 Score =  102 bits (255), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 63/191 (32%), Positives = 100/191 (52%), Gaps = 39/191 (20%)

Query: 222 GKLLRTIFVGNLPLK-VKKKTLIKEFIKF--------------------GEIDSVRIRSV 260
            K  RT+FVGN+P + +  K + KEF +                       ++S+R RS+
Sbjct: 133 AKAERTVFVGNVPHEAITDKKVYKEFKQLVAQRKLSKEDEDDEEQKAEKYAVESIRFRSI 192

Query: 261 PIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACP 320
              +  +PRK A +Q++++   DSV+AY+V+  +++  AA   N +V   +H+R D    
Sbjct: 193 -AFEEALPRKVAFVQQKLHHTRDSVNAYVVYAEKEAVTAACKLNGSVFHDHHLRFDSVAH 251

Query: 321 PRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHM 378
           P        AP +D K++VFVGNL F+  +E +++ F  CG       +E VR++R P  
Sbjct: 252 P--------AP-HDRKRSVFVGNLDFEESEESLWKHFMSCG------PIEYVRIVRDPKT 296

Query: 379 RVGKGIAYVLF 389
            VGKG AYV F
Sbjct: 297 NVGKGFAYVQF 307

Involved in pre-25S rRNA processing.

Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (taxid: 284811)

>sp|Q6BTS9|NOP12_DEBHA Nucleolar protein 12 OS=Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) GN=NOP12 PE=3 SV=2

 Score =  100 bits (249), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 64/171 (37%), Positives = 94/171 (54%), Gaps = 18/171 (10%)

Query: 226 RTIFVGNLPLKV-----KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINE 280
           RT+FVGN+   V       K   K F ++G+I S+R RS+   D  +PRK A  +K+++ 
Sbjct: 159 RTVFVGNVNASVVGSKPMYKKFKKLFSQYGKIQSIRFRSISFDDA-VPRKVAFAKKKLHS 217

Query: 281 NADSVHAYIVF-KSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTV 339
           + D+++AY+VF + E S +     N       H+R+D    P        AP  D K+T+
Sbjct: 218 SRDTLNAYVVFAEKEPSLKCVPKLNATEFEHAHLRVDHVAHP--------AP-KDNKRTI 268

Query: 340 FVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFK 390
           FVGNL F+ K+E +++ F    D  + VE+VRVIR     VGKG A V FK
Sbjct: 269 FVGNLDFEEKEETLWRYFNSKTD--NDVESVRVIRDAKTNVGKGFALVQFK 317

Involved in pre-25S rRNA processing.

Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) (taxid: 284592)

>sp|Q6FUS6|NOP12_CANGA Nucleolar protein 12 OS=Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) GN=NOP12 PE=3 SV=1

 Score = 94.0 bits (232), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/188 (37%), Positives = 100/188 (53%), Gaps = 33/188 (17%)

Query: 219 DDEGKLLRTIFVGNLPLKVK-KKTLIKEFIK-FGEID-----------SVRIRSVPIIDT 265
           D+  K  RTIFVGNL  +V   K+  K F K F  ID           S+R RSV   D 
Sbjct: 105 DEIEKASRTIFVGNLSNEVIISKSTYKLFQKLFNNIDDDDENKKLPIQSIRFRSVSFEDA 164

Query: 266 KIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA--FNMAVIGGNHIRLDRACPPRK 323
            +PRK A +Q++++++  SV+AYIV+K +      L    N  V    H+R+D    P  
Sbjct: 165 -LPRKVAFVQQKLHKSRASVNAYIVYKEQSPLLNKLIKRLNGQVFSNRHLRVDSITHP-- 221

Query: 324 KLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVG 381
                 AP +D +++VFVGNL F+  +E +++ F  CG      S+E VR++R P   +G
Sbjct: 222 ------AP-HDKQRSVFVGNLDFEEDEESLWKHFGACG------SIEYVRIVRDPKTNMG 268

Query: 382 KGIAYVLF 389
           KG AYV F
Sbjct: 269 KGFAYVQF 276

Involved in pre-25S rRNA processing.

Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (taxid: 284593)

>sp|Q08208|NOP12_YEAST Nucleolar protein 12 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=NOP12 PE=1 SV=1

 Score = 91.7 bits (226), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 65/204 (31%), Positives = 103/204 (50%), Gaps = 48/204 (23%)

Query: 219 DDEGKLLRTIFVGN-LPLKVKKKTLIKEFIK-FG-------------------------- 250
           D+  K  RT+F+GN L   +  K + KEF K FG                          
Sbjct: 141 DELEKAERTVFIGNILSTVITSKKVYKEFKKLFGTNPIAETEESGNEKEEESSKKSDNNE 200

Query: 251 -EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-FNMAVI 308
             I+S+R RS+   D  +PRK A +Q++ +++ D+++AYIV+K++ +     +  N  V 
Sbjct: 201 FAIESIRFRSISF-DEALPRKVAFVQQKFHKSRDTINAYIVYKNKSAVRKICSNLNAVVF 259

Query: 309 GGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESS 366
             +H+R+D    P        AP +D K+++FVGNL F+  +E +++ F  CG       
Sbjct: 260 QDHHLRVDSVAHP--------AP-HDKKRSIFVGNLDFEEIEESLWKHFEPCG------D 304

Query: 367 VEAVRVIRHPHMRVGKGIAYVLFK 390
           +E VR+IR     +GKG AYV FK
Sbjct: 305 IEYVRIIRDSKTNMGKGFAYVQFK 328

Involved in pre-25S rRNA processing.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

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	393
224138160	487	predicted protein [Populus trichocarpa]	0.814	0.657	0.534	1e-101
224071371	491	predicted protein [Populus trichocarpa]	0.814	0.651	0.547	3e-99
255573457	830	RNA binding protein, putative [Ricinus c	0.567	0.268	0.741	7e-92
356529724	519	PREDICTED: nucleolar protein 12-like [Gl	0.875	0.662	0.516	3e-88
225427165	541	PREDICTED: uncharacterized protein LOC10	0.933	0.678	0.526	1e-86
356496350	515	PREDICTED: nucleolar protein 12-like [Gl	0.867	0.662	0.515	1e-84
449462029	559	PREDICTED: LOW QUALITY PROTEIN: uncharac	0.923	0.649	0.476	9e-81
169219255	566	putative RNA recognition motif-containin	0.905	0.628	0.482	3e-80
15237960	501	RNA recognition motif-containing protein	0.567	0.445	0.683	3e-80
21554835	501	unknown [Arabidopsis thaliana]	0.567	0.445	0.679	1e-79

>gi|224138160|ref|XP_002326533.1| predicted protein [Populus trichocarpa] gi|222833855|gb|EEE72332.1| predicted protein [Populus trichocarpa]

 Score =  376 bits (965), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 209/391 (53%), Positives = 254/391 (64%), Gaps = 71/391 (18%)

Query: 3   DKKKSEDNNISAPSSIFTTLFGGIPNESTVASSLFSDSNPFKRQHRESQSAENESIFNPM 62
           D   ++++  SA S +F TLF G  +++   SSLFSDSNPFKR+  + +S EN S     
Sbjct: 10  DTSTAQNHTASALSDVFQTLFSGA-DQTASTSSLFSDSNPFKRKPEDPKSNENPST---- 64

Query: 63  NSDSLDSNNSE-LKKIKKTRQEKPNPDLPDAEGAATKTLSLSNKSTKLIYPRSILGFEPN 121
           + D+   N  E  +K+KK + E PN                             LGFEP 
Sbjct: 65  DVDTQKPNFYETTEKLKKVKTENPN-----------------------------LGFEP- 94

Query: 122 GTIENEIKKEHSSNVGSESYLNRQKQNSNFSVEGKKRSENKKTKKRKRDDVEKDYVEKKY 181
                   KE  +  G                           KKRKRDD+E++Y  KKY
Sbjct: 95  --------KEEETLRGR--------------------------KKRKRDDLEREYEAKKY 120

Query: 182 GVIAKEEEGKKVGVGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKT 241
           G +   EE   V VG KRK  D +  D+LV ++ EGFDDE KLLRT+FVGNLPLKVKKKT
Sbjct: 121 GPVVDNEENASVVVGAKRKNTD-DAADVLVSKESEGFDDESKLLRTVFVGNLPLKVKKKT 179

Query: 242 LIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL 301
           LIKEF KFG+++SVRIRSVPI ++KIPRKGAIL K+ N+N DSVHAY+VFK+EQS EA+L
Sbjct: 180 LIKEFSKFGDVESVRIRSVPIAESKIPRKGAILLKKFNDNVDSVHAYVVFKNEQSAEASL 239

Query: 302 AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLN 361
           + NMAV+GGNHIR+DRACPPRKKLKG DAPLYD K+TVFVGNLPFDVKDEE+YQLF G+ 
Sbjct: 240 SHNMAVVGGNHIRVDRACPPRKKLKGSDAPLYDNKRTVFVGNLPFDVKDEELYQLFTGIK 299

Query: 362 DLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           DL SS+EAVRVIR PH+ +GKGIAYVLFKTR
Sbjct: 300 DLASSIEAVRVIRDPHVGLGKGIAYVLFKTR 330

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224071371|ref|XP_002303427.1| predicted protein [Populus trichocarpa] gi|222840859|gb|EEE78406.1| predicted protein [Populus trichocarpa]

 Score =  368 bits (944), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 212/387 (54%), Positives = 253/387 (65%), Gaps = 67/387 (17%)

Query: 7   SEDNNISAPSSIFTTLFGGIPNESTVASSLFSDSNPFKRQHRESQSAENESIFNPMNSDS 66
           ++ N +SA S IF  LF G  N++    SLF+DSNPFKR+  + +S EN S     N+D 
Sbjct: 14  TQKNIVSASSDIFKFLFSGA-NQTAATFSLFTDSNPFKRKPDDPKSNENPS----ANADI 68

Query: 67  LDSN-NSELKKIKKTRQEKPNPDLPDAEGAATKTLSLSNKSTKLIYPRSILGFEPNGTIE 125
            D N N    K+KK + +  NP+                           LG EP     
Sbjct: 69  QDPNFNGTAMKLKKVKTQ--NPN---------------------------LGLEPK---- 95

Query: 126 NEIKKEHSSNVGSESYLNRQKQNSNFSVEGKKRSENKKTKKRKRDDVEKDYVEKKYGVIA 185
                        E  LN                  +K KKRKRDD+E +Y  KKYG + 
Sbjct: 96  ------------EEKTLN---------------ESGRKRKKRKRDDLESEYEAKKYGPVV 128

Query: 186 KEEEGKKVGVGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKE 245
             EE  +V VG KRKKAD +  D+LV ++ EGFDDE KLLRT+FVGNLPLKVKKK LIKE
Sbjct: 129 NNEENVRVVVGAKRKKAD-DAADVLVSKEGEGFDDERKLLRTVFVGNLPLKVKKKALIKE 187

Query: 246 FIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNM 305
           F KFGE++S+RIRS+PI ++KIPRKGAIL K+ N+NADSVHAYIVF +EQS EA+L  NM
Sbjct: 188 FSKFGEVESLRIRSMPITESKIPRKGAILLKKFNDNADSVHAYIVFNTEQSAEASLTHNM 247

Query: 306 AVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLES 365
           AV+GGNHIR+DRACPPRKKLKG DAPLYD K+TVFVGNLPFDVKDEEIYQLF G+ DL S
Sbjct: 248 AVVGGNHIRVDRACPPRKKLKGSDAPLYDNKRTVFVGNLPFDVKDEEIYQLFTGIKDLAS 307

Query: 366 SVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           S+EAVRVIRHPH+ +GKGIAYVLFKTR
Sbjct: 308 SIEAVRVIRHPHIGLGKGIAYVLFKTR 334

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255573457|ref|XP_002527654.1| RNA binding protein, putative [Ricinus communis] gi|223532959|gb|EEF34725.1| RNA binding protein, putative [Ricinus communis]

 Score =  343 bits (881), Expect = 7e-92,   Method: Compositional matrix adjust.
 Identities = 166/224 (74%), Positives = 192/224 (85%), Gaps = 1/224 (0%)

Query: 170 DDVEKDYVEKKYGVIAKEEEGKKVGVGEKRKKADNETEDMLVHRKE-EGFDDEGKLLRTI 228
           DD+E +Y  KKYG          V VGEKRKKA+N  EDMLV ++  EGFDDE KLLRT+
Sbjct: 106 DDIESEYEAKKYGSPEVSRNAVVVAVGEKRKKAENAEEDMLVSKEGGEGFDDESKLLRTV 165

Query: 229 FVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAY 288
           FVGNLPLK+KKKTL+KEF +FGEIDSVRIRSVPI+DTKIPRKGA++ K+IN++ADSVHAY
Sbjct: 166 FVGNLPLKMKKKTLVKEFSQFGEIDSVRIRSVPIVDTKIPRKGAVILKKINDSADSVHAY 225

Query: 289 IVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDV 348
           IVFK+EQS EA+LA NMAVIGGNHIR+DRACPPRKKLKGE  PLYD K+T+FVGNLPFDV
Sbjct: 226 IVFKTEQSAEASLANNMAVIGGNHIRVDRACPPRKKLKGEATPLYDNKRTLFVGNLPFDV 285

Query: 349 KDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           KDEEIYQLF G+ DLESS+EAVRVIR  ++ +G+GIAYVLFKTR
Sbjct: 286 KDEEIYQLFSGIKDLESSIEAVRVIRDSYVGLGRGIAYVLFKTR 329

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356529724|ref|XP_003533438.1| PREDICTED: nucleolar protein 12-like [Glycine max]

 Score =  332 bits (850), Expect = 3e-88,   Method: Compositional matrix adjust.
 Identities = 204/395 (51%), Positives = 263/395 (66%), Gaps = 51/395 (12%)

Query: 4   KKKSEDNNISAPSSIFTTLFGGIPNESTV--ASSLFSDSNPFKRQHRESQSAENESIFNP 61
           ++ S+ + +S PSSIF+ LF   P  +T   A+SLFSD NPF+R+      + N +  NP
Sbjct: 10  QQSSQTDTVSTPSSIFSKLFAIAPERTTATTAASLFSDDNPFRRKPTPLSDSTNRTQ-NP 68

Query: 62  MNSD---SLDSNNSELKKIKKTRQEK-PNPDLPDAEGAATKTLSLSNKSTKLIYPRSILG 117
            + D   + DS   + +K  K + +K P P    A       +  S+KS K         
Sbjct: 69  NDGDHPVNTDSGEEKKRKRNKEKTDKTPAP----AIDTVVSVIEASDKSEK--------- 115

Query: 118 FEPNGTIENEIKKEHSSNVGSESYLNRQKQNSNFSVEGKKRSENKKTKKRKRDDVEKDYV 177
                      K++  S+ G +  +                +E    +KRKR +VEKD+ 
Sbjct: 116 -----------KRKRDSDEGKDLIVG---------------AEASGKRKRKRGEVEKDWE 149

Query: 178 EKKYGVIAKEEEGKKVGVGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKV 237
           EKKYG++ +  E K VG+  KRK  D+   DM+V +  EGFDDE KLLRT+FVGNLPLKV
Sbjct: 150 EKKYGIVEEGLENKTVGI--KRKTLDDPA-DMMVSK--EGFDDEDKLLRTVFVGNLPLKV 204

Query: 238 KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQST 297
           KKKTL+KEF KFGE++SVRIRSVPI DTK PRKGAIL K+IN+ ADSVHAYIVFK+EQS 
Sbjct: 205 KKKTLLKEFKKFGEVESVRIRSVPIQDTKKPRKGAILAKKINDAADSVHAYIVFKTEQSA 264

Query: 298 EAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF 357
           +A+L+ NM+++ GNHIR+DRACPPRKK KGE  PLYD K+TVFVGNLPFDVKDEE+YQLF
Sbjct: 265 QASLSHNMSLVEGNHIRVDRACPPRKKHKGESTPLYDDKRTVFVGNLPFDVKDEELYQLF 324

Query: 358 CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           CG+++LESS+EAVRV+R PH+ VGKGIAYVLFKT+
Sbjct: 325 CGISNLESSIEAVRVVRDPHLNVGKGIAYVLFKTK 359

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225427165|ref|XP_002277589.1| PREDICTED: uncharacterized protein LOC100266124 [Vitis vinifera]

 Score =  326 bits (835), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 212/403 (52%), Positives = 274/403 (67%), Gaps = 36/403 (8%)

Query: 2   MDKKKSEDNNISAPSS--IFTTLFGGIPNESTVASSLFSDSNPFKRQHRESQSAENESIF 59
           M KKK +D     P S  +F TLFG +P +   + SLFSDSNPF+R  + S S++     
Sbjct: 1   MGKKKPKD-----PESGDVFKTLFGYLPKDDASSRSLFSDSNPFRR--KPSLSSQTLPFE 53

Query: 60  NPMNSDSLDSNNSELKKIKKTRQ-EKPNPDLPDAEGAATKTLSLSNKSTKLIYPRSILGF 118
           NP   DS      E+KK K+T + ++ +  L DA  A        +K+ KL  P   LG 
Sbjct: 54  NPSIPDS------EVKKRKRTEETDETSQTLEDAPKAQHLVEPKKSKNDKLRNPN--LGS 105

Query: 119 EPNGTIENEIKKEHSS---NVGSESYLNRQKQNSNFSVEGKKRSENKKTKKRKR-----D 170
           E N  + N + + + +   N G    L  +  N N   E K+  +++K K++K+     D
Sbjct: 106 ESNEELLNSVSESNKTLKKNKGKYIILGSE-GNPNSGSEVKEMVDSEKGKEKKKKKRKRD 164

Query: 171 DVEKDYVEKKYGVIAKEEEGKKVGVGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFV 230
           ++E++Y  + YG +AK E     GVGEKRK   N  E MLV +  EGFDDE KLLRT+FV
Sbjct: 165 EIEEEYEAQHYGTVAKVE-----GVGEKRKSVVNPAE-MLVSK--EGFDDESKLLRTVFV 216

Query: 231 GNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIV 290
           GNLPLK+KKK L+KEF  FGE+ SVRIRSVPI+D+K PRKGAI+ K+IN++ DSVHAYIV
Sbjct: 217 GNLPLKIKKKALLKEFSVFGEVQSVRIRSVPILDSKKPRKGAIISKKINDSVDSVHAYIV 276

Query: 291 FKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGE-DAPLYDIKKTVFVGNLPFDVK 349
           FK+E+S + +L+ NM+VIGGNHIR+DRACPPRKKLKGE DA LYD K+TVFVGNLPFDVK
Sbjct: 277 FKTEESAQTSLSHNMSVIGGNHIRVDRACPPRKKLKGENDASLYDNKRTVFVGNLPFDVK 336

Query: 350 DEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
            EEIYQLFCG++ LESS+EAVRV+R+PH  VGKGIAY+LFKT+
Sbjct: 337 AEEIYQLFCGIDSLESSIEAVRVVRNPHTSVGKGIAYILFKTK 379

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356496350|ref|XP_003517031.1| PREDICTED: nucleolar protein 12-like [Glycine max]

 Score =  320 bits (819), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 203/394 (51%), Positives = 262/394 (66%), Gaps = 53/394 (13%)

Query: 4   KKKSEDNNISAPSSIFTTLFGGIPNESTV--ASSLFSDSNPFKRQHRESQSAENESIFNP 61
           ++ SE + +S PSSIF+ LF   P ++T   A+SLFSD NPF+R+      + N +  NP
Sbjct: 10  QQSSETDAVSTPSSIFSKLFANAPEQTTATAAASLFSDDNPFRRKSAPLSYSTNRTQ-NP 68

Query: 62  MNSD---SLDSNNSELKKIKKTRQEKPNPDLPDAEGAATKTLSLSNKSTKLIYPRSILGF 118
            N D   + DS+  + +K  K +   P PD                 +  +I P      
Sbjct: 69  NNGDHPVNTDSSEEKKRKRTKDKTSAPAPD-----------------TVSVIEPLE---- 107

Query: 119 EPNGTIENEIKKEHSSNVGSESYLNRQKQNSNFSVEGKKRSENKKTKKRKRDDVEKDYVE 178
           EP    + +  +    +VG+E+   R                     KRKRD+VEK++ E
Sbjct: 108 EPGKKRKRDSDEGKDLSVGAEAIGKR---------------------KRKRDEVEKEWEE 146

Query: 179 KKYGVIAKEEEGKKVGVGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVK 238
           KKYG + +  E K VG+  KRK  D+   DM+V +  EGFD+E KLLRT+FVGNLPLKVK
Sbjct: 147 KKYGAVEEGIENKTVGI--KRKTLDDPA-DMMVSK--EGFDNEDKLLRTVFVGNLPLKVK 201

Query: 239 KKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE 298
           KKTL+KEF KFGE++SVRIRSVPI DTK PRKGAIL K+IN+ ADSVHAYIVFK+EQS +
Sbjct: 202 KKTLLKEFKKFGEVESVRIRSVPIQDTKKPRKGAILAKKINDAADSVHAYIVFKTEQSAQ 261

Query: 299 AALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFC 358
           A+LA NM+++ GNHIR+DRACPPRKK KGE  PLYD K+TVFVGNLPFDVKDEE+Y+LFC
Sbjct: 262 ASLAHNMSLVEGNHIRVDRACPPRKKHKGESTPLYDNKRTVFVGNLPFDVKDEELYKLFC 321

Query: 359 GLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           G+++LESS+EA+RV+R PH+ VGKGIAYVLFKT+
Sbjct: 322 GISNLESSIEAIRVVRDPHLNVGKGIAYVLFKTK 355

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449462029|ref|XP_004148744.1| PREDICTED: LOW QUALITY PROTEIN: uncharacterized protein LOC101206555 [Cucumis sativus]

 Score =  306 bits (785), Expect = 9e-81,   Method: Compositional matrix adjust.
 Identities = 197/413 (47%), Positives = 264/413 (63%), Gaps = 50/413 (12%)

Query: 1   MMDKKKSEDNNISAPSSIFTTLFG--GIPNESTVASSLFSDSNPFKRQHRESQSAENESI 58
           M + K ++   +++  S+F TLFG  G+ N      S+FS  NPF+R+            
Sbjct: 1   MGNNKITDXPTVASTFSVFDTLFGSAGVENPPV---SIFSTDNPFRRKA----------- 46

Query: 59  FNPMNSDSLDSNNSELKKIKKTRQEKPNPDLPDAEGAATKTLSLS----------NKSTK 108
                SDS+    +E+ + KK + ++   DL   EG  T +              ++   
Sbjct: 47  -----SDSVPPPPAEISR-KKGKDKRVGIDLDSTEGVKTSSEIKKSKKKEKKKSLDRELD 100

Query: 109 LIYPRSILGFEPNGTIENEIKKEHSSNVGSESYLNRQKQNSNFSVEGKKRSEN----KKT 164
            +      GFE  G +++  KK+  + +GSE+         +   EG K  EN    K+ 
Sbjct: 101 NVDDDGERGFESQGGLKDSSKKK-GTVLGSET------SEKSHGFEGSKLGENVKLMKER 153

Query: 165 KKRKRDDVEKDYVEKKYGV--IAKEE-EGKKVGVGEKRKKADNETEDMLVHRKEEGFDDE 221
           KKRKRD++E++Y  KKYGV  +A++E EG    V  K++KA ++  +MLV +  EGFDDE
Sbjct: 154 KKRKRDELEREYEAKKYGVSDVAEDEVEGSGGNVVGKKRKALDDPSEMLVTK--EGFDDE 211

Query: 222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPI--IDTKIPRKGAILQKQIN 279
            KLLRT+FVGNLPLKVKKK L KEF +FGEIDSVRIRSVPI   ++K PRKGAI+ K++N
Sbjct: 212 SKLLRTVFVGNLPLKVKKKALAKEFSQFGEIDSVRIRSVPIDIANSKKPRKGAIISKKLN 271

Query: 280 ENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTV 339
           E ADS HAY+VFK+E+S +A+L+ NMAV  GNHIR+DRACPP KKLK  + P+YD K+TV
Sbjct: 272 EAADSSHAYVVFKTEESAQASLSHNMAVFAGNHIRVDRACPPHKKLKVGNGPIYDPKRTV 331

Query: 340 FVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           FVGNLPFDVKDEE+YQLFCG++++ SSVEAVRVIR P + VGKG AYV FKTR
Sbjct: 332 FVGNLPFDVKDEELYQLFCGIDNMGSSVEAVRVIRDPKVNVGKGFAYVFFKTR 384

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|169219255|gb|ACA50448.1| putative RNA recognition motif-containing protein [Cucumis sativus]

 Score =  305 bits (780), Expect = 3e-80,   Method: Compositional matrix adjust.
 Identities = 196/406 (48%), Positives = 259/406 (63%), Gaps = 50/406 (12%)

Query: 8   EDNNISAPSSIFTTLFG--GIPNESTVASSLFSDSNPFKRQHRESQSAENESIFNPMNSD 65
           E   +++  S+F TLFG  G+ N      S+FS  NPF+R+                 SD
Sbjct: 15  ETPTVASTFSVFDTLFGSAGVENPPV---SIFSTDNPFRRKA----------------SD 55

Query: 66  SLDSNNSELKKIKKTRQEKPNPDLPDAEGAATKTLSLS----------NKSTKLIYPRSI 115
           S+    +E+ + KK + ++   DL   EG  T +              ++    +     
Sbjct: 56  SVPPPPAEISR-KKGKDKRVGIDLDSTEGVKTSSEIKKSKKKEKKKSLDRELDNVDDDGE 114

Query: 116 LGFEPNGTIENEIKKEHSSNVGSESYLNRQKQNSNFSVEGKKRSEN----KKTKKRKRDD 171
            GFE  G +++  KK+  + +GSE+         +   EG K  EN    K+ KKRKRD+
Sbjct: 115 RGFESQGGLKDSSKKK-GTVLGSET------SEKSHGFEGSKLGENVKLMKERKKRKRDE 167

Query: 172 VEKDYVEKKYGV--IAKEE-EGKKVGVGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTI 228
           +E++Y  KKYGV  +A++E EG    V  K++KA ++  +MLV +  EGFDDE KLLRT+
Sbjct: 168 LEREYEAKKYGVSDVAEDEVEGSGGNVVGKKRKALDDPSEMLVTK--EGFDDESKLLRTV 225

Query: 229 FVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPI--IDTKIPRKGAILQKQINENADSVH 286
           FVGNLPLKVKKK L KEF +FGEIDSVRIRSVPI   ++K PRKGAI+ K++NE ADS H
Sbjct: 226 FVGNLPLKVKKKALAKEFSQFGEIDSVRIRSVPIDIANSKKPRKGAIISKKLNEAADSSH 285

Query: 287 AYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPF 346
           AY+VFK+E+S  A+L+ NMAV  GNHIR+DRACPP KKLK  + P+YD K+TVFVGNLPF
Sbjct: 286 AYVVFKTEESAWASLSHNMAVFAGNHIRVDRACPPHKKLKVGNGPIYDPKRTVFVGNLPF 345

Query: 347 DVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           DVKDEE+YQLFCG++++ SSVEAVRVIR P + VGKG AYV FKTR
Sbjct: 346 DVKDEELYQLFCGIDNMGSSVEAVRVIRDPKVNVGKGFAYVFFKTR 391

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15237960|ref|NP_199496.1| RNA recognition motif-containing protein [Arabidopsis thaliana] gi|8809667|dbj|BAA97218.1| unnamed protein product [Arabidopsis thaliana] gi|32441262|gb|AAP81806.1| At5g46840 [Arabidopsis thaliana] gi|110736326|dbj|BAF00133.1| hypothetical protein [Arabidopsis thaliana] gi|332008049|gb|AED95432.1| RNA recognition motif-containing protein [Arabidopsis thaliana]

 Score =  305 bits (780), Expect = 3e-80,   Method: Compositional matrix adjust.
 Identities = 158/231 (68%), Positives = 191/231 (82%), Gaps = 8/231 (3%)

Query: 163 KTKKRKRDDVEKDYVEKKYGVIAKEEEGKKVGVGEKRKKADNETEDMLVHRKEEGFDDEG 222
           K KKRKRD++E +Y  KKYG +    E K+  VGEKRKKAD E  D +V +  EGFDDE 
Sbjct: 115 KRKKRKRDEIENEYETKKYGSV----EMKEKKVGEKRKKAD-EVADTMVSK--EGFDDES 167

Query: 223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENA 282
           KLLRT+FVGNLPLKVKKK ++KEF KFGE++SVRIRSVPI+D+K  RKGAI+ KQINE A
Sbjct: 168 KLLRTVFVGNLPLKVKKKVILKEFSKFGEVESVRIRSVPIVDSKRTRKGAIMLKQINEKA 227

Query: 283 DSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKG-EDAPLYDIKKTVFV 341
            SVHAY+VF++EQS  A+LA NM++I GNH+R+DRACPPRKK KG +D  LYD K+TVF+
Sbjct: 228 SSVHAYVVFETEQSAAASLAHNMSLIDGNHVRVDRACPPRKKQKGHDDTHLYDPKRTVFM 287

Query: 342 GNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           GNLPFDVKDEE+YQLF G ++LE+S+EAVRVIR PH+ +GKGIAYVLFKTR
Sbjct: 288 GNLPFDVKDEEVYQLFTGKSNLENSIEAVRVIRDPHLNIGKGIAYVLFKTR 338

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|21554835|gb|AAM63703.1| unknown [Arabidopsis thaliana]

 Score =  302 bits (774), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 157/231 (67%), Positives = 190/231 (82%), Gaps = 8/231 (3%)

Query: 163 KTKKRKRDDVEKDYVEKKYGVIAKEEEGKKVGVGEKRKKADNETEDMLVHRKEEGFDDEG 222
           K KKRKRD++E +Y   KYG +    E K+  VGEKRKKAD E  D +V +  EGFDDE 
Sbjct: 115 KRKKRKRDEIENEYETXKYGSV----EMKEKKVGEKRKKAD-EVADTMVSK--EGFDDES 167

Query: 223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENA 282
           KLLRT+FVGNLPLKVKKK ++KEF KFGE++SVRIRSVPI+D+K  RKGAI+ KQINE A
Sbjct: 168 KLLRTVFVGNLPLKVKKKVILKEFSKFGEVESVRIRSVPIVDSKRTRKGAIMLKQINEKA 227

Query: 283 DSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKG-EDAPLYDIKKTVFV 341
            SVHAY+VF++EQS  A+LA NM++I GNH+R+DRACPPRKK KG +D  LYD K+TVF+
Sbjct: 228 SSVHAYVVFETEQSAAASLAHNMSLIDGNHVRVDRACPPRKKQKGHDDTHLYDPKRTVFM 287

Query: 342 GNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           GNLPFDVKDEE+YQLF G ++LE+S+EAVRVIR PH+ +GKGIAYVLFKTR
Sbjct: 288 GNLPFDVKDEEVYQLFTGKSNLENSIEAVRVIRDPHLNIGKGIAYVLFKTR 338

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	393
TAIR|locus:2172937	501	AT5G46840 [Arabidopsis thalian	0.475	0.373	0.705	5.2e-77
ZFIN|ZDB-GENE-040718-77	411	rbm34 "RNA binding motif prote	0.442	0.423	0.391	3.2e-26
DICTYBASE|DDB_G0289941	481	DDB_G0289941 "Nucleolar protei	0.394	0.322	0.363	3e-25
CGD|CAL0002615	454	orf19.809 [Candida albicans (t	0.389	0.337	0.4	3.5e-24
POMBASE|SPAC16E8.06c	438	nop12 "RNA-binding protein Nop	0.379	0.340	0.377	1e-23
MGI|MGI:1098653	375	Rbm34 "RNA binding motif prote	0.407	0.426	0.371	2.6e-22
UNIPROTKB|P42696	430	RBM34 "RNA-binding protein 34"	0.435	0.397	0.371	3.7e-22
UNIPROTKB|F1NIM5	392	RBM34 "Uncharacterized protein	0.417	0.418	0.368	4.3e-22
UNIPROTKB|J9NU83	344	RBM34 "Uncharacterized protein	0.424	0.485	0.363	5.5e-22
UNIPROTKB|F1RGW8	424	RBM34 "Uncharacterized protein	0.424	0.393	0.363	1.3e-21

TAIR|locus:2172937 AT5G46840 [Arabidopsis thaliana (taxid:3702)]

 Score = 703 (252.5 bits), Expect = 5.2e-77, Sum P(2) = 5.2e-77
 Identities = 134/190 (70%), Positives = 163/190 (85%)

Query:   204 NETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPII 263
             +E  D +V +  EGFDDE KLLRT+FVGNLPLKVKKK ++KEF KFGE++SVRIRSVPI+
Sbjct:   151 DEVADTMVSK--EGFDDESKLLRTVFVGNLPLKVKKKVILKEFSKFGEVESVRIRSVPIV 208

Query:   264 DTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRK 323
             D+K  RKGAI+ KQINE A SVHAY+VF++EQS  A+LA NM++I GNH+R+DRACPPRK
Sbjct:   209 DSKRTRKGAIMLKQINEKASSVHAYVVFETEQSAAASLAHNMSLIDGNHVRVDRACPPRK 268

Query:   324 KLKG-EDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGK 382
             K KG +D  LYD K+TVF+GNLPFDVKDEE+YQLF G ++LE+S+EAVRVIR PH+ +GK
Sbjct:   269 KQKGHDDTHLYDPKRTVFMGNLPFDVKDEEVYQLFTGKSNLENSIEAVRVIRDPHLNIGK 328

Query:   383 GIAYVLFKTR 392
             GIAYVLFKTR
Sbjct:   329 GIAYVLFKTR 338

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0006312 "mitotic recombination" evidence=RCA

GO:0009560 "embryo sac egg cell differentiation" evidence=RCA

ZFIN|ZDB-GENE-040718-77 rbm34 "RNA binding motif protein 34" [Danio rerio (taxid:7955)]

 Score = 296 (109.3 bits), Expect = 3.2e-26, P = 3.2e-26
 Identities = 76/194 (39%), Positives = 112/194 (57%)

Query:   203 DNETEDMLVHRKEEGFDDEG--KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSV 260
             ++E E    H+K   F+ E   K+ RT+FVGNLP   KKK L+  F K G I+SVR RSV
Sbjct:   124 EDEEERPTKHKKTVKFNAEERLKMKRTVFVGNLPSSCKKKDLLSVFKKSGVIESVRFRSV 183

Query:   261 PIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVI-GGNHIRLDRAC 319
                D  + RK A +Q++++    +++AYIVFK E+S   AL +N   I  G +IR+DR  
Sbjct:   184 IREDPTMSRKVAAIQRKVHPKKQNINAYIVFKEEESATDALKWNGHEIQAGFYIRVDRVS 243

Query:   320 PPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPH 377
                K         +D K+++FVGNLP+D+ +  +   F  CG      ++EAVR++R   
Sbjct:   244 QHSK---------HDHKRSIFVGNLPYDISELPLQNHFQECG------NIEAVRLVRDRD 288

Query:   378 MRVGKGIAYVLFKT 391
               +GKG  YVLF++
Sbjct:   289 SGMGKGFGYVLFES 302

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

DICTYBASE|DDB_G0289941 DDB_G0289941 "Nucleolar protein 12" [Dictyostelium discoideum (taxid:44689)]

 Score = 267 (99.0 bits), Expect = 3.0e-25, Sum P(2) = 3.0e-25
 Identities = 61/168 (36%), Positives = 95/168 (56%)

Query:   226 RTIFVGNLPLKVKKKTLIKEFIK-FGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADS 284
             RT+FV N+ L   K   +K+  K FG+I+S+R RS+P+      RK   ++K+ +E  ++
Sbjct:   257 RTVFVSNINLNHAKDNELKQLFKPFGQIESIRFRSIPLSSIDGNRKETFIKKEFHEKRET 316

Query:   285 VHAYIVFKS-EQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGN 343
              +AYIVFK    + +AA   N     G H+R+D A    K  K  DA      KT+F+GN
Sbjct:   317 CNAYIVFKQIADAKKAAKQMNGKEAFGKHLRVDMA--DHKPTKASDA------KTIFIGN 368

Query:   344 LPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
             +P++ ++EE++ +F   +     V +VR+IR  H  +GKG  YV F T
Sbjct:   369 IPYETEEEELFLIF---DKTFGDVVSVRIIRDSHTNIGKGFGYVNFST 413

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

CGD|CAL0002615 orf19.809 [Candida albicans (taxid:5476)]

 Score = 280 (103.6 bits), Expect = 3.5e-24, P = 3.5e-24
 Identities = 68/170 (40%), Positives = 101/170 (59%)

Query:   226 RTIFVGNLPLKV-KKKTLIKEF---IK-FGEIDSVRIRSVPIIDTKIPRKGAILQKQINE 280
             RT+FVGN+P  V   K + K F    K +G+IDS+R RS+   D  +PRK A  +K +++
Sbjct:   159 RTVFVGNVPADVITSKIIAKNFKNLFKHYGKIDSIRYRSISF-DEHLPRKVAFAKKNLHK 217

Query:   281 NADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVF 340
             + DSV+AYIV+K + ++ AA   N  V   +H+R+D    P  K         D K+T+F
Sbjct:   218 SRDSVNAYIVYKEKPASIAAKELNATVFEDHHLRVDHVSHPAPK---------DNKRTIF 268

Query:   341 VGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFK 390
             VGNL F+ K+E +++ F   + L+  VE+VR+IR     +GKG A V FK
Sbjct:   269 VGNLDFEEKEETLWKYFN--SKLDQDVESVRIIRDSKTNLGKGFALVQFK 316

GO:0005730 "nucleolus" evidence=IEA

GO:0030684 "preribosome" evidence=IEA

GO:0000463 "maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)" evidence=IEA

POMBASE|SPAC16E8.06c nop12 "RNA-binding protein Nop12 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 275 (101.9 bits), Expect = 1.0e-23, P = 1.0e-23
 Identities = 65/172 (37%), Positives = 98/172 (56%)

Query:   226 RTIFVGNLPLKV--KK---KTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINE 280
             +T+FV NLP +V   K   K L K F +FG +DS+R RS+   +  IPRK A  +K+ + 
Sbjct:   164 KTVFVNNLPARVVTNKGDYKDLTKHFRQFGAVDSIRFRSLAFSEA-IPRKVAFFEKKFHS 222

Query:   281 NADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVF 340
               D+V+AYIVF+   S  +AL+ N  +    H+R+D    P  +         D K+ VF
Sbjct:   223 ERDTVNAYIVFRDSSSARSALSLNGTMFMDRHLRVDSVSHPMPQ---------DTKRCVF 273

Query:   341 VGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFK 390
             VGNL F+ ++E +++ F  CG      S++ VR++R P   +GKG AY+ FK
Sbjct:   274 VGNLAFEAEEEPLWRYFGDCG------SIDYVRIVRDPKTNLGKGFAYIQFK 319

GO:0003723 "RNA binding" evidence=ISM

GO:0005730 "nucleolus" evidence=ISO;IDA

GO:0006364 "rRNA processing" evidence=ISO

MGI|MGI:1098653 Rbm34 "RNA binding motif protein 34" [Mus musculus (taxid:10090)]

 Score = 259 (96.2 bits), Expect = 2.6e-22, P = 2.6e-22
 Identities = 68/183 (37%), Positives = 106/183 (57%)

Query:   211 VHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRK 270
             V+ +EE   +E    RT+FVGNLP+   KK L   F ++G+++SVR RSV   +  + +K
Sbjct:   178 VNPEEERLKNE----RTVFVGNLPVTCNKKKLKSFFKEYGQVESVRFRSVMPAEGTLTKK 233

Query:   271 GAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIG-GNHIRLDRACPPRKKLKGED 329
              A ++++ + +  S++AY+VFK E +   AL  N A I  G  IR+D A     +    D
Sbjct:   234 LAAIKRKFHPDQKSINAYVVFKDESAAAKALQRNGAQIAEGFRIRVDLA----SETASRD 289

Query:   330 APLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYV 387
                   K++VFVGNLP+ ++D  + + F  CG      S+ AVR++R+P   VG+G  YV
Sbjct:   290 ------KRSVFVGNLPYKIEDSALEEHFLDCG------SIVAVRIVRNPLTGVGRGFGYV 337

Query:   388 LFK 390
             LF+
Sbjct:   338 LFE 340

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|P42696 RBM34 "RNA-binding protein 34" [Homo sapiens (taxid:9606)]

 Score = 261 (96.9 bits), Expect = 3.7e-22, P = 3.7e-22
 Identities = 72/194 (37%), Positives = 112/194 (57%)

Query:   204 NETEDMLV-HRKEEGFDDEGKLL---RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRS 259
             ++TED +V  RK+   + E + L   RT+FVGNLP+   KK L   F ++G+I+SVR RS
Sbjct:   159 DDTEDTVVSQRKKIQINQEEERLKNERTVFVGNLPVTCNKKKLKSFFKEYGQIESVRFRS 218

Query:   260 VPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIG-GNHIRLDRA 318
             +   +  + +K A ++++I+ +  +++AY+VFK E +   AL  N A I  G  IR+D A
Sbjct:   219 LIPAEGTLSKKLAAIKRKIHPDQKNINAYVVFKEESAATQALKRNGAQIADGFRIRVDLA 278

Query:   319 CPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHP 376
                  +    D      K++VFVGNLP+ V++  I + F  CG      S+ AVR++R  
Sbjct:   279 ----SETSSRD------KRSVFVGNLPYKVEESAIEKHFLDCG------SIMAVRIVRDK 322

Query:   377 HMRVGKGIAYVLFK 390
                +GKG  YVLF+
Sbjct:   323 MTGIGKGFGYVLFE 336

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|F1NIM5 RBM34 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 258 (95.9 bits), Expect = 4.3e-22, P = 4.3e-22
 Identities = 67/182 (36%), Positives = 103/182 (56%)

Query:   213 RKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSV-PIIDTKIPRKG 271
             +K+   ++  K  RT+FVGNLP+    + L   F ++G+I+S+R RSV P  DT + RK 
Sbjct:   134 KKKNEAEEMIKNKRTVFVGNLPVDCTAQMLKSLFKEYGQIESIRFRSVVPAEDT-LSRKL 192

Query:   272 AILQKQINENADSVHAYIVFKSEQSTEAALAFNM---AVIGGNHIRLDRACPPRKKLKGE 328
             A ++++I+ N   ++AY+VFK E+    AL +      V  G HIR+D A       K  
Sbjct:   193 AAIKRKIHPNVKYINAYVVFKEERDAVKALNYKRNGTEVASGFHIRVDSAS------KNS 246

Query:   329 DAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVL 388
                L+D K++VF+GNL +D+ D  + + F    D    V AVR++R     +GKG  YVL
Sbjct:   247 ---LHDNKRSVFLGNLAYDISDSAVREHFADCGD----VVAVRIVRDRQSGMGKGFGYVL 299

Query:   389 FK 390
             F+
Sbjct:   300 FE 301

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

UNIPROTKB|J9NU83 RBM34 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 256 (95.2 bits), Expect = 5.5e-22, P = 5.5e-22
 Identities = 69/190 (36%), Positives = 109/190 (57%)

Query:   204 NETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPII 263
             N+ + + ++++EE   +E    RT+FVGNLP+   KK L   F ++G+IDSVR RS+   
Sbjct:   164 NQRKKIEINQEEEKLKNE----RTVFVGNLPVTCNKKKLKSFFREYGQIDSVRFRSLIPA 219

Query:   264 DTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIG-GNHIRLDRACPPR 322
             +  + +K A ++++I+ +   ++AY+VFK E S   AL  N A I  G  IR+D A    
Sbjct:   220 EGTLSKKLAAIKRKIHPDQKYINAYVVFKDESSATKALKRNGAQIADGFRIRVDLA---- 275

Query:   323 KKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRV 380
              +    D      K++VFVGNLP+ V++  + + F  CG      S+ AVR++R     V
Sbjct:   276 SETSSRD------KRSVFVGNLPYKVEESAVEEHFLDCG------SIVAVRIVRDRVTGV 323

Query:   381 GKGIAYVLFK 390
             G+G  YVLF+
Sbjct:   324 GRGFGYVLFE 333

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1RGW8 RBM34 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 256 (95.2 bits), Expect = 1.3e-21, P = 1.3e-21
 Identities = 69/190 (36%), Positives = 108/190 (56%)

Query:   204 NETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPII 263
             N    +  +++EE   +E    RT+FVGNLP+   KK L   F ++G+I+SVR RS+   
Sbjct:   163 NPRRKIQTNKEEERLKNE----RTVFVGNLPVTCNKKKLKSFFKEYGQIESVRFRSLIPA 218

Query:   264 DTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIG-GNHIRLDRACPPR 322
             +  + +K A ++++I+ +  +++AY+VFK E +   AL  N A I  G  IR+D A    
Sbjct:   219 EGTLSKKLAAIKRKIHPDQKNINAYVVFKDESAAAKALERNGAQIADGFRIRVDLA---- 274

Query:   323 KKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRV 380
              +    D      K++VFVGNLP+ V++  + + F  CG      SV AVR++R P   V
Sbjct:   275 SETSSRD------KRSVFVGNLPYKVEESAVEKHFLDCG------SVVAVRIVRDPVTGV 322

Query:   381 GKGIAYVLFK 390
             G+G  YVLF+
Sbjct:   323 GRGFGYVLFE 332

GO:0005730 "nucleolus" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	393
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	6e-32
cd12669	105	cd12669, RRM1_Nop12p_like, RNA recognition motif 1	2e-19
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	2e-18
smart00360	73	smart00360, RRM, RNA recognition motif	6e-09
smart00360	73	smart00360, RRM, RNA recognition motif	1e-08
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-08
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-08
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	3e-08
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	8e-08
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	6e-06
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	1e-05
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-05
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-05
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	3e-05
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	4e-05
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	5e-05
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	5e-05
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	6e-05
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	8e-05
cd12294	102	cd12294, RRM_Rrp7A, RNA recognition motif in ribos	9e-05
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-04
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	3e-04
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	5e-04
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	5e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	5e-04
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	6e-04
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	7e-04
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	8e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	8e-04
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	8e-04
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	0.001
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	0.001
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	0.001
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	0.002
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	0.002
cd12420	79	cd12420, RRM_RBPMS_like, RNA recognition motif in	0.002
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	0.002
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	0.002
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	0.002
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	0.003
cd12508	80	cd12508, RRM2_ESRPs_Fusilli, RNA recognition motif	0.003
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	0.004

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

 Score =  115 bits (291), Expect = 6e-32
 Identities = 48/91 (52%), Positives = 66/91 (72%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           RT+FVGNLPL  KKK L K F +FG I+SVR RSVP+ + K+P+K A ++K+ ++  D+V
Sbjct: 1   RTVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNV 60

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLD 316
           +AY+VFK E+S E AL  N     G+HIR+D
Sbjct: 61  NAYVVFKEEESAEKALKLNGTEFEGHHIRVD 91

This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 91

>gnl|CDD|241113 cd12669, RRM1_Nop12p_like, RNA recognition motif 1 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 82.1 bits (203), Expect = 2e-19
 Identities = 40/105 (38%), Positives = 61/105 (58%), Gaps = 9/105 (8%)

Query: 226 RTIFVGNLPL-KVKKKTLIKEFIK-------FGEIDSVRIRSVPIIDTKIPRKGAILQKQ 277
           RT+FVGN+P+  V  K++ K+  K       FG+I+S+R RS+      +PRK A ++K 
Sbjct: 1   RTVFVGNVPIDVVTSKSVYKDLKKHFLNLAPFGKIESIRFRSISFATDALPRKVAFIKKD 60

Query: 278 INENADSVHAYIVFK-SEQSTEAALAFNMAVIGGNHIRLDRACPP 321
           ++   DSV+AYIV+K    + +AA   N  V  G H+R+D    P
Sbjct: 61  LHSERDSVNAYIVYKTPALAAKAAKKLNGTVFLGRHLRVDSVAHP 105

This subgroup corresponds to the RRM1 of Nop12p which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 105

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

 Score = 78.4 bits (194), Expect = 2e-18
 Identities = 29/58 (50%), Positives = 39/58 (67%), Gaps = 8/58 (13%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRV 393
           +VFVGNLPFD+++EE+ + F  CG       VEAVR++R     +GKG  YVLFKT+ 
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCG------DVEAVRIVRDRKTGIGKGFGYVLFKTKD 52

This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 73

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

 Score = 51.8 bits (125), Expect = 6e-09
 Identities = 26/90 (28%), Positives = 44/90 (48%), Gaps = 18/90 (20%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVH 286
           T+FVGNLP    ++ L + F KFG+++SVR+      +T   +                 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDK--ETGKSKG---------------F 43

Query: 287 AYIVFKSEQSTEAAL-AFNMAVIGGNHIRL 315
           A++ F+SE+  E AL A N   + G  +++
Sbjct: 44  AFVEFESEEDAEKALEALNGKELDGRPLKV 73

Length = 73

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

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 4/55 (7%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           T+FVGNLP D  +EE+ +LF     +ES    VR++R       KG A+V F++ 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVES----VRLVRDKETGKSKGFAFVEFESE 51

Length = 73

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

 Score = 51.2 bits (123), Expect = 1e-08
 Identities = 29/90 (32%), Positives = 43/90 (47%), Gaps = 19/90 (21%)

Query: 228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHA 287
           +FVGNLP    ++ L + F KFGEI+SVRI    + D     KG               A
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRI----VRDKDGKSKG--------------FA 42

Query: 288 YIVFKSEQSTEAAL-AFNMAVIGGNHIRLD 316
           ++ F+S +  E AL A N   + G  +++ 
Sbjct: 43  FVEFESPEDAEKALEALNGKELDGRKLKVS 72

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

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

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 21/56 (37%), Positives = 33/56 (58%), Gaps = 4/56 (7%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           +TVF+ NLPFD  +EE+ +LF    +    V+  R+++       KG A+V FKT+
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGE----VKYARIVKDKLTGHSKGTAFVKFKTK 52

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

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

 Score = 49.9 bits (120), Expect = 3e-08
 Identities = 29/85 (34%), Positives = 41/85 (48%), Gaps = 14/85 (16%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           R I+V NL  K+ +  L   F KFGE++S+R          IP+K    Q ++N      
Sbjct: 1   REIYVRNLDFKLDEDDLRGIFSKFGEVESIR----------IPKKQDEKQGRLNNG---- 46

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGG 310
            A++ FK   S E AL  N   +GG
Sbjct: 47  FAFVTFKDASSAENALQLNGTELGG 71

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|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 49.1 bits (117), Expect = 8e-08
 Identities = 25/54 (46%), Positives = 34/54 (62%), Gaps = 8/54 (14%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFK 390
           VFVGNL F+  +E ++++F  CG       +E VR++R P   VGKG AYV FK
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCG------GIEYVRIVRDPKTNVGKGFAYVQFK 49

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 43.4 bits (103), Expect = 6e-06
 Identities = 20/56 (35%), Positives = 33/56 (58%), Gaps = 9/56 (16%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           +FVGNLP D  +E++ +LF   G       +E+VR++R    +  KG A+V F++ 
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFG------EIESVRIVRDKDGK-SKGFAFVEFESP 49

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

 Score = 42.5 bits (101), Expect = 1e-05
 Identities = 27/90 (30%), Positives = 44/90 (48%), Gaps = 19/90 (21%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADSV 285
           ++FVGNLP  ++++ L K F   G++++VRI    + D K    KG              
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRI----VRDRKTGIGKG-------------- 42

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRL 315
             Y++FK++ S   AL  N   + G  IR+
Sbjct: 43  FGYVLFKTKDSVALALKLNGIKLKGRKIRV 72

This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 73

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

 Score = 42.5 bits (101), Expect = 1e-05
 Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 6/54 (11%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           ++V NLP  V +E++ + F         VE VR++R+      +G A+V F + 
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGK----VEGVRLVRNKDR--PRGFAFVEFASP 48

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

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

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 4/57 (7%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           K TV+V NLPF + + +++++F         V  V +++    R  KG+A++LF  R
Sbjct: 1   KSTVYVSNLPFSLTNNDLHKIFSKY----GKVVKVTIVKDKETRKSKGVAFILFLDR 53

This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. . Length = 78

>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 4/51 (7%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLF 389
           +FVGNL FD  ++ IY+ F         + +VR+   P     KG  YV F
Sbjct: 1   LFVGNLSFDADEDSIYEAFGE----YGEISSVRLPTDPDSGRPKGFGYVEF 47

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

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 27/84 (32%), Positives = 40/84 (47%), Gaps = 18/84 (21%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVH 286
           T+FV NL   V +  L K F K GEI  VR+    + + K   KG              +
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRL----VKNYKGKSKG--------------Y 42

Query: 287 AYIVFKSEQSTEAALAFNMAVIGG 310
           AY+ F++E+S + AL  +  +I G
Sbjct: 43  AYVEFENEESVQEALKLDRELIKG 66

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

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

 Score = 41.0 bits (97), Expect = 4e-05
 Identities = 20/55 (36%), Positives = 31/55 (56%), Gaps = 9/55 (16%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
           +FVGNLP D  +E++  LF   G       +E++R++R    R  KG A+V F+ 
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFG------PIESIRIVRDETGR-SKGFAFVEFED 48

(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|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 40.8 bits (96), Expect = 5e-05
 Identities = 23/57 (40%), Positives = 34/57 (59%), Gaps = 8/57 (14%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP--HMRVGKGIAYVLFKTR 392
           T ++GNLP+DV +E+I + F GLN     V +VR+ R P    R+ +G  Y  F+ R
Sbjct: 3   TAYLGNLPYDVTEEDIKEFFRGLN-----VSSVRLPREPGDPGRL-RGFGYAEFEDR 53

This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation. . Length = 77

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

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 21/57 (36%), Positives = 29/57 (50%), Gaps = 8/57 (14%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           TVFV  L   V++ ++Y+ F   G       V  VR+IR  + R  KG+AYV F   
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAG------KVRDVRIIRDRNSRRSKGVAYVEFYDE 51

This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

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

 Score = 40.8 bits (96), Expect = 6e-05
 Identities = 23/92 (25%), Positives = 39/92 (42%), Gaps = 18/92 (19%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVH 286
           T+FVGNL    ++  L + F + GE+  VRI                   Q ++      
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRI------------------AQDDDGRSKGF 42

Query: 287 AYIVFKSEQSTEAALAFNMAVIGGNHIRLDRA 318
            ++ F +E+  + AL  +   + G  IR+D A
Sbjct: 43  GHVEFATEEGAQKALEKSGEELLGREIRVDLA 74

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

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

 Score = 40.3 bits (95), Expect = 8e-05
 Identities = 29/88 (32%), Positives = 41/88 (46%), Gaps = 19/88 (21%)

Query: 228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHA 287
           +FVGNLP    ++ L   F KFG I+S+RI    + D     KG               A
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRI----VRDETGRSKG--------------FA 42

Query: 288 YIVFKSEQSTEAAL-AFNMAVIGGNHIR 314
           ++ F+ E+  E AL A N   +GG  +R
Sbjct: 43  FVEFEDEEDAEKALEALNGKELGGRELR 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|240740 cd12294, RRM_Rrp7A, RNA recognition motif in ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar proteins

 Score = 40.8 bits (96), Expect = 9e-05
 Identities = 21/85 (24%), Positives = 37/85 (43%), Gaps = 14/85 (16%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           RT+FV N+P    +++L + F + G+++SV ++  P          A  +   ++     
Sbjct: 1   RTLFVLNVPPYCTEESLKRLFSRCGKVESVELQEKP--------GPAESEDLTSKFFPPK 52

Query: 286 H------AYIVFKSEQSTEAALAFN 304
                  AY+VFK   S   AL   
Sbjct: 53  PIKGFKVAYVVFKKPSSLSRALKLK 77

This subfamily corresponds to the RRM of Rrp7A, also termed gastric cancer antigen Zg14, a homolog of yeast ribosomal RNA-processing protein 7 (Rrp7p), and mainly found in Metazoa. Rrp7p is an essential yeast protein involved in pre-rRNA processing and ribosome assembly, and is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle. In contrast, the cellular function of Rrp7A remains unclear currently. Rrp7A harbors an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal Rrp7 domain. . Length = 102

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

 Score = 39.8 bits (94), Expect = 1e-04
 Identities = 22/88 (25%), Positives = 39/88 (44%), Gaps = 20/88 (22%)

Query: 228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHA 287
           ++V NLP  V ++ L + F  +G+++ VR+                     N++     A
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLV-------------------RNKDRPRGFA 41

Query: 288 YIVFKSEQSTEAALA-FNMAVIGGNHIR 314
           ++ F S +  EAAL   N  V+ G  +R
Sbjct: 42  FVEFASPEDAEAALKKLNGLVLDGRTLR 69

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

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

 Score = 43.3 bits (102), Expect = 2e-04
 Identities = 55/245 (22%), Positives = 92/245 (37%), Gaps = 34/245 (13%)

Query: 154 EGKKRSENKKTKKRKRDDVEKDYVEKKY-GVIAKEEEGKKVGVGEKRKKADNETEDML-V 211
              K  E  + + R RD   +      Y G   +            R       +D    
Sbjct: 16  RSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYRPRGDRSYRRDDRRSG 75

Query: 212 HRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKG 271
              +E   +  +  RT+FV  L LK +++ L + F K G++  V+     I D    R  
Sbjct: 76  RNTKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQC----IKDRNSRRSK 131

Query: 272 AILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRL-------DRACPPRKK 324
            +             AY+ F   +S   ALA    ++ G  I +       +RA      
Sbjct: 132 GV-------------AYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAATH 178

Query: 325 LKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGI 384
             G D P +     ++VGNL F++ ++E+ Q+F    D+E     V++ R P     KG 
Sbjct: 179 QPG-DIPNF---LKLYVGNLHFNITEQELRQIFEPFGDIED----VQLHRDPETGRSKGF 230

Query: 385 AYVLF 389
            ++ F
Sbjct: 231 GFIQF 235

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

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 24/93 (25%), Positives = 42/93 (45%), Gaps = 25/93 (26%)

Query: 225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADS 284
           + T++VG L  +V +K L   F +FGEI S+ +         +PR+              
Sbjct: 1   ITTLYVGGLGERVTEKDLRDHFYQFGEIRSITV---------VPRQQC------------ 39

Query: 285 VHAYIVFKSEQSTEAAL--AFNMAVIGGNHIRL 315
             A++ F + ++ E A    FN  +I G  ++L
Sbjct: 40  --AFVTFTTREAAEKAAERLFNKLIINGRRLKL 70

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

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

 Score = 38.2 bits (89), Expect = 5e-04
 Identities = 25/91 (27%), Positives = 46/91 (50%), Gaps = 19/91 (20%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           RT+FVGNL + + ++ L + F ++G ++ V        D K P +G         NA   
Sbjct: 3   RTLFVGNLEITITEEELRRAFERYGVVEDV--------DIKRPPRG-------QGNA--- 44

Query: 286 HAYIVFKS-EQSTEAALAFNMAVIGGNHIRL 315
           +A++ F + + +  A +A +   IG N I++
Sbjct: 45  YAFVKFLNLDMAHRAKVAMSGQYIGRNQIKI 75

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

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

 Score = 38.1 bits (89), Expect = 5e-04
 Identities = 28/90 (31%), Positives = 37/90 (41%), Gaps = 24/90 (26%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVH 286
           T+FVG L   V +  L   F  FGEI  V+I   P      P KG               
Sbjct: 3   TVFVGGLDPAVTEDELRSLFGPFGEIVYVKI---P------PGKGC-------------- 39

Query: 287 AYIVFKSEQSTEAALA-FNMAVIGGNHIRL 315
            ++ F    + EAA+      +IGG+ IRL
Sbjct: 40  GFVQFVHRAAAEAAIQQLQGTIIGGSRIRL 69

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

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

 Score = 37.9 bits (89), Expect = 5e-04
 Identities = 22/96 (22%), Positives = 37/96 (38%), Gaps = 25/96 (26%)

Query: 228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHA 287
           +FVG L   V +  L + F +FG +  V I                  K+ +   D   A
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEII-----------------KKKDAGPDRGFA 44

Query: 288 YIVFKSEQSTEAAL-----AFNMAVIGGNHIRLDRA 318
           YI     +++EA L       N     G+ ++++ A
Sbjct: 45  YIDL---RTSEAQLKKCKSTLNGTKWKGSVLKIEEA 77

This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. Length = 78

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

 Score = 38.4 bits (90), Expect = 6e-04
 Identities = 26/104 (25%), Positives = 46/104 (44%), Gaps = 20/104 (19%)

Query: 225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADS 284
             T+FVG L L+  ++TL + F ++G+I   R+R V  I T   +               
Sbjct: 3   YLTLFVGRLSLQTTEETLREVFSRYGDI--RRLRLVRDIVTGFSKG-------------- 46

Query: 285 VHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKG 327
            +A++ ++ E+    A    +  VI G+ I +D      + L G
Sbjct: 47  -YAFVEYEHERDALRAYRDAHKLVIDGSEIFVDFER--ERTLPG 87

This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain. Length = 93

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

 Score = 37.7 bits (88), Expect = 7e-04
 Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 8/52 (15%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYV 387
            +FV NLP D  +  ++QLF   G      +V  V+VIR       KG  +V
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFG------AVTNVKVIRDLTTNKCKGYGFV 48

This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

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

 Score = 37.6 bits (88), Expect = 8e-04
 Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 9/57 (15%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           TVFV NL + V ++E+ +LF  CG       +  VR++++   +  KG AYV F+  
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCG------EITDVRLVKNYKGKS-KGYAYVEFENE 50

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

 Score = 37.7 bits (88), Expect = 8e-04
 Identities = 19/89 (21%), Positives = 35/89 (39%), Gaps = 19/89 (21%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           RTI VG +   + +  L + F   GE+  VR+        +                   
Sbjct: 1   RTIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARF------------------ 42

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIR 314
            A++ F   +S  +AL  +  ++GG+ +R
Sbjct: 43  -AFVEFADAESALSALNLSGTLLGGHPLR 70

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

>gnl|CDD|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 = 37.5 bits (88), Expect = 8e-04
 Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 4/55 (7%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
            V +  LPF   +E+I   F GL+      + + ++     R   G AYV F + 
Sbjct: 1   VVRLRGLPFSATEEDIRDFFSGLDIPP---DGIHIVYDDDGR-PTGEAYVEFASP 51

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 13/32 (40%), Positives = 20/32 (62%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRI 257
           RT+F+ NLP    ++ L + F +FGE+   RI
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARI 32

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

>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 5/55 (9%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           T FVGNLPF+    ++  +F  L     SV++VR++R       KG  YV F+  
Sbjct: 3   TAFVGNLPFNTVQGDLDAIFKDL-----SVKSVRLVRDKETDKFKGFCYVEFEDV 52

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

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 14/30 (46%), Positives = 22/30 (73%)

Query: 228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRI 257
           ++VGNL  KV ++ L +EF +FG + SV+I
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKI 33

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

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

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 8/56 (14%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
            +FVGNLP+D   E++   F   G         +VR++        KG A+V F T
Sbjct: 2   ILFVGNLPYDTTAEDLLAHFKNAGAPP------SVRLLTDKKTGKSKGCAFVEFDT 51

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

>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 23/88 (26%), Positives = 37/88 (42%), Gaps = 19/88 (21%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           RTI+VGNL        L++ F + GE+  VR+                     +E   + 
Sbjct: 5   RTIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAG-------------------DETQPTR 45

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHI 313
           +A++ F  + S   AL  N A+ GG  +
Sbjct: 46  YAFVEFAEQTSVINALKLNGAMFGGRPL 73

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

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

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 5/56 (8%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKG-IAYVLFKTR 392
           T+FV  LP DVK+ E+  LF      E+S    R++        K  + +V F + 
Sbjct: 2   TLFVSGLPSDVKERELAHLFRPFPGYEAS----RLVFKEKKGGEKQPVGFVDFSSA 53

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

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

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 7/52 (13%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFK 390
           ++V NLPF +  EE+Y LF           A+R IR  + +  +G A+V+++
Sbjct: 5   LYVRNLPFKISSEELYDLF-------GKYGAIRQIRIGNTKETRGTAFVVYE 49

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

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

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 25/92 (27%), Positives = 40/92 (43%), Gaps = 19/92 (20%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           RT+FVGNL  +V ++ L + F++ G          P+   KIP+      K         
Sbjct: 2   RTLFVGNLDARVTEEILYELFLQAG----------PLEGVKIPKDPNGKPKSF------- 44

Query: 286 HAYIVFKSEQSTEAALA-FNMAVIGGNHIRLD 316
            A++ FK E S   A+   N   + G  +R+ 
Sbjct: 45  -AFVTFKHEVSVPYAIQLLNGIRLFGRELRIK 75

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

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

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 4/54 (7%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
            ++VGNLP++V +E++  LF         V + RVI        +G  +V  +T
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQ----FGEVTSARVITDRETGRSRGFGFVEMET 50

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

 Score = 36.0 bits (84), Expect = 0.003
 Identities = 26/79 (32%), Positives = 35/79 (44%), Gaps = 19/79 (24%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADSV 285
           T+FV  L LKV+++ L + F K G++  VRI    I D    R KG              
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAGKVRDVRI----IRDRNSRRSKGV------------- 43

Query: 286 HAYIVFKSEQSTEAALAFN 304
            AY+ F  E+S   AL   
Sbjct: 44  -AYVEFYDEESVPLALGLT 61

This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|240952 cd12508, RRM2_ESRPs_Fusilli, RNA recognition motif 2 in epithelial splicing regulatory protein ESRP1, ESRP2, Drosophila RNA-binding protein Fusilli and similar proteins

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 1/48 (2%)

Query: 344 LPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
           LP+     +I   F GL  +    + +  +  P  R   G A+VLF+T
Sbjct: 9   LPYSATAADILAFFGGLCPVVGGPDGILFVTGPDGR-PTGDAFVLFET 55

This subfamily corresponds to the RRM2 of ESRPs and Fusilli. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of the fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. They are highly conserved paralogs and specifically bind to GU-rich binding site. ESRP1 and ESRP2 contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes Drosophila fusilli (fus) gene encoding RNA-binding protein Fusilli.Loss of fusilli activity causes lethality during embryogenesis in flies. Drosophila Fusilli can regulate endogenous FGFR2 splicing and functions as a splicing factor. It shows high sequence homology to ESRPs and contains three RRMs as well. It also has an N-terminal domain with unknown function and a C-terminal domain particularly rich in alanine, glutamine, and serine. . Length = 80

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

 Score = 36.0 bits (84), Expect = 0.004
 Identities = 21/92 (22%), Positives = 42/92 (45%), Gaps = 12/92 (13%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           R ++VGNLP  + ++ L+  F     + +  +   P           +L  QIN   +  
Sbjct: 2   RRLYVGNLPPGITEEELVDFF--NQAMLAAGLNQAP--------GNPVLSVQINP--EKN 49

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDR 317
            A++ F++ +   AALA +  +  G  +++ R
Sbjct: 50  FAFVEFRTVEEATAALALDGIIFKGQPLKIRR 81

The subfamily corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 82

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	393
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.94
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.92
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.92
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.92
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.9
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.89
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.88
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.85
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.85
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.85
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.84
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.84
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.84
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.83
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.83
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.83
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.82
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.81
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.8
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.79
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.77
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.73
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.72
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.71
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.7
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.69
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.68
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.68
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.66
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.66
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.6
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.58
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.54
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.53
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.48
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.48
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.48
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.46
PLN03120	260	nucleic acid binding protein; Provisional	99.45
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.43
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.43
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.42
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.37
PLN03121	243	nucleic acid binding protein; Provisional	99.33
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.31
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.3
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.29
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.28
PLN03213	759	repressor of silencing 3; Provisional	99.26
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.26
smart00362	72	RRM_2 RNA recognition motif.	99.24
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.24
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.23
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.23
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.19
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.16
KOG0122	270	consensus Translation initiation factor 3, subunit	99.15
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.15
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.14
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.11
smart00360	71	RRM RNA recognition motif.	99.1
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.08
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.06
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.06
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.0
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.99
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	98.95
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.92
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	98.89
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.89
KOG4210	285	consensus Nuclear localization sequence binding pr	98.88
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.87
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.85
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	98.84
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.84
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.8
smart00361	70	RRM_1 RNA recognition motif.	98.79
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.77
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.75
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.74
KOG0122	270	consensus Translation initiation factor 3, subunit	98.73
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.73
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.71
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.69
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.67
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.62
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.62
smart00362	72	RRM_2 RNA recognition motif.	98.62
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.56
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	98.53
smart00360	71	RRM RNA recognition motif.	98.51
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.51
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.5
KOG0151	877	consensus Predicted splicing regulator, contains R	98.48
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.47
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.43
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.41
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.41
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.38
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	98.38
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.36
KOG4207	256	consensus Predicted splicing factor, SR protein su	98.34
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.29
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	98.27
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.26
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.25
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.24
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.2
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.19
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.17
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.15
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.14
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.1
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.05
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	97.97
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	97.96
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.86
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.71
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	97.67
KOG0226	290	consensus RNA-binding proteins [General function p	97.64
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.62
smart00361	70	RRM_1 RNA recognition motif.	97.53
KOG0226	290	consensus RNA-binding proteins [General function p	97.53
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.49
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.48
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.47
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	97.42
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.38
KOG4210	285	consensus Nuclear localization sequence binding pr	97.21
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	97.17
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.17
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.08
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.07
PLN03213	759	repressor of silencing 3; Provisional	97.01
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	96.9
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.88
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	96.85
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	96.79
KOG3152	278	consensus TBP-binding protein, activator of basal	96.77
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.7
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	96.63
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	96.54
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.48
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.45
KOG1995	351	consensus Conserved Zn-finger protein [General fun	96.42
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	96.35
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.28
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	96.18
KOG1548	382	consensus Transcription elongation factor TAT-SF1	96.18
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.17
KOG0533	243	consensus RRM motif-containing protein [RNA proces	96.12
KOG4660	549	consensus Protein Mei2, essential for commitment t	95.82
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	95.82
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	95.29
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	95.21
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	95.17
KOG2314	698	consensus Translation initiation factor 3, subunit	95.02
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	94.95
KOG1996	378	consensus mRNA splicing factor [RNA processing and	94.69
KOG0151	877	consensus Predicted splicing regulator, contains R	94.61
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	94.07
PLN03120	260	nucleic acid binding protein; Provisional	93.99
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	93.93
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	93.87
PLN03121	243	nucleic acid binding protein; Provisional	93.69
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	93.58
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	93.17
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	93.16
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	93.15
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	91.73
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	90.94
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	90.53
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	89.34
KOG1855	484	consensus Predicted RNA-binding protein [General f	88.47
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	88.07
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	87.37
KOG2135	526	consensus Proteins containing the RNA recognition	86.77
KOG1995	351	consensus Conserved Zn-finger protein [General fun	86.67
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	86.13
KOG2068	327	consensus MOT2 transcription factor [Transcription	86.11
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	84.72
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	83.05
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	82.72
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	82.26

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.94  E-value=6.3e-26  Score=227.02  Aligned_cols=139  Identities=21%  Similarity=0.341  Sum_probs=123.8

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|||+|||+++|+++|+++|..||.|.+|+|+.+..                 ++.++|||||+|.+.++|..|| .
T Consensus       106 ~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~-----------------tg~srGyaFVeF~~~e~A~~Ai~~  168 (346)
T TIGR01659       106 SGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYK-----------------TGYSFGYAFVDFGSEADSQRAIKN  168 (346)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCC-----------------CCccCcEEEEEEccHHHHHHHHHH
Confidence            468999999999999999999999999999999977652                 2346699999999999999999 6


Q ss_pred             hcCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCc
Q 016231          303 FNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGK  382 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~k  382 (393)
                      ||+..|.++.|.|.++.+...         .....+|||+|||+.+|+++|+++|..|    |.|..|+|++|..+|.++
T Consensus       169 LnG~~l~gr~i~V~~a~p~~~---------~~~~~~lfV~nLp~~vtee~L~~~F~~f----G~V~~v~i~~d~~tg~~k  235 (346)
T TIGR01659       169 LNGITVRNKRLKVSYARPGGE---------SIKDTNLYVTNLPRTITDDQLDTIFGKY----GQIVQKNILRDKLTGTPR  235 (346)
T ss_pred             cCCCccCCceeeeeccccccc---------ccccceeEEeCCCCcccHHHHHHHHHhc----CCEEEEEEeecCCCCccc
Confidence            999999999999999865321         1234689999999999999999999999    999999999999999999


Q ss_pred             cEEEEEeeec
Q 016231          383 GIAYVLFKTR  392 (393)
Q Consensus       383 GfaFVeF~t~  392 (393)
                      |||||+|.++
T Consensus       236 G~aFV~F~~~  245 (346)
T TIGR01659       236 GVAFVRFNKR  245 (346)
T ss_pred             eEEEEEECCH
Confidence            9999999874

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

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

Probab=99.92  E-value=7.5e-25  Score=231.30  Aligned_cols=148  Identities=18%  Similarity=0.366  Sum_probs=124.4

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|||||||+.+++++|+.+|..||.|.+|+|+.++.                 +++++|||||+|.+.++|+.|| .
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~-----------------TgkskGfAFVeF~s~e~A~~Ai~~  168 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPA-----------------TGKHKGFAFVEYEVPEAAQLALEQ  168 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCC-----------------CCCcCCeEEEEeCcHHHHHHHHHh
Confidence            468999999999999999999999999999999987652                 2346799999999999999999 6


Q ss_pred             hcCceeCCeEEEEeecCCCcccCCCC--CCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCC
Q 016231          303 FNMAVIGGNHIRLDRACPPRKKLKGE--DAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRV  380 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~~~~~~~~--~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~  380 (393)
                      |||..|.|+.|.|.+...........  .........+|||+|||+++++++|+++|+.|    |.|.+|+|++|+.+|.
T Consensus       169 lnG~~i~GR~IkV~rp~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~F----G~I~svrl~~D~~tgk  244 (612)
T TIGR01645       169 MNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAF----GEIVKCQLARAPTGRG  244 (612)
T ss_pred             cCCeEEecceeeecccccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhc----CCeeEEEEEecCCCCC
Confidence            99999999999998754321111000  01112245799999999999999999999999    9999999999999999


Q ss_pred             CccEEEEEeeec
Q 016231          381 GKGIAYVLFKTR  392 (393)
Q Consensus       381 ~kGfaFVeF~t~  392 (393)
                      ++|||||+|.+.
T Consensus       245 sKGfGFVeFe~~  256 (612)
T TIGR01645       245 HKGYGFIEYNNL  256 (612)
T ss_pred             cCCeEEEEECCH
Confidence            999999999873

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.92  E-value=1.2e-24  Score=216.12  Aligned_cols=138  Identities=17%  Similarity=0.353  Sum_probs=123.2

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      ..+|||+|||+.+|+++|+++|+.||+|.+|+|++++.                 ++.++|||||+|.+.++|..|| .|
T Consensus         3 ~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~-----------------~g~s~g~afV~f~~~~~A~~Ai~~l   65 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKV-----------------TGQSLGYGFVNYVRPEDAEKAVNSL   65 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCC-----------------CCccceEEEEEECcHHHHHHHHhhc
Confidence            57899999999999999999999999999999988652                 2347799999999999999999 69


Q ss_pred             cCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCcc
Q 016231          304 NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKG  383 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kG  383 (393)
                      ||..|.|+.|.|.++.+...         .....+|||+|||..+++++|+.+|+.|    |.|..++|+.+..+|.++|
T Consensus        66 ~g~~l~g~~i~v~~a~~~~~---------~~~~~~l~v~~l~~~~~~~~l~~~f~~~----G~i~~~~~~~~~~~~~~~g  132 (352)
T TIGR01661        66 NGLRLQNKTIKVSYARPSSD---------SIKGANLYVSGLPKTMTQHELESIFSPF----GQIITSRILSDNVTGLSKG  132 (352)
T ss_pred             ccEEECCeeEEEEeeccccc---------ccccceEEECCccccCCHHHHHHHHhcc----CCEEEEEEEecCCCCCcCc
Confidence            99999999999999865421         1234689999999999999999999999    9999999999988899999


Q ss_pred             EEEEEeeec
Q 016231          384 IAYVLFKTR  392 (393)
Q Consensus       384 faFVeF~t~  392 (393)
                      ||||+|.+.
T Consensus       133 ~~fv~f~~~  141 (352)
T TIGR01661       133 VGFIRFDKR  141 (352)
T ss_pred             EEEEEECCH
Confidence            999999863

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

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

Probab=99.92  E-value=2.1e-24  Score=222.16  Aligned_cols=152  Identities=24%  Similarity=0.367  Sum_probs=127.1

Q ss_pred             cCCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHH
Q 016231          220 DEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (393)
Q Consensus       220 ~~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~  299 (393)
                      +.....++|||+|||+.+++++|.++|+.||.|..|+|+.+..  +               +.++|||||+|.+.++|..
T Consensus        84 ~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~--~---------------~~skg~afVeF~~~e~A~~  146 (457)
T TIGR01622        84 EAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRN--S---------------RRSKGVAYVEFYDVESVIK  146 (457)
T ss_pred             ccccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCC--C---------------CCcceEEEEEECCHHHHHH
Confidence            3345679999999999999999999999999999999977542  2               2366999999999999999


Q ss_pred             HHHhcCceeCCeEEEEeecCCCcccCCC---CCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecC
Q 016231          300 ALAFNMAVIGGNHIRLDRACPPRKKLKG---EDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP  376 (393)
Q Consensus       300 Al~lng~~~~Gr~I~V~~a~~~~~~~~~---~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~  376 (393)
                      ||.|+|..|.|+.|.|..+.........   ..........+|||+|||..+++++|+++|..|    |.|..|.|++++
T Consensus       147 Al~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~----G~i~~v~~~~d~  222 (457)
T TIGR01622       147 ALALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPF----GDIEDVQLHRDP  222 (457)
T ss_pred             HHHhCCCEECCeeeEEeecchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhc----CCeEEEEEEEcC
Confidence            9999999999999999887543221111   001112236899999999999999999999999    999999999999


Q ss_pred             CCCCCccEEEEEeeec
Q 016231          377 HMRVGKGIAYVLFKTR  392 (393)
Q Consensus       377 ~tg~~kGfaFVeF~t~  392 (393)
                      .+|.++|||||+|.+.
T Consensus       223 ~~g~~~g~afV~f~~~  238 (457)
T TIGR01622       223 ETGRSKGFGFIQFHDA  238 (457)
T ss_pred             CCCccceEEEEEECCH
Confidence            9999999999999863

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.90  E-value=1.5e-22  Score=201.21  Aligned_cols=147  Identities=24%  Similarity=0.349  Sum_probs=119.5

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      .++|||+|||+.+++++|..+|..||.|..++++.+..                 .+.++|||||+|.+.++|+.|| .|
T Consensus        89 ~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~-----------------~~~~~g~~fv~f~~~~~A~~ai~~l  151 (352)
T TIGR01661        89 GANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNV-----------------TGLSKGVGFIRFDKRDEADRAIKTL  151 (352)
T ss_pred             cceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCC-----------------CCCcCcEEEEEECCHHHHHHHHHHh
Confidence            56899999999999999999999999999999976542                 1236699999999999999999 79


Q ss_pred             cCceeCC--eEEEEeecCCCcccCC--------------CCC--------------------------------------
Q 016231          304 NMAVIGG--NHIRLDRACPPRKKLK--------------GED--------------------------------------  329 (393)
Q Consensus       304 ng~~~~G--r~I~V~~a~~~~~~~~--------------~~~--------------------------------------  329 (393)
                      ||..+.|  +.|.|.++..+.....              ...                                      
T Consensus       152 ~g~~~~g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  231 (352)
T TIGR01661       152 NGTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQ  231 (352)
T ss_pred             CCCccCCCceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhh
Confidence            9999877  6788888754321000              000                                      


Q ss_pred             -------------CC------------------CcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCC
Q 016231          330 -------------AP------------------LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHM  378 (393)
Q Consensus       330 -------------~~------------------~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~t  378 (393)
                                   .+                  ....+.+|||+|||+++++++|+++|+.|    |.|.+|+|++|+.+
T Consensus       232 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~f----G~v~~v~i~~d~~t  307 (352)
T TIGR01661       232 QHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPF----GAVQNVKIIRDLTT  307 (352)
T ss_pred             hcccccccccccCCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhC----CCeEEEEEeEcCCC
Confidence                         00                  00112369999999999999999999999    99999999999999


Q ss_pred             CCCccEEEEEeeec
Q 016231          379 RVGKGIAYVLFKTR  392 (393)
Q Consensus       379 g~~kGfaFVeF~t~  392 (393)
                      |.++|||||+|.+.
T Consensus       308 ~~skG~aFV~F~~~  321 (352)
T TIGR01661       308 NQCKGYGFVSMTNY  321 (352)
T ss_pred             CCccceEEEEECCH
Confidence            99999999999874

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

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

Probab=99.89  E-value=9.2e-23  Score=215.79  Aligned_cols=137  Identities=23%  Similarity=0.390  Sum_probs=119.5

Q ss_pred             EEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-HhcC
Q 016231          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNM  305 (393)
Q Consensus       227 tVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~lng  305 (393)
                      +|||||||+++|+++|+++|+.||.|.+|+|+++..  +               ++++|||||+|.+.++|+.|| .+|+
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~--t---------------~~s~G~afV~F~~~~~A~~Al~~ln~   64 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSV--T---------------RRSLGYGYVNFQNPADAERALETMNF   64 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCC--C---------------CCcceEEEEEECCHHHHHHHHHHhCC
Confidence            699999999999999999999999999999988652  1               236699999999999999999 7999


Q ss_pred             ceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEE
Q 016231          306 AVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIA  385 (393)
Q Consensus       306 ~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfa  385 (393)
                      ..|.|+.|+|.|+......       ......+|||+|||.++++++|+++|+.|    |.|.+|+|+++ .+|.++|||
T Consensus        65 ~~i~gk~i~i~~s~~~~~~-------~~~~~~~vfV~nLp~~~~~~~L~~~F~~~----G~i~~~~i~~~-~~g~skg~a  132 (562)
T TIGR01628        65 KRLGGKPIRIMWSQRDPSL-------RRSGVGNIFVKNLDKSVDNKALFDTFSKF----GNILSCKVATD-ENGKSRGYG  132 (562)
T ss_pred             CEECCeeEEeecccccccc-------cccCCCceEEcCCCccCCHHHHHHHHHhc----CCcceeEeeec-CCCCcccEE
Confidence            9999999999997532111       12234689999999999999999999999    99999999999 478899999


Q ss_pred             EEEeeec
Q 016231          386 YVLFKTR  392 (393)
Q Consensus       386 FVeF~t~  392 (393)
                      ||+|.+.
T Consensus       133 fV~F~~~  139 (562)
T TIGR01628       133 FVHFEKE  139 (562)
T ss_pred             EEEECCH
Confidence            9999864

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

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

Probab=99.88  E-value=3.3e-22  Score=208.34  Aligned_cols=145  Identities=20%  Similarity=0.427  Sum_probs=116.5

Q ss_pred             cCCCcccEEEEeCCCccCCHHHHHHHhccc------------CCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEE
Q 016231          220 DEGKLLRTIFVGNLPLKVKKKTLIKEFIKF------------GEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHA  287 (393)
Q Consensus       220 ~~~~~~rtVFVgNLp~~~tee~L~~~Fs~~------------G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~A  287 (393)
                      ......++|||||||+.+|+++|..||..|            +.|..+.+                       +.++|||
T Consensus       170 ~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~-----------------------~~~kg~a  226 (509)
T TIGR01642       170 QATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI-----------------------NKEKNFA  226 (509)
T ss_pred             cCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE-----------------------CCCCCEE
Confidence            445668999999999999999999999975            23333333                       1255899


Q ss_pred             EEeeCCHHHHHHHHHhcCceeCCeEEEEeecCCCcccC--------CC------------CCCCCcCCcceeeeCCCCCC
Q 016231          288 YIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKL--------KG------------EDAPLYDIKKTVFVGNLPFD  347 (393)
Q Consensus       288 FVeF~s~e~A~~Al~lng~~~~Gr~I~V~~a~~~~~~~--------~~------------~~~~~~~~~~tLfVgNLp~~  347 (393)
                      ||+|.+.++|..||.|||..|.|+.|.|.+........        ..            .........++|||+|||+.
T Consensus       227 fVeF~~~e~A~~Al~l~g~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~  306 (509)
T TIGR01642       227 FLEFRTVEEATFAMALDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLY  306 (509)
T ss_pred             EEEeCCHHHHhhhhcCCCeEeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCC
Confidence            99999999999999999999999999997653211000        00            00011234579999999999


Q ss_pred             CCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeee
Q 016231          348 VKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT  391 (393)
Q Consensus       348 ~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t  391 (393)
                      +++++|+++|+.|    |.|..|.|+.++.+|.++|||||+|.+
T Consensus       307 ~~~~~l~~~f~~~----G~i~~~~~~~~~~~g~~~g~afv~f~~  346 (509)
T TIGR01642       307 LGEDQIKELLESF----GDLKAFNLIKDIATGLSKGYAFCEYKD  346 (509)
T ss_pred             CCHHHHHHHHHhc----CCeeEEEEEecCCCCCcCeEEEEEECC
Confidence            9999999999999    999999999999999999999999976

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

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.85  E-value=6.2e-21  Score=180.23  Aligned_cols=141  Identities=23%  Similarity=0.437  Sum_probs=120.9

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      ..-||||.|...++-+.|++.|..||+|..+++++|..                 +++++||+||.|.+.++|+.|| .|
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~-----------------T~KsKGYgFVSf~~k~dAEnAI~~M  124 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMN-----------------TGKSKGYGFVSFPNKEDAENAIQQM  124 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeeccc-----------------CCcccceeEEeccchHHHHHHHHHh
Confidence            56799999999999999999999999999999988762                 3457799999999999999999 79


Q ss_pred             cCceeCCeEEEEeecCCCcccCCCC-----C--CCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecC
Q 016231          304 NMAVIGGNHIRLDRACPPRKKLKGE-----D--APLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP  376 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~~~~~~~-----~--~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~  376 (393)
                      ||+.|.+|.|+-.|+.++....-..     +  ........+|||||++.-+|+++|++.|..|    |.|..|||..+ 
T Consensus       125 nGqWlG~R~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~f----G~I~EVRvFk~-  199 (321)
T KOG0148|consen  125 NGQWLGRRTIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPF----GPIQEVRVFKD-  199 (321)
T ss_pred             CCeeeccceeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccC----CcceEEEEecc-
Confidence            9999999999999997643111110     0  1224456899999999999999999999999    99999999988 


Q ss_pred             CCCCCccEEEEEeeec
Q 016231          377 HMRVGKGIAYVLFKTR  392 (393)
Q Consensus       377 ~tg~~kGfaFVeF~t~  392 (393)
                           +|||||.|.+.
T Consensus       200 -----qGYaFVrF~tk  210 (321)
T KOG0148|consen  200 -----QGYAFVRFETK  210 (321)
T ss_pred             -----cceEEEEecch
Confidence                 68999999874

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.85  E-value=5.6e-21  Score=194.16  Aligned_cols=146  Identities=32%  Similarity=0.456  Sum_probs=121.5

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      ...|.|+||||.+.+.+|..+|+.||.|..|.|++.+  +                +.-+|||||.|....+|..|| .+
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~--d----------------gklcGFaFV~fk~~~dA~~Al~~~  178 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK--D----------------GKLCGFAFVQFKEKKDAEKALEFF  178 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC--C----------------CCccceEEEEEeeHHHHHHHHHhc
Confidence            4679999999999999999999999999999996533  2                234599999999999999999 69


Q ss_pred             cCceeCCeEEEEeecCCCcccCC---------------------------------------------------------
Q 016231          304 NMAVIGGNHIRLDRACPPRKKLK---------------------------------------------------------  326 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~~~~~---------------------------------------------------------  326 (393)
                      |+..|.||+|.|+||.+......                                                         
T Consensus       179 N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~  258 (678)
T KOG0127|consen  179 NGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEES  258 (678)
T ss_pred             cCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccc
Confidence            99999999999999843211000                                                         


Q ss_pred             ------CCCC--C----------------CcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCc
Q 016231          327 ------GEDA--P----------------LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGK  382 (393)
Q Consensus       327 ------~~~~--~----------------~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~k  382 (393)
                            .++.  +                ......+|||+|||+++|+++|.++|+.|    |.|.++.|+.++.||.++
T Consensus       259 Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskF----G~v~ya~iV~~k~T~~sk  334 (678)
T KOG0127|consen  259 EEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKF----GEVKYAIIVKDKDTGHSK  334 (678)
T ss_pred             cccccccccccccccCcccchhccccccccccccceEEEecCCccccHHHHHHHHHhh----ccceeEEEEeccCCCCcc
Confidence                  0000  0                01113799999999999999999999999    999999999999999999


Q ss_pred             cEEEEEeeec
Q 016231          383 GIAYVLFKTR  392 (393)
Q Consensus       383 GfaFVeF~t~  392 (393)
                      |.|||.|.+.
T Consensus       335 GtAFv~Fkt~  344 (678)
T KOG0127|consen  335 GTAFVKFKTQ  344 (678)
T ss_pred             cceEEEeccH
Confidence            9999999875

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

Probab=99.85  E-value=1e-20  Score=200.21  Aligned_cols=146  Identities=23%  Similarity=0.389  Sum_probs=122.4

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|||+|||+++|+++|+.+|+.||.|.+|.++++.   .               +.++|||||.|.+.++|..|+ .
T Consensus       177 ~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~---~---------------g~~~G~afV~F~~~e~A~~Av~~  238 (562)
T TIGR01628       177 KFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG---S---------------GRSRGFAFVNFEKHEDAAKAVEE  238 (562)
T ss_pred             CCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECC---C---------------CCcccEEEEEECCHHHHHHHHHH
Confidence            35789999999999999999999999999999997653   1               236699999999999999999 6


Q ss_pred             hcCceeC----CeEEEEeecCCCcccCC---------CCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEE
Q 016231          303 FNMAVIG----GNHIRLDRACPPRKKLK---------GEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEA  369 (393)
Q Consensus       303 lng~~~~----Gr~I~V~~a~~~~~~~~---------~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~  369 (393)
                      +|+..|.    |+.|.|.++........         ...........+|||+||+..+++++|+++|+.|    |.|.+
T Consensus       239 l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~----G~i~~  314 (562)
T TIGR01628       239 MNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSEC----GEITS  314 (562)
T ss_pred             hCCcEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhc----CCeEE
Confidence            9999999    99999998865432210         0001112345689999999999999999999999    99999


Q ss_pred             EEEeecCCCCCCccEEEEEeeec
Q 016231          370 VRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       370 VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      |+|+.| .+|.++|||||+|.+.
T Consensus       315 ~~i~~d-~~g~~~g~gfV~f~~~  336 (562)
T TIGR01628       315 AKVMLD-EKGVSRGFGFVCFSNP  336 (562)
T ss_pred             EEEEEC-CCCCcCCeEEEEeCCH
Confidence            999999 7899999999999874

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

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.84  E-value=1.6e-20  Score=187.33  Aligned_cols=134  Identities=25%  Similarity=0.408  Sum_probs=117.4

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...+-||||.||.++.|++|.-+|...|+|..+|||++++  +               |.+||||||.|.+.+.|+.|+ 
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~--s---------------G~nRGYAFVtf~~Ke~Aq~Aik  143 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPF--S---------------GDNRGYAFVTFCTKEEAQEAIK  143 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeeccc--C---------------CCCcceEEEEeecHHHHHHHHH
Confidence            3468899999999999999999999999999999999874  2               346799999999999999999 


Q ss_pred             HhcCcee-CCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecC-CCC
Q 016231          302 AFNMAVI-GGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP-HMR  379 (393)
Q Consensus       302 ~lng~~~-~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~-~tg  379 (393)
                      .||+.+| .|+.|.|+.+.               ...+|||||||.++++++|.+.|...+.  | |+.|.|+..+ +..
T Consensus       144 ~lnn~Eir~GK~igvc~Sv---------------an~RLFiG~IPK~k~keeIlee~~kVte--G-VvdVivy~~p~dk~  205 (506)
T KOG0117|consen  144 ELNNYEIRPGKLLGVCVSV---------------ANCRLFIGNIPKTKKKEEILEEMKKVTE--G-VVDVIVYPSPDDKT  205 (506)
T ss_pred             HhhCccccCCCEeEEEEee---------------ecceeEeccCCccccHHHHHHHHHhhCC--C-eeEEEEecCccccc
Confidence            6999877 69999999874               3469999999999999999999999853  4 6778877776 467


Q ss_pred             CCccEEEEEeee
Q 016231          380 VGKGIAYVLFKT  391 (393)
Q Consensus       380 ~~kGfaFVeF~t  391 (393)
                      ++||||||+|.+
T Consensus       206 KNRGFaFveYe~  217 (506)
T KOG0117|consen  206 KNRGFAFVEYES  217 (506)
T ss_pred             cccceEEEEeec
Confidence            899999999976

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

Probab=99.84  E-value=1.4e-20  Score=198.39  Aligned_cols=134  Identities=22%  Similarity=0.351  Sum_probs=110.3

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|||+|||+++++++|+.+|+.||.|.+|+|+++.   +               +.++|||||+|.+.++|+.|| .
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~---s---------------G~sRGfaFV~F~~~e~A~~Ai~~  118 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDF---S---------------GQNRGYAFVTFCGKEEAKEAVKL  118 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECC---C---------------CCccceEEEEeCCHHHHHHHHHH
Confidence            35899999999999999999999999999999997762   2               346799999999999999999 6


Q ss_pred             hcCceeC-CeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCC
Q 016231          303 FNMAVIG-GNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVG  381 (393)
Q Consensus       303 lng~~~~-Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~  381 (393)
                      ||+..|. |+.|.|.++.               ..++|||+|||.++++++|.++|..+..  |.+..|.+......+.+
T Consensus       119 lng~~i~~Gr~l~V~~S~---------------~~~rLFVgNLP~~~TeeeL~eeFskv~e--gvv~vIv~~~~~~kgKn  181 (578)
T TIGR01648       119 LNNYEIRPGRLLGVCISV---------------DNCRLFVGGIPKNKKREEILEEFSKVTE--GVVDVIVYHSAADKKKN  181 (578)
T ss_pred             cCCCeecCCccccccccc---------------cCceeEeecCCcchhhHHHHHHhhcccC--CceEEEEeccccccCcc
Confidence            9998885 7887776653               2468999999999999999999999832  33333334444456788


Q ss_pred             ccEEEEEeeec
Q 016231          382 KGIAYVLFKTR  392 (393)
Q Consensus       382 kGfaFVeF~t~  392 (393)
                      +|||||+|.+.
T Consensus       182 RGFAFVeF~s~  192 (578)
T TIGR01648       182 RGFAFVEYESH  192 (578)
T ss_pred             CceEEEEcCCH
Confidence            99999999873

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.

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

Probab=99.84  E-value=5.1e-20  Score=192.03  Aligned_cols=138  Identities=22%  Similarity=0.265  Sum_probs=113.4

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH-
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~-  302 (393)
                      ++++|||+|||+.+++++|+++|+.||.|.+|.|+.                       ++|||||+|.+.++|..|+. 
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~-----------------------~k~~afVef~~~e~A~~Ai~~   57 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLP-----------------------GKRQALVEFEDEESAKACVNF   57 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEEC-----------------------CCCEEEEEeCchHHHHHHHHH
Confidence            378999999999999999999999999999998853                       33799999999999999994 


Q ss_pred             --hcCceeCCeEEEEeecCCCcccCCCC---CCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCC
Q 016231          303 --FNMAVIGGNHIRLDRACPPRKKLKGE---DAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPH  377 (393)
Q Consensus       303 --lng~~~~Gr~I~V~~a~~~~~~~~~~---~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~  377 (393)
                        +++..|.|+.|.|.++..........   .........+|||+||++.+|+++|+++|+.|    |.|..|.|+++. 
T Consensus        58 ~~~~~~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~----G~V~~v~i~~~~-  132 (481)
T TIGR01649        58 ATSVPIYIRGQPAFFNYSTSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPY----GKVLRIVTFTKN-  132 (481)
T ss_pred             hhcCCceEcCeEEEEEecCCcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhcc----CCEEEEEEEecC-
Confidence              57899999999999986543211110   01111234589999999999999999999999    999999998774 


Q ss_pred             CCCCccEEEEEeeec
Q 016231          378 MRVGKGIAYVLFKTR  392 (393)
Q Consensus       378 tg~~kGfaFVeF~t~  392 (393)
                         .+|+|||+|.+.
T Consensus       133 ---~~~~afVef~~~  144 (481)
T TIGR01649       133 ---NVFQALVEFESV  144 (481)
T ss_pred             ---CceEEEEEECCH
Confidence               247999999873

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

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.83  E-value=9.5e-21  Score=188.20  Aligned_cols=145  Identities=21%  Similarity=0.420  Sum_probs=121.4

Q ss_pred             CCcCCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHH
Q 016231          218 FDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQST  297 (393)
Q Consensus       218 ~~~~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A  297 (393)
                      .+..+...-.+|||.||..++|.+|+.+|++||.|.+|.|++|+.+                 +.++|||||.|.+.++|
T Consensus        27 ~d~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t-----------------~~s~gcCFv~~~trk~a   89 (510)
T KOG0144|consen   27 TDNPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKST-----------------GQSKGCCFVKYYTRKEA   89 (510)
T ss_pred             CCCCCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeeccccc-----------------CcccceEEEEeccHHHH
Confidence            3444455778999999999999999999999999999999887642                 34679999999999999


Q ss_pred             HHHH-Hh-cCceeCC--eEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEe
Q 016231          298 EAAL-AF-NMAVIGG--NHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVI  373 (393)
Q Consensus       298 ~~Al-~l-ng~~~~G--r~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~  373 (393)
                      ..|+ +| |...|.|  .+|.|.++......        ....++||||-|+..+|+.+|+++|..|    |.|+.|+|+
T Consensus        90 ~~a~~Alhn~ktlpG~~~pvqvk~Ad~E~er--------~~~e~KLFvg~lsK~~te~evr~iFs~f----G~Ied~~il  157 (510)
T KOG0144|consen   90 DEAINALHNQKTLPGMHHPVQVKYADGERER--------IVEERKLFVGMLSKQCTENEVREIFSRF----GHIEDCYIL  157 (510)
T ss_pred             HHHHHHhhcccccCCCCcceeecccchhhhc--------cccchhhhhhhccccccHHHHHHHHHhh----Cccchhhhe
Confidence            9999 55 4556766  56777777543321        1235789999999999999999999999    999999999


Q ss_pred             ecCCCCCCccEEEEEeeec
Q 016231          374 RHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       374 ~d~~tg~~kGfaFVeF~t~  392 (393)
                      +|+ .|.+||+|||+|.++
T Consensus       158 rd~-~~~sRGcaFV~fstk  175 (510)
T KOG0144|consen  158 RDP-DGLSRGCAFVKFSTK  175 (510)
T ss_pred             ecc-cccccceeEEEEehH
Confidence            996 599999999999875

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.83  E-value=1.9e-20  Score=168.15  Aligned_cols=140  Identities=24%  Similarity=0.459  Sum_probs=121.4

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ....|||||||+..++++.|+++|-++|+|..+.|+++..+.                 .+.|||||+|.++++|+.|+ 
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~-----------------~~qGygF~Ef~~eedadYAik   69 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQ-----------------KHQGYGFAEFRTEEDADYAIK   69 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcc-----------------cccceeEEEEechhhhHHHHH
Confidence            346899999999999999999999999999999998876432                 35699999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEE-EEEeecCCCCC
Q 016231          302 AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEA-VRVIRHPHMRV  380 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~-VrI~~d~~tg~  380 (393)
                      -||+..+.|++|+|..+....        .....+..|||+||.+.+++.-|++.|+.|    |.|.. -.|++++.||.
T Consensus        70 iln~VkLYgrpIrv~kas~~~--------~nl~vganlfvgNLd~~vDe~~L~dtFsaf----G~l~~~P~i~rd~~tg~  137 (203)
T KOG0131|consen   70 ILNMVKLYGRPIRVNKASAHQ--------KNLDVGANLFVGNLDPEVDEKLLYDTFSAF----GVLISPPKIMRDPDTGN  137 (203)
T ss_pred             HHHHHHhcCceeEEEeccccc--------ccccccccccccccCcchhHHHHHHHHHhc----cccccCCcccccccCCC
Confidence            599999999999999987221        112334789999999999999999999999    77665 47999999999


Q ss_pred             CccEEEEEeee
Q 016231          381 GKGIAYVLFKT  391 (393)
Q Consensus       381 ~kGfaFVeF~t  391 (393)
                      ++|||||-|.+
T Consensus       138 ~~~~g~i~~~s  148 (203)
T KOG0131|consen  138 PKGFGFINYAS  148 (203)
T ss_pred             CCCCeEEechh
Confidence            99999999976

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.83  E-value=3.9e-20  Score=188.11  Aligned_cols=145  Identities=21%  Similarity=0.339  Sum_probs=122.5

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hhc
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~ln  304 (393)
                      .||||++||+.++.++|.++|+.+|+|..+.+++++    +.             ..+|||+||.|+..++++.|+ ..+
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~----gs-------------~~~RGfgfVtFam~ED~qrA~~e~~   68 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNK----GS-------------SEKRGFGFVTFAMEEDVQRALAETE   68 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCC----Cc-------------ccccCccceeeehHhHHHHHHHHhh
Confidence            799999999999999999999999999999996654    22             237799999999999999999 689


Q ss_pred             CceeCCeEEEEeecCCCcccCCC-------------CC----CCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCe
Q 016231          305 MAVIGGNHIRLDRACPPRKKLKG-------------ED----APLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSV  367 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~~~~~~~~-------------~~----~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I  367 (393)
                      +..|.||.|+|..+.+.......             +.    .....+..+|+|+||||.+...+|..+|+.|    |.|
T Consensus        69 ~~kf~Gr~l~v~~A~~R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~----G~V  144 (678)
T KOG0127|consen   69 QSKFEGRILNVDPAKKRARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNF----GKV  144 (678)
T ss_pred             cCcccceecccccccccccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhc----ceE
Confidence            99999999999999765333211             00    1112346799999999999999999999999    999


Q ss_pred             EEEEEeecCCCCCCccEEEEEeeec
Q 016231          368 EAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       368 ~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..|.||+.++.+.| |||||+|...
T Consensus       145 ~Ei~IP~k~dgklc-GFaFV~fk~~  168 (678)
T KOG0127|consen  145 VEIVIPRKKDGKLC-GFAFVQFKEK  168 (678)
T ss_pred             EEEEcccCCCCCcc-ceEEEEEeeH
Confidence            99999999887777 9999999763

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

Probab=99.82  E-value=2.5e-19  Score=186.88  Aligned_cols=142  Identities=18%  Similarity=0.262  Sum_probs=114.9

Q ss_pred             CcccEEEEeCCCc-cCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          223 KLLRTIFVGNLPL-KVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~-~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ...++|||+|||+ .+|+++|+.+|+.||.|.+|+|+.+                      .+|||||+|.+.++|..||
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~----------------------~~g~afV~f~~~~~A~~Ai  330 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKN----------------------KKETALIEMADPYQAQLAL  330 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeC----------------------CCCEEEEEECCHHHHHHHH
Confidence            4578999999998 6999999999999999999999653                      1389999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCCcccCC-------C----CC-----------------CCCcCCcceeeeCCCCCCCCHHH
Q 016231          302 -AFNMAVIGGNHIRLDRACPPRKKLK-------G----ED-----------------APLYDIKKTVFVGNLPFDVKDEE  352 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~~~~~~-------~----~~-----------------~~~~~~~~tLfVgNLp~~~teed  352 (393)
                       .||+..|.|+.|.|.++........       .    .+                 .....++.+|||+|||+++++++
T Consensus       331 ~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~  410 (481)
T TIGR01649       331 THLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEED  410 (481)
T ss_pred             HHhCCCEECCceEEEEEcccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHH
Confidence             6999999999999998754211000       0    00                 00124567999999999999999


Q ss_pred             HHHHhhcCCCCCCC--eEEEEEeecCCCCCCccEEEEEeeec
Q 016231          353 IYQLFCGLNDLESS--VEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       353 L~e~F~~~~~~~G~--I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      |+++|..|    |.  |..|++.... + ..+|||||+|.+.
T Consensus       411 L~~lF~~~----G~~~i~~ik~~~~~-~-~~~~~gfVeF~~~  446 (481)
T TIGR01649       411 LKELFAEN----GVHKVKKFKFFPKD-N-ERSKMGLLEWESV  446 (481)
T ss_pred             HHHHHHhc----CCccceEEEEecCC-C-CcceeEEEEcCCH
Confidence            99999999    77  8888886543 3 3689999999873

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).

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.81  E-value=3.8e-20  Score=180.67  Aligned_cols=146  Identities=18%  Similarity=0.387  Sum_probs=123.7

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      -|.||||.|.|.+.|+.|+..|..||+|.+|.+-+++.                 +++|+|||||+|.-++.|+.|+ .|
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~-----------------T~kHKgFAFVEYEvPEaAqLAlEqM  175 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPA-----------------TGKHKGFAFVEYEVPEAAQLALEQM  175 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccc-----------------cccccceEEEEEeCcHHHHHHHHHh
Confidence            47899999999999999999999999999999988874                 3457899999999999999999 69


Q ss_pred             cCceeCCeEEEEeecCCCcccCCCCC--CCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCC
Q 016231          304 NMAVIGGNHIRLDRACPPRKKLKGED--APLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVG  381 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~~~~~~~~--~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~  381 (393)
                      ||.+++||.|.|.+.+.-...+..-+  ......-.+|||..++++++++||+.+|+.|    |.|..|.|.+++.++.+
T Consensus       176 Ng~mlGGRNiKVgrPsNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAF----G~I~~C~LAr~pt~~~H  251 (544)
T KOG0124|consen  176 NGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAF----GEIVKCQLARAPTGRGH  251 (544)
T ss_pred             ccccccCccccccCCCCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhh----cceeeEEeeccCCCCCc
Confidence            99999999999987653211111100  0001124799999999999999999999999    99999999999999999


Q ss_pred             ccEEEEEeee
Q 016231          382 KGIAYVLFKT  391 (393)
Q Consensus       382 kGfaFVeF~t  391 (393)
                      +|||||+|.+
T Consensus       252 kGyGfiEy~n  261 (544)
T KOG0124|consen  252 KGYGFIEYNN  261 (544)
T ss_pred             cceeeEEecc
Confidence            9999999975

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

Probab=99.80  E-value=7.8e-19  Score=183.06  Aligned_cols=148  Identities=19%  Similarity=0.255  Sum_probs=116.2

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|||+|||+.+|+++|.++|..||.|..+.|+.++.                 ++.++|||||+|.+.++|..|| .
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~-----------------~g~~~g~afv~f~~~~~a~~A~~~  356 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIA-----------------TGLSKGYAFCEYKDPSVTDVAIAA  356 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC-----------------CCCcCeEEEEEECCHHHHHHHHHH
Confidence            458999999999999999999999999999999976541                 2346799999999999999999 7


Q ss_pred             hcCceeCCeEEEEeecCCCcccCCCCC-------------------CCCcCCcceeeeCCCCCCC----------CHHHH
Q 016231          303 FNMAVIGGNHIRLDRACPPRKKLKGED-------------------APLYDIKKTVFVGNLPFDV----------KDEEI  353 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~~~~~~~~~-------------------~~~~~~~~tLfVgNLp~~~----------teedL  353 (393)
                      |||..|.|+.|.|.++...........                   .....++.+|+|.||....          ..++|
T Consensus       357 l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl  436 (509)
T TIGR01642       357 LNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDV  436 (509)
T ss_pred             cCCCEECCeEEEEEECccCCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHH
Confidence            999999999999999864321110000                   0012356789999996431          23679


Q ss_pred             HHHhhcCCCCCCCeEEEEEeecC---CCCCCccEEEEEeeec
Q 016231          354 YQLFCGLNDLESSVEAVRVIRHP---HMRVGKGIAYVLFKTR  392 (393)
Q Consensus       354 ~e~F~~~~~~~G~I~~VrI~~d~---~tg~~kGfaFVeF~t~  392 (393)
                      +++|+.|    |.|..|.|+++.   .++.+.|||||+|.+.
T Consensus       437 ~~~f~~~----G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~  474 (509)
T TIGR01642       437 KTEFSKY----GPLINIVIPRPNGDRNSTPGVGKVFLEYADV  474 (509)
T ss_pred             HHHHHhc----CCeeEEEeeccCcCCCcCCCcceEEEEECCH
Confidence            9999999    999999999763   3456789999999874

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

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.79  E-value=3.1e-19  Score=167.95  Aligned_cols=139  Identities=19%  Similarity=0.361  Sum_probs=125.3

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      ...|.|.-||.++|+++|+.+|...|+|++|+|++++.                 +|++-||+||.|.++.+|+.|+ .|
T Consensus        41 kTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKi-----------------tGqSLGYGFVNYv~p~DAe~Aintl  103 (360)
T KOG0145|consen   41 KTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKI-----------------TGQSLGYGFVNYVRPKDAEKAINTL  103 (360)
T ss_pred             cceeeeeecccccCHHHHHHHhhcccceeeeeeeeccc-----------------cccccccceeeecChHHHHHHHhhh
Confidence            45688999999999999999999999999999999874                 3457799999999999999999 79


Q ss_pred             cCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCcc
Q 016231          304 NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKG  383 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kG  383 (393)
                      ||-.+..+.|.|.++.|...         ......|||.+||..+|..+|.++|++|    |.|..-||+.|.-+|.+||
T Consensus       104 NGLrLQ~KTIKVSyARPSs~---------~Ik~aNLYvSGlPktMtqkelE~iFs~f----GrIItSRiL~dqvtg~srG  170 (360)
T KOG0145|consen  104 NGLRLQNKTIKVSYARPSSD---------SIKDANLYVSGLPKTMTQKELEQIFSPF----GRIITSRILVDQVTGLSRG  170 (360)
T ss_pred             cceeeccceEEEEeccCChh---------hhcccceEEecCCccchHHHHHHHHHHh----hhhhhhhhhhhcccceecc
Confidence            99999999999999976533         2234589999999999999999999999    9999999999999999999


Q ss_pred             EEEEEeeecC
Q 016231          384 IAYVLFKTRV  393 (393)
Q Consensus       384 faFVeF~t~~  393 (393)
                      .|||.|+.++
T Consensus       171 VgFiRFDKr~  180 (360)
T KOG0145|consen  171 VGFIRFDKRI  180 (360)
T ss_pred             eeEEEecchh
Confidence            9999998653

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.77  E-value=1e-18  Score=182.39  Aligned_cols=147  Identities=23%  Similarity=0.353  Sum_probs=121.3

Q ss_pred             EEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-HhcCc
Q 016231          228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMA  306 (393)
Q Consensus       228 VFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~lng~  306 (393)
                      |||.||+|++|.++|..+|..+|.|.+|.|...+...              +...|+|||||+|.+.++|+.|+ .|+|+
T Consensus       518 lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~--------------~k~lSmGfgFVEF~~~e~A~~a~k~lqgt  583 (725)
T KOG0110|consen  518 LFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPA--------------NKYLSMGFGFVEFAKPESAQAALKALQGT  583 (725)
T ss_pred             hhhhcCCcccchhHHHHHHHhcCeEEEEEEecccccc--------------ccccccceeEEEecCHHHHHHHHHHhcCc
Confidence            9999999999999999999999999999885533111              12348899999999999999999 69999


Q ss_pred             eeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEE
Q 016231          307 VIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAY  386 (393)
Q Consensus       307 ~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaF  386 (393)
                      .|.|+.|.|.++.......-+...+.....+.|+|+|||+.++..+|+.+|..|    |.|.+|||+.....+.++||||
T Consensus       584 vldGH~l~lk~S~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aF----GqlksvRlPKK~~k~a~rGF~F  659 (725)
T KOG0110|consen  584 VLDGHKLELKISENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAF----GQLKSVRLPKKIGKGAHRGFGF  659 (725)
T ss_pred             eecCceEEEEeccCccccccccccccccccceeeeeccchHHHHHHHHHHHhcc----cceeeeccchhhcchhhcccee
Confidence            999999999998722111111122223346799999999999999999999999    9999999998866778899999


Q ss_pred             EEeeec
Q 016231          387 VLFKTR  392 (393)
Q Consensus       387 VeF~t~  392 (393)
                      |+|-++
T Consensus       660 v~f~t~  665 (725)
T KOG0110|consen  660 VDFLTP  665 (725)
T ss_pred             eeccCc
Confidence            999764

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.73  E-value=1.4e-17  Score=163.69  Aligned_cols=145  Identities=21%  Similarity=0.370  Sum_probs=127.0

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHh
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~l  303 (393)
                      ..++||||+|+|.++++.|+.+|.+||.|..|.+++++.+  +               .++||+||+|.+...+.++|..
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t--~---------------rsrgFgfv~f~~~~~v~~vl~~   67 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPST--G---------------RSRGFGFVTFATPEGVDAVLNA   67 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCC--C---------------CcccccceecCCCcchheeecc
Confidence            4789999999999999999999999999999999998743  2               3669999999999999999977


Q ss_pred             cCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCcc
Q 016231          304 NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKG  383 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kG  383 (393)
                      ..+.|.|+.|.+..+.+.........   ......|||++||.++++.+|++.|.+|    |.|..+-++.|..+..++|
T Consensus        68 ~~h~~dgr~ve~k~av~r~~~~~~~~---~~~tkkiFvGG~~~~~~e~~~r~yfe~~----g~v~~~~~~~d~~~~~~rg  140 (311)
T KOG4205|consen   68 RTHKLDGRSVEPKRAVSREDQTKVGR---HLRTKKIFVGGLPPDTTEEDFKDYFEQF----GKVADVVIMYDKTTSRPRG  140 (311)
T ss_pred             cccccCCccccceeccCccccccccc---ccceeEEEecCcCCCCchHHHhhhhhcc----ceeEeeEEeeccccccccc
Confidence            77889999999999987654332221   2256799999999999999999999999    8999999999999999999


Q ss_pred             EEEEEeeec
Q 016231          384 IAYVLFKTR  392 (393)
Q Consensus       384 faFVeF~t~  392 (393)
                      ||||+|.++
T Consensus       141 Fgfv~~~~e  149 (311)
T KOG4205|consen  141 FGFVTFDSE  149 (311)
T ss_pred             ceeeEeccc
Confidence            999999875

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.72  E-value=3.1e-17  Score=165.65  Aligned_cols=123  Identities=24%  Similarity=0.430  Sum_probs=110.9

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hhc
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~ln  304 (393)
                      ..||||   +++|+..|.++|+.+|+|.+|+++++. +                   +-|||||.|.++.+|..|| ++|
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t-------------------slgy~yvnf~~~~da~~A~~~~n   58 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T-------------------SLGYAYVNFQQPADAERALDTMN   58 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C-------------------ccceEEEecCCHHHHHHHHHHcC
Confidence            369999   999999999999999999999998864 2                   3489999999999999999 799


Q ss_pred             CceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccE
Q 016231          305 MAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGI  384 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGf  384 (393)
                      ...+.|++|+|.|+..-.              ..|||.||+++++..+|.++|+.|    |.|.+|++.++. .| ++||
T Consensus        59 ~~~~~~~~~rim~s~rd~--------------~~~~i~nl~~~~~~~~~~d~f~~~----g~ilS~kv~~~~-~g-~kg~  118 (369)
T KOG0123|consen   59 FDVLKGKPIRIMWSQRDP--------------SLVFIKNLDESIDNKSLYDTFSEF----GNILSCKVATDE-NG-SKGY  118 (369)
T ss_pred             CcccCCcEEEeehhccCC--------------ceeeecCCCcccCcHHHHHHHHhh----cCeeEEEEEEcC-CC-ceee
Confidence            999999999999985321              229999999999999999999999    999999999995 45 9999


Q ss_pred             EEEEeeec
Q 016231          385 AYVLFKTR  392 (393)
Q Consensus       385 aFVeF~t~  392 (393)
                       ||+|.++
T Consensus       119 -FV~f~~e  125 (369)
T KOG0123|consen  119 -FVQFESE  125 (369)
T ss_pred             -EEEeCCH
Confidence             9999875

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

Probab=99.71  E-value=9.7e-17  Score=169.54  Aligned_cols=138  Identities=25%  Similarity=0.366  Sum_probs=106.4

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCC-eeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGE-IDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~-I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      .++|||+|||+.+++++|.++|+.++. +..+.+...+ .+               .++++|||||+|.+.++|..|+ .
T Consensus       138 ~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~-~~---------------kgKnRGFAFVeF~s~edAa~Airk  201 (578)
T TIGR01648       138 NCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSA-AD---------------KKKNRGFAFVEYESHRAAAMARRK  201 (578)
T ss_pred             CceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccc-cc---------------cCccCceEEEEcCCHHHHHHHHHH
Confidence            588999999999999999999999864 4444332111 11               1247799999999999999999 5


Q ss_pred             hcC--ceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCC
Q 016231          303 FNM--AVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRV  380 (393)
Q Consensus       303 lng--~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~  380 (393)
                      |+.  ..+.|+.|.|.|+.+.....    .......++|||+|||+++++++|+++|+.|..  |.|..|.++       
T Consensus       202 L~~gki~l~Gr~I~VdwA~p~~~~d----~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~--G~I~rV~~~-------  268 (578)
T TIGR01648       202 LMPGRIQLWGHVIAVDWAEPEEEVD----EDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKP--GKVERVKKI-------  268 (578)
T ss_pred             hhccceEecCceEEEEeeccccccc----ccccccccEEEEeCCCCCCCHHHHHHHHHhcCC--CceEEEEee-------
Confidence            543  46789999999987543211    112334579999999999999999999999832  789999875       


Q ss_pred             CccEEEEEeeec
Q 016231          381 GKGIAYVLFKTR  392 (393)
Q Consensus       381 ~kGfaFVeF~t~  392 (393)
                       +|||||+|.++
T Consensus       269 -rgfAFVeF~s~  279 (578)
T TIGR01648       269 -RDYAFVHFEDR  279 (578)
T ss_pred             -cCeEEEEeCCH
Confidence             45999999874

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

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

Probab=99.70  E-value=4e-16  Score=160.78  Aligned_cols=143  Identities=19%  Similarity=0.309  Sum_probs=111.3

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      .++|||+|||+.+|+++|+.+|+.||.|..|.|+.++.                 ++.++|||||+|.+.++|..|| .|
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~-----------------~g~~~g~afV~f~~~e~A~~A~~~l  248 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPE-----------------TGRSKGFGFIQFHDAEEAKEALEVM  248 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCC-----------------CCccceEEEEEECCHHHHHHHHHhc
Confidence            68999999999999999999999999999999977542                 2246699999999999999999 69


Q ss_pred             cCceeCCeEEEEeecCCCcccC--------------------------------CCC-----------------------
Q 016231          304 NMAVIGGNHIRLDRACPPRKKL--------------------------------KGE-----------------------  328 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~~~~--------------------------------~~~-----------------------  328 (393)
                      ||..|.|+.|.|.++.......                                ...                       
T Consensus       249 ~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  328 (457)
T TIGR01622       249 NGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRD  328 (457)
T ss_pred             CCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhcccccc
Confidence            9999999999999953210000                                000                       


Q ss_pred             -----CCC---------------------CcCCcceeeeCCCCCCCC----------HHHHHHHhhcCCCCCCCeEEEEE
Q 016231          329 -----DAP---------------------LYDIKKTVFVGNLPFDVK----------DEEIYQLFCGLNDLESSVEAVRV  372 (393)
Q Consensus       329 -----~~~---------------------~~~~~~tLfVgNLp~~~t----------eedL~e~F~~~~~~~G~I~~VrI  372 (393)
                           ..+                     ...+..+|+|.||....+          .+||++.|..|    |.|..|.|
T Consensus       329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~----G~v~~v~v  404 (457)
T TIGR01622       329 GIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKY----GGVVHIYV  404 (457)
T ss_pred             ccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhc----CCeeEEEE
Confidence                 000                     113457899999955544          36899999999    99999999


Q ss_pred             eecCCCCCCccEEEEEeeec
Q 016231          373 IRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       373 ~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...    ...|++||.|.+.
T Consensus       405 ~~~----~~~G~~fV~F~~~  420 (457)
T TIGR01622       405 DTK----NSAGKIYLKFSSV  420 (457)
T ss_pred             eCC----CCceeEEEEECCH
Confidence            643    3679999999874

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.

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.69  E-value=1.2e-16  Score=150.55  Aligned_cols=146  Identities=26%  Similarity=0.342  Sum_probs=118.9

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      ...|||.+||..+|..+|..+|+.||.|..-||..+..                 ++.++|.+||.|....+|+.|| .|
T Consensus       127 ~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqv-----------------tg~srGVgFiRFDKr~EAe~AIk~l  189 (360)
T KOG0145|consen  127 DANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQV-----------------TGLSRGVGFIRFDKRIEAEEAIKGL  189 (360)
T ss_pred             ccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcc-----------------cceecceeEEEecchhHHHHHHHhc
Confidence            46799999999999999999999999998777755432                 3457799999999999999999 69


Q ss_pred             cCceeCC--eEEEEeecCCCcccCC-------------------------C-------------CCCCC-----------
Q 016231          304 NMAVIGG--NHIRLDRACPPRKKLK-------------------------G-------------EDAPL-----------  332 (393)
Q Consensus       304 ng~~~~G--r~I~V~~a~~~~~~~~-------------------------~-------------~~~~~-----------  332 (393)
                      ||+.-.|  -+|.|.++..|.....                         .             ..+++           
T Consensus       190 NG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~  269 (360)
T KOG0145|consen  190 NGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGV  269 (360)
T ss_pred             cCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeee
Confidence            9998877  5688888754421100                         0             00000           


Q ss_pred             -----cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeee
Q 016231          333 -----YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT  391 (393)
Q Consensus       333 -----~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t  391 (393)
                           .....+|||-||.+++++.-|+++|.+|    |.|.+|.|++|..+++|+|||||...+
T Consensus       270 ~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpF----GAv~nVKvirD~ttnkCKGfgFVtMtN  329 (360)
T KOG0145|consen  270 NLPGGPGGGWCIFVYNLSPDADESILWQLFGPF----GAVTNVKVIRDFTTNKCKGFGFVTMTN  329 (360)
T ss_pred             ccCCCCCCeeEEEEEecCCCchHhHHHHHhCcc----cceeeEEEEecCCcccccceeEEEecc
Confidence                 1124789999999999999999999999    999999999999999999999999754

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.68  E-value=8.7e-17  Score=153.57  Aligned_cols=116  Identities=19%  Similarity=0.376  Sum_probs=106.3

Q ss_pred             EEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH-hcC
Q 016231          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-FNM  305 (393)
Q Consensus       227 tVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~-lng  305 (393)
                      .|||||||..+++.+|+.+|.+||.|.+|.|+.                         -||||...+...+..||. |||
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvK-------------------------NYgFVHiEdktaaedairNLhg   58 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGKVLECDIVK-------------------------NYGFVHIEDKTAAEDAIRNLHG   58 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCceEeeeeec-------------------------ccceEEeecccccHHHHhhccc
Confidence            599999999999999999999999999999943                         399999999999999994 999


Q ss_pred             ceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEE
Q 016231          306 AVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIA  385 (393)
Q Consensus       306 ~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfa  385 (393)
                      ..|+|..|.|..+...           ...+.+|+||||.+.++.++|+..|+.|    |.|..|.|++|        |+
T Consensus        59 YtLhg~nInVeaSksK-----------sk~stkl~vgNis~tctn~ElRa~fe~y----gpviecdivkd--------y~  115 (346)
T KOG0109|consen   59 YTLHGVNINVEASKSK-----------SKASTKLHVGNISPTCTNQELRAKFEKY----GPVIECDIVKD--------YA  115 (346)
T ss_pred             ceecceEEEEEecccc-----------CCCccccccCCCCccccCHHHhhhhccc----CCceeeeeecc--------ee
Confidence            9999999999998654           2356899999999999999999999999    99999999866        89


Q ss_pred             EEEee
Q 016231          386 YVLFK  390 (393)
Q Consensus       386 FVeF~  390 (393)
                      ||.|.
T Consensus       116 fvh~d  120 (346)
T KOG0109|consen  116 FVHFD  120 (346)
T ss_pred             EEEEe
Confidence            99996

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.68  E-value=1.3e-17  Score=170.40  Aligned_cols=152  Identities=20%  Similarity=0.327  Sum_probs=126.6

Q ss_pred             cCCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHH
Q 016231          220 DEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (393)
Q Consensus       220 ~~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~  299 (393)
                      .+++..+|||+-.|+..++.-+|.+||+.+|.|..|+|+++.+  +               +.++|.|||+|.+.+++..
T Consensus       174 ~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~--s---------------~rskgi~Yvef~D~~sVp~  236 (549)
T KOG0147|consen  174 PEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRN--S---------------RRSKGIAYVEFCDEQSVPL  236 (549)
T ss_pred             chHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeecccc--c---------------hhhcceeEEEEecccchhh
Confidence            3456689999999999999999999999999999999988763  2               2366999999999999999


Q ss_pred             HHHhcCceeCCeEEEEeecCCCcccCCCC----C-CCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEee
Q 016231          300 ALAFNMAVIGGNHIRLDRACPPRKKLKGE----D-APLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIR  374 (393)
Q Consensus       300 Al~lng~~~~Gr~I~V~~a~~~~~~~~~~----~-~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~  374 (393)
                      ||.|.|+.+.|.+|.|+............    . .....+-..||||||++++++++|+.+|++|    |.|..|.++.
T Consensus       237 aiaLsGqrllg~pv~vq~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepf----g~Ie~v~l~~  312 (549)
T KOG0147|consen  237 AIALSGQRLLGVPVIVQLSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPF----GKIENVQLTK  312 (549)
T ss_pred             HhhhcCCcccCceeEecccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCc----ccceeeeecc
Confidence            99999999999999999875432221110    0 1112233449999999999999999999999    9999999999


Q ss_pred             cCCCCCCccEEEEEeeec
Q 016231          375 HPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       375 d~~tg~~kGfaFVeF~t~  392 (393)
                      |..||.++|||||+|.+.
T Consensus       313 d~~tG~skgfGfi~f~~~  330 (549)
T KOG0147|consen  313 DSETGRSKGFGFITFVNK  330 (549)
T ss_pred             ccccccccCcceEEEecH
Confidence            988999999999999763

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.66  E-value=4.5e-16  Score=155.70  Aligned_cols=138  Identities=26%  Similarity=0.385  Sum_probs=111.3

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCC-eeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGE-IDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~-I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ...+.|||||||.+.++++|.+.|.+.++ |+.|.+...+.                +..+|||||||+|.+...|..|-
T Consensus       162 van~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~----------------dk~KNRGFaFveYe~H~~Aa~aR  225 (506)
T KOG0117|consen  162 VANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPD----------------DKTKNRGFAFVEYESHRAAAMAR  225 (506)
T ss_pred             eecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCcc----------------ccccccceEEEEeecchhHHHHH
Confidence            34688999999999999999999999875 56666644331                12358899999999999988887


Q ss_pred             -H-hcCc-eeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCC
Q 016231          302 -A-FNMA-VIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHM  378 (393)
Q Consensus       302 -~-lng~-~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~t  378 (393)
                       + +++. .+.|+.|.|.||.+....    +...+.....|||+||+.++|++.|..+|+.|    |.|+.|..++|   
T Consensus       226 rKl~~g~~klwgn~~tVdWAep~~e~----ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~----G~veRVkk~rD---  294 (506)
T KOG0117|consen  226 RKLMPGKIKLWGNAITVDWAEPEEEP----DEDTMSKVKVLYVRNLMESTTEETLKKLFNEF----GKVERVKKPRD---  294 (506)
T ss_pred             hhccCCceeecCCcceeeccCcccCC----ChhhhhheeeeeeeccchhhhHHHHHHHHHhc----cceEEeecccc---
Confidence             3 4544 689999999999765321    11134456899999999999999999999999    99999999877   


Q ss_pred             CCCccEEEEEeeec
Q 016231          379 RVGKGIAYVLFKTR  392 (393)
Q Consensus       379 g~~kGfaFVeF~t~  392 (393)
                           ||||.|.+|
T Consensus       295 -----YaFVHf~eR  303 (506)
T KOG0117|consen  295 -----YAFVHFAER  303 (506)
T ss_pred             -----eeEEeecch
Confidence                 999999876

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.66  E-value=5.4e-16  Score=156.63  Aligned_cols=138  Identities=26%  Similarity=0.405  Sum_probs=119.1

Q ss_pred             EEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-HhcCc
Q 016231          228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMA  306 (393)
Q Consensus       228 VFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~lng~  306 (393)
                      |||.||+..++-.+|..+|+.||.|.+|++.++..   +                ++|| ||+|.+++.|..|+ .+||.
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~---g----------------~kg~-FV~f~~e~~a~~ai~~~ng~  138 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN---G----------------SKGY-FVQFESEESAKKAIEKLNGM  138 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC---C----------------ceee-EEEeCCHHHHHHHHHHhcCc
Confidence            99999999999999999999999999999987651   1                5689 99999999999999 79999


Q ss_pred             eeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEE
Q 016231          307 VIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAY  386 (393)
Q Consensus       307 ~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaF  386 (393)
                      .+.|+.|.|............... ....-..+||.|++.+++++.|..+|..+    |.|.++.++.+. .|.++||||
T Consensus       139 ll~~kki~vg~~~~~~er~~~~~~-~~~~~t~v~vk~~~~~~~~~~l~~~f~~~----g~i~s~~v~~~~-~g~~~~~gf  212 (369)
T KOG0123|consen  139 LLNGKKIYVGLFERKEEREAPLGE-YKKRFTNVYVKNLEEDSTDEELKDLFSAY----GSITSVAVMRDS-IGKSKGFGF  212 (369)
T ss_pred             ccCCCeeEEeeccchhhhcccccc-hhhhhhhhheeccccccchHHHHHhhccc----CcceEEEEeecC-CCCCCCccc
Confidence            999999999988764433222212 23345689999999999999999999999    999999999995 677999999


Q ss_pred             EEeee
Q 016231          387 VLFKT  391 (393)
Q Consensus       387 VeF~t  391 (393)
                      |.|.+
T Consensus       213 v~f~~  217 (369)
T KOG0123|consen  213 VNFEN  217 (369)
T ss_pred             eeecC
Confidence            99976

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.60  E-value=9.3e-15  Score=132.06  Aligned_cols=138  Identities=22%  Similarity=0.343  Sum_probs=110.8

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      +..++|||||||.++.+.+|..+|.+||.|..|.|...+    +.+                +||||+|.++.+|+.|| 
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~----g~p----------------pfafVeFEd~RDAeDAiy   63 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP----GPP----------------PFAFVEFEDPRDAEDAIY   63 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC----CCC----------------CeeEEEecCccchhhhhh
Confidence            457899999999999999999999999999999883322    222                59999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCCcccCCC-----------------CCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCC
Q 016231          302 AFNMAVIGGNHIRLDRACPPRKKLKG-----------------EDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLE  364 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~~~~~~-----------------~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~  364 (393)
                      .-+|..+.|..|+|.++..-......                 ...+.......|.|.+||++.+++||++++...    
T Consensus        64 gRdGYdydg~rLRVEfprggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmRea----  139 (241)
T KOG0105|consen   64 GRDGYDYDGCRLRVEFPRGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREA----  139 (241)
T ss_pred             cccccccCcceEEEEeccCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhh----
Confidence            69999999999999998543211100                 002223345789999999999999999999997    


Q ss_pred             CCeEEEEEeecCCCCCCccEEEEEeee
Q 016231          365 SSVEAVRVIRHPHMRVGKGIAYVLFKT  391 (393)
Q Consensus       365 G~I~~VrI~~d~~tg~~kGfaFVeF~t  391 (393)
                      |.|-...+.+|       |+|.|+|..
T Consensus       140 GdvCfadv~rD-------g~GvV~~~r  159 (241)
T KOG0105|consen  140 GDVCFADVQRD-------GVGVVEYLR  159 (241)
T ss_pred             CCeeeeeeecc-------cceeeeeee
Confidence            99998898887       367888854

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

Probab=99.58  E-value=1.6e-14  Score=128.02  Aligned_cols=82  Identities=20%  Similarity=0.380  Sum_probs=72.9

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+++|+++|+++|..||.|.+|.|+.++.                 +++++|||||+|.+.++|+.|| 
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~-----------------tg~~kGfaFV~F~~~e~A~~Al~   94 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRE-----------------TGRSRGFGFVNFNDEGAATAAIS   94 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCC-----------------CCCcceEEEEEECCHHHHHHHHH
Confidence            3467899999999999999999999999999999977652                 2346799999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCC
Q 016231          302 AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~  321 (393)
                      .||+..|.|+.|.|.++...
T Consensus        95 ~lng~~i~Gr~l~V~~a~~~  114 (144)
T PLN03134         95 EMDGKELNGRHIRVNPANDR  114 (144)
T ss_pred             HcCCCEECCEEEEEEeCCcC
Confidence            69999999999999998654

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.54  E-value=6.1e-14  Score=130.35  Aligned_cols=140  Identities=26%  Similarity=0.383  Sum_probs=112.4

Q ss_pred             cccEEEEeCCCccCCHHHHHH----HhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHH
Q 016231          224 LLRTIFVGNLPLKVKKKTLIK----EFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~----~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~  299 (393)
                      +..||||.||+..+..++|+.    +|++||.|..|....                    +.+.||-|||.|.+.+.|-.
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k--------------------t~KmRGQA~VvFk~~~~As~   67 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK--------------------TPKMRGQAFVVFKETEAASA   67 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC--------------------CCCccCceEEEecChhHHHH
Confidence            456999999999999998888    999999999887632                    22377999999999999999


Q ss_pred             HH-HhcCceeCCeEEEEeecCCCcccCC------------------------CCC-----------------CCCcCCcc
Q 016231          300 AL-AFNMAVIGGNHIRLDRACPPRKKLK------------------------GED-----------------APLYDIKK  337 (393)
Q Consensus       300 Al-~lng~~~~Gr~I~V~~a~~~~~~~~------------------------~~~-----------------~~~~~~~~  337 (393)
                      |+ .|+|..|.|+.++|++|+....-..                        .+.                 .....+..
T Consensus        68 A~r~l~gfpFygK~mriqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~  147 (221)
T KOG4206|consen   68 ALRALQGFPFYGKPMRIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNN  147 (221)
T ss_pred             HHHHhcCCcccCchhheecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCce
Confidence            99 7999999999999999864311000                        000                 11245668


Q ss_pred             eeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       338 tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .||+.|||..++.+.|..+|++|    +--..||++..     -.|+|||+|.++
T Consensus       148 ilf~~niP~es~~e~l~~lf~qf----~g~keir~i~~-----~~~iAfve~~~d  193 (221)
T KOG4206|consen  148 ILFLTNIPSESESEMLSDLFEQF----PGFKEIRLIPP-----RSGIAFVEFLSD  193 (221)
T ss_pred             EEEEecCCcchhHHHHHHHHhhC----cccceeEeccC-----CCceeEEecchh
Confidence            99999999999999999999999    45678888765     367999999875

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

Probab=99.53  E-value=1.5e-13  Score=126.97  Aligned_cols=141  Identities=30%  Similarity=0.512  Sum_probs=110.8

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      .++|||+|||+.+|+++|..+|..||.|..|.+..+.  .               .+.++|||||.|.+.++|..|+ .+
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~--~---------------~~~~~g~~~v~f~~~~~~~~a~~~~  177 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDR--E---------------TGKSRGFAFVEFESEESAEKAIEEL  177 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeecc--c---------------cCccCceEEEEecCHHHHHHHHHHc
Confidence            6999999999999999999999999999999997654  2               2346799999999999999999 69


Q ss_pred             cCceeCCeEEEEeecCC---CcccCC------------CCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeE
Q 016231          304 NMAVIGGNHIRLDRACP---PRKKLK------------GEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVE  368 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~---~~~~~~------------~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~  368 (393)
                      ++..|.|+.|.|.++..   +.....            ............++++|++..++..++..+|..+    |.+.
T Consensus       178 ~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~  253 (306)
T COG0724         178 NGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSR----GDIV  253 (306)
T ss_pred             CCCeECCceeEeeccccccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhcccc----ccce
Confidence            99999999999999642   111111            0011224456789999999999999999999998    8887


Q ss_pred             EEEEeecCCCCCCccEEE
Q 016231          369 AVRVIRHPHMRVGKGIAY  386 (393)
Q Consensus       369 ~VrI~~d~~tg~~kGfaF  386 (393)
                      .+.+...........+.+
T Consensus       254 ~~~~~~~~~~~~~~~~~~  271 (306)
T COG0724         254 RASLPPSKDGKIPKSRSF  271 (306)
T ss_pred             eeeccCCCCCcccccccc
Confidence            777766654443444444

>PF00076 RRM_1: RNA recognition motif

Probab=99.48  E-value=2.2e-13  Score=103.39  Aligned_cols=69  Identities=35%  Similarity=0.598  Sum_probs=61.9

Q ss_pred             EEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-HhcCc
Q 016231          228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMA  306 (393)
Q Consensus       228 VFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~lng~  306 (393)
                      |||+|||+++|+++|+.+|+.||.|..+.++...   .               +.++|||||+|.+.++|..|+ .+|+.
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~---~---------------~~~~~~a~V~F~~~~~a~~a~~~l~g~   62 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNS---S---------------GKSKGYAFVEFESEEDAEKALEELNGK   62 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEET---T---------------SSEEEEEEEEESSHHHHHHHHHHHTTE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccc---c---------------ccccceEEEEEcCHHHHHHHHHHcCCC
Confidence            7999999999999999999999999999986641   1               235699999999999999999 59999


Q ss_pred             eeCCeEEE
Q 016231          307 VIGGNHIR  314 (393)
Q Consensus       307 ~~~Gr~I~  314 (393)
                      .|.|+.|+
T Consensus        63 ~~~~~~ir   70 (70)
T PF00076_consen   63 KINGRKIR   70 (70)
T ss_dssp             EETTEEEE
T ss_pred             EECccCcC
Confidence            99999985

(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 ....

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=99.48  E-value=3.5e-13  Score=137.44  Aligned_cols=153  Identities=25%  Similarity=0.392  Sum_probs=112.3

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ..-++.||||+||++++|+.|...|..||.+. |.++.........+.+|           +.||+|+.|.++.++..-|
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkG-----------s~~YvflvFe~E~sV~~Ll  323 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKG-----------SYGYVFLVFEDERSVQSLL  323 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCC-----------cccEEEEEecchHHHHHHH
Confidence            45678999999999999999999999999876 77754322222333322           4469999999999988766


Q ss_pred             HhcCceeCCeEEEEeecCCCcccCC--------------CCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCe
Q 016231          302 AFNMAVIGGNHIRLDRACPPRKKLK--------------GEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSV  367 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~~~~~--------------~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I  367 (393)
                      .-.-  +....+.++.+.+..+...              -+.....++.+|||||+||..++.++|..+|...   ||.|
T Consensus       324 ~aC~--~~~~~~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~l---yGgV  398 (520)
T KOG0129|consen  324 SACS--EGEGNYYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDL---FGGV  398 (520)
T ss_pred             HHHh--hcccceEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHh---cCce
Confidence            2111  1233333333322211110              0123457789999999999999999999999965   5999


Q ss_pred             EEEEEeecCCCCCCccEEEEEeee
Q 016231          368 EAVRVIRHPHMRVGKGIAYVLFKT  391 (393)
Q Consensus       368 ~~VrI~~d~~tg~~kGfaFVeF~t  391 (393)
                      ..+-|-+|+.-+.++|-|-|+|.+
T Consensus       399 ~yaGIDtD~k~KYPkGaGRVtFsn  422 (520)
T KOG0129|consen  399 LYVGIDTDPKLKYPKGAGRVTFSN  422 (520)
T ss_pred             EEEEeccCcccCCCCCcceeeecc
Confidence            999999999999999999999976

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.48  E-value=7.9e-14  Score=132.35  Aligned_cols=110  Identities=25%  Similarity=0.433  Sum_probs=90.7

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHh
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~l  303 (393)
                      ..||||||||+.++||+-|..||++.|.|.+++|+.+                                           
T Consensus         5 ~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~-------------------------------------------   41 (321)
T KOG0148|consen    5 EPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD-------------------------------------------   41 (321)
T ss_pred             CCceEEeeccChhhHHHHHHHHHHhccccccceeehh-------------------------------------------
Confidence            4699999999999999999999999999998887331                                           


Q ss_pred             cCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCcc
Q 016231          304 NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKG  383 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kG  383 (393)
                              .|.|.+++.+..+.+..    ....--|||+.|...++-++|++.|..|    |+|..++|++|+.|++++|
T Consensus        42 --------e~~v~wa~~p~nQsk~t----~~~hfhvfvgdls~eI~~e~lr~aF~pF----GevS~akvirD~~T~KsKG  105 (321)
T KOG0148|consen   42 --------ELKVNWATAPGNQSKPT----SNQHFHVFVGDLSPEIDNEKLREAFAPF----GEVSDAKVIRDMNTGKSKG  105 (321)
T ss_pred             --------hhccccccCcccCCCCc----cccceeEEehhcchhcchHHHHHHhccc----cccccceEeecccCCcccc
Confidence                    45566666552222111    1124569999999999999999999999    9999999999999999999


Q ss_pred             EEEEEeeec
Q 016231          384 IAYVLFKTR  392 (393)
Q Consensus       384 faFVeF~t~  392 (393)
                      ||||.|-++
T Consensus       106 YgFVSf~~k  114 (321)
T KOG0148|consen  106 YGFVSFPNK  114 (321)
T ss_pred             eeEEeccch
Confidence            999999654

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.46  E-value=9.2e-13  Score=133.66  Aligned_cols=143  Identities=23%  Similarity=0.325  Sum_probs=110.6

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhc
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~ln  304 (393)
                      ..-|-+++|||.+|+++|..||+.|+ |.++.+.+.    ++               +.+|-|||+|.+.++++.||+.+
T Consensus        10 ~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~----~G---------------r~sGeA~Ve~~seedv~~Alkkd   69 (510)
T KOG4211|consen   10 AFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRR----NG---------------RPSGEAYVEFTSEEDVEKALKKD   69 (510)
T ss_pred             ceEEEecCCCccccHHHHHHHHhcCc-eeEEEEecc----CC---------------CcCcceEEEeechHHHHHHHHhh
Confidence            45688999999999999999999998 677766442    23               35589999999999999999999


Q ss_pred             CceeCCeEEEEeecCCCcccC--CCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEE-EEEeecCCCCCC
Q 016231          305 MAVIGGNHIRLDRACPPRKKL--KGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEA-VRVIRHPHMRVG  381 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~~~~~~--~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~-VrI~~d~~tg~~  381 (393)
                      ...+..|.|.|-.+.......  +........+...|-+++||+.||++||.++|+...    .|.. |.++.+ ..+++
T Consensus        70 R~~mg~RYIEVf~~~~~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~----Iv~~gi~l~~d-~rgR~  144 (510)
T KOG4211|consen   70 RESMGHRYIEVFTAGGAEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLE----IVPDGILLPMD-QRGRP  144 (510)
T ss_pred             HHHhCCceEEEEccCCccccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCc----ccccceeeecc-CCCCc
Confidence            999999999998875432211  111111113456899999999999999999999972    2333 456666 46889


Q ss_pred             ccEEEEEeeec
Q 016231          382 KGIAYVLFKTR  392 (393)
Q Consensus       382 kGfaFVeF~t~  392 (393)
                      .|-|||+|.+.
T Consensus       145 tGEAfVqF~sq  155 (510)
T KOG4211|consen  145 TGEAFVQFESQ  155 (510)
T ss_pred             ccceEEEecCH
Confidence            99999999874

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.45  E-value=2.7e-13  Score=129.78  Aligned_cols=76  Identities=30%  Similarity=0.383  Sum_probs=69.4

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhc
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~ln  304 (393)
                      .++|||+|||+.+|+++|++||+.||.|.+|+|+++..                    ++|||||+|.+.++|..||.||
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~--------------------~~GfAFVtF~d~eaAe~AllLn   63 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE--------------------RSQIAYVTFKDPQGAETALLLS   63 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC--------------------CCCEEEEEeCcHHHHHHHHHhc
Confidence            57999999999999999999999999999999966431                    3489999999999999999999


Q ss_pred             CceeCCeEEEEeecCC
Q 016231          305 MAVIGGNHIRLDRACP  320 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~  320 (393)
                      |..|.|+.|.|.++..
T Consensus        64 G~~l~gr~V~Vt~a~~   79 (260)
T PLN03120         64 GATIVDQSVTITPAED   79 (260)
T ss_pred             CCeeCCceEEEEeccC
Confidence            9999999999999853

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.43  E-value=2.4e-13  Score=135.89  Aligned_cols=76  Identities=25%  Similarity=0.391  Sum_probs=67.2

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      .+.||||-|+..+||.+|+++|++||.|++|+|++++.                  +.+||||||.|.+.+.|..|| .|
T Consensus       124 e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~------------------~~sRGcaFV~fstke~A~~Aika~  185 (510)
T KOG0144|consen  124 ERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPD------------------GLSRGCAFVKFSTKEMAVAAIKAL  185 (510)
T ss_pred             chhhhhhhccccccHHHHHHHHHhhCccchhhheeccc------------------ccccceeEEEEehHHHHHHHHHhh
Confidence            57899999999999999999999999999999988762                  357899999999999999999 69


Q ss_pred             cCc-eeCC--eEEEEeec
Q 016231          304 NMA-VIGG--NHIRLDRA  318 (393)
Q Consensus       304 ng~-~~~G--r~I~V~~a  318 (393)
                      ||. .+.|  .+|.|.|+
T Consensus       186 ng~~tmeGcs~PLVVkFA  203 (510)
T KOG0144|consen  186 NGTQTMEGCSQPLVVKFA  203 (510)
T ss_pred             ccceeeccCCCceEEEec
Confidence            986 5655  56888877

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.43  E-value=7.9e-13  Score=125.43  Aligned_cols=77  Identities=23%  Similarity=0.383  Sum_probs=64.4

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..+.||||-|...-.|++++.+|..||.|.+|.+.+-+                  ++.++|||||.|.+.-+|+.|| .
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~------------------dg~sKGCAFVKf~s~~eAqaAI~a   79 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP------------------DGNSKGCAFVKFSSHAEAQAAINA   79 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC------------------CCCCCCceEEEeccchHHHHHHHH
Confidence            45889999999999999999999999999999986654                  3457799999999999999999 7


Q ss_pred             hcCc-eeCC--eEEEEeec
Q 016231          303 FNMA-VIGG--NHIRLDRA  318 (393)
Q Consensus       303 lng~-~~~G--r~I~V~~a  318 (393)
                      |||. .+.|  ..|.|.++
T Consensus        80 LHgSqTmpGASSSLVVK~A   98 (371)
T KOG0146|consen   80 LHGSQTMPGASSSLVVKFA   98 (371)
T ss_pred             hcccccCCCCccceEEEec
Confidence            8876 4444  44666654

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.42  E-value=2.7e-13  Score=116.11  Aligned_cols=80  Identities=20%  Similarity=0.343  Sum_probs=69.4

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      +.++|||||||++.++|++|+++|+.||+|..|.|=.+.+                 +.+.+|||||+|.+.++|..||.
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~-----------------kktpCGFCFVeyy~~~dA~~Alr   96 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRF-----------------KKTPCGFCFVEYYSRDDAEDALR   96 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccC-----------------CcCccceEEEEEecchhHHHHHH
Confidence            3489999999999999999999999999999887633221                 23467999999999999999995


Q ss_pred             -hcCceeCCeEEEEeecC
Q 016231          303 -FNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       303 -lng~~~~Gr~I~V~~a~  319 (393)
                       ++++.+..+.|+|+|..
T Consensus        97 yisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   97 YISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             HhccCcccccceeeeccc
Confidence             99999999999999974

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.37  E-value=3.4e-12  Score=97.93  Aligned_cols=69  Identities=29%  Similarity=0.536  Sum_probs=58.3

Q ss_pred             EEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH-hcCc
Q 016231          228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-FNMA  306 (393)
Q Consensus       228 VFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~-lng~  306 (393)
                      |||+|||+++++++|..+|+.||.|..|++....  +                +..+|+|||+|.+.++|..|+. +++.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~--~----------------~~~~~~a~v~f~~~~~a~~al~~~~~~   62 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNK--D----------------GQSRGFAFVEFSSEEDAKRALELLNGK   62 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEEST--T----------------SSEEEEEEEEESSHHHHHHHHHHHTTE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeee--c----------------cccCCEEEEEeCCHHHHHHHHHHCCCc
Confidence            7999999999999999999999999999996542  1                2356999999999999999995 6669


Q ss_pred             eeCCeEEE
Q 016231          307 VIGGNHIR  314 (393)
Q Consensus       307 ~~~Gr~I~  314 (393)
                      .|.|+.|+
T Consensus        63 ~~~g~~l~   70 (70)
T PF14259_consen   63 EIDGRKLR   70 (70)
T ss_dssp             EETTEEEE
T ss_pred             EECCEEcC
Confidence            99999885

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 ....

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.33  E-value=6.2e-12  Score=118.98  Aligned_cols=76  Identities=26%  Similarity=0.264  Sum_probs=68.9

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhc
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~ln  304 (393)
                      ..||||+||++.+|+++|++||+.||.|.+|+|+++.                    ...|||||+|.++++++.||.|+
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~--------------------et~gfAfVtF~d~~aaetAllLn   64 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG--------------------EYACTAYVTFKDAYALETAVLLS   64 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC--------------------CcceEEEEEECCHHHHHHHHhcC
Confidence            5799999999999999999999999999999997642                    13479999999999999999999


Q ss_pred             CceeCCeEEEEeecCC
Q 016231          305 MAVIGGNHIRLDRACP  320 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~  320 (393)
                      |..|.++.|.|.....
T Consensus        65 Ga~l~d~~I~It~~~~   80 (243)
T PLN03121         65 GATIVDQRVCITRWGQ   80 (243)
T ss_pred             CCeeCCceEEEEeCcc
Confidence            9999999999988653

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.31  E-value=1.7e-11  Score=122.93  Aligned_cols=146  Identities=21%  Similarity=0.320  Sum_probs=115.8

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhc-ccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFI-KFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs-~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      .|.|||.||||++...+|+.+|. ..|+|.-|.|..+.   ++               +.+|||.|+|.+++.+++|+ .
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~---~G---------------K~rGcavVEFk~~E~~qKa~E~  105 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE---SG---------------KARGCAVVEFKDPENVQKALEK  105 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc---CC---------------CcCCceEEEeeCHHHHHHHHHH
Confidence            57799999999999999999998 58999999986653   33               46699999999999999999 6


Q ss_pred             hcCceeCCeEEEEeecCCCcccC-----------------------------------------CCCCCC----------
Q 016231          303 FNMAVIGGNHIRLDRACPPRKKL-----------------------------------------KGEDAP----------  331 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~~~~~-----------------------------------------~~~~~~----------  331 (393)
                      ||...+.||+|.|.-....+..+                                         ..++..          
T Consensus       106 lnk~~~~GR~l~vKEd~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~  185 (608)
T KOG4212|consen  106 LNKYEVNGRELVVKEDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMS  185 (608)
T ss_pred             hhhccccCceEEEeccCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccc
Confidence            99999999999997542100000                                         000000          


Q ss_pred             -------------------------CcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEE
Q 016231          332 -------------------------LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAY  386 (393)
Q Consensus       332 -------------------------~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaF  386 (393)
                                               ..+....+||.||.+.+....|.+.|.-.    |.|++|.+-.|. -|.++|||.
T Consensus       186 ~~~~~~~~~~lfgl~~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmA----Gkv~~vdf~idK-eG~s~G~~v  260 (608)
T KOG4212|consen  186 NDYNNSSNYNLFGLSASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMA----GKVQSVDFSIDK-EGNSRGFAV  260 (608)
T ss_pred             cccccchhhhcccchhhhhhhccCCCCCccceeeeeccccccchHHHHHHhccc----eeeeeeceeecc-ccccCCeeE
Confidence                                     01123679999999999999999999876    999999999995 579999999


Q ss_pred             EEeeecC
Q 016231          387 VLFKTRV  393 (393)
Q Consensus       387 VeF~t~~  393 (393)
                      ++|..+|
T Consensus       261 i~y~hpv  267 (608)
T KOG4212|consen  261 IEYDHPV  267 (608)
T ss_pred             EEecchH
Confidence            9998764

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.30  E-value=4.6e-12  Score=113.82  Aligned_cols=76  Identities=26%  Similarity=0.454  Sum_probs=69.5

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      .+.||||||+..+++.+|...|..||+|.+|+|-+.|                      -|||||+|.+..+|+.|+ .|
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP----------------------PGfAFVEFed~RDA~DAvr~L   67 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP----------------------PGFAFVEFEDPRDAEDAVRYL   67 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC----------------------CCceEEeccCcccHHHHHhhc
Confidence            6889999999999999999999999999999996644                      189999999999999999 79


Q ss_pred             cCceeCCeEEEEeecCCCc
Q 016231          304 NMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~  322 (393)
                      +|..|.|..|.|.++....
T Consensus        68 DG~~~cG~r~rVE~S~G~~   86 (195)
T KOG0107|consen   68 DGKDICGSRIRVELSTGRP   86 (195)
T ss_pred             CCccccCceEEEEeecCCc
Confidence            9999999999999987543

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.29  E-value=5.2e-12  Score=118.13  Aligned_cols=78  Identities=24%  Similarity=0.356  Sum_probs=68.9

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhc
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~ln  304 (393)
                      -.+||||||+|.+..+.|+.+|.+||+|++..+++|..  +               ++|+||+||+|.+.++|..|++--
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~--t---------------~rskGyGfVTf~d~~aa~rAc~dp   74 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKN--T---------------GRSKGYGFVTFRDAEAATRACKDP   74 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccC--C---------------ccccceeeEEeecHHHHHHHhcCC
Confidence            46799999999999999999999999999999988652  2               347799999999999999999766


Q ss_pred             CceeCCeEEEEeecC
Q 016231          305 MAVIGGNHIRLDRAC  319 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~  319 (393)
                      .-.|+||+..|..+.
T Consensus        75 ~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   75 NPIIDGRKANCNLAS   89 (247)
T ss_pred             CCcccccccccchhh
Confidence            678999999998875

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

Probab=99.28  E-value=1.3e-11  Score=131.27  Aligned_cols=80  Identities=20%  Similarity=0.400  Sum_probs=71.7

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|||+|||+++++++|+.+|+.||.|.+|+|++++.  +               +.++|||||+|.+.++|..|| .
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~--t---------------gksKGfGFVeFe~~e~A~kAI~a  265 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPT--G---------------RGHKGYGFIEYNNLQSQSEAIAS  265 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCC--C---------------CCcCCeEEEEECCHHHHHHHHHH
Confidence            457899999999999999999999999999999977652  2               236699999999999999999 7


Q ss_pred             hcCceeCCeEEEEeecCC
Q 016231          303 FNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~  320 (393)
                      ||+..|+|+.|+|.++..
T Consensus       266 mNg~elgGr~LrV~kAi~  283 (612)
T TIGR01645       266 MNLFDLGGQYLRVGKCVT  283 (612)
T ss_pred             hCCCeeCCeEEEEEecCC
Confidence            999999999999999864

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.

>PLN03213 repressor of silencing 3; Provisional

Probab=99.26  E-value=1.5e-11  Score=124.69  Aligned_cols=75  Identities=28%  Similarity=0.412  Sum_probs=67.5

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCH--HHHHHHH-
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSE--QSTEAAL-  301 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~--e~A~~Al-  301 (393)
                      ..+||||||++.+++++|+.+|+.||.|.+|.|++.    ++                 ||||||+|.+.  .++..|| 
T Consensus        10 gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE----TG-----------------RGFAFVEMssdddaEeeKAIS   68 (759)
T PLN03213         10 GVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT----KG-----------------RSFAYIDFSPSSTNSLTKLFS   68 (759)
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc----cC-----------------CceEEEEecCCcHHHHHHHHH
Confidence            578999999999999999999999999999999642    22                 48999999987  6788999 


Q ss_pred             HhcCceeCCeEEEEeecCC
Q 016231          302 AFNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~  320 (393)
                      .|||..|.|+.|+|..|.+
T Consensus        69 aLNGAEWKGR~LKVNKAKP   87 (759)
T PLN03213         69 TYNGCVWKGGRLRLEKAKE   87 (759)
T ss_pred             HhcCCeecCceeEEeeccH
Confidence            7999999999999999965

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.26  E-value=7.3e-11  Score=109.75  Aligned_cols=148  Identities=24%  Similarity=0.341  Sum_probs=103.4

Q ss_pred             cCCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHH
Q 016231          220 DEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (393)
Q Consensus       220 ~~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~  299 (393)
                      ++...-|||||.+||.++..-+|..+|..|-.-+.+.|....   .+.             .-.+-+|||.|.+.+.|.+
T Consensus        29 ~~~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Ts---k~~-------------~~~~pvaFatF~s~q~A~a   92 (284)
T KOG1457|consen   29 DEPGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTS---KGD-------------QVCKPVAFATFTSHQFALA   92 (284)
T ss_pred             ccccccceeeeccCCcccCHHHHHHHhccCCCccceeeeecc---CCC-------------ccccceEEEEecchHHHHH
Confidence            334457999999999999999999999998766666664322   110             1123599999999999999


Q ss_pred             HH-HhcCceeC---CeEEEEeecCCCcccC--CC---------------------------C---CC-------------
Q 016231          300 AL-AFNMAVIG---GNHIRLDRACPPRKKL--KG---------------------------E---DA-------------  330 (393)
Q Consensus       300 Al-~lng~~~~---Gr~I~V~~a~~~~~~~--~~---------------------------~---~~-------------  330 (393)
                      |+ .|||..|+   +..|++..+....+..  +.                           +   ..             
T Consensus        93 amnaLNGvrFDpE~~stLhiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al  172 (284)
T KOG1457|consen   93 AMNALNGVRFDPETGSTLHIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADAL  172 (284)
T ss_pred             HHHHhcCeeeccccCceeEeeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccC
Confidence            99 79999985   6888888774321100  00                           0   00             


Q ss_pred             --------------------------------CCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCC
Q 016231          331 --------------------------------PLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHM  378 (393)
Q Consensus       331 --------------------------------~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~t  378 (393)
                                                      .....+.||||.||..++++++|+.+|..|..    ...++|...  .
T Consensus       173 ~~~~~t~~~~l~a~~~~~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~g----f~~l~~~~~--~  246 (284)
T KOG1457|consen  173 KENDTTKSEALSAPDSKAPSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPG----FHILKIRAR--G  246 (284)
T ss_pred             CCccccchhhhhhhhhcCCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCC----ceEEEEecC--C
Confidence                                            00112468999999999999999999999942    344454221  2


Q ss_pred             CCCccEEEEEeee
Q 016231          379 RVGKGIAYVLFKT  391 (393)
Q Consensus       379 g~~kGfaFVeF~t  391 (393)
                        .-..|||+|.+
T Consensus       247 --g~~vaf~~~~~  257 (284)
T KOG1457|consen  247 --GMPVAFADFEE  257 (284)
T ss_pred             --CcceEeecHHH
Confidence              34589999964

>smart00362 RRM_2 RNA recognition motif

Probab=99.24  E-value=4.7e-11  Score=89.12  Aligned_cols=71  Identities=39%  Similarity=0.655  Sum_probs=62.5

Q ss_pred             EEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-HhcC
Q 016231          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNM  305 (393)
Q Consensus       227 tVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~lng  305 (393)
                      +|||+|||..++.++|+.+|..||.|..+.+...+    +               .++|+|||+|.+.+.|..|+ .+++
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~----~---------------~~~~~~~v~f~~~~~a~~a~~~~~~   61 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT----G---------------KSKGFAFVEFESEEDAEKAIEALNG   61 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC----C---------------CCCceEEEEeCCHHHHHHHHHHhCC
Confidence            59999999999999999999999999999885532    1               25589999999999999999 6899


Q ss_pred             ceeCCeEEEEe
Q 016231          306 AVIGGNHIRLD  316 (393)
Q Consensus       306 ~~~~Gr~I~V~  316 (393)
                      ..+.|+.|.|.
T Consensus        62 ~~~~~~~i~v~   72 (72)
T smart00362       62 TKLGGRPLRVE   72 (72)
T ss_pred             cEECCEEEeeC
Confidence            99999998873

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.24  E-value=2.3e-11  Score=117.02  Aligned_cols=79  Identities=27%  Similarity=0.400  Sum_probs=71.6

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      +-+||||+-|+++++|..|+..|+.||+|..|+|+++..  +               ++++|||||+|.++.++..|. .
T Consensus       100 Py~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~v--T---------------gkskGYAFIeye~erdm~~AYK~  162 (335)
T KOG0113|consen  100 PYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKV--T---------------GKSKGYAFIEYEHERDMKAAYKD  162 (335)
T ss_pred             ccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecc--c---------------CCccceEEEEeccHHHHHHHHHh
Confidence            479999999999999999999999999999999988753  2               346699999999999999999 6


Q ss_pred             hcCceeCCeEEEEeecC
Q 016231          303 FNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~  319 (393)
                      .+|..|+|+.|.|+.-.
T Consensus       163 adG~~Idgrri~VDvER  179 (335)
T KOG0113|consen  163 ADGIKIDGRRILVDVER  179 (335)
T ss_pred             ccCceecCcEEEEEecc
Confidence            89999999999998763

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.23  E-value=1.6e-12  Score=117.29  Aligned_cols=81  Identities=23%  Similarity=0.400  Sum_probs=72.9

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      +.+.-|||||||+..||-+|...|++||+|+.|.|+++.  .               +|+|+||||+.|.+..+...|+ 
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk--~---------------TGKSKGFaFLcYEDQRSTILAVD   95 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDK--K---------------TGKSKGFAFLCYEDQRSTILAVD   95 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecC--C---------------CCcccceEEEEecCccceEEEEe
Confidence            346889999999999999999999999999999998876  2               3457799999999999998898 


Q ss_pred             HhcCceeCCeEEEEeecCC
Q 016231          302 AFNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~  320 (393)
                      .|||..|.||.|+|+....
T Consensus        96 N~NGiki~gRtirVDHv~~  114 (219)
T KOG0126|consen   96 NLNGIKILGRTIRVDHVSN  114 (219)
T ss_pred             ccCCceecceeEEeeeccc
Confidence            7999999999999998754

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.23  E-value=4.2e-11  Score=120.35  Aligned_cols=80  Identities=23%  Similarity=0.321  Sum_probs=69.4

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      ..+|||+|||+.+|+++|+++|+.||.|..|+|+++..  +               ++++|||||+|.+.++|+.|| .|
T Consensus       193 ~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~--t---------------g~~kG~aFV~F~~~e~A~~Ai~~l  255 (346)
T TIGR01659       193 DTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKL--T---------------GTPRGVAFVRFNKREEAQEAISAL  255 (346)
T ss_pred             cceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCC--C---------------CccceEEEEEECCHHHHHHHHHHh
Confidence            56899999999999999999999999999999976542  2               335699999999999999999 69


Q ss_pred             cCceeCC--eEEEEeecCCC
Q 016231          304 NMAVIGG--NHIRLDRACPP  321 (393)
Q Consensus       304 ng~~~~G--r~I~V~~a~~~  321 (393)
                      |+..|.|  +.|.|.++...
T Consensus       256 ng~~~~g~~~~l~V~~a~~~  275 (346)
T TIGR01659       256 NNVIPEGGSQPLTVRLAEEH  275 (346)
T ss_pred             CCCccCCCceeEEEEECCcc
Confidence            9998876  78999988643

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).

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.19  E-value=2.5e-11  Score=113.58  Aligned_cols=130  Identities=18%  Similarity=0.386  Sum_probs=104.3

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hhc
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~ln  304 (393)
                      ..||||+||+.+.+.+|..||..||.|..|.+.                         .||+||+|.+..+|.-|+ .+|
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk-------------------------~gf~fv~fed~rda~Dav~~l~   56 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK-------------------------NGFGFVEFEDPRDADDAVHDLD   56 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee-------------------------cccceeccCchhhhhcccchhc
Confidence            359999999999999999999999999988871                         279999999999999999 899


Q ss_pred             CceeCCeEEEEeecCCCcccC----CCC----C---CCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEe
Q 016231          305 MAVIGGNHIRLDRACPPRKKL----KGE----D---APLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVI  373 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~~~~~~----~~~----~---~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~  373 (393)
                      +..|.|-.+.|.++...+..+    .++    .   .........|+|.|++..+.+.+|.++|+.+    |.++...+ 
T Consensus        57 ~~~l~~e~~vve~~r~~~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~----g~~~~~~~-  131 (216)
T KOG0106|consen   57 GKELCGERLVVEHARGKRRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPA----GEVTYVDA-  131 (216)
T ss_pred             CceecceeeeeecccccccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhccc----CCCchhhh-
Confidence            999999889998886432111    000    0   1112234678999999999999999999999    88865544 


Q ss_pred             ecCCCCCCccEEEEEeeec
Q 016231          374 RHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       374 ~d~~tg~~kGfaFVeF~t~  392 (393)
                             .+++|||+|.++
T Consensus       132 -------~~~~~~v~Fs~~  143 (216)
T KOG0106|consen  132 -------RRNFAFVEFSEQ  143 (216)
T ss_pred             -------hccccceeehhh
Confidence                   467999999864

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.16  E-value=3.5e-11  Score=110.74  Aligned_cols=78  Identities=26%  Similarity=0.419  Sum_probs=71.6

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      -.+|-|-||.+.|+.++|+.+|.+||.|-.|.|+++++                 +.+++|||||.|....+|+.|| +|
T Consensus        13 m~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~-----------------Tr~sRgFaFVrf~~k~daedA~dam   75 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRY-----------------TRQSRGFAFVRFHDKRDAEDALDAM   75 (256)
T ss_pred             ceeEEecceeccCCHHHHHHHHHHhCcccceecccccc-----------------cccccceeEEEeeecchHHHHHHhh
Confidence            46799999999999999999999999999999988874                 2357799999999999999999 79


Q ss_pred             cCceeCCeEEEEeecC
Q 016231          304 NMAVIGGNHIRLDRAC  319 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~  319 (393)
                      +|.+|+|+.|.|++|.
T Consensus        76 DG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   76 DGAVLDGRELRVQMAR   91 (256)
T ss_pred             cceeeccceeeehhhh
Confidence            9999999999999984

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.15  E-value=1.4e-10  Score=109.04  Aligned_cols=81  Identities=22%  Similarity=0.272  Sum_probs=73.1

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|-|.|||.++++.+|.++|..||.|..|.|.++.  .++               .++|||||.|.+.++|.+|| .
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK--~TG---------------~~kGFAFVtF~sRddA~rAI~~  250 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDK--ETG---------------LSKGFAFVTFESRDDAARAIAD  250 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEcc--ccC---------------cccceEEEEEecHHHHHHHHHH
Confidence            46889999999999999999999999999999998765  344               46699999999999999999 6


Q ss_pred             hcCceeCCeEEEEeecCCC
Q 016231          303 FNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~  321 (393)
                      |||.-++.--|+|.|+.|.
T Consensus       251 LnG~gyd~LILrvEwskP~  269 (270)
T KOG0122|consen  251 LNGYGYDNLILRVEWSKPS  269 (270)
T ss_pred             ccCcccceEEEEEEecCCC
Confidence            9999999999999999763

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.15  E-value=3.4e-10  Score=84.83  Aligned_cols=73  Identities=38%  Similarity=0.601  Sum_probs=63.9

Q ss_pred             EEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-HhcC
Q 016231          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNM  305 (393)
Q Consensus       227 tVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~lng  305 (393)
                      +|||+|||+.+++++|+.+|..||.|..+.+...+..                  ..+|+|||+|.+.++|..|+ .+++
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~------------------~~~~~~~v~f~s~~~a~~a~~~~~~   62 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT------------------KSKGFAFVEFEDEEDAEKALEALNG   62 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC------------------CcceEEEEEECCHHHHHHHHHHhCC
Confidence            4899999999999999999999999999998664421                  24589999999999999999 6999


Q ss_pred             ceeCCeEEEEee
Q 016231          306 AVIGGNHIRLDR  317 (393)
Q Consensus       306 ~~~~Gr~I~V~~  317 (393)
                      ..+.|+.|.|.+
T Consensus        63 ~~~~~~~~~v~~   74 (74)
T cd00590          63 KELGGRPLRVEF   74 (74)
T ss_pred             CeECCeEEEEeC
Confidence            999999998863

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).

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.14  E-value=6.8e-11  Score=115.08  Aligned_cols=78  Identities=19%  Similarity=0.357  Sum_probs=70.1

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      .+.|+|.||||...+.||+.+|.+||.|.+|.|+.+.    ..               |+||+||+|.+.++|+.|- +|
T Consensus        96 pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE----RG---------------SKGFGFVTmen~~dadRARa~L  156 (376)
T KOG0125|consen   96 PKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE----RG---------------SKGFGFVTMENPADADRARAEL  156 (376)
T ss_pred             CceeEeecCCccccCccHHHHHHhhCceeeEEEEecc----CC---------------CCccceEEecChhhHHHHHHHh
Confidence            4789999999999999999999999999999996532    22               6699999999999999999 79


Q ss_pred             cCceeCCeEEEEeecCCC
Q 016231          304 NMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~  321 (393)
                      ||+.+.||+|.|..+...
T Consensus       157 Hgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen  157 HGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             hcceeeceEEEEeccchh
Confidence            999999999999998653

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.11  E-value=3.2e-10  Score=94.18  Aligned_cols=77  Identities=19%  Similarity=0.345  Sum_probs=68.7

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      .+.|||+|||+++|.+++.++|..||.|..|||=..                    ...+|-|||.|.+..+|..|+ .|
T Consensus        18 nriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~--------------------k~TrGTAFVVYedi~dAk~A~dhl   77 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNT--------------------KETRGTAFVVYEDIFDAKKACDHL   77 (124)
T ss_pred             heeEEEecCCccccHHHHHHHhhcccceEEEEecCc--------------------cCcCceEEEEehHhhhHHHHHHHh
Confidence            688999999999999999999999999999998211                    125699999999999999999 79


Q ss_pred             cCceeCCeEEEEeecCCC
Q 016231          304 NMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~  321 (393)
                      +|.-+.++.+.|.+..+.
T Consensus        78 sg~n~~~ryl~vlyyq~~   95 (124)
T KOG0114|consen   78 SGYNVDNRYLVVLYYQPE   95 (124)
T ss_pred             cccccCCceEEEEecCHH
Confidence            999999999999988654

>smart00360 RRM RNA recognition motif

Probab=99.10  E-value=3.8e-10  Score=83.71  Aligned_cols=70  Identities=36%  Similarity=0.544  Sum_probs=60.6

Q ss_pred             EeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-HhcCcee
Q 016231          230 VGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVI  308 (393)
Q Consensus       230 VgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~lng~~~  308 (393)
                      |+|||..+++++|+.+|..||.|..+.+...+.                 .+.++|||||+|.+.++|..|+ .+++..+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~-----------------~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~   63 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKD-----------------TGKSKGFAFVEFESEEDAEKALEALNGKEL   63 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCC-----------------CCCCCceEEEEeCCHHHHHHHHHHcCCCee
Confidence            689999999999999999999999998865431                 1236699999999999999999 6899999


Q ss_pred             CCeEEEEe
Q 016231          309 GGNHIRLD  316 (393)
Q Consensus       309 ~Gr~I~V~  316 (393)
                      .|+.|.|.
T Consensus        64 ~~~~~~v~   71 (71)
T smart00360       64 DGRPLKVK   71 (71)
T ss_pred             CCcEEEeC
Confidence            99998873

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

Probab=99.08  E-value=2.2e-10  Score=101.58  Aligned_cols=56  Identities=20%  Similarity=0.416  Sum_probs=52.2

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ....++|||+|||+.+++++|+++|..|    |.|..|+|+.|+.++.++|||||+|.++
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~----G~I~~v~i~~d~~tg~~kGfaFV~F~~~   86 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHF----GDVVDAKVIVDRETGRSRGFGFVNFNDE   86 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcC----CCeEEEEEEecCCCCCcceEEEEEECCH
Confidence            3456799999999999999999999999    9999999999999999999999999874

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.06  E-value=4.8e-10  Score=118.19  Aligned_cols=146  Identities=25%  Similarity=0.385  Sum_probs=109.4

Q ss_pred             cCCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHH
Q 016231          220 DEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (393)
Q Consensus       220 ~~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~  299 (393)
                      ...+....|+|+|||..+..++|..+|..||+|..|.|+  +   .+                  -.|+|+|.++.+|..
T Consensus       380 ~~~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp--~---~G------------------~~aiv~fl~p~eAr~  436 (725)
T KOG0110|consen  380 QAERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLP--P---GG------------------TGAIVEFLNPLEARK  436 (725)
T ss_pred             hhhhhcceeeeccCccccccHHHHHHhhcccccceeecC--c---cc------------------ceeeeeecCccchHH
Confidence            355666889999999999999999999999999988552  2   11                  159999999999999


Q ss_pred             HH-HhcCceeCCeEEEEeecCCCccc-------C-------------------CC---CC------CCC------cCCcc
Q 016231          300 AL-AFNMAVIGGNHIRLDRACPPRKK-------L-------------------KG---ED------APL------YDIKK  337 (393)
Q Consensus       300 Al-~lng~~~~Gr~I~V~~a~~~~~~-------~-------------------~~---~~------~~~------~~~~~  337 (393)
                      |+ .|..+.+...++.+.|+......       .                   .+   .+      .+.      .....
T Consensus       437 Afrklaysr~k~~plyle~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t  516 (725)
T KOG0110|consen  437 AFRKLAYSRFKSAPLYLEWAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETET  516 (725)
T ss_pred             HHHHhchhhhccCccccccChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccch
Confidence            99 68888888888877776211000       0                   00   00      000      01123


Q ss_pred             eeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCC---CCccEEEEEeeec
Q 016231          338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMR---VGKGIAYVLFKTR  392 (393)
Q Consensus       338 tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg---~~kGfaFVeF~t~  392 (393)
                      +|||.||++++|.++|..+|..+    |.|.+|.|...++..   .+.|||||+|.++
T Consensus       517 ~lfvkNlnf~Tt~e~l~~~F~k~----G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~  570 (725)
T KOG0110|consen  517 KLFVKNLNFDTTLEDLEDLFSKQ----GTVLSIEISKKKDPANKYLSMGFGFVEFAKP  570 (725)
T ss_pred             hhhhhcCCcccchhHHHHHHHhc----CeEEEEEEeccccccccccccceeEEEecCH
Confidence            39999999999999999999998    999999998775422   3459999999874

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.06  E-value=1.5e-10  Score=107.52  Aligned_cols=83  Identities=28%  Similarity=0.458  Sum_probs=74.0

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..||||||+|...+|+.-|...|-.||.|..|.++.+-  .               .+++||||||+|...++|.+|| .
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDy--e---------------sqkHRgFgFVefe~aEDAaaAiDN   71 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDY--E---------------SQKHRGFGFVEFEEAEDAAAAIDN   71 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccch--h---------------cccccceeEEEeeccchhHHHhhc
Confidence            46899999999999999999999999999999986653  2               2348899999999999999999 7


Q ss_pred             hcCceeCCeEEEEeecCCCcc
Q 016231          303 FNMAVIGGNHIRLDRACPPRK  323 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~~~  323 (393)
                      ||+..|.||.|+|.++.|...
T Consensus        72 MnesEL~GrtirVN~AkP~ki   92 (298)
T KOG0111|consen   72 MNESELFGRTIRVNLAKPEKI   92 (298)
T ss_pred             CchhhhcceeEEEeecCCccc
Confidence            999999999999999987643

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.00  E-value=1.7e-09  Score=111.45  Aligned_cols=76  Identities=25%  Similarity=0.463  Sum_probs=67.4

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hhc
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~ln  304 (393)
                      +.||||||.+++++++|+..|..||.|..|.++.+.  .++               .++||+||+|.+.++|..|+ .||
T Consensus       279 ~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~--~tG---------------~skgfGfi~f~~~~~ar~a~e~ln  341 (549)
T KOG0147|consen  279 RRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDS--ETG---------------RSKGFGFITFVNKEDARKALEQLN  341 (549)
T ss_pred             hhhhhcccccCchHHHHhhhccCcccceeeeecccc--ccc---------------cccCcceEEEecHHHHHHHHHHhc
Confidence            349999999999999999999999999999996654  233               46699999999999999998 799


Q ss_pred             CceeCCeEEEEeec
Q 016231          305 MAVIGGNHIRLDRA  318 (393)
Q Consensus       305 g~~~~Gr~I~V~~a  318 (393)
                      |..|-|+.|.|...
T Consensus       342 gfelAGr~ikV~~v  355 (549)
T KOG0147|consen  342 GFELAGRLIKVSVV  355 (549)
T ss_pred             cceecCceEEEEEe
Confidence            99999999998764

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.99  E-value=8.8e-10  Score=113.25  Aligned_cols=78  Identities=26%  Similarity=0.421  Sum_probs=71.5

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hhc
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~ln  304 (393)
                      +.|||||||+++++++|..+|+..|.|.+++++.|+  +++.               .+||||++|.+.+.+..|+ .||
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~--~tG~---------------~~G~~f~~~~~~~~~~~a~~~lN   81 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDR--ETGK---------------PKGFGFCEFTDEETAERAIRNLN   81 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccc--cCCC---------------cCceeeEecCchhhHHHHHHhcC
Confidence            889999999999999999999999999999998876  4444               4599999999999999999 699


Q ss_pred             CceeCCeEEEEeecCC
Q 016231          305 MAVIGGNHIRLDRACP  320 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~  320 (393)
                      |..+.||.|+|.++..
T Consensus        82 g~~~~gr~l~v~~~~~   97 (435)
T KOG0108|consen   82 GAEFNGRKLRVNYASN   97 (435)
T ss_pred             CcccCCceEEeecccc
Confidence            9999999999999853

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=98.95  E-value=9.7e-10  Score=103.02  Aligned_cols=53  Identities=23%  Similarity=0.447  Sum_probs=50.7

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      -++||||||+|.++.+.|+..|++|    |+|...-|+.|..+|+++|||||+|.+.
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqf----GeI~eavvitd~~t~rskGyGfVTf~d~   64 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQF----GEIVEAVVITDKNTGRSKGYGFVTFRDA   64 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHh----CceEEEEEEeccCCccccceeeEEeecH
Confidence            3689999999999999999999999    9999999999999999999999999874

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=98.92  E-value=1.9e-09  Score=93.51  Aligned_cols=78  Identities=19%  Similarity=0.295  Sum_probs=69.6

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      .-.|||.++...+|+++|...|..||+|..|.|-.+.  .               +|-.+|||+|+|.+...|++|+ .+
T Consensus        72 GwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDR--R---------------tGy~KGYaLvEYet~keAq~A~~~~  134 (170)
T KOG0130|consen   72 GWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDR--R---------------TGYVKGYALVEYETLKEAQAAIDAL  134 (170)
T ss_pred             eEEEEEeccCcchhHHHHHHHHhhcccccceeecccc--c---------------cccccceeeeehHhHHHHHHHHHhc
Confidence            5779999999999999999999999999999884433  2               3446699999999999999999 79


Q ss_pred             cCceeCCeEEEEeecC
Q 016231          304 NMAVIGGNHIRLDRAC  319 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~  319 (393)
                      ||..|.|..|.|+|+.
T Consensus       135 Ng~~ll~q~v~VDw~F  150 (170)
T KOG0130|consen  135 NGAELLGQNVSVDWCF  150 (170)
T ss_pred             cchhhhCCceeEEEEE
Confidence            9999999999999985

>PF00076 RRM_1: RNA recognition motif

Probab=98.89  E-value=2e-09  Score=81.41  Aligned_cols=49  Identities=37%  Similarity=0.734  Sum_probs=46.2

Q ss_pred             eeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       339 LfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      |||+|||+.+++++|+++|..|    |.|..+.+..+ .++..+|||||+|.++
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~----g~i~~~~~~~~-~~~~~~~~a~V~F~~~   49 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQF----GKIESIKVMRN-SSGKSKGYAFVEFESE   49 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTT----STEEEEEEEEE-TTSSEEEEEEEEESSH
T ss_pred             cEEcCCCCcCCHHHHHHHHHHh----hhccccccccc-ccccccceEEEEEcCH
Confidence            7999999999999999999999    99999999998 6789999999999874

(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 ....

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.89  E-value=3.4e-10  Score=105.06  Aligned_cols=123  Identities=24%  Similarity=0.307  Sum_probs=100.6

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      .+||||+||...++++-|.++|-+.|+|..|.|+.+..   +.               -+ ||||.|.++-++..|+ -+
T Consensus         9 drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d---~~---------------~k-Fa~v~f~~E~sv~~a~~L~   69 (267)
T KOG4454|consen    9 DRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD---QE---------------QK-FAYVFFPNENSVQLAGQLE   69 (267)
T ss_pred             hhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc---CC---------------Cc-eeeeecccccchhhhhhhc
Confidence            58999999999999999999999999999999865431   11               12 9999999999999999 58


Q ss_pred             cCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCcc
Q 016231          304 NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKG  383 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kG  383 (393)
                      ||..+.++.|.|..-+...-             .-     |...++.+.+...|+..    |.|..+|+.++.+ |.++.
T Consensus        70 ng~~l~~~e~q~~~r~G~sh-------------ap-----ld~r~~~ei~~~v~s~a----~p~~~~R~~~~~d-~rnrn  126 (267)
T KOG4454|consen   70 NGDDLEEDEEQRTLRCGNSH-------------AP-----LDERVTEEILYEVFSQA----GPIEGVRIPTDND-GRNRN  126 (267)
T ss_pred             ccchhccchhhcccccCCCc-------------ch-----hhhhcchhhheeeeccc----CCCCCcccccccc-CCccC
Confidence            99999888887755432100             01     45558889999999987    8999999999975 88999


Q ss_pred             EEEEEe
Q 016231          384 IAYVLF  389 (393)
Q Consensus       384 faFVeF  389 (393)
                      ++||++
T Consensus       127 ~~~~~~  132 (267)
T KOG4454|consen  127 FGFVTY  132 (267)
T ss_pred             ccchhh
Confidence            999986

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.88  E-value=1.1e-09  Score=107.38  Aligned_cols=148  Identities=22%  Similarity=0.218  Sum_probs=111.5

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      ....++|+|++.+.+.+.++..++..+|.+..+.+....                 +...++||++|.|...+.+..||.
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~-----------------~~~~sk~~~s~~f~~ks~~~~~l~  148 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLE-----------------DSLSSKGGLSVHFAGKSQFFAALE  148 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhc-----------------cccccccceeeccccHHHHHHHHH
Confidence            347899999999999999999999999976665552211                 123467999999999999999998


Q ss_pred             hcCc-eeCCeEEEEeecCCCcccCCC-CCCCCcCCcceee-eCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCC
Q 016231          303 FNMA-VIGGNHIRLDRACPPRKKLKG-EDAPLYDIKKTVF-VGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMR  379 (393)
Q Consensus       303 lng~-~~~Gr~I~V~~a~~~~~~~~~-~~~~~~~~~~tLf-VgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg  379 (393)
                      +.+. .+.++.+.............. .......+..++| |+||++.++.++|+.+|..+    |.|..++++.++.+|
T Consensus       149 ~s~~~~~~~~~~~~dl~~~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~----~~i~~~r~~~~~~s~  224 (285)
T KOG4210|consen  149 ESGSKVLDGNKGEKDLNTRRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSS----GEITSVRLPTDEESG  224 (285)
T ss_pred             hhhccccccccccCcccccccccccchhcccccCccccceeecccccccchHHHhhhccCc----CcceeeccCCCCCcc
Confidence            7775 555555555444322210100 1011223344555 99999999999999999998    999999999999999


Q ss_pred             CCccEEEEEeee
Q 016231          380 VGKGIAYVLFKT  391 (393)
Q Consensus       380 ~~kGfaFVeF~t  391 (393)
                      .++|||||.|.+
T Consensus       225 ~~kg~a~~~~~~  236 (285)
T KOG4210|consen  225 DSKGFAYVDFSA  236 (285)
T ss_pred             chhhhhhhhhhh
Confidence            999999999964

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.87  E-value=3.9e-08  Score=96.67  Aligned_cols=156  Identities=22%  Similarity=0.300  Sum_probs=106.8

Q ss_pred             CcCCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHH
Q 016231          219 DDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE  298 (393)
Q Consensus       219 ~~~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~  298 (393)
                      .-+..-+..|||.|||.++|-+++.++|+.||.|.     +++  .++.++--   .=+-+.|+-+|-|.+.|...+++.
T Consensus       128 ~~~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~-----~d~--~t~epk~K---lYrd~~G~lKGDaLc~y~K~ESVe  197 (382)
T KOG1548|consen  128 NPEPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIM-----RDP--QTGEPKVK---LYRDNQGKLKGDALCCYIKRESVE  197 (382)
T ss_pred             CcccccCceEEecCCCCcccHHHHHHHHHhcceEe-----ccC--CCCCeeEE---EEecCCCCccCceEEEeecccHHH
Confidence            33344466799999999999999999999999653     222  22222200   001123567799999999999999


Q ss_pred             HHH-HhcCceeCCeEEEEeecCCCcccC----------------------C-----C--CCCCCcCCcceeeeCCCC---
Q 016231          299 AAL-AFNMAVIGGNHIRLDRACPPRKKL----------------------K-----G--EDAPLYDIKKTVFVGNLP---  345 (393)
Q Consensus       299 ~Al-~lng~~~~Gr~I~V~~a~~~~~~~----------------------~-----~--~~~~~~~~~~tLfVgNLp---  345 (393)
                      .|+ -|++..|.|+.|+|..|....+..                      .     .  .+.+.....++|.|.||=   
T Consensus       198 LA~~ilDe~~~rg~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~  277 (382)
T KOG1548|consen  198 LAIKILDEDELRGKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPE  277 (382)
T ss_pred             HHHHHhCcccccCcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHH
Confidence            999 599999999999999985321100                      0     0  011223345789999972   


Q ss_pred             -CCCC-------HHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          346 -FDVK-------DEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       346 -~~~t-------eedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                       +..+       +++|.+-++.|    |.|..|-|.-.    .+.|.+-|.|.+.
T Consensus       278 ~~~~~~~l~~dlkedl~eec~K~----G~v~~vvv~d~----hPdGvvtV~f~n~  324 (382)
T KOG1548|consen  278 DFEKNPDLLNDLKEDLTEECEKF----GQVRKVVVYDR----HPDGVVTVSFRNN  324 (382)
T ss_pred             HhccCHHHHHHHHHHHHHHHHHh----CCcceEEEecc----CCCceeEEEeCCh
Confidence             2233       45666778888    99999987533    3678899999874

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.85  E-value=3.9e-08  Score=98.40  Aligned_cols=137  Identities=20%  Similarity=0.297  Sum_probs=107.0

Q ss_pred             ccEEEEeCCCc-cCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          225 LRTIFVGNLPL-KVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       225 ~rtVFVgNLp~-~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ...|.|.||.. .+|.+.|..+|+-||.|..|.|....    +                  --|.|+|.+...|+.|+ .
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk----k------------------d~ALIQmsd~~qAqLA~~h  354 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK----K------------------DNALIQMSDGQQAQLAMEH  354 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC----C------------------cceeeeecchhHHHHHHHH
Confidence            67899999965 58999999999999999999996533    1                  26999999999999999 6


Q ss_pred             hcCceeCCeEEEEeecCCCcccCCC----------CC----------------CCCcCCcceeeeCCCCCCCCHHHHHHH
Q 016231          303 FNMAVIGGNHIRLDRACPPRKKLKG----------ED----------------APLYDIKKTVFVGNLPFDVKDEEIYQL  356 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~~~~~~~----------~~----------------~~~~~~~~tLfVgNLp~~~teedL~e~  356 (393)
                      |+|..|.|+.|+|..+.+..-....          +.                ...+.++.+|.+.|+|.++++++|+.+
T Consensus       355 L~g~~l~gk~lrvt~SKH~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~  434 (492)
T KOG1190|consen  355 LEGHKLYGKKLRVTLSKHTNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNL  434 (492)
T ss_pred             hhcceecCceEEEeeccCccccCCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHh
Confidence            9999999999999998764322111          00                012456789999999999999999999


Q ss_pred             hhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeee
Q 016231          357 FCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT  391 (393)
Q Consensus       357 F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t  391 (393)
                      |...+   |.|....+.     ++.+-+|++++.+
T Consensus       435 f~~~g---~~vkafkff-----~kd~kmal~q~~s  461 (492)
T KOG1190|consen  435 FQEPG---GQVKAFKFF-----QKDRKMALPQLES  461 (492)
T ss_pred             hhcCC---ceEEeeeec-----CCCcceeecccCC
Confidence            99873   555555543     2345688888765

>PF14259 RRM_6: RNA recognition motif (a

Probab=98.84  E-value=4.2e-09  Score=80.61  Aligned_cols=49  Identities=31%  Similarity=0.649  Sum_probs=44.4

Q ss_pred             eeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       339 LfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      |||+|||+++++++|+++|+.|    |.|..|++..+.+ |.++|+|||+|.++
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~----g~v~~v~~~~~~~-~~~~~~a~v~f~~~   49 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRF----GPVEKVRLIKNKD-GQSRGFAFVEFSSE   49 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTS----SBEEEEEEEESTT-SSEEEEEEEEESSH
T ss_pred             CEEeCCCCCCCHHHHHHHHHhc----CCcceEEEEeeec-cccCCEEEEEeCCH
Confidence            7999999999999999999999    8999999999977 99999999999874

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 ....

>PF13893 RRM_5: RNA recognition motif

Probab=98.84  E-value=1.3e-08  Score=75.13  Aligned_cols=55  Identities=27%  Similarity=0.458  Sum_probs=47.3

Q ss_pred             HHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-HhcCceeCCeEEEEeec
Q 016231          242 LIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRA  318 (393)
Q Consensus       242 L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~lng~~~~Gr~I~V~~a  318 (393)
                      |..+|+.||.|..|.+...                      .+|+|||+|.+.++|..|+ .||+..|.|+.|.|.+|
T Consensus         1 L~~~f~~fG~V~~i~~~~~----------------------~~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKK----------------------KRGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETT----------------------STTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeC----------------------CCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            6889999999999988331                      1279999999999999999 69999999999999875

(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 ....

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.80  E-value=1.6e-09  Score=98.21  Aligned_cols=56  Identities=20%  Similarity=0.568  Sum_probs=52.0

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +..+.-|||||||+.+|+-||.-+|++|    |+|..|.|++|..||.++||||+.|.+.
T Consensus        32 YkdsA~Iyiggl~~~LtEgDil~VFSqy----Ge~vdinLiRDk~TGKSKGFaFLcYEDQ   87 (219)
T KOG0126|consen   32 YKDSAYIYIGGLPYELTEGDILCVFSQY----GEIVDINLIRDKKTGKSKGFAFLCYEDQ   87 (219)
T ss_pred             cccceEEEECCCcccccCCcEEEEeecc----CceEEEEEEecCCCCcccceEEEEecCc
Confidence            4456789999999999999999999999    9999999999999999999999999763

>smart00361 RRM_1 RNA recognition motif

Probab=98.79  E-value=2.6e-08  Score=77.21  Aligned_cols=62  Identities=21%  Similarity=0.366  Sum_probs=50.1

Q ss_pred             HHHHHHHhc----ccCCeeEEE-EeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-HhcCceeCCeE
Q 016231          239 KKTLIKEFI----KFGEIDSVR-IRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNH  312 (393)
Q Consensus       239 ee~L~~~Fs----~~G~I~sVr-i~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~lng~~~~Gr~  312 (393)
                      +++|+.+|+    .||.|.+|. ++.++....               +.++|||||.|.+.++|..|+ .|||..+.|+.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~---------------~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~   66 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYE---------------NHKRGNVYITFERSEDAARAIVDLNGRYFDGRT   66 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCC---------------CCCcEEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            578889998    999999985 544332111               236699999999999999999 69999999999


Q ss_pred             EEE
Q 016231          313 IRL  315 (393)
Q Consensus       313 I~V  315 (393)
                      |.+
T Consensus        67 l~~   69 (70)
T smart00361       67 VKA   69 (70)
T ss_pred             EEe
Confidence            986

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.77  E-value=4.8e-10  Score=120.15  Aligned_cols=125  Identities=30%  Similarity=0.337  Sum_probs=106.5

Q ss_pred             CCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       221 ~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      +.+...++||+||++.+.+.+|...|..+|.+..+++.  ...+.+.               -+|+|||+|..++++.+|
T Consensus       663 ~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~--~h~n~~~---------------~rG~~Y~~F~~~~~~~aa  725 (881)
T KOG0128|consen  663 EIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIV--IHKNEKR---------------FRGKAYVEFLKPEHAGAA  725 (881)
T ss_pred             HHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHH--HHhhccc---------------cccceeeEeecCCchhhh
Confidence            34567899999999999999999999999988877764  1223333               459999999999999999


Q ss_pred             HHhcCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCC
Q 016231          301 LAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRV  380 (393)
Q Consensus       301 l~lng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~  380 (393)
                      +.++...+.|                         ...|||.|+|+..|.++|+.+|..+    |.++++++++.. .|+
T Consensus       726 V~f~d~~~~g-------------------------K~~v~i~g~pf~gt~e~~k~l~~~~----gn~~~~~~vt~r-~gk  775 (881)
T KOG0128|consen  726 VAFRDSCFFG-------------------------KISVAISGPPFQGTKEELKSLASKT----GNVTSLRLVTVR-AGK  775 (881)
T ss_pred             hhhhhhhhhh-------------------------hhhhheeCCCCCCchHHHHhhcccc----CCccccchhhhh-ccc
Confidence            9877766666                         2479999999999999999999999    999999999885 699


Q ss_pred             CccEEEEEeeec
Q 016231          381 GKGIAYVLFKTR  392 (393)
Q Consensus       381 ~kGfaFVeF~t~  392 (393)
                      ++|.|||.|.++
T Consensus       776 pkg~a~v~y~~e  787 (881)
T KOG0128|consen  776 PKGKARVDYNTE  787 (881)
T ss_pred             cccceeccCCCc
Confidence            999999999875

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.75  E-value=2e-08  Score=106.84  Aligned_cols=111  Identities=23%  Similarity=0.333  Sum_probs=84.3

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      .--++|||||+|+..+++.+|..+|..||.|.+|.++-                       ++|||||.+...++|..||
T Consensus       418 sV~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~-----------------------~R~cAfI~M~~RqdA~kal  474 (894)
T KOG0132|consen  418 SVCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP-----------------------PRGCAFIKMVRRQDAEKAL  474 (894)
T ss_pred             eEeeeeeeeccccchhhHHHHHHHHHhcccceeEeecc-----------------------CCceeEEEEeehhHHHHHH
Confidence            34579999999999999999999999999999998822                       5589999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhc
Q 016231          302 -AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCG  359 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~  359 (393)
                       +|+...+.++.|.|.|+....-+....+-    -...+=|.-||+..-..+|..++..
T Consensus       475 qkl~n~kv~~k~Iki~Wa~g~G~kse~k~~----wD~~lGVt~IP~~kLt~dl~~~~eg  529 (894)
T KOG0132|consen  475 QKLSNVKVADKTIKIAWAVGKGPKSEYKDY----WDVELGVTYIPWEKLTDDLEAWCEG  529 (894)
T ss_pred             HHHhcccccceeeEEeeeccCCcchhhhhh----hhcccCeeEeehHhcCHHHHHhhhh
Confidence             89999999999999999754322210000    0112334446777555557777654

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.74  E-value=2e-08  Score=104.30  Aligned_cols=147  Identities=20%  Similarity=0.402  Sum_probs=115.5

Q ss_pred             CcCCCcccEEEEeCCCccCCHHHHHHHhccc-----------C-CeeEEEEeeecccCCCCCccchhhhhhcccCCCceE
Q 016231          219 DDEGKLLRTIFVGNLPLKVKKKTLIKEFIKF-----------G-EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVH  286 (393)
Q Consensus       219 ~~~~~~~rtVFVgNLp~~~tee~L~~~Fs~~-----------G-~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~  286 (393)
                      .......+.+||+++|+.++++.+..+|..-           | .+..|.|-                       ....|
T Consensus       169 ~~~t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n-----------------------~~~nf  225 (500)
T KOG0120|consen  169 SQATRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLN-----------------------LEKNF  225 (500)
T ss_pred             cchhhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeec-----------------------ccccc
Confidence            3445567889999999999999999999863           2 24445441                       23469


Q ss_pred             EEEeeCCHHHHHHHHHhcCceeCCeEEEEeecCCCcccCCC----------C----CCCCcCCcceeeeCCCCCCCCHHH
Q 016231          287 AYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKG----------E----DAPLYDIKKTVFVGNLPFDVKDEE  352 (393)
Q Consensus       287 AFVeF~s~e~A~~Al~lng~~~~Gr~I~V~~a~~~~~~~~~----------~----~~~~~~~~~tLfVgNLp~~~teed  352 (393)
                      ||++|.+.+.|..|+.+++..+.|+.+.+............          .    ..........+||+|||..+++.+
T Consensus       226 a~ie~~s~~~at~~~~~~~~~f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q  305 (500)
T KOG0120|consen  226 AFIEFRSISEATEAMALDGIIFEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQ  305 (500)
T ss_pred             eeEEecCCCchhhhhcccchhhCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHH
Confidence            99999999999999999999999998887654321111100          0    011234567899999999999999


Q ss_pred             HHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          353 IYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       353 L~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +.++...|    |.+...+++.|..+|.++||||.+|.++
T Consensus       306 ~~Ell~~f----g~lk~f~lv~d~~~g~skg~af~ey~dp  341 (500)
T KOG0120|consen  306 VKELLDSF----GPLKAFRLVKDSATGNSKGFAFCEYCDP  341 (500)
T ss_pred             HHHHHHhc----ccchhheeecccccccccceeeeeeeCC
Confidence            99999999    9999999999999999999999999764

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=98.73  E-value=1.5e-08  Score=95.65  Aligned_cols=56  Identities=30%  Similarity=0.497  Sum_probs=52.6

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+...+|-|.||+.++++++|+++|..|    |.|..|.|.+|..||.+||||||.|.++
T Consensus       186 R~D~~tvRvtNLsed~~E~dL~eLf~~f----g~i~rvylardK~TG~~kGFAFVtF~sR  241 (270)
T KOG0122|consen  186 RDDEATVRVTNLSEDMREDDLEELFRPF----GPITRVYLARDKETGLSKGFAFVTFESR  241 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhhcc----CccceeEEEEccccCcccceEEEEEecH
Confidence            3456789999999999999999999999    9999999999999999999999999876

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.73  E-value=1.4e-08  Score=100.84  Aligned_cols=146  Identities=18%  Similarity=0.283  Sum_probs=105.9

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhccc----CCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKF----GEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~----G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      .-.|-+++||+++++.++..||..-    |..+.|-+++.+                  +++-.|-|||.|..+++|+.|
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp------------------dgrpTGdAFvlfa~ee~aq~a  222 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP------------------DGRPTGDAFVLFACEEDAQFA  222 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC------------------CCCcccceEEEecCHHHHHHH
Confidence            3458889999999999999999843    233456665543                  223558999999999999999


Q ss_pred             HHhcCceeCCeEEEEeecCCCc----------ccCCC------------CCCCCcCCcceeeeCCCCCCCCHHHHHHHhh
Q 016231          301 LAFNMAVIGGNHIRLDRACPPR----------KKLKG------------EDAPLYDIKKTVFVGNLPFDVKDEEIYQLFC  358 (393)
Q Consensus       301 l~lng~~~~Gr~I~V~~a~~~~----------~~~~~------------~~~~~~~~~~tLfVgNLp~~~teedL~e~F~  358 (393)
                      |..|...++-|.|.+-++....          .....            ...+......+|-+++||+..+.++|..+|.
T Consensus       223 L~khrq~iGqRYIElFRSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~Flg  302 (508)
T KOG1365|consen  223 LRKHRQNIGQRYIELFRSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLG  302 (508)
T ss_pred             HHHHHHHHhHHHHHHHHHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHH
Confidence            9877777777777665542110          00000            0011223367899999999999999999999


Q ss_pred             cCCCCCCCeEE--EEEeecCCCCCCccEEEEEeeec
Q 016231          359 GLNDLESSVEA--VRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       359 ~~~~~~G~I~~--VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .|.   -.|..  |.++.+ ..|++.|-|||+|.+.
T Consensus       303 dFa---~~i~f~gVHmv~N-~qGrPSGeAFIqm~na  334 (508)
T KOG1365|consen  303 DFA---TDIRFQGVHMVLN-GQGRPSGEAFIQMRNA  334 (508)
T ss_pred             HHh---hhcccceeEEEEc-CCCCcChhhhhhhhhh
Confidence            984   35555  888888 5799999999999763

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=98.71  E-value=1.6e-08  Score=97.62  Aligned_cols=56  Identities=23%  Similarity=0.444  Sum_probs=53.2

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .++-+||||+-|+.++++..|+..|+.|    |.|..|+||+|..||.++|||||+|.++
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~Y----G~IkrirlV~d~vTgkskGYAFIeye~e  153 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKY----GPIKRIRLVRDKVTGKSKGYAFIEYEHE  153 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhc----CcceeEEEeeecccCCccceEEEEeccH
Confidence            4677999999999999999999999999    9999999999999999999999999874

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.69  E-value=5.2e-08  Score=95.88  Aligned_cols=78  Identities=28%  Similarity=0.550  Sum_probs=68.8

Q ss_pred             CCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       221 ~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      ++....|||||||-..+++.+|+.+|-+||+|.+|++..                       ..|+|||+|.+..+|+.|
T Consensus       224 eD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~-----------------------~~~CAFv~ftTR~aAE~A  280 (377)
T KOG0153|consen  224 EDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILP-----------------------RKGCAFVTFTTREAAEKA  280 (377)
T ss_pred             cccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeec-----------------------ccccceeeehhhHHHHHH
Confidence            345578999999998999999999999999999999833                       237999999999999999


Q ss_pred             H--HhcCceeCCeEEEEeecCCC
Q 016231          301 L--AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       301 l--~lng~~~~Gr~I~V~~a~~~  321 (393)
                      .  .+|...|+|++|.|.|..+.
T Consensus       281 ae~~~n~lvI~G~Rl~i~Wg~~~  303 (377)
T KOG0153|consen  281 AEKSFNKLVINGFRLKIKWGRPK  303 (377)
T ss_pred             HHhhcceeeecceEEEEEeCCCc
Confidence            8  38888899999999999873

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.67  E-value=2.9e-08  Score=97.76  Aligned_cols=82  Identities=23%  Similarity=0.268  Sum_probs=72.5

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ..+...|||.-|.+-+|.++|.-+|+.||.|.+|.++++..  +               |-+-.||||+|.+.+++++|.
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~k--t---------------gdsLqyaFiEFen~escE~Ay  298 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRK--T---------------GDSLQYAFIEFENKESCEQAY  298 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEeccc--c---------------cchhheeeeeecchhhHHHHH
Confidence            34568899999999999999999999999999999988752  2               234469999999999999998


Q ss_pred             -HhcCceeCCeEEEEeecCC
Q 016231          302 -AFNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~  320 (393)
                       +|+...|..+.|.|.++..
T Consensus       299 FKMdNvLIDDrRIHVDFSQS  318 (479)
T KOG0415|consen  299 FKMDNVLIDDRRIHVDFSQS  318 (479)
T ss_pred             hhhcceeeccceEEeehhhh
Confidence             9999999999999999854

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

Probab=98.62  E-value=5.8e-08  Score=89.62  Aligned_cols=53  Identities=38%  Similarity=0.757  Sum_probs=50.7

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+|||+|||+.+++++|+++|..|    |.|..|+|+.+..+|.++|||||+|.++
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~----g~~~~~~~~~d~~~~~~~g~~~v~f~~~  167 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKF----GPVKRVRLVRDRETGKSRGFAFVEFESE  167 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhc----CceeEEEeeeccccCccCceEEEEecCH
Confidence            5899999999999999999999999    9999999999998999999999999874

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.62  E-value=3.1e-07  Score=93.99  Aligned_cols=144  Identities=22%  Similarity=0.291  Sum_probs=106.1

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeE-EEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDS-VRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~s-Vri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      ....|-+++|||.+|+++|.+||+-+-.|.. |.|+.++                  .+..+|=|||+|.+.+.|+.||.
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~------------------rgR~tGEAfVqF~sqe~ae~Al~  163 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ------------------RGRPTGEAFVQFESQESAEIALG  163 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC------------------CCCcccceEEEecCHHHHHHHHH
Confidence            4578999999999999999999998765544 3333322                  23367999999999999999998


Q ss_pred             hcCceeCCeEEEEeecCCC-------------------cc--cCCC---------------------------------C
Q 016231          303 FNMAVIGGNHIRLDRACPP-------------------RK--KLKG---------------------------------E  328 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~-------------------~~--~~~~---------------------------------~  328 (393)
                      .|...|..|.|.|..+...                   ..  ..+.                                 .
T Consensus       164 rhre~iGhRYIEvF~Ss~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~  243 (510)
T KOG4211|consen  164 RHRENIGHRYIEVFRSSRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQ  243 (510)
T ss_pred             HHHHhhccceEEeehhHHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCcccc
Confidence            8888888888888765210                   00  0000                                 0


Q ss_pred             C-----------------C--C-----------CcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCC
Q 016231          329 D-----------------A--P-----------LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHM  378 (393)
Q Consensus       329 ~-----------------~--~-----------~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~t  378 (393)
                      +                 .  +           .......+++++||+..+..++..+|...     ....|.|-..+ +
T Consensus       244 d~~~~gs~~~~~~~~~~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl-----~p~~v~i~ig~-d  317 (510)
T KOG4211|consen  244 DYGNFGSYGGGRDPNYPVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPL-----NPYRVHIEIGP-D  317 (510)
T ss_pred             ccccccccccccccccCCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCC-----CceeEEEEeCC-C
Confidence            0                 0  0           00112568899999999999999999986     45588887775 6


Q ss_pred             CCCccEEEEEeee
Q 016231          379 RVGKGIAYVLFKT  391 (393)
Q Consensus       379 g~~kGfaFVeF~t  391 (393)
                      |+..|-|+|+|.|
T Consensus       318 Gr~TGEAdveF~t  330 (510)
T KOG4211|consen  318 GRATGEADVEFAT  330 (510)
T ss_pred             CccCCcceeeccc
Confidence            9999999999976

>smart00362 RRM_2 RNA recognition motif

Probab=98.62  E-value=8.8e-08  Score=71.16  Aligned_cols=49  Identities=39%  Similarity=0.746  Sum_probs=45.5

Q ss_pred             eeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       338 tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +|||+|||..++.++|+++|..|    |.|..+.+..++  +.++|+|||+|.+.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~----g~v~~~~~~~~~--~~~~~~~~v~f~~~   49 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKF----GPIESVKIPKDT--GKSKGFAFVEFESE   49 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhc----CCEEEEEEecCC--CCCCceEEEEeCCH
Confidence            58999999999999999999999    999999999886  78899999999874

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=98.56  E-value=7.2e-08  Score=87.54  Aligned_cols=81  Identities=28%  Similarity=0.364  Sum_probs=68.7

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeE-EEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDS-VRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~s-Vri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ...||||||.+.+++..|+..|+.||.|.+ -.|++++  +++.               .+|||||.|.+.+.+.+|+ .
T Consensus        96 ganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~--~tg~---------------~~~~g~i~~~sfeasd~ai~s  158 (203)
T KOG0131|consen   96 GANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDP--DTGN---------------PKGFGFINYASFEASDAAIGS  158 (203)
T ss_pred             cccccccccCcchhHHHHHHHHHhccccccCCcccccc--cCCC---------------CCCCeEEechhHHHHHHHHHH
Confidence            377999999999999999999999998754 2565655  2333               4589999999999999999 7


Q ss_pred             hcCceeCCeEEEEeecCCCc
Q 016231          303 FNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~~  322 (393)
                      +||+.+..+.|.|.++....
T Consensus       159 ~ngq~l~nr~itv~ya~k~~  178 (203)
T KOG0131|consen  159 MNGQYLCNRPITVSYAFKKD  178 (203)
T ss_pred             hccchhcCCceEEEEEEecC
Confidence            99999999999999987543

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=98.53  E-value=1e-07  Score=82.19  Aligned_cols=53  Identities=28%  Similarity=0.501  Sum_probs=49.8

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +.|||||||++.+++++|+++|+.|    |.|..|.+-.|..+-.+=|||||+|.++
T Consensus        36 S~tvyVgNlSfyttEEqiyELFs~c----G~irriiMGLdr~kktpCGFCFVeyy~~   88 (153)
T KOG0121|consen   36 SCTVYVGNLSFYTTEEQIYELFSKC----GDIRRIIMGLDRFKKTPCGFCFVEYYSR   88 (153)
T ss_pred             cceEEEeeeeeeecHHHHHHHHHhc----cchheeEeccccCCcCccceEEEEEecc
Confidence            5799999999999999999999999    9999999999998888999999999764

>smart00360 RRM RNA recognition motif

Probab=98.51  E-value=2.2e-07  Score=68.64  Aligned_cols=48  Identities=42%  Similarity=0.741  Sum_probs=44.8

Q ss_pred             eCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          341 VGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       341 VgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      |+|||..+++++|+++|+.|    |.|..+.+..++.++.++|||||+|.+.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~----g~v~~~~i~~~~~~~~~~~~a~v~f~~~   48 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKF----GKIESVRLVRDKDTGKSKGFAFVEFESE   48 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhh----CCEeEEEEEeCCCCCCCCceEEEEeCCH
Confidence            68999999999999999999    9999999999988899999999999864

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=98.51  E-value=1.2e-07  Score=91.54  Aligned_cols=75  Identities=17%  Similarity=0.322  Sum_probs=68.8

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      .+.+.+||||||.+.++-.+|+..|..||+|..|.|+.                         +|+||.|.-.++|..|+
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk-------------------------dy~fvh~d~~eda~~ai  129 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK-------------------------DYAFVHFDRAEDAVEAI  129 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeeec-------------------------ceeEEEEeeccchHHHH
Confidence            44578899999999999999999999999999999943                         59999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCC
Q 016231          302 -AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~  321 (393)
                       .||+++|.|+++.|+.+...
T Consensus       130 r~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen  130 RGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             hcccccccccceeeeeeeccc
Confidence             79999999999999998654

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.50  E-value=6.8e-08  Score=104.35  Aligned_cols=135  Identities=19%  Similarity=0.266  Sum_probs=107.7

Q ss_pred             CcCCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHH
Q 016231          219 DDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE  298 (393)
Q Consensus       219 ~~~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~  298 (393)
                      .++....+|||+|||+..+++.+|+..|..+|.|..|.|-+.++                  ++..-||||.|.+...+.
T Consensus       366 ~DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~------------------~~esa~~f~~~~n~dmtp  427 (975)
T KOG0112|consen  366 LDDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI------------------KTESAYAFVSLLNTDMTP  427 (975)
T ss_pred             ccchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC------------------CcccchhhhhhhccccCc
Confidence            35567789999999999999999999999999999999855432                  123349999999999999


Q ss_pred             HHH-HhcCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCC
Q 016231          299 AAL-AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPH  377 (393)
Q Consensus       299 ~Al-~lng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~  377 (393)
                      .|+ .+.+..|....+++.+..+           ...+.+.++|++|+..+....|...|..|    |.|..|.+-    
T Consensus       428 ~ak~e~s~~~I~~g~~r~glG~~-----------kst~ttr~~sgglg~w~p~~~l~r~fd~f----Gpir~Idy~----  488 (975)
T KOG0112|consen  428 SAKFEESGPLIGNGTHRIGLGQP-----------KSTPTTRLQSGGLGPWSPVSRLNREFDRF----GPIRIIDYR----  488 (975)
T ss_pred             ccchhhcCCccccCccccccccc-----------ccccceeeccCCCCCCChHHHHHHHhhcc----Ccceeeecc----
Confidence            887 7888777655555554432           24467899999999999999999999999    899887762    


Q ss_pred             CCCCccEEEEEeeec
Q 016231          378 MRVGKGIAYVLFKTR  392 (393)
Q Consensus       378 tg~~kGfaFVeF~t~  392 (393)
                      -|  --||||.|.++
T Consensus       489 hg--q~yayi~yes~  501 (975)
T KOG0112|consen  489 HG--QPYAYIQYESP  501 (975)
T ss_pred             cC--CcceeeecccC
Confidence            22  34999999764

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.48  E-value=2.7e-07  Score=97.70  Aligned_cols=90  Identities=24%  Similarity=0.400  Sum_probs=76.7

Q ss_pred             CCCCcCCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHH
Q 016231          216 EGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQ  295 (393)
Q Consensus       216 ~~~~~~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e  295 (393)
                      ..+|+.+.....|||+||++.+++..|...|..||+|.+|+|+......... |             .+-|+||-|.+..
T Consensus       165 gsfDdgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~-r-------------~r~cgfvafmnR~  230 (877)
T KOG0151|consen  165 GSFDDGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKR-R-------------ERNCGFVAFMNRA  230 (877)
T ss_pred             CcCCCCCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhc-c-------------ccccceeeehhhh
Confidence            4467778888999999999999999999999999999999998765322221 1             3459999999999


Q ss_pred             HHHHHH-HhcCceeCCeEEEEeecC
Q 016231          296 STEAAL-AFNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       296 ~A~~Al-~lng~~~~Gr~I~V~~a~  319 (393)
                      +|++|+ .|+|..+.++.+.+.|+.
T Consensus       231 D~era~k~lqg~iv~~~e~K~gWgk  255 (877)
T KOG0151|consen  231 DAERALKELQGIIVMEYEMKLGWGK  255 (877)
T ss_pred             hHHHHHHHhcceeeeeeeeeecccc
Confidence            999999 799999999999999984

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.47  E-value=4.6e-07  Score=83.76  Aligned_cols=80  Identities=16%  Similarity=0.296  Sum_probs=67.8

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhccc-CCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKF-GEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~-G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..-+||+.||+.+.+..|..+|.+| |.|..+++-|..                 .+|.|+|||||+|.+.+.|..|- .
T Consensus        49 ~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnk-----------------rTGNSKgYAFVEFEs~eVA~IaAET  111 (214)
T KOG4208|consen   49 EGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNK-----------------RTGNSKGYAFVEFESEEVAKIAAET  111 (214)
T ss_pred             ccceeecccccchhHHHHhhhhhhcCCeeEEEEeeccc-----------------ccCCcCceEEEEeccHHHHHHHHHH
Confidence            4569999999999999999999998 677777763432                 25668899999999999999888 6


Q ss_pred             hcCceeCCeEEEEeecCCC
Q 016231          303 FNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~  321 (393)
                      ||+..|.|+.|.|....+.
T Consensus       112 MNNYLl~e~lL~c~vmppe  130 (214)
T KOG4208|consen  112 MNNYLLMEHLLECHVMPPE  130 (214)
T ss_pred             hhhhhhhhheeeeEEeCch
Confidence            9999999999999887554

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.43  E-value=3.9e-07  Score=94.38  Aligned_cols=81  Identities=15%  Similarity=0.339  Sum_probs=70.2

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...+.|||.+|+..+...+|+.+|++||.|+-..++++.    ..|-             -++|+||++.+...|..|| 
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNa----RsPG-------------aRCYGfVTMSts~eAtkCI~  465 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNA----RSPG-------------ARCYGFVTMSTSAEATKCIE  465 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecC----CCCC-------------cceeEEEEecchHHHHHHHH
Confidence            346889999999999999999999999999999886643    2221             4589999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCC
Q 016231          302 AFNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~  320 (393)
                      .|+.+.|.|+.|.|..+..
T Consensus       466 hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  466 HLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             Hhhhhhhcceeeeeeeccc
Confidence            6999999999999998853

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.41  E-value=4.3e-07  Score=89.96  Aligned_cols=115  Identities=21%  Similarity=0.284  Sum_probs=85.4

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhc
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~ln  304 (393)
                      ...||||+||.++++++|+.+|.+||.|..+.++.+.  .+..               .+||+||.|.+++++..++...
T Consensus        97 tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~--~~~~---------------~rgFgfv~~~~e~sVdkv~~~~  159 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDK--TTSR---------------PRGFGFVTFDSEDSVDKVTLQK  159 (311)
T ss_pred             eeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecc--cccc---------------cccceeeEeccccccceecccc
Confidence            5689999999999999999999999999988887765  2333               5599999999999999999888


Q ss_pred             CceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcC
Q 016231          305 MAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGL  360 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~  360 (393)
                      -+.|+|+.+.|..|.+.........    .........|++-..+.-.|..+|..|
T Consensus       160 f~~~~gk~vevkrA~pk~~~~~~~~----~~~~~~~~~~~g~~~~~~~l~~~~~g~  211 (311)
T KOG4205|consen  160 FHDFNGKKVEVKRAIPKEVMQSTKS----SVSTRGKGNNLGNGRTGFFLKKYFKGY  211 (311)
T ss_pred             eeeecCceeeEeeccchhhcccccc----ccccccccccccccccccccchhcccc
Confidence            9999999999999987644322111    011122222444444455566666666

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.41  E-value=8.2e-07  Score=92.42  Aligned_cols=146  Identities=21%  Similarity=0.304  Sum_probs=106.0

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      .+.+||+|||...++.++.+++..||++....++.+..  +               +.++||||.+|.+......|+ .|
T Consensus       289 ~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~--~---------------g~skg~af~ey~dpsvtd~A~agL  351 (500)
T KOG0120|consen  289 PNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSA--T---------------GNSKGFAFCEYCDPSVTDQAIAGL  351 (500)
T ss_pred             cchhhhccCcCccCHHHHHHHHHhcccchhheeecccc--c---------------ccccceeeeeeeCCcchhhhhccc
Confidence            46799999999999999999999999999988866552  1               236699999999999999999 69


Q ss_pred             cCceeCCeEEEEeecCCCcccCCCCC---------------CCCcCCcceeeeCCC--CCCC-CH-------HHHHHHhh
Q 016231          304 NMAVIGGNHIRLDRACPPRKKLKGED---------------APLYDIKKTVFVGNL--PFDV-KD-------EEIYQLFC  358 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~~~~~~~~---------------~~~~~~~~tLfVgNL--p~~~-te-------edL~e~F~  358 (393)
                      ||..+.+..|.|+.++..........               .....++..|.+.|+  |.++ .+       ++|+.-+.
T Consensus       352 nGm~lgd~~lvvq~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~  431 (500)
T KOG0120|consen  352 NGMQLGDKKLVVQRAIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECA  431 (500)
T ss_pred             chhhhcCceeEeehhhccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhc
Confidence            99999999999999875432221110               112334566666665  2222 12       23444456


Q ss_pred             cCCCCCCCeEEEEEeec-C--CCCCCccEEEEEeee
Q 016231          359 GLNDLESSVEAVRVIRH-P--HMRVGKGIAYVLFKT  391 (393)
Q Consensus       359 ~~~~~~G~I~~VrI~~d-~--~tg~~kGfaFVeF~t  391 (393)
                      .|    |.|.+|.|+++ .  ...-+-|--||+|.+
T Consensus       432 k~----g~v~~v~ipr~~~~~~~~~G~GkVFVefas  463 (500)
T KOG0120|consen  432 KF----GAVRSVEIPRPYPDENPVPGTGKVFVEFAD  463 (500)
T ss_pred             cc----CceeEEecCCCCCCCCcCCCcccEEEEecC
Confidence            66    99999999998 2  222345667999986

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=98.38  E-value=8.3e-07  Score=66.18  Aligned_cols=50  Identities=44%  Similarity=0.788  Sum_probs=45.5

Q ss_pred             eeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       338 tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +|+|+|||..+++++|+++|+.|    |.|..+.+..++.+ .++|+|||+|.+.
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~----g~i~~~~~~~~~~~-~~~~~~~v~f~s~   50 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKF----GKVESVRIVRDKDT-KSKGFAFVEFEDE   50 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhc----CCEEEEEEeeCCCC-CcceEEEEEECCH
Confidence            58999999999999999999999    89999999988654 7799999999864

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).

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=98.38  E-value=4.3e-07  Score=88.94  Aligned_cols=54  Identities=26%  Similarity=0.475  Sum_probs=48.2

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+..++|+|.|||+..-+.||+.+|..|    |.|.+|.|+.+. -| +||||||+|.+.
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kf----G~VldVEIIfNE-RG-SKGFGFVTmen~  146 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKF----GKVLDVEIIFNE-RG-SKGFGFVTMENP  146 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhh----CceeeEEEEecc-CC-CCccceEEecCh
Confidence            4456899999999999999999999999    999999999883 34 899999999864

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=98.36  E-value=7.7e-07  Score=88.18  Aligned_cols=80  Identities=21%  Similarity=0.414  Sum_probs=70.9

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      +.-..|||..+.++.+++||+..|..||+|..|.|-+.+.                 .+.|+||+||+|.+..+...|+ 
T Consensus       208 k~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt-----------------~~~HkGyGfiEy~n~qs~~eAia  270 (544)
T KOG0124|consen  208 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPT-----------------GRGHKGYGFIEYNNLQSQSEAIA  270 (544)
T ss_pred             HhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCC-----------------CCCccceeeEEeccccchHHHhh
Confidence            3457899999999999999999999999999999977652                 1237899999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecC
Q 016231          302 AFNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~  319 (393)
                      .||-..++|..|+|..+.
T Consensus       271 sMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  271 SMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             hcchhhcccceEeccccc
Confidence            699999999999998774

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=98.34  E-value=5.9e-07  Score=83.17  Aligned_cols=58  Identities=22%  Similarity=0.383  Sum_probs=53.4

Q ss_pred             CCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          331 PLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       331 ~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +..+.-.+|.|-||-+-++.++|+.+|+.|    |.|-.|.|++|+.|+.++|||||-|..+
T Consensus         8 Pdv~gm~SLkVdNLTyRTspd~LrrvFekY----G~vgDVyIPrdr~Tr~sRgFaFVrf~~k   65 (256)
T KOG4207|consen    8 PDVEGMTSLKVDNLTYRTSPDDLRRVFEKY----GRVGDVYIPRDRYTRQSRGFAFVRFHDK   65 (256)
T ss_pred             CCcccceeEEecceeccCCHHHHHHHHHHh----CcccceecccccccccccceeEEEeeec
Confidence            345667899999999999999999999999    9999999999999999999999999763

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.29  E-value=1.1e-06  Score=83.96  Aligned_cols=78  Identities=22%  Similarity=0.276  Sum_probs=69.0

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhc
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~ln  304 (393)
                      ...|||||+.+.+|.+.|..+|..||.|..|.|+.+.+.                 ++.+|||||+|.+.+.++.||.||
T Consensus       101 ~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~-----------------~~~k~~~yvef~~~~~~~~ay~l~  163 (231)
T KOG4209|consen  101 APSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFR-----------------GHPKGFAYVEFSSYELVEEAYKLD  163 (231)
T ss_pred             CceEEEeccccccccchhhheeeccCCccceeeeccccC-----------------CCcceeEEEecccHhhhHHHhhcC
Confidence            578999999999999999999999999998888776532                 235599999999999999999999


Q ss_pred             CceeCCeEEEEeecC
Q 016231          305 MAVIGGNHIRLDRAC  319 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~  319 (393)
                      +..|.|+.|.|.+..
T Consensus       164 gs~i~~~~i~vt~~r  178 (231)
T KOG4209|consen  164 GSEIPGPAIEVTLKR  178 (231)
T ss_pred             Ccccccccceeeeee
Confidence            999999999998764

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.27  E-value=1.3e-06  Score=72.85  Aligned_cols=52  Identities=25%  Similarity=0.676  Sum_probs=45.9

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeee
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT  391 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t  391 (393)
                      .+..+.|||+|||+.+|.+++.++|..|    |.|..|||-..+.   -+|-|||.|.+
T Consensus        15 pevnriLyirNLp~~ITseemydlFGky----g~IrQIRiG~~k~---TrGTAFVVYed   66 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITSEEMYDLFGKY----GTIRQIRIGNTKE---TRGTAFVVYED   66 (124)
T ss_pred             hhhheeEEEecCCccccHHHHHHHhhcc----cceEEEEecCccC---cCceEEEEehH
Confidence            3456899999999999999999999999    9999999976654   58999999975

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.26  E-value=8.9e-07  Score=91.32  Aligned_cols=52  Identities=27%  Similarity=0.620  Sum_probs=50.2

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..|||||+|+++++++|..+|...    |.|.+++++.|+.+|.++||||++|.+.
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~----g~v~s~~~v~D~~tG~~~G~~f~~~~~~   70 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGV----GPVLSFRLVYDRETGKPKGFGFCEFTDE   70 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhcc----CccceeeecccccCCCcCceeeEecCch
Confidence            799999999999999999999998    9999999999999999999999999874

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=98.25  E-value=1.7e-06  Score=87.47  Aligned_cols=74  Identities=20%  Similarity=0.284  Sum_probs=64.3

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      .+..|+|||+|||++.|.+.|++-|..||.|..+.|+.     .+               +++|  .|.|.++++|+.|+
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime-----~G---------------kskG--VVrF~s~edAEra~  590 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME-----NG---------------KSKG--VVRFFSPEDAERAC  590 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHhccceehhhhhc-----cC---------------Cccc--eEEecCHHHHHHHH
Confidence            45679999999999999999999999999998887732     22               2445  89999999999999


Q ss_pred             -HhcCceeCCeEEEEee
Q 016231          302 -AFNMAVIGGNHIRLDR  317 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~  317 (393)
                       .||+..+.||.|.|.+
T Consensus       591 a~Mngs~l~Gr~I~V~y  607 (608)
T KOG4212|consen  591 ALMNGSRLDGRNIKVTY  607 (608)
T ss_pred             HHhccCcccCceeeeee
Confidence             5999999999999976

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.24  E-value=1.3e-06  Score=83.56  Aligned_cols=84  Identities=26%  Similarity=0.410  Sum_probs=72.1

Q ss_pred             CCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       221 ~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      +..+.|.|||-.||....+.+|..+|-.||-|.+.++-.|+.                 +.+|++|+||.|.+..++++|
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRA-----------------TNQSKCFGFVSfDNp~SaQaA  343 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRA-----------------TNQSKCFGFVSFDNPASAQAA  343 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhc-----------------cccccceeeEecCCchhHHHH
Confidence            344579999999999999999999999999999988855442                 234778999999999999999


Q ss_pred             H-HhcCceeCCeEEEEeecCCC
Q 016231          301 L-AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       301 l-~lng~~~~Gr~I~V~~a~~~  321 (393)
                      | .|||..|.-++|.|+.-.+.
T Consensus       344 IqAMNGFQIGMKRLKVQLKRPk  365 (371)
T KOG0146|consen  344 IQAMNGFQIGMKRLKVQLKRPK  365 (371)
T ss_pred             HHHhcchhhhhhhhhhhhcCcc
Confidence            9 89999999899998876554

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.20  E-value=1.3e-05  Score=80.03  Aligned_cols=150  Identities=18%  Similarity=0.213  Sum_probs=103.6

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhc
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~ln  304 (393)
                      ...|-.++|||..++.+|..||.-.--..-.+.+..   .....              -.|.|.|.|.+.+.-+.|++.+
T Consensus        60 ~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG---~~qgr--------------Rnge~lvrf~d~e~RdlalkRh  122 (508)
T KOG1365|consen   60 NVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCL---NAQGR--------------RNGEALVRFVDPEGRDLALKRH  122 (508)
T ss_pred             ceEEEecCCCCCcccCCHHHHHhhhhccccceeeee---hhhhc--------------cccceEEEecCchhhhhhhHhh
Confidence            455677899999999999999985421111111111   11122              2289999999999999999888


Q ss_pred             CceeCCeEEEEeecCCCcccCC-C---CCC---CCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCC
Q 016231          305 MAVIGGNHIRLDRACPPRKKLK-G---EDA---PLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPH  377 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~~~~~~~-~---~~~---~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~  377 (393)
                      ...+.+|.|.|-.+....--.. +   ...   ......-.|-+++||+++++.++..+|...-.+.|..+.|-+++.+ 
T Consensus       123 khh~g~ryievYka~ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-  201 (508)
T KOG1365|consen  123 KHHMGTRYIEVYKATGEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-  201 (508)
T ss_pred             hhhccCCceeeeccCchhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-
Confidence            8889999999977754311000 0   000   1122345688889999999999999995321223567788888886 


Q ss_pred             CCCCccEEEEEeeec
Q 016231          378 MRVGKGIAYVLFKTR  392 (393)
Q Consensus       378 tg~~kGfaFVeF~t~  392 (393)
                      .|+..|-|||.|..+
T Consensus       202 dgrpTGdAFvlfa~e  216 (508)
T KOG1365|consen  202 DGRPTGDAFVLFACE  216 (508)
T ss_pred             CCCcccceEEEecCH
Confidence            589999999999875

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.19  E-value=3.5e-06  Score=86.53  Aligned_cols=80  Identities=21%  Similarity=0.320  Sum_probs=66.3

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      ....+|||+|||++++..+|.++|..||.|...+|.....                 .+.+-+||||+|.+..+++.||.
T Consensus       286 ~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~-----------------~~~~~~fgFV~f~~~~~~~~~i~  348 (419)
T KOG0116|consen  286 ADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSP-----------------GGKNPCFGFVEFENAAAVQNAIE  348 (419)
T ss_pred             ecccceEeecCCCCCCHHHHHHHHhhcccccccceEEecc-----------------CCCcCceEEEEEeecchhhhhhh
Confidence            4456699999999999999999999999999988855321                 01123799999999999999997


Q ss_pred             hcCceeCCeEEEEeecC
Q 016231          303 FNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~  319 (393)
                      -+-..++|+.+.|.--.
T Consensus       349 Asp~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  349 ASPLEIGGRKLNVEEKR  365 (419)
T ss_pred             cCccccCCeeEEEEecc
Confidence            77888999999997653

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.17  E-value=9e-07  Score=82.62  Aligned_cols=54  Identities=19%  Similarity=0.412  Sum_probs=51.0

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeee
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT  391 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t  391 (393)
                      ...++||||+|...+++.-|...|-+|    |.|..|.|+.|..++++||||||+|.-
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPF----GDI~dIqiPlDyesqkHRgFgFVefe~   61 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPF----GDIKDIQIPLDYESQKHRGFGFVEFEE   61 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccc----cchhhcccccchhcccccceeEEEeec
Confidence            356899999999999999999999999    999999999999999999999999964

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.15  E-value=1.1e-06  Score=87.83  Aligned_cols=143  Identities=21%  Similarity=0.185  Sum_probs=104.8

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhcC
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNM  305 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~lng  305 (393)
                      ..|-|.||.+.+|.++++.||.-+|.|..++|.... .+...+             ...-.|||.|.+...+..|..|-.
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~-~d~~~p-------------v~sRtcyVkf~d~~sv~vaQhLtn   73 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNV-DDSKIP-------------VISRTCYVKFLDSQSVTVAQHLTN   73 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCC-CCccCc-------------ceeeeEEEeccCCcceeHHhhhcc
Confidence            479999999999999999999999999999984321 122222             234589999999999999998989


Q ss_pred             ceeCCeEEEEeecCCCcc-----------------------cCCCCC--------------CCC----------cCCcce
Q 016231          306 AVIGGNHIRLDRACPPRK-----------------------KLKGED--------------APL----------YDIKKT  338 (393)
Q Consensus       306 ~~~~Gr~I~V~~a~~~~~-----------------------~~~~~~--------------~~~----------~~~~~t  338 (393)
                      +.|-++.|.|.++...-.                       .+.++.              .|.          .+..++
T Consensus        74 tvfvdraliv~p~~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt  153 (479)
T KOG4676|consen   74 TVFVDRALIVRPYGDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRT  153 (479)
T ss_pred             ceeeeeeEEEEecCCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhh
Confidence            999999988876532100                       000000              000          112378


Q ss_pred             eeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEee
Q 016231          339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFK  390 (393)
Q Consensus       339 LfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~  390 (393)
                      |+|++|+..|...++.++|+.+    |.|...++....    ..-+|-|.|.
T Consensus       154 ~~v~sl~~~~~l~e~~e~f~r~----Gev~ya~~ask~----~s~~c~~sf~  197 (479)
T KOG4676|consen  154 REVQSLISAAILPESGESFERK----GEVSYAHTASKS----RSSSCSHSFR  197 (479)
T ss_pred             hhhhcchhhhcchhhhhhhhhc----chhhhhhhhccC----CCcchhhhHh
Confidence            9999999999999999999999    899888875443    3456777774

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.14  E-value=1.8e-06  Score=89.57  Aligned_cols=71  Identities=32%  Similarity=0.459  Sum_probs=63.0

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      +-..++|||-|||..++.++|..+|+.||+|..|+.-  +                    ..+|.+||+|.+..+|+.|+
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t--~--------------------~~~~~~~v~FyDvR~A~~Al  129 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRET--P--------------------NKRGIVFVEFYDVRDAERAL  129 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcc--c--------------------ccCceEEEEEeehHhHHHHH
Confidence            4457999999999999999999999999999887651  1                    24589999999999999999


Q ss_pred             -HhcCceeCCeEEE
Q 016231          302 -AFNMAVIGGNHIR  314 (393)
Q Consensus       302 -~lng~~~~Gr~I~  314 (393)
                       +||+..|.|+.|.
T Consensus       130 k~l~~~~~~~~~~k  143 (549)
T KOG4660|consen  130 KALNRREIAGKRIK  143 (549)
T ss_pred             HHHHHHHhhhhhhc
Confidence             7999999999888

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.10  E-value=8.4e-06  Score=78.11  Aligned_cols=79  Identities=23%  Similarity=0.380  Sum_probs=67.0

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      ..+|+|.|||+.|+.++|.++|..||.+..+-+-.++   .               +.+.|.|-|.|...++|..|+ .+
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~---~---------------G~s~Gta~v~~~r~~DA~~avk~~  144 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR---A---------------GRSLGTADVSFNRRDDAERAVKKY  144 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC---C---------------CCCCccceeeecchHhHHHHHHHh
Confidence            4789999999999999999999999977766663322   2               235699999999999999999 79


Q ss_pred             cCceeCCeEEEEeecCCC
Q 016231          304 NMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~  321 (393)
                      |+..+.|+.|.+....++
T Consensus       145 ~gv~ldG~~mk~~~i~~~  162 (243)
T KOG0533|consen  145 NGVALDGRPMKIEIISSP  162 (243)
T ss_pred             cCcccCCceeeeEEecCc
Confidence            999999999999887654

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.05  E-value=6.6e-06  Score=82.75  Aligned_cols=137  Identities=16%  Similarity=0.191  Sum_probs=93.9

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH-
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~-  302 (393)
                      +++.|.++|||++++|.+|..++..||.|..+.+..-      .                 --|||+|.+.++|..-+. 
T Consensus        27 pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkG------k-----------------nQAflem~d~~sAvtmv~~   83 (492)
T KOG1190|consen   27 PSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKG------K-----------------NQAFLEMADEESAVTMVNY   83 (492)
T ss_pred             CcceeEeccCCccccHHHHHHhcccccceeeeeeecc------c-----------------hhhhhhhcchhhhhheeec
Confidence            5789999999999999999999999999998876321      1                 279999999998776331 


Q ss_pred             --hcCceeCCeEEEEeecCCCcccC--------------------------CC-----CCCCCcCCcceeeeCCCCCCCC
Q 016231          303 --FNMAVIGGNHIRLDRACPPRKKL--------------------------KG-----EDAPLYDIKKTVFVGNLPFDVK  349 (393)
Q Consensus       303 --lng~~~~Gr~I~V~~a~~~~~~~--------------------------~~-----~~~~~~~~~~tLfVgNLp~~~t  349 (393)
                        ----.+.|+.|.|+++....-..                          ..     .......+-.+++|+|+-+.++
T Consensus        84 y~~~~p~lr~~~~yiq~sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVs  163 (492)
T KOG1190|consen   84 YTSVTPVLRGQPIYIQYSNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVS  163 (492)
T ss_pred             ccccCccccCcceeehhhhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeE
Confidence              11224678888888763210000                          00     0001112345789999999999


Q ss_pred             HHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeee
Q 016231          350 DEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT  391 (393)
Q Consensus       350 eedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t  391 (393)
                      -+-|+++|+.|    |.|..|.-...  +  ..--|.|+|.+
T Consensus       164 lDVLHqvFS~f----G~VlKIiTF~K--n--n~FQALvQy~d  197 (492)
T KOG1190|consen  164 LDVLHQVFSKF----GFVLKIITFTK--N--NGFQALVQYTD  197 (492)
T ss_pred             HHHHHHHHhhc----ceeEEEEEEec--c--cchhhhhhccc
Confidence            99999999999    88875543322  1  11236777765

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=97.97  E-value=1.1e-05  Score=74.73  Aligned_cols=57  Identities=26%  Similarity=0.479  Sum_probs=52.1

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .....-+||+.+|.-+.+.+|...|.+|+   |.|..+|+.|+..||.++|||||+|.++
T Consensus        46 ~~~~g~~~~~~~p~g~~e~~~~~~~~q~~---g~v~r~rlsRnkrTGNSKgYAFVEFEs~  102 (214)
T KOG4208|consen   46 QEIEGVVYVDHIPHGFFETEILNYFRQFG---GTVTRFRLSRNKRTGNSKGYAFVEFESE  102 (214)
T ss_pred             cCCccceeecccccchhHHHHhhhhhhcC---CeeEEEEeecccccCCcCceEEEEeccH
Confidence            44567899999999999999999999983   8999999999999999999999999875

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=97.96  E-value=7e-06  Score=71.55  Aligned_cols=53  Identities=19%  Similarity=0.265  Sum_probs=50.5

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeee
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT  391 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t  391 (393)
                      ....|||.+++..+++++|.+.|..|    |.|.+|.|-.|.-||..+|||.|+|.+
T Consensus        71 EGwIi~VtgvHeEatEedi~d~F~dy----GeiKNihLNLDRRtGy~KGYaLvEYet  123 (170)
T KOG0130|consen   71 EGWIIFVTGVHEEATEEDIHDKFADY----GEIKNIHLNLDRRTGYVKGYALVEYET  123 (170)
T ss_pred             eeEEEEEeccCcchhHHHHHHHHhhc----ccccceeeccccccccccceeeeehHh
Confidence            46789999999999999999999999    999999999999999999999999975

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=97.86  E-value=0.00021  Score=71.50  Aligned_cols=143  Identities=14%  Similarity=0.153  Sum_probs=107.6

Q ss_pred             CCcccEEEEeCCCcc-CCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLK-VKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~-~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      ..+.+.+.|.+|... ++-+-|..+|=.||.|..|.+++..                      .|-|.|++.+..+++.|
T Consensus       284 ~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk----------------------~gtamVemgd~~aver~  341 (494)
T KOG1456|consen  284 GAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK----------------------PGTAMVEMGDAYAVERA  341 (494)
T ss_pred             CCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc----------------------cceeEEEcCcHHHHHHH
Confidence            345788999999865 6788999999999999999997643                      27999999999999999


Q ss_pred             H-HhcCceeCCeEEEEeecCCCcccC-------------------C---------CCCCCCcCCcceeeeCCCCCCCCHH
Q 016231          301 L-AFNMAVIGGNHIRLDRACPPRKKL-------------------K---------GEDAPLYDIKKTVFVGNLPFDVKDE  351 (393)
Q Consensus       301 l-~lng~~~~Gr~I~V~~a~~~~~~~-------------------~---------~~~~~~~~~~~tLfVgNLp~~~tee  351 (393)
                      + .||+..+.|.+|.|+.+....-..                   +         ......+.++.+|..-|.|..+|++
T Consensus       342 v~hLnn~~lfG~kl~v~~SkQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe  421 (494)
T KOG1456|consen  342 VTHLNNIPLFGGKLNVCVSKQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEE  421 (494)
T ss_pred             HHHhccCccccceEEEeeccccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEEecCCCccCHH
Confidence            9 699999999999999875321000                   0         0012235678899999999999999


Q ss_pred             HHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeee
Q 016231          352 EIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT  391 (393)
Q Consensus       352 dL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t  391 (393)
                      .|..+|.....   ...+|+|..-.  ....--|.++|.+
T Consensus       422 ~l~~i~nek~v---~~~svkvFp~k--serSssGllEfe~  456 (494)
T KOG1456|consen  422 QLIGICNEKDV---PPTSVKVFPLK--SERSSSGLLEFEN  456 (494)
T ss_pred             HHHHHhhhcCC---CcceEEeeccc--ccccccceeeeeh
Confidence            99999987632   24566665443  2223356777765

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

Probab=97.71  E-value=0.00029  Score=58.53  Aligned_cols=77  Identities=21%  Similarity=0.195  Sum_probs=57.4

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcc--cCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIK--FGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~--~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      .||.|+|||-..|.+.|.+++..  .|...-+.|+.|.                 ....+.|||||-|.+++.|..-. .
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf-----------------~~~~N~GYAFVNf~~~~~~~~F~~~   64 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDF-----------------KNKCNLGYAFVNFTSPQAAIRFYKA   64 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeec-----------------cCCCceEEEEEEcCCHHHHHHHHHH
Confidence            58999999999999999998875  3444445554443                 12347799999999999999877 6


Q ss_pred             hcCceeC----CeEEEEeecC
Q 016231          303 FNMAVIG----GNHIRLDRAC  319 (393)
Q Consensus       303 lng~~~~----Gr~I~V~~a~  319 (393)
                      ++|..|.    .+.+.|.+|.
T Consensus        65 f~g~~w~~~~s~Kvc~i~yAr   85 (97)
T PF04059_consen   65 FNGKKWPNFNSKKVCEISYAR   85 (97)
T ss_pred             HcCCccccCCCCcEEEEehhH
Confidence            8988875    3445555553

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

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=97.67  E-value=3.6e-05  Score=76.39  Aligned_cols=56  Identities=20%  Similarity=0.304  Sum_probs=52.6

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..|.+.|||.-|.+-++.+||.-+|+.|    |.|.+|.|++|..||.+..||||+|.+.
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrF----G~i~sceVIRD~ktgdsLqyaFiEFen~  291 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRF----GKIVSCEVIRDRKTGDSLQYAFIEFENK  291 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhc----ccceeeeEEecccccchhheeeeeecch
Confidence            4567899999999999999999999999    9999999999999999999999999864

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=97.64  E-value=3.9e-05  Score=73.21  Aligned_cols=143  Identities=20%  Similarity=0.222  Sum_probs=94.7

Q ss_pred             ccEEEEeCCCccCCHHH-H--HHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          225 LRTIFVGNLPLKVKKKT-L--IKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~-L--~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      .-..|++|+-..+..+- |  ...|+.|-.+....++++.                  .+.-++++|+.|........+-
T Consensus        96 vf~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~------------------p~~~~~~~~~~~k~s~a~~k~~  157 (290)
T KOG0226|consen   96 VFRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDR------------------PQPIRPEAFESFKASDALLKAE  157 (290)
T ss_pred             cccccccccccccCCCCCCcchhhhccchhhhhhhhhhcC------------------CCccCcccccCcchhhhhhhhc
Confidence            34577777766665554 2  4556655544433332221                  1234589999999777666665


Q ss_pred             -HhcCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCC
Q 016231          302 -AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRV  380 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~  380 (393)
                       .-++..+.-+.|++..........   .....+...+||+|.|.-+++.+-|...|..|.    .-...++++|.-||+
T Consensus       158 ~~~~~Kki~~~~VR~a~gtswedPs---l~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfp----sf~~akviRdkRTgK  230 (290)
T KOG0226|consen  158 TEKEKKKIGKPPVRLAAGTSWEDPS---LAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFP----SFQKAKVIRDKRTGK  230 (290)
T ss_pred             cccccccccCcceeeccccccCCcc---cccCccccceeecccccccccHHHHHHHHHhcc----chhhccccccccccc
Confidence             455555555555555443221110   011133457999999999999999999999994    456678899999999


Q ss_pred             CccEEEEEeeec
Q 016231          381 GKGIAYVLFKTR  392 (393)
Q Consensus       381 ~kGfaFVeF~t~  392 (393)
                      ++|||||.|.+.
T Consensus       231 SkgygfVSf~~p  242 (290)
T KOG0226|consen  231 SKGYGFVSFRDP  242 (290)
T ss_pred             cccceeeeecCH
Confidence            999999999864

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.62  E-value=0.00018  Score=58.10  Aligned_cols=67  Identities=21%  Similarity=0.235  Sum_probs=45.1

Q ss_pred             cEEEEeCCCccCCHHHHHH----HhcccC-CeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          226 RTIFVGNLPLKVKKKTLIK----EFIKFG-EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~----~Fs~~G-~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      ..|||.|||.+.+...|+.    ++..|| .|.+|                           +.|.|+|.|.+.+.|..|
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v---------------------------~~~tAilrF~~~~~A~RA   55 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV---------------------------SGGTAILRFPNQEFAERA   55 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-----------------------------TT-EEEEESSHHHHHHH
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE---------------------------eCCEEEEEeCCHHHHHHH
Confidence            3599999999988776655    555676 34333                           126899999999999999


Q ss_pred             H-HhcCceeCCeEEEEeecC
Q 016231          301 L-AFNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       301 l-~lng~~~~Gr~I~V~~a~  319 (393)
                      + .|+|..+.|+.|.|.+..
T Consensus        56 ~KRmegEdVfG~kI~v~~~~   75 (90)
T PF11608_consen   56 QKRMEGEDVFGNKISVSFSP   75 (90)
T ss_dssp             HHHHTT--SSSS--EEESS-
T ss_pred             HHhhcccccccceEEEEEcC
Confidence            9 799999999999999874

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

>smart00361 RRM_1 RNA recognition motif

Probab=97.53  E-value=0.00012  Score=56.56  Aligned_cols=39  Identities=18%  Similarity=0.296  Sum_probs=33.2

Q ss_pred             HHHHHHHhh----cCCCCCCCeEEEE-EeecCCC--CCCccEEEEEeeec
Q 016231          350 DEEIYQLFC----GLNDLESSVEAVR-VIRHPHM--RVGKGIAYVLFKTR  392 (393)
Q Consensus       350 eedL~e~F~----~~~~~~G~I~~Vr-I~~d~~t--g~~kGfaFVeF~t~  392 (393)
                      +++|+++|+    .|    |.|..|. |+.++.+  |.++|||||+|.+.
T Consensus         2 ~~~l~~~~~~~~~~f----G~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~   47 (70)
T smart00361        2 DEDFEREFSEEEEYF----GEVGKINKIYIDNVGYENHKRGNVYITFERS   47 (70)
T ss_pred             chhHHHHHHHHHHhc----CCeeEEEEEEeCCCCCCCCCcEEEEEEECCH
Confidence            578899998    88    9999995 7777666  89999999999874

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=97.53  E-value=0.00011  Score=70.09  Aligned_cols=77  Identities=19%  Similarity=0.336  Sum_probs=65.5

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      ...||+|.|.-.++.+.|...|.+|-.....+++++.                 .+++++||+||.|.+..++..|| +|
T Consensus       190 DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdk-----------------RTgKSkgygfVSf~~pad~~rAmrem  252 (290)
T KOG0226|consen  190 DFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDK-----------------RTGKSKGYGFVSFRDPADYVRAMREM  252 (290)
T ss_pred             cceeecccccccccHHHHHHHHHhccchhhccccccc-----------------cccccccceeeeecCHHHHHHHHHhh
Confidence            4679999999999999999999999876666665543                 24568899999999999999999 79


Q ss_pred             cCceeCCeEEEEeec
Q 016231          304 NMAVIGGNHIRLDRA  318 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a  318 (393)
                      ||..++.|.|.+.-+
T Consensus       253 ~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  253 NGKYVGSRPIKLRKS  267 (290)
T ss_pred             cccccccchhHhhhh
Confidence            999999998877554

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.49  E-value=0.00019  Score=76.47  Aligned_cols=145  Identities=14%  Similarity=0.093  Sum_probs=101.6

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhc
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~ln  304 (393)
                      .+.+-+.++++++...++++||...- |.++.|..+..   +.+              ..|-++|.|....+++.|+.-|
T Consensus       311 ~~y~~~~gm~fn~~~nd~rkfF~g~~-~~~~~l~~~~v---~~~--------------~tG~~~v~f~~~~~~q~A~~rn  372 (944)
T KOG4307|consen  311 KYYNNYKGMEFNNDFNDGRKFFPGRN-AQSTDLSENRV---APP--------------QTGRKTVMFTPQAPFQNAFTRN  372 (944)
T ss_pred             hheeeecccccccccchhhhhcCccc-ccccchhhhhc---CCC--------------cCCceEEEecCcchHHHHHhcC
Confidence            35566789999999999999987532 23333322211   111              2589999999999999999888


Q ss_pred             CceeCCeEEEEeecCCCc-------cc-C-------C--------------CCC-CCCcCCcceeeeCCCCCCCCHHHHH
Q 016231          305 MAVIGGNHIRLDRACPPR-------KK-L-------K--------------GED-APLYDIKKTVFVGNLPFDVKDEEIY  354 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~~~-------~~-~-------~--------------~~~-~~~~~~~~tLfVgNLp~~~teedL~  354 (393)
                      ...+-.|.|.|..+....       .. .       .              ++. .........|||..||..++..++.
T Consensus       373 ~~~~~~R~~q~~P~g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v  452 (944)
T KOG4307|consen  373 PSDDVNRPFQTGPPGNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPV  452 (944)
T ss_pred             chhhhhcceeecCCCccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchh
Confidence            888888888886542110       00 0       0              000 0112345789999999999999999


Q ss_pred             HHhhcCCCCCCCeEE-EEEeecCCCCCCccEEEEEeeec
Q 016231          355 QLFCGLNDLESSVEA-VRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       355 e~F~~~~~~~G~I~~-VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ++|...    -.|+. |.|.+.| ++..++.|||.|..+
T Consensus       453 ~~f~~~----~~Ved~I~lt~~P-~~~~~~~afv~F~~~  486 (944)
T KOG4307|consen  453 NKFMGA----AAVEDFIELTRLP-TDLLRPAAFVAFIHP  486 (944)
T ss_pred             hhhhhh----hhhhheeEeccCC-cccccchhhheeccc
Confidence            999876    34555 7777775 788999999999763

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

Probab=97.48  E-value=0.0002  Score=59.44  Aligned_cols=54  Identities=19%  Similarity=0.230  Sum_probs=48.5

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +||-|+|||...|.++|.+++...-  .|...-+.||.|..++-+.|||||-|.+.
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~--~g~yDF~YLPiDf~~~~N~GYAFVNf~~~   55 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHF--KGKYDFFYLPIDFKNKCNLGYAFVNFTSP   55 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhc--cCcceEEEeeeeccCCCceEEEEEEcCCH
Confidence            5899999999999999999996552  48999999999999999999999999764

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

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=97.47  E-value=0.00072  Score=67.75  Aligned_cols=135  Identities=16%  Similarity=0.237  Sum_probs=99.5

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      ..+-.|.|++|-..+++.+|.+-++.||+|.-|.++..       .                -.|.|+|.+.+.|..|+.
T Consensus        29 ~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~-------~----------------r~alvefedi~~akn~Vn   85 (494)
T KOG1456|consen   29 NPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPH-------K----------------RQALVEFEDIEGAKNCVN   85 (494)
T ss_pred             CCCceEEEeccccccchhHHHHHHhcCCceEEEEeccc-------c----------------ceeeeeeccccchhhhee
Confidence            34677999999999999999999999999987765221       1                279999999999999983


Q ss_pred             ---hcCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceee--eCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCC
Q 016231          303 ---FNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVF--VGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPH  377 (393)
Q Consensus       303 ---lng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLf--VgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~  377 (393)
                         -+...+.|..-.+.++........+++..  .+...|.  |-|--+.+|-+-|+.++..+    |.|..|-|.+.  
T Consensus        86 faa~n~i~i~gq~Al~NyStsq~i~R~g~es~--~pN~VLl~TIlNp~YpItvDVly~Icnp~----GkVlRIvIfkk--  157 (494)
T KOG1456|consen   86 FAADNQIYIAGQQALFNYSTSQCIERPGDESA--TPNKVLLFTILNPQYPITVDVLYTICNPQ----GKVLRIVIFKK--  157 (494)
T ss_pred             hhccCcccccCchhhcccchhhhhccCCCCCC--CCCeEEEEEeecCccccchhhhhhhcCCC----CceEEEEEEec--
Confidence               45556777777777775443333333222  2233333  44666778999999999998    99998888766  


Q ss_pred             CCCCccEEEEEeee
Q 016231          378 MRVGKGIAYVLFKT  391 (393)
Q Consensus       378 tg~~kGfaFVeF~t  391 (393)
                      +|.   .|.|+|++
T Consensus       158 ngV---QAmVEFds  168 (494)
T KOG1456|consen  158 NGV---QAMVEFDS  168 (494)
T ss_pred             cce---eeEEeech
Confidence            454   69999986

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.42  E-value=0.00015  Score=71.90  Aligned_cols=49  Identities=31%  Similarity=0.575  Sum_probs=43.8

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeecC
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRV  393 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~~  393 (393)
                      ...+|||+||...+++.+|+++|.+|    |.|.+|+++..      +|.|||+|.+++
T Consensus       227 ~I~tLyIg~l~d~v~e~dIrdhFyqy----Geirsi~~~~~------~~CAFv~ftTR~  275 (377)
T KOG0153|consen  227 SIKTLYIGGLNDEVLEQDIRDHFYQY----GEIRSIRILPR------KGCAFVTFTTRE  275 (377)
T ss_pred             ceeEEEecccccchhHHHHHHHHhhc----CCeeeEEeecc------cccceeeehhhH
Confidence            45799999999999999999999999    99999999755      569999999863

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.38  E-value=8.8e-05  Score=75.11  Aligned_cols=108  Identities=18%  Similarity=0.254  Sum_probs=85.6

Q ss_pred             EEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-HhcC
Q 016231          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNM  305 (393)
Q Consensus       227 tVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~lng  305 (393)
                      .+|+|||.+.++..+|..+|...---.+-.++.                       ..|||||.+.+...|..|+ .++|
T Consensus         3 klyignL~p~~~psdl~svfg~ak~~~~g~fl~-----------------------k~gyafvd~pdq~wa~kaie~~sg   59 (584)
T KOG2193|consen    3 KLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV-----------------------KSGYAFVDCPDQQWANKAIETLSG   59 (584)
T ss_pred             cccccccCCCCChHHHHHHhccccCCCCcceee-----------------------ecceeeccCCchhhhhhhHHhhch
Confidence            589999999999999999998642111111111                       2389999999999999999 5776


Q ss_pred             c-eeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEE
Q 016231          306 A-VIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRV  372 (393)
Q Consensus       306 ~-~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI  372 (393)
                      . .+.|..+.|..+-+..           .-++.+-|+|+|+..-++-|..++..|    |.|..|..
T Consensus        60 k~elqGkr~e~~~sv~kk-----------qrsrk~Qirnippql~wevld~Ll~qy----g~ve~~eq  112 (584)
T KOG2193|consen   60 KVELQGKRQEVEHSVPKK-----------QRSRKIQIRNIPPQLQWEVLDSLLAQY----GTVENCEQ  112 (584)
T ss_pred             hhhhcCceeeccchhhHH-----------HHhhhhhHhcCCHHHHHHHHHHHHhcc----CCHhHhhh
Confidence            5 6889999998876442           234679999999999999999999999    88988865

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.21  E-value=0.0002  Score=70.54  Aligned_cols=81  Identities=32%  Similarity=0.484  Sum_probs=67.0

Q ss_pred             cccEEE-EeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          224 LLRTIF-VGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       224 ~~rtVF-VgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      ...++| |+||++.++.++|..+|..+|.|..++++..+  .++.               ..|||||.|........++.
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~--~s~~---------------~kg~a~~~~~~~~~~~~~~~  245 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDE--ESGD---------------SKGFAYVDFSAGNSKKLALN  245 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCC--Cccc---------------hhhhhhhhhhhchhHHHHhh
Confidence            345666 99999999999999999999999999986543  3333               55999999999999888885


Q ss_pred             hcCceeCCeEEEEeecCCC
Q 016231          303 FNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~  321 (393)
                      .+...+.|+++.+....+.
T Consensus       246 ~~~~~~~~~~~~~~~~~~~  264 (285)
T KOG4210|consen  246 DQTRSIGGRPLRLEEDEPR  264 (285)
T ss_pred             cccCcccCcccccccCCCC
Confidence            4677889999999887654

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=97.17  E-value=0.00051  Score=70.81  Aligned_cols=52  Identities=19%  Similarity=0.282  Sum_probs=43.8

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeee
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT  391 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t  391 (393)
                      ..+|||+|||++++..+|.++|..|    |.|...+|..-...+...+||||+|.+
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~F----G~Ik~~~I~vr~~~~~~~~fgFV~f~~  339 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQF----GPIKEGGIQVRSPGGKNPCFGFVEFEN  339 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhc----ccccccceEEeccCCCcCceEEEEEee
Confidence            4569999999999999999999999    999999887654234444999999976

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=97.17  E-value=0.00036  Score=65.67  Aligned_cols=67  Identities=15%  Similarity=0.269  Sum_probs=53.8

Q ss_pred             CCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       221 ~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      ..+...||||.||..++||++|+.+|+.|-....++|+-    ..+                 +..|||+|.+.+.|..|
T Consensus       206 ~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~----~~g-----------------~~vaf~~~~~~~~at~a  264 (284)
T KOG1457|consen  206 GARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA----RGG-----------------MPVAFADFEEIEQATDA  264 (284)
T ss_pred             cchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec----CCC-----------------cceEeecHHHHHHHHHH
Confidence            345568899999999999999999999998776666621    122                 24899999999999999


Q ss_pred             H-HhcCcee
Q 016231          301 L-AFNMAVI  308 (393)
Q Consensus       301 l-~lng~~~  308 (393)
                      | .|+|..|
T Consensus       265 m~~lqg~~~  273 (284)
T KOG1457|consen  265 MNHLQGNLL  273 (284)
T ss_pred             HHHhhccee
Confidence            9 6887655

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=97.08  E-value=0.00038  Score=66.58  Aligned_cols=55  Identities=29%  Similarity=0.315  Sum_probs=50.6

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeee
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT  391 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t  391 (393)
                      ......+||+|+.+.+|.+++..+|+.|    |.|..|.|+.|...|.++|||||+|.+
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~C----g~i~~~ti~~d~~~~~~k~~~yvef~~  152 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESC----GGINRVTVPKDKFRGHPKGFAYVEFSS  152 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeecc----CCccceeeeccccCCCcceeEEEeccc
Confidence            3356799999999999999999999999    899999999999999999999999976

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.07  E-value=6.1e-05  Score=81.70  Aligned_cols=145  Identities=20%  Similarity=0.188  Sum_probs=108.7

Q ss_pred             cEEEEeCCCccCCHH-HHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCce-EEEEeeCCHHHHHHHHHh
Q 016231          226 RTIFVGNLPLKVKKK-TLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV-HAYIVFKSEQSTEAALAF  303 (393)
Q Consensus       226 rtVFVgNLp~~~tee-~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG-~AFVeF~s~e~A~~Al~l  303 (393)
                      +...+.|+.+..... ..+..|..+|.|..|+++..     +..             .+.+ ++++.+....+++.|...
T Consensus       572 ~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~-----g~k-------------~h~q~~~~~~~s~~~~~esat~p  633 (881)
T KOG0128|consen  572 REKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKR-----GFK-------------AHEQPQQQKVQSKHGSAESATVP  633 (881)
T ss_pred             hhhcccCCCcchhhHHhhHHHhhcccccccccCccc-----ccc-------------ccccchhhhhhccccchhhcccc
Confidence            446777887777665 67788899999999987321     111             1223 889999999999999988


Q ss_pred             cCceeCCeEEEEeecCCCcccCCCCCCC-CcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCc
Q 016231          304 NMAVIGGNHIRLDRACPPRKKLKGEDAP-LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGK  382 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~~~~~~~~~~-~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~k  382 (393)
                      .+.-+.++.+.|..+.+..........+ ..-...++||.||+..+.+.+|...|..+    |.|..++|......+..|
T Consensus       634 a~~~~a~~~~av~~ad~~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~----~~~e~vqi~~h~n~~~~r  709 (881)
T KOG0128|consen  634 AGGALANRSAAVGLADAEEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPS----GTIEVVQIVIHKNEKRFR  709 (881)
T ss_pred             cccccCCccccCCCCCchhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCcc----chhhhHHHHHHhhccccc
Confidence            8999999999998886544211111110 01123589999999999999999999998    778888887666789999


Q ss_pred             cEEEEEeeec
Q 016231          383 GIAYVLFKTR  392 (393)
Q Consensus       383 GfaFVeF~t~  392 (393)
                      |+|||.|..+
T Consensus       710 G~~Y~~F~~~  719 (881)
T KOG0128|consen  710 GKAYVEFLKP  719 (881)
T ss_pred             cceeeEeecC
Confidence            9999999754

>PLN03213 repressor of silencing 3; Provisional

Probab=97.01  E-value=0.00082  Score=69.42  Aligned_cols=39  Identities=23%  Similarity=0.393  Sum_probs=35.7

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCC
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMR  379 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg  379 (393)
                      ...+||||||++.+++++|..+|..|    |.|..|.|++.  +|
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeF----GsVkdVEIpRE--TG   47 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPM----GTVDAVEFVRT--KG   47 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhc----CCeeEEEEecc--cC
Confidence            45799999999999999999999999    99999999954  67

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=96.90  E-value=0.00099  Score=71.97  Aligned_cols=48  Identities=23%  Similarity=0.570  Sum_probs=43.0

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .++|||||+|+..+++.||.++|+.|    |.|.+|.++-      ++|+|||....+
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feef----GeiqSi~li~------~R~cAfI~M~~R  467 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEF----GEIQSIILIP------PRGCAFIKMVRR  467 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhc----ccceeEeecc------CCceeEEEEeeh
Confidence            46899999999999999999999999    9999999853      589999997654

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.88  E-value=0.0016  Score=64.60  Aligned_cols=115  Identities=13%  Similarity=0.295  Sum_probs=75.0

Q ss_pred             cEEEEeCCCccCCHHH----H--HHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHH
Q 016231          226 RTIFVGNLPLKVKKKT----L--IKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (393)
Q Consensus       226 rtVFVgNLp~~~tee~----L--~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~  299 (393)
                      .-|||-+||+.+-.++    |  .++|.+||.|..|.+-+.  +.+            .+...+---.||.|.+.++|..
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkk--t~s------------~nst~~h~gvYITy~~kedAar  180 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKK--TSS------------LNSTASHAGVYITYSTKEDAAR  180 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEeccc--ccc------------cccccccceEEEEecchHHHHH
Confidence            4599999999876555    3  369999999998877221  110            1111111234999999999999


Q ss_pred             HH-HhcCceeCCeEEEEeecCCCc--ccCCCCCCCCcCCcceeeeCCCC---CCCCHHHHHHHh
Q 016231          300 AL-AFNMAVIGGNHIRLDRACPPR--KKLKGEDAPLYDIKKTVFVGNLP---FDVKDEEIYQLF  357 (393)
Q Consensus       300 Al-~lng~~~~Gr~I~V~~a~~~~--~~~~~~~~~~~~~~~tLfVgNLp---~~~teedL~e~F  357 (393)
                      || +.+|..++||.|+..+.....  ...+   ........+.|+.--.   .+++.++|...=
T Consensus       181 cIa~vDgs~~DGr~lkatYGTTKYCtsYLR---n~~CpNp~CMyLHEpg~e~Ds~tK~el~n~q  241 (480)
T COG5175         181 CIAEVDGSLLDGRVLKATYGTTKYCTSYLR---NAVCPNPDCMYLHEPGPEKDSLTKDELCNSQ  241 (480)
T ss_pred             HHHHhccccccCceEeeecCchHHHHHHHc---CCCCCCCCeeeecCCCcccccccHHHHhhhh
Confidence            99 799999999999998764221  0011   1123345677766433   236788887554

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=96.85  E-value=0.00075  Score=63.66  Aligned_cols=71  Identities=23%  Similarity=0.382  Sum_probs=61.0

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...+.++|.||+..+...+|..+|..+|.+..+.+                         ..+++||+|...++|..|| 
T Consensus        97 ~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~-------------------------~~~~~~v~Fs~~~da~ra~~  151 (216)
T KOG0106|consen   97 RTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA-------------------------RRNFAFVEFSEQEDAKRALE  151 (216)
T ss_pred             cccceeeeccchhhhhHHHHhhhhcccCCCchhhh-------------------------hccccceeehhhhhhhhcch
Confidence            34577999999999999999999999998854443                         2269999999999999999 


Q ss_pred             HhcCceeCCeEEEEeec
Q 016231          302 AFNMAVIGGNHIRLDRA  318 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a  318 (393)
                      .|++..+.|+.|.+...
T Consensus       152 ~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen  152 KLDGKKLNGRRISVEKN  168 (216)
T ss_pred             hccchhhcCceeeeccc
Confidence            79999999999999444

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=96.79  E-value=0.0048  Score=58.17  Aligned_cols=77  Identities=22%  Similarity=0.288  Sum_probs=62.9

Q ss_pred             cCCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHH
Q 016231          220 DEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (393)
Q Consensus       220 ~~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~  299 (393)
                      ....+..++|+.|||..++.+.|..+|.+|.....|+++..                      -.|.|||+|.+...+..
T Consensus       141 ~~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~----------------------~~~iAfve~~~d~~a~~  198 (221)
T KOG4206|consen  141 QMAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPP----------------------RSGIAFVEFLSDRQASA  198 (221)
T ss_pred             cCCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccC----------------------CCceeEEecchhhhhHH
Confidence            34566899999999999999999999999998899988432                      12799999999999888


Q ss_pred             HH-HhcCceeC-CeEEEEeec
Q 016231          300 AL-AFNMAVIG-GNHIRLDRA  318 (393)
Q Consensus       300 Al-~lng~~~~-Gr~I~V~~a  318 (393)
                      |. .+++..+- ...+.|.++
T Consensus       199 a~~~lq~~~it~~~~m~i~~a  219 (221)
T KOG4206|consen  199 AQQALQGFKITKKNTMQITFA  219 (221)
T ss_pred             HhhhhccceeccCceEEeccc
Confidence            88 68777665 666666654

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.77  E-value=0.0014  Score=62.73  Aligned_cols=84  Identities=20%  Similarity=0.302  Sum_probs=60.1

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ....||+++||+.+...-|+++|+.||.|-.|.|-...  ++  .+ .+-..+..+.+...--|+|+|.+...|..+. .
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~--~s--~~-~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~  147 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPED--DS--KR-AARKRKGGNYKKLYSEGWVEFISKRVAKRIAEL  147 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchh--hH--HH-HHHhhcCCCccccchhHHHHHHHHHHHHHHHHH
Confidence            45779999999999999999999999999999883322  11  00 0000111122233345789999999999877 7


Q ss_pred             hcCceeCCeE
Q 016231          303 FNMAVIGGNH  312 (393)
Q Consensus       303 lng~~~~Gr~  312 (393)
                      ||+..|.|+.
T Consensus       148 Lnn~~Iggkk  157 (278)
T KOG3152|consen  148 LNNTPIGGKK  157 (278)
T ss_pred             hCCCccCCCC
Confidence            9999998875

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.70  E-value=0.0015  Score=66.46  Aligned_cols=83  Identities=28%  Similarity=0.305  Sum_probs=64.6

Q ss_pred             cCCCCcCCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeee---cccCCCCCccchhhhhhcccCCCceEEEEee
Q 016231          215 EEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSV---PIIDTKIPRKGAILQKQINENADSVHAYIVF  291 (393)
Q Consensus       215 ~~~~~~~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~---~~~~~~~~rkga~~~~k~~~~~srG~AFVeF  291 (393)
                      -..++.+.-+++||.+-|||.+-.-+.|.++|+.||.|.+|+|+..   +....+.++       ++.....+-+|+|+|
T Consensus       221 lp~~~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~-------~~~~~~tk~~AlvEy  293 (484)
T KOG1855|consen  221 LPEFDEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPK-------KYFELQTKECALVEY  293 (484)
T ss_pred             CCCccccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCc-------cchhhhhhhhhhhhh
Confidence            4456666678999999999999999999999999999999999765   332333333       333334556899999


Q ss_pred             CCHHHHHHHHHhc
Q 016231          292 KSEQSTEAALAFN  304 (393)
Q Consensus       292 ~s~e~A~~Al~ln  304 (393)
                      ...+.|..|.++.
T Consensus       294 e~~~~A~KA~e~~  306 (484)
T KOG1855|consen  294 EEVEAARKARELL  306 (484)
T ss_pred             hhhHHHHHHHHhh
Confidence            9999999998654

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=96.63  E-value=0.0013  Score=61.89  Aligned_cols=54  Identities=26%  Similarity=0.380  Sum_probs=47.5

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeecC
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRV  393 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~~  393 (393)
                      +..+||||+||...++++-|.++|-+.    |.|..|.|+.+.+ +..+ ||||.|.+++
T Consensus         7 e~drtl~v~n~~~~v~eelL~Elfiqa----GPV~kv~ip~~~d-~~~k-Fa~v~f~~E~   60 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQA----GPVYKVGIPSGQD-QEQK-FAYVFFPNEN   60 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhcc----CceEEEeCCCCcc-CCCc-eeeeeccccc
Confidence            345899999999999999999999997    9999999998864 5566 9999998874

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=96.54  E-value=0.0052  Score=51.72  Aligned_cols=53  Identities=21%  Similarity=0.367  Sum_probs=34.4

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      +.|+|.+++..++-++|+.+|+.||.|.-|.+..      +.                 --|||.|.+.++|+.|+
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~------G~-----------------~~g~VRf~~~~~A~~a~   54 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSR------GD-----------------TEGYVRFKTPEAAQKAL   54 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--T------T------------------SEEEEEESS---HHHHH
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecC------CC-----------------CEEEEEECCcchHHHHH
Confidence            5689999999999999999999999988887722      11                 27999999999999998

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=96.48  E-value=0.015  Score=48.56  Aligned_cols=82  Identities=16%  Similarity=0.184  Sum_probs=50.6

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEE-EeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVR-IRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVr-i~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~l  303 (393)
                      .+.|.|=+.|+. ....|..+|++||.|.+.. +.+..   .+..        ............|.|.+..+|..||..
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~---~~~~--------~~~~~~~~NWi~I~Y~~~~~A~rAL~~   73 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSS---SGIN--------PYPIPSGGNWIHITYDNPLSAQRALQK   73 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG---------------------E-CCTTEEEEEESSHHHHHHHHTT
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccc---cccc--------cccCCCCCCEEEEECCCHHHHHHHHHh
Confidence            466888899988 4466778999999987664 10000   0000        000011235899999999999999999


Q ss_pred             cCceeCCeEEE-Eeec
Q 016231          304 NMAVIGGNHIR-LDRA  318 (393)
Q Consensus       304 ng~~~~Gr~I~-V~~a  318 (393)
                      ||..|.|.-|. |.++
T Consensus        74 NG~i~~g~~mvGV~~~   89 (100)
T PF05172_consen   74 NGTIFSGSLMVGVKPC   89 (100)
T ss_dssp             TTEEETTCEEEEEEE-
T ss_pred             CCeEEcCcEEEEEEEc
Confidence            99999986554 5544

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.45  E-value=0.006  Score=44.99  Aligned_cols=52  Identities=27%  Similarity=0.505  Sum_probs=41.0

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      +.|-|.+.|....+. |..+|..||+|..+.+..                       ..-++||.|.+..+|+.||
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~-----------------------~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPE-----------------------STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCC-----------------------CCcEEEEEECCHHHHHhhC
Confidence            568889998776644 555899999999988731                       1138999999999999985

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=96.42  E-value=0.0039  Score=62.29  Aligned_cols=89  Identities=24%  Similarity=0.235  Sum_probs=68.9

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      .....+|||-+||..+++.+|..+|.+||.|..     +  ..+..|+. .+-+.+ .++..+|-|.|.|.+...|++|+
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikr-----n--K~t~kPki-~~y~dk-eT~~~KGeatvS~~D~~~akaai  133 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKR-----N--KRTGKPKI-KIYTDK-ETGAPKGEATVSYEDPPAAKAAI  133 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceecc-----C--CCCCCcch-hccccc-cccCcCCceeeeecChhhhhhhh
Confidence            344678999999999999999999999997532     1  12223332 122222 66778899999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecC
Q 016231          302 -AFNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~  319 (393)
                       -+++..|.|..|.|..+.
T Consensus       134 ~~~agkdf~gn~ikvs~a~  152 (351)
T KOG1995|consen  134 EWFAGKDFCGNTIKVSLAE  152 (351)
T ss_pred             hhhccccccCCCchhhhhh
Confidence             599999999999998874

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=96.35  E-value=0.0043  Score=65.19  Aligned_cols=52  Identities=15%  Similarity=0.323  Sum_probs=48.5

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeee
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT  391 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t  391 (393)
                      .+.|||.+|...+-..+|..||+.|    |.|....++++.-+-..++||||++.+
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKy----GKVvGAKVVTNaRsPGaRCYGfVTMSt  456 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKY----GKVVGAKVVTNARSPGARCYGFVTMST  456 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHh----cceeceeeeecCCCCCcceeEEEEecc
Confidence            5789999999999999999999999    999999999998888889999999875

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=96.28  E-value=0.01  Score=61.91  Aligned_cols=63  Identities=29%  Similarity=0.413  Sum_probs=53.3

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhc-ccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFI-KFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs-~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      .+.+|||||+||--++.++|..+|. -||.|.-+-|-+|+  .-+.|+               |-|-|.|.+..+-.+||
T Consensus       368 DprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~--k~KYPk---------------GaGRVtFsnqqsYi~AI  430 (520)
T KOG0129|consen  368 DPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDP--KLKYPK---------------GAGRVTFSNQQAYIKAI  430 (520)
T ss_pred             CccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCc--ccCCCC---------------CcceeeecccHHHHHHH
Confidence            3579999999999999999999999 59999988885543  234444               89999999999999999


Q ss_pred             H
Q 016231          302 A  302 (393)
Q Consensus       302 ~  302 (393)
                      .
T Consensus       431 s  431 (520)
T KOG0129|consen  431 S  431 (520)
T ss_pred             h
Confidence            4

>PF13893 RRM_5: RNA recognition motif

Probab=96.18  E-value=0.0069  Score=44.23  Aligned_cols=31  Identities=26%  Similarity=0.710  Sum_probs=25.8

Q ss_pred             HHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          353 IYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       353 L~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      |+++|+.|    |.|..|.+....     +|+|||+|.+.
T Consensus         1 L~~~f~~f----G~V~~i~~~~~~-----~~~a~V~f~~~   31 (56)
T PF13893_consen    1 LYKLFSKF----GEVKKIKIFKKK-----RGFAFVEFASV   31 (56)
T ss_dssp             HHHHHTTT----S-EEEEEEETTS-----TTEEEEEESSH
T ss_pred             ChHHhCCc----ccEEEEEEEeCC-----CCEEEEEECCH
Confidence            68899999    999999997663     68999999874

(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 ....

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=96.18  E-value=0.021  Score=56.97  Aligned_cols=78  Identities=15%  Similarity=0.252  Sum_probs=61.6

Q ss_pred             CCcccEEEEeCCC----ccCC-------HHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEe
Q 016231          222 GKLLRTIFVGNLP----LKVK-------KKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIV  290 (393)
Q Consensus       222 ~~~~rtVFVgNLp----~~~t-------ee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVe  290 (393)
                      .+..+||.|.||=    +..+       .++|.+-..+||.|.+|.+.-.                     ..-|.+-|.
T Consensus       262 ~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~---------------------hPdGvvtV~  320 (382)
T KOG1548|consen  262 ARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDR---------------------HPDGVVTVS  320 (382)
T ss_pred             ccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEecc---------------------CCCceeEEE
Confidence            4567999999992    2233       4566677889999999877221                     133899999


Q ss_pred             eCCHHHHHHHH-HhcCceeCCeEEEEeecCC
Q 016231          291 FKSEQSTEAAL-AFNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       291 F~s~e~A~~Al-~lng~~~~Gr~I~V~~a~~  320 (393)
                      |.+.+.|..|| .|+|..|.||.|.......
T Consensus       321 f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG  351 (382)
T KOG1548|consen  321 FRNNEEADQCIQTMDGRWFDGRQLTASIWDG  351 (382)
T ss_pred             eCChHHHHHHHHHhcCeeecceEEEEEEeCC
Confidence            99999999999 6999999999999887653

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=96.17  E-value=0.013  Score=63.01  Aligned_cols=74  Identities=20%  Similarity=0.346  Sum_probs=61.3

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCe-eEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEI-DSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I-~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      +.|-|.|+|++++-++|.+||..|-.+ .+|+|++   .+.+.               -.|-|.|-|.+.+.|..|. .|
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~---nd~G~---------------pTGe~mvAfes~~eAr~A~~dl  929 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRR---NDDGV---------------PTGECMVAFESQEEARRASMDL  929 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEee---cCCCC---------------cccceeEeecCHHHHHhhhhcc
Confidence            478899999999999999999999866 4455533   23343               4589999999999999998 79


Q ss_pred             cCceeCCeEEEEee
Q 016231          304 NMAVIGGNHIRLDR  317 (393)
Q Consensus       304 ng~~~~Gr~I~V~~  317 (393)
                      +++.|..|.|.+..
T Consensus       930 ~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  930 DGQKIRNRVVSLRI  943 (944)
T ss_pred             ccCcccceeEEEEe
Confidence            99999999988764

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=96.12  E-value=0.0072  Score=58.15  Aligned_cols=52  Identities=31%  Similarity=0.433  Sum_probs=47.5

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+|+|.|||..++.+||+++|..|    |.+..+-|..++ .|.+.|.|-|.|..+
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~----~~~~r~~vhy~~-~G~s~Gta~v~~~r~  134 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEF----GELKRVAVHYDR-AGRSLGTADVSFNRR  134 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHh----ccceEEeeccCC-CCCCCccceeeecch
Confidence            3689999999999999999999999    889999999995 699999999999753

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=95.82  E-value=0.0071  Score=63.41  Aligned_cols=50  Identities=24%  Similarity=0.405  Sum_probs=44.2

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeee
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT  391 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t  391 (393)
                      ..+.++|+|-|||.+++.++|+.+|+.|    |+|..|+.-+.     .+|.+||+|.+
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~y----Geir~ir~t~~-----~~~~~~v~FyD  121 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAY----GEIREIRETPN-----KRGIVFVEFYD  121 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhh----cchhhhhcccc-----cCceEEEEEee
Confidence            4567899999999999999999999999    99999876444     58999999976

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=95.82  E-value=0.04  Score=49.01  Aligned_cols=74  Identities=23%  Similarity=0.383  Sum_probs=52.5

Q ss_pred             CCcccEEEEeCCC-----c-cCCH---HHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeC
Q 016231          222 GKLLRTIFVGNLP-----L-KVKK---KTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFK  292 (393)
Q Consensus       222 ~~~~rtVFVgNLp-----~-~~te---e~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~  292 (393)
                      .++..||.|.=+.     . ...+   .+|...|..||.+.-||+..                         |.-+|+|.
T Consensus        24 GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~-------------------------~~mwVTF~   78 (146)
T PF08952_consen   24 GPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVG-------------------------DTMWVTFR   78 (146)
T ss_dssp             --TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEET-------------------------TCEEEEES
T ss_pred             CCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeC-------------------------CeEEEEEC
Confidence            3446788777665     1 2222   26777888999988777722                         46899999


Q ss_pred             CHHHHHHHHHhcCceeCCeEEEEeecCC
Q 016231          293 SEQSTEAALAFNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       293 s~e~A~~Al~lng~~~~Gr~I~V~~a~~  320 (393)
                      +.++|-+|+.++|..++|+.|.|..-++
T Consensus        79 dg~sALaals~dg~~v~g~~l~i~LKtp  106 (146)
T PF08952_consen   79 DGQSALAALSLDGIQVNGRTLKIRLKTP  106 (146)
T ss_dssp             SCHHHHHHHHGCCSEETTEEEEEEE---
T ss_pred             ccHHHHHHHccCCcEECCEEEEEEeCCc
Confidence            9999999999999999999999987654

; PDB: 1UFW_A 2DNR_A.

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=95.29  E-value=0.022  Score=54.83  Aligned_cols=76  Identities=17%  Similarity=0.143  Sum_probs=64.8

Q ss_pred             HHHHHH-HhcCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEee
Q 016231          296 STEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIR  374 (393)
Q Consensus       296 ~A~~Al-~lng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~  374 (393)
                      -|..|- +|++....|+.++|.++..                ..|||.||+.-++.+.|.+.|+.|    |.|...-++.
T Consensus         6 ~ae~ak~eLd~~~~~~~~lr~rfa~~----------------a~l~V~nl~~~~sndll~~~f~~f----g~~e~av~~v   65 (275)
T KOG0115|consen    6 LAEIAKRELDGRFPKGRSLRVRFAMH----------------AELYVVNLMQGASNDLLEQAFRRF----GPIERAVAKV   65 (275)
T ss_pred             HHHHHHHhcCCCCCCCCceEEEeecc----------------ceEEEEecchhhhhHHHHHhhhhc----Cccchheeee
Confidence            345555 6999999999999999863                489999999999999999999999    8998877777


Q ss_pred             cCCCCCCccEEEEEeeec
Q 016231          375 HPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       375 d~~tg~~kGfaFVeF~t~  392 (393)
                      | +.+.+.|-++|.|..+
T Consensus        66 D-~r~k~t~eg~v~~~~k   82 (275)
T KOG0115|consen   66 D-DRGKPTREGIVEFAKK   82 (275)
T ss_pred             c-ccccccccchhhhhcc
Confidence            7 5688899999999764

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=95.21  E-value=0.026  Score=62.20  Aligned_cols=78  Identities=29%  Similarity=0.405  Sum_probs=65.4

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      .....+|||+|+.++....|...|..||.|..|.+..      +.                 -||||.|.+...++.|+ 
T Consensus       453 t~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h------gq-----------------~yayi~yes~~~aq~a~~  509 (975)
T KOG0112|consen  453 TPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH------GQ-----------------PYAYIQYESPPAAQAATH  509 (975)
T ss_pred             ccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc------CC-----------------cceeeecccCccchhhHH
Confidence            4457799999999999999999999999998887721      11                 39999999999999999 


Q ss_pred             HhcCceeCC--eEEEEeecCCCcc
Q 016231          302 AFNMAVIGG--NHIRLDRACPPRK  323 (393)
Q Consensus       302 ~lng~~~~G--r~I~V~~a~~~~~  323 (393)
                      .|.|..|.|  +.|+|.++..+..
T Consensus       510 ~~rgap~G~P~~r~rvdla~~~~~  533 (975)
T KOG0112|consen  510 DMRGAPLGGPPRRLRVDLASPPGA  533 (975)
T ss_pred             HHhcCcCCCCCcccccccccCCCC
Confidence            688888876  7799999876543

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=95.17  E-value=0.024  Score=51.82  Aligned_cols=37  Identities=30%  Similarity=0.503  Sum_probs=34.1

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecC
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP  376 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~  376 (393)
                      ...||||||+..+++.||..+|..|    |.|.+|-|.+.|
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~y----G~lrsvWvArnP   46 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKY----GPLRSVWVARNP   46 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhc----CcceeEEEeecC
Confidence            5789999999999999999999999    899998888766

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=95.02  E-value=0.048  Score=57.60  Aligned_cols=74  Identities=18%  Similarity=0.153  Sum_probs=55.6

Q ss_pred             ccEEEEeCCCccC------CHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHH
Q 016231          225 LRTIFVGNLPLKV------KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE  298 (393)
Q Consensus       225 ~rtVFVgNLp~~~------tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~  298 (393)
                      ...|+|-|+|.--      -...|..+|+.+|+|..+.++-+.   .+.               ..||.|++|.+..+|+
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e---~gg---------------tkG~lf~E~~~~~~A~  119 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDE---EGG---------------TKGYLFVEYASMRDAK  119 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCc---cCC---------------eeeEEEEEecChhhHH
Confidence            4679999998532      234677899999999888775433   222               4599999999999999


Q ss_pred             HHH-HhcCceeCC-eEEEEe
Q 016231          299 AAL-AFNMAVIGG-NHIRLD  316 (393)
Q Consensus       299 ~Al-~lng~~~~G-r~I~V~  316 (393)
                      .|+ .|||..|+- +...|.
T Consensus       120 ~aVK~l~G~~ldknHtf~v~  139 (698)
T KOG2314|consen  120 KAVKSLNGKRLDKNHTFFVR  139 (698)
T ss_pred             HHHHhcccceecccceEEee
Confidence            999 799998865 444444

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=94.95  E-value=0.017  Score=61.13  Aligned_cols=76  Identities=16%  Similarity=0.173  Sum_probs=61.1

Q ss_pred             CCCcccEEEEeCCCccCCHHHHHHHhc-ccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHH
Q 016231          221 EGKLLRTIFVGNLPLKVKKKTLIKEFI-KFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (393)
Q Consensus       221 ~~~~~rtVFVgNLp~~~tee~L~~~Fs-~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~  299 (393)
                      ....+..|||.||-.-+|.-+|+.++. .+|.|...+|  +.+                     +..|||.|.+.+.|.+
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm--DkI---------------------KShCyV~yss~eEA~a  496 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM--DKI---------------------KSHCYVSYSSVEEAAA  496 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHHHH--HHh---------------------hcceeEecccHHHHHH
Confidence            445678899999999999999999999 5777776644  221                     1489999999999988


Q ss_pred             HH-HhcCcee---CCeEEEEeecC
Q 016231          300 AL-AFNMAVI---GGNHIRLDRAC  319 (393)
Q Consensus       300 Al-~lng~~~---~Gr~I~V~~a~  319 (393)
                      -. +|||..|   +++.|.+.+..
T Consensus       497 tr~AlhnV~WP~sNPK~L~adf~~  520 (718)
T KOG2416|consen  497 TREALHNVQWPPSNPKHLIADFVR  520 (718)
T ss_pred             HHHHHhccccCCCCCceeEeeecc
Confidence            88 7999987   57888888763

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=94.69  E-value=0.081  Score=51.91  Aligned_cols=65  Identities=20%  Similarity=0.269  Sum_probs=51.5

Q ss_pred             HHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-HhcCceeCCeEEEEee
Q 016231          239 KKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDR  317 (393)
Q Consensus       239 ee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~lng~~~~Gr~I~V~~  317 (393)
                      ++++.+.+.+||.|..|.|..++......                ..-.||+|...++|..|+ .|||..|+||.++.++
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~de----------------avRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~F  363 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDE----------------AVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACF  363 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccch----------------hheeeeeeccHHHHHHHHHhcCCceecceeeehee
Confidence            45778889999999999886665322211                135899999999999998 7999999999998877


Q ss_pred             cC
Q 016231          318 AC  319 (393)
Q Consensus       318 a~  319 (393)
                      ..
T Consensus       364 yn  365 (378)
T KOG1996|consen  364 YN  365 (378)
T ss_pred             cc
Confidence            53

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=94.61  E-value=0.032  Score=60.23  Aligned_cols=54  Identities=20%  Similarity=0.404  Sum_probs=45.5

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecC---CCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP---HMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~---~tg~~kGfaFVeF~t~  392 (393)
                      .++.|||+||++.++++.|...|..|    |.|.+|+|+.-.   .....+.+|||-|-++
T Consensus       173 ~TTNlyv~Nlnpsv~E~~ll~tfGrf----gPlasvKimwpRtEeEk~r~r~cgfvafmnR  229 (877)
T KOG0151|consen  173 QTTNLYVGNLNPSVDENFLLRTFGRF----GPLASVKIMWPRTEEEKRRERNCGFVAFMNR  229 (877)
T ss_pred             cccceeeecCCccccHHHHHHHhccc----Ccccceeeecccchhhhccccccceeeehhh
Confidence            46789999999999999999999999    999999987654   2334577999999764

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=94.07  E-value=0.14  Score=47.39  Aligned_cols=61  Identities=10%  Similarity=0.097  Sum_probs=51.7

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ....|.|.+||+..+.++|+.+....|.|.-..+-++                        |++.|+|...+++..|+ .
T Consensus       114 Se~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD------------------------g~GvV~~~r~eDMkYAvr~  169 (241)
T KOG0105|consen  114 SEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD------------------------GVGVVEYLRKEDMKYAVRK  169 (241)
T ss_pred             cceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc------------------------cceeeeeeehhhHHHHHHh
Confidence            3467999999999999999999999999876655221                        69999999999999999 6


Q ss_pred             hcCcee
Q 016231          303 FNMAVI  308 (393)
Q Consensus       303 lng~~~  308 (393)
                      |+.+.+
T Consensus       170 ld~~~~  175 (241)
T KOG0105|consen  170 LDDQKF  175 (241)
T ss_pred             hccccc
Confidence            776655

>PLN03120 nucleic acid binding protein; Provisional

Probab=93.99  E-value=0.042  Score=53.39  Aligned_cols=27  Identities=26%  Similarity=0.401  Sum_probs=25.0

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCC
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLND  362 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~  362 (393)
                      .++|||+|||+.+++++|+++|+.||.
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~   30 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGD   30 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCC
Confidence            479999999999999999999999973

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=93.93  E-value=0.044  Score=54.86  Aligned_cols=76  Identities=16%  Similarity=0.238  Sum_probs=57.4

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCC--eeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH-
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGE--IDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-  302 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~--I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~-  302 (393)
                      -.+|||||-|++|+++|.+.+...|-  +..+++-.     ..            ..|+++|||+|...+..++..-|. 
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFE-----NR------------~NGQSKG~AL~~~~SdAa~Kq~Mei  143 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFE-----NR------------TNGQSKGYALLVLNSDAAVKQTMEI  143 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhh-----cc------------cCCcccceEEEEecchHHHHHHHHh
Confidence            45999999999999999999998883  23333311     11            135788999999999998888884 


Q ss_pred             hcCceeCCeEEEEeec
Q 016231          303 FNMAVIGGNHIRLDRA  318 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a  318 (393)
                      |-...|.|..-.|..+
T Consensus       144 LP~k~iHGQ~P~V~~~  159 (498)
T KOG4849|consen  144 LPTKTIHGQSPTVLSY  159 (498)
T ss_pred             cccceecCCCCeeecc
Confidence            7777888877666554

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=93.87  E-value=0.063  Score=49.28  Aligned_cols=80  Identities=14%  Similarity=0.071  Sum_probs=46.4

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcc-cCCee---EEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIK-FGEID---SVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~-~G~I~---sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      ...|.|++||+++|+++++..++. ++...   .+.-.. +......              ....-|||.|.+.+++..-
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~-~~~~~~~--------------~~~SRaYi~F~~~~~~~~F   71 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKY-GKKSFKP--------------PTYSRAYINFKNPEDLLEF   71 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEE-S-SSSTT--------------S--EEEEEEESSCHHHHHH
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCC-CCccCCC--------------CcceEEEEEeCCHHHHHHH
Confidence            568999999999999999998887 66542   222100 0000011              1235799999999998777


Q ss_pred             H-HhcCceeCC-----eEEEEeecC
Q 016231          301 L-AFNMAVIGG-----NHIRLDRAC  319 (393)
Q Consensus       301 l-~lng~~~~G-----r~I~V~~a~  319 (393)
                      + .++|..|.+     ....|.+|.
T Consensus        72 ~~~~~g~~F~D~kg~~~~~~VE~Ap   96 (176)
T PF03467_consen   72 RDRFDGHVFVDSKGNEYPAVVEFAP   96 (176)
T ss_dssp             HHHCTTEEEE-TTS-EEEEEEEE-S
T ss_pred             HHhcCCcEEECCCCCCcceeEEEcc
Confidence            7 688887732     334455553

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>PLN03121 nucleic acid binding protein; Provisional

Probab=93.69  E-value=0.059  Score=51.72  Aligned_cols=28  Identities=21%  Similarity=0.277  Sum_probs=25.7

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCC
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLND  362 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~  362 (393)
                      ..++|||+||++.+|+++|+++|+.||.
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~   31 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGA   31 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCC
Confidence            4589999999999999999999999973

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=93.58  E-value=0.3  Score=39.61  Aligned_cols=51  Identities=16%  Similarity=0.332  Sum_probs=37.7

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      +..||+ .|......||..+|+.||.|. |.++.+                        .-|||.....+.|..++.
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d------------------------TSAfV~l~~r~~~~~v~~   60 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND------------------------TSAFVALHNRDQAKVVMN   60 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT------------------------TEEEEEECCCHHHHHHHH
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC------------------------CcEEEEeecHHHHHHHHH
Confidence            445555 999999999999999999976 666332                        269999999999999883

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=93.17  E-value=0.12  Score=43.45  Aligned_cols=46  Identities=26%  Similarity=0.246  Sum_probs=29.9

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..|+|.+++..++.++|+++|+.|    |.|.+|.+.+..      ..|||-|.++
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~----g~V~yVD~~~G~------~~g~VRf~~~   47 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQF----GEVAYVDFSRGD------TEGYVRFKTP   47 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS------EEEEE--TT-------SEEEEEESS-
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhc----CCcceEEecCCC------CEEEEEECCc
Confidence            368899999999999999999999    899999986652      3789999874

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=93.16  E-value=0.034  Score=55.60  Aligned_cols=54  Identities=17%  Similarity=0.308  Sum_probs=46.2

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeee
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT  391 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t  391 (393)
                      ..++|||||-|-+|++||.+.+...+.  ..|..+.+.-+..+|.++|||.|...+
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~--~~~~dmKFFENR~NGQSKG~AL~~~~S  133 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGL--AQFADMKFFENRTNGQSKGYALLVLNS  133 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhH--HHHhhhhhhhcccCCcccceEEEEecc
Confidence            468999999999999999999987743  467778888888899999999998654

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=93.15  E-value=0.041  Score=52.95  Aligned_cols=62  Identities=26%  Similarity=0.357  Sum_probs=48.4

Q ss_pred             HHHHHHhc-ccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-HhcCceeCCeEEEEee
Q 016231          240 KTLIKEFI-KFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDR  317 (393)
Q Consensus       240 e~L~~~Fs-~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~lng~~~~Gr~I~V~~  317 (393)
                      ++|...|. +||+|.++.+....    +.              .-.|-+||.|...++|++|+ .||+..|.|++|.+.+
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl----~~--------------hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~  144 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNL----GD--------------HLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAEL  144 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc----ch--------------hhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeee
Confidence            45555566 89999988664322    11              13478999999999999999 7999999999999988


Q ss_pred             cC
Q 016231          318 AC  319 (393)
Q Consensus       318 a~  319 (393)
                      +.
T Consensus       145 ~p  146 (260)
T KOG2202|consen  145 SP  146 (260)
T ss_pred             cC
Confidence            63

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=91.73  E-value=0.71  Score=35.29  Aligned_cols=50  Identities=16%  Similarity=0.322  Sum_probs=40.9

Q ss_pred             cEEEEeCCCccCCHHHHHHHhccc----CCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKF----GEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~----G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ..|+|+|+. +++.++|..+|..|    ++ ..|.|+-+.                        -|-|.|.+...|..||
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~-~~IEWIdDt------------------------ScNvvf~d~~~A~~AL   59 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGP-FRIEWIDDT------------------------SCNVVFKDEETAARAL   59 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCC-ceEEEecCC------------------------cEEEEECCHHHHHHHH
Confidence            469999994 57889999999998    54 567775443                        5899999999999998

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=90.94  E-value=0.2  Score=40.89  Aligned_cols=72  Identities=19%  Similarity=0.161  Sum_probs=47.0

Q ss_pred             EEEeeCCHHHHHHHHHh--cCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhh
Q 016231          287 AYIVFKSEQSTEAALAF--NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFC  358 (393)
Q Consensus       287 AFVeF~s~e~A~~Al~l--ng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~  358 (393)
                      |.|+|....-|+..+.+  +...+++..+.|............-........++|.|.|||..+.+++|++.++
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~qv~~~vs~rtVlvsgip~~l~ee~l~D~Le   74 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKFQVFSGVSKRTVLVSGIPDVLDEEELRDKLE   74 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEEEEEEcccCCEEEEeCCCCCCChhhheeeEE
Confidence            68999999999998853  3445666666665442111100000011233568999999999999999988764

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=90.53  E-value=0.96  Score=40.32  Aligned_cols=74  Identities=24%  Similarity=0.227  Sum_probs=53.5

Q ss_pred             CCcccEEEEeCCCccC----CHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHH
Q 016231          222 GKLLRTIFVGNLPLKV----KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQST  297 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~----tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A  297 (393)
                      +.+-.||.|+=|..++    +-..+...++.||+|.+|.+.       |.                 --|.|.|.+..+|
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-------Gr-----------------qsavVvF~d~~SA  138 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-------GR-----------------QSAVVVFKDITSA  138 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-------CC-----------------ceEEEEehhhHHH
Confidence            3456788887555443    444566677889999999872       11                 2699999999999


Q ss_pred             HHHHHhcCceeCCeEEEEeecC
Q 016231          298 EAALAFNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       298 ~~Al~lng~~~~Gr~I~V~~a~  319 (393)
                      -.|+..-+....|..+.+.|-.
T Consensus       139 C~Av~Af~s~~pgtm~qCsWqq  160 (166)
T PF15023_consen  139 CKAVSAFQSRAPGTMFQCSWQQ  160 (166)
T ss_pred             HHHHHhhcCCCCCceEEeeccc
Confidence            9999433446778888887753

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=89.34  E-value=0.62  Score=34.24  Aligned_cols=45  Identities=22%  Similarity=0.426  Sum_probs=35.0

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +.|-|.|.+++.. +.|..+|..|    |.|..+.+..      ...+.||.|.++
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~f----GeI~~~~~~~------~~~~~~l~y~~~   46 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASF----GEIVDIYVPE------STNWMYLKYKSR   46 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhc----CCEEEEEcCC------CCcEEEEEECCH
Confidence            5788889988766 4466688889    9999999862      244899999875

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=88.47  E-value=0.79  Score=47.25  Aligned_cols=38  Identities=24%  Similarity=0.469  Sum_probs=35.0

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRH  375 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d  375 (393)
                      -+.++|.+-|||.+-.-+.|.+||..|    |.|.+|||..-
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~----G~IksIRIckP  266 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTV----GSIKSIRICKP  266 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcc----cceeeeeecCC
Confidence            367999999999999999999999999    99999999766

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=88.07  E-value=0.43  Score=48.63  Aligned_cols=52  Identities=19%  Similarity=0.317  Sum_probs=43.5

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCC---CCCCccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPH---MRVGKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~---tg~~kGfaFVeF~t~  392 (393)
                      ..|.|.||.+++|.++++.||...    |.|..++|+....   .......|||.|.+.
T Consensus         8 ~vIqvanispsat~dqm~tlFg~l----GkI~elrlyp~~~d~~~pv~sRtcyVkf~d~   62 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNL----GKIPELRLYPNVDDSKIPVISRTCYVKFLDS   62 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhc----cccccccccCCCCCccCcceeeeEEEeccCC
Confidence            489999999999999999999988    9999999977442   234567999999764

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=87.37  E-value=0.13  Score=55.32  Aligned_cols=112  Identities=13%  Similarity=0.098  Sum_probs=77.7

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...-+|||||+...+..+-+...+..||.|-++..  +                        -|+|..|........|+ 
T Consensus        38 ~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr--~------------------------~fgf~~f~~~~~~~ra~r   91 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKR--D------------------------KFGFCEFLKHIGDLRASR   91 (668)
T ss_pred             CCCceeEecchhhhhhHHHHHHHHhhCCcchhhhh--h------------------------hhcccchhhHHHHHHHHH
Confidence            34678999999999999999999999998765433  1                        18999999999998888 


Q ss_pred             HhcCceeCCeEEEEeecC----CCcccC--CCCCCCCcC---CcceeeeCCCCCCCCHHHHHHHhhcC
Q 016231          302 AFNMAVIGGNHIRLDRAC----PPRKKL--KGEDAPLYD---IKKTVFVGNLPFDVKDEEIYQLFCGL  360 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~----~~~~~~--~~~~~~~~~---~~~tLfVgNLp~~~teedL~e~F~~~  360 (393)
                      .++...++|..+.+..-.    .+.+..  .........   ..+-++|+|+|..+........|..-
T Consensus        92 ~~t~~~~~~~kl~~~~d~q~~~n~~k~~~~~~~~~~~f~p~~srr~e~i~~k~~~l~~~~~~~~~~is  159 (668)
T KOG2253|consen   92 LLTELNIDDQKLIENVDEQTIENADKEKSIANKESHKFVPSSSRRQESIQNKPLSLDEQIHKKSLQIS  159 (668)
T ss_pred             HhcccCCCcchhhccchhhhhcCccccccchhhhhcccCCchhHHHHHhhccccchhHHHHHHHHhcc
Confidence            567777778777665521    000000  000011111   14678999999988888777777654

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=86.77  E-value=0.36  Score=50.22  Aligned_cols=73  Identities=25%  Similarity=0.401  Sum_probs=59.1

Q ss_pred             ccEEEEeCCCccC-CHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHh
Q 016231          225 LRTIFVGNLPLKV-KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~-tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~l  303 (393)
                      .+.|-+.-.|+.. |-.+|..+|.+||.|..|.+...+                       -.|.|+|.+..+|-.|...
T Consensus       372 hs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~-----------------------~~a~vTF~t~aeag~a~~s  428 (526)
T KOG2135|consen  372 HSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSS-----------------------LHAVVTFKTRAEAGEAYAS  428 (526)
T ss_pred             cchhhhhccCCCCchHhhhhhhhhhcCccccccccCch-----------------------hhheeeeeccccccchhcc
Confidence            4555566666664 568999999999999998872211                       2699999999999888889


Q ss_pred             cCceeCCeEEEEeecCC
Q 016231          304 NMAVIGGNHIRLDRACP  320 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~  320 (393)
                      ++..|+||.|.|.|..+
T Consensus       429 ~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  429 HGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             ccceecCceeEEEEecC
Confidence            99999999999999876

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=86.67  E-value=0.57  Score=47.16  Aligned_cols=54  Identities=19%  Similarity=0.268  Sum_probs=47.4

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeE--------EEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVE--------AVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~--------~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...+|||-+||..++..+|.++|.+|    |.|.        -|.|.+|..|+.++|-|-|.|.+.
T Consensus        65 ~~~ti~v~g~~d~~~~~~~~~~f~qc----g~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~  126 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCENDNADFFLQC----GVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDP  126 (351)
T ss_pred             ccccceeeccCccchHHHHHHHHhhc----ceeccCCCCCCcchhccccccccCcCCceeeeecCh
Confidence            35699999999999999999999999    6664        377888989999999999999874

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=86.13  E-value=2.3  Score=42.18  Aligned_cols=70  Identities=20%  Similarity=0.237  Sum_probs=52.4

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhcC
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNM  305 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~lng  305 (393)
                      .-|-|-++|+... ..|..+|..||.|..+...          ++|             -+-+|.|.+.-+|++||..||
T Consensus       198 ~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~----------~ng-------------NwMhirYssr~~A~KALskng  253 (350)
T KOG4285|consen  198 TWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP----------SNG-------------NWMHIRYSSRTHAQKALSKNG  253 (350)
T ss_pred             ceEEEeccCccch-hHHHHHHHhhCeeeeeecC----------CCC-------------ceEEEEecchhHHHHhhhhcC
Confidence            4466668887755 4566789999999876541          111             389999999999999999999


Q ss_pred             ceeCCeE-EEEeecC
Q 016231          306 AVIGGNH-IRLDRAC  319 (393)
Q Consensus       306 ~~~~Gr~-I~V~~a~  319 (393)
                      ++|+|.. |-|..|.
T Consensus       254 ~ii~g~vmiGVkpCt  268 (350)
T KOG4285|consen  254 TIIDGDVMIGVKPCT  268 (350)
T ss_pred             eeeccceEEeeeecC
Confidence            9998855 4566654

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=86.11  E-value=0.36  Score=48.19  Aligned_cols=81  Identities=16%  Similarity=0.363  Sum_probs=58.0

Q ss_pred             ccEEEEeCCCccCCHHHHH---HHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          225 LRTIFVGNLPLKVKKKTLI---KEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~---~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ..-+||-+|+.....+.+.   ++|.+||.|..|.+-+++..  .. .          .+ ...-+||+|...++|..||
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~--~s-~----------~~-~~~s~yITy~~~eda~rci  142 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSS--SS-S----------SG-GTCSVYITYEEEEDADRCI  142 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCccc--cc-C----------CC-CCCcccccccchHhhhhHH
Confidence            3558999999886555443   48999999999988554310  00 0          00 1123899999999999999


Q ss_pred             -HhcCceeCCeEEEEeecC
Q 016231          302 -AFNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~  319 (393)
                       ..+|..+.|+.+......
T Consensus       143 ~~v~g~~~dg~~lka~~gt  161 (327)
T KOG2068|consen  143 DDVDGFVDDGRALKASLGT  161 (327)
T ss_pred             HHhhhHHhhhhhhHHhhCC
Confidence             699999999987766654

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=84.72  E-value=8.7  Score=32.64  Aligned_cols=66  Identities=17%  Similarity=0.188  Sum_probs=45.6

Q ss_pred             cEEEEeCCCccCCHHHHHHHhccc-CCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKF-GEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~-G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      ..+-+...|+-++-++|..+.+.+ ..|..++|+++..                   .++-.+.+.|.+..+|.... .+
T Consensus        14 ~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~-------------------pnrymVLikF~~~~~Ad~Fy~~f   74 (110)
T PF07576_consen   14 TLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT-------------------PNRYMVLIKFRDQESADEFYEEF   74 (110)
T ss_pred             eEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC-------------------CceEEEEEEECCHHHHHHHHHHh
Confidence            344445555556666676555554 4577888876532                   14468999999999999988 79


Q ss_pred             cCceeCC
Q 016231          304 NMAVIGG  310 (393)
Q Consensus       304 ng~~~~G  310 (393)
                      ||..|+.
T Consensus        75 NGk~Fns   81 (110)
T PF07576_consen   75 NGKPFNS   81 (110)
T ss_pred             CCCccCC
Confidence            9988753

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=83.05  E-value=1.5  Score=42.41  Aligned_cols=59  Identities=17%  Similarity=0.260  Sum_probs=47.9

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      ..|||.||+.-+.-+.|..-|+.||+|....+.-+.                  .++..|-++|.|...-.+..|+.
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~------------------r~k~t~eg~v~~~~k~~a~~a~r   90 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD------------------RGKPTREGIVEFAKKPNARKAAR   90 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc------------------cccccccchhhhhcchhHHHHHH
Confidence            569999999999999999999999999765553322                  12355789999999999999984

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=82.72  E-value=1.6  Score=38.05  Aligned_cols=84  Identities=17%  Similarity=0.097  Sum_probs=60.2

Q ss_pred             eEEEEeeCCHHHHHHHHHhcCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCC-CCHHHHHHHhhcCCCC
Q 016231          285 VHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFD-VKDEEIYQLFCGLNDL  363 (393)
Q Consensus       285 G~AFVeF~s~e~A~~Al~lng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~-~teedL~e~F~~~~~~  363 (393)
                      |+..+.|.+.+++..++......+.|..+.+..-.+......   .......--|-|.|||.. ++++-|..+-+.+   
T Consensus        56 ~~fl~~F~~~~d~~~vl~~~p~~~~~~~~~l~~W~~~~~~~~---~~~~~~~vWVri~glP~~~~~~~~~~~i~~~i---  129 (153)
T PF14111_consen   56 NLFLFQFESEEDRQRVLKGGPWNFNGHFLILQRWSPDFNPSE---VKFEHIPVWVRIYGLPLHLWSEEILKAIGSKI---  129 (153)
T ss_pred             CeEEEEEEeccceeEEEecccccccccchhhhhhcccccccc---cceeccchhhhhccCCHHHhhhHHHHHHHHhc---
Confidence            699999999999999998777888888888876653211110   001112234677799998 6788888998888   


Q ss_pred             CCCeEEEEEeec
Q 016231          364 ESSVEAVRVIRH  375 (393)
Q Consensus       364 ~G~I~~VrI~~d  375 (393)
                       |.+..+.....
T Consensus       130 -G~~i~vD~~t~  140 (153)
T PF14111_consen  130 -GEPIEVDENTL  140 (153)
T ss_pred             -CCeEEEEcCCC
Confidence             89988876443

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=82.26  E-value=8  Score=40.39  Aligned_cols=67  Identities=15%  Similarity=0.254  Sum_probs=57.1

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhccc-CCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKF-GEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~-G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      +..|+|-.+|..+|-.||..|+..+ -.|.+|+|+++...                   ++-.+.|.|.+..+|..-. .
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~p-------------------nrymvLIkFr~q~da~~Fy~e  134 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMP-------------------NRYMVLIKFRDQADADTFYEE  134 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCC-------------------ceEEEEEEeccchhHHHHHHH
Confidence            7889999999999999999999875 56899999886532                   3357999999999999988 7


Q ss_pred             hcCceeCC
Q 016231          303 FNMAVIGG  310 (393)
Q Consensus       303 lng~~~~G  310 (393)
                      +||..|+.
T Consensus       135 fNGk~Fn~  142 (493)
T KOG0804|consen  135 FNGKQFNS  142 (493)
T ss_pred             cCCCcCCC
Confidence            99998864

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	393
1wi8_A	104	Solution Structure Of The Rna Binding Domain Of Euk		5e-04
2krr_A	180	Solution Structure Of The Rbd1,2 Domains From Human		7e-04
2j76_E	100	Solution Structure And Rna Interactions Of The Rna		7e-04
1fje_B	175	Solution Structure Of Nucleolin Rbd12 In Complex Wi		9e-04

>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic Initiation Factor 4b Length = 104

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 31/54 (57%), Gaps = 6/54 (11%)
Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP-HMRVGKGIAYVLFK 390
           T F+GNLP+DV +E I + F GLN     + AVR+ R P +    KG  Y  F+
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLN-----ISAVRLPREPSNPERLKGFGYAEFE 65

>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human Nucleoli Length = 180

Iteration: 1
 Score = 41.6 bits (96), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 31/107 (28%), Positives = 52/107 (48%), Gaps = 16/107 (14%)
Query: 287 AYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPF 346
            Y+ F+S +  E AL      + GN I+L++        KG+D+      +T+   NLP+
Sbjct: 51  GYVDFESAEDLEKALELTGLKVFGNEIKLEKP-------KGKDSKKERDARTLLAKNLPY 103
Query: 347 DVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRV 393
            V  +E+ ++F      E + E +R++        KGIAY+ FKT  
Sbjct: 104 KVTQDELKEVF------EDAAE-IRLVSKDGKS--KGIAYIEFKTEA 141

>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna Recognition Motif From Eukaryotic Translation Initiation Factor 4b Length = 100

Iteration: 1
 Score = 41.6 bits (96), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 31/54 (57%), Gaps = 6/54 (11%)
Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP-HMRVGKGIAYVLFK 390
           T F+GNLP+DV +E I + F GLN     + AVR+ R P +    KG  Y  F+
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGLN-----ISAVRLPREPSNPERLKGFGYAEFE 69

>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre Rna Length = 175

Iteration: 1
 Score = 41.6 bits (96), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 30/105 (28%), Positives = 53/105 (50%), Gaps = 16/105 (15%)
Query: 287 AYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPF 346
            Y+ F+S +  E AL      + GN I+L+       K KG D+      +T+   NL F
Sbjct: 57  GYVDFESAEDLEKALELTGLKVFGNEIKLE-------KPKGRDSKKVRAARTLLAKNLSF 109
Query: 347 DVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
           ++ ++E+ ++F      E ++E +R++        KGIAY+ FK+
Sbjct: 110 NITEDELKEVF------EDALE-IRLVSQDGK--SKGIAYIEFKS 145

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	393
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-21
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-05
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	6e-21
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-08
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-17
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-05
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-17
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	7e-07
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-17
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-04
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	9e-16
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	7e-06
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	4e-15
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-05
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	4e-15
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	4e-07
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-15
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-07
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-14
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	7e-07
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	6e-13
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	6e-13
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-04
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	8e-13
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-11
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-04
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	7e-11
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-09
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	5e-10
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	9e-10
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	5e-04
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-09
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	3e-06
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-09
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-08
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	2e-09
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	4e-04
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	4e-09
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	6e-07
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	6e-09
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	3e-04
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	6e-09
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-05
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	7e-09
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	5e-05
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	9e-09
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	4e-07
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-09
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-06
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-08
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	3e-06
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-08
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	3e-05
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-08
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	7e-07
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-08
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	6e-07
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-08
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	8e-06
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	3e-08
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	4e-05
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-08
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	4e-08
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	2e-05
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	5e-08
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	6e-07
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	5e-08
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	3e-07
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	5e-08
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	9e-06
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	7e-08
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	5e-06
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	8e-08
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-05
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-07
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-05
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-07
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-07
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	9e-04
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-07
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	4e-06
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	2e-07
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	8e-04
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-07
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-07
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	5e-04
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-07
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-05
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	4e-07
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-06
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-07
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-04
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	5e-07
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	9e-05
2div_A	99	TRNA selenocysteine associated protein; structural	6e-07
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	7e-07
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	8e-07
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	7e-04
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	9e-07
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-04
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-06
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	3e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-06
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-06
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-06
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-06
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-06
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	7e-05
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-06
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-04
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-06
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	5e-04
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-06
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	3e-06
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	3e-06
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	7e-04
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-06
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-06
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	6e-05
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	4e-06
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	4e-04
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	4e-06
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	4e-06
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-04
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	4e-06
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-06
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-04
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	5e-06
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-06
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	5e-06
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	6e-04
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	5e-06
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	6e-06
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-04
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	6e-06
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	6e-06
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	5e-04
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	6e-06
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-04
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	7e-06
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	7e-06
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	8e-06
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-05
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-05
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-05
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	2e-05
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-05
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-05
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-05
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	4e-04
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-05
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-05
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	3e-05
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	3e-05
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	3e-05
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	3e-05
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-04
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-05
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-04
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	4e-05
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	5e-04
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	4e-05
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	4e-05
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	5e-05
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	6e-05
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	7e-05
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	6e-04
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	7e-05
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	8e-05
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-04
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	8e-05
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-04
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-04
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-04
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	1e-04
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-04
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-04
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-04
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-04
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	3e-04
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-04
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-04
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-04
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-04
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	2e-04
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-04
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-04
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	2e-04
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-04
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-04
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	3e-04
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	3e-04
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	6e-04
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	3e-04
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-04
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	4e-04
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	4e-04
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	4e-04
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	4e-04
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	4e-04
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	5e-04
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	5e-04
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	8e-04
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	5e-04
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	5e-04
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	6e-04
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	7e-04
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	9e-04
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	9e-04
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	9e-04

>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 = 88.8 bits (221), Expect = 4e-21
 Identities = 29/171 (16%), Positives = 68/171 (39%), Gaps = 33/171 (19%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVR-IRSVPIIDTKIPR-KGAILQKQINENAD 283
           R ++VGN+P  + ++ ++  F     +  +      P++  +I + K             
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------------ 52

Query: 284 SVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGN 343
              A++ F+S   T  A+AF+  +  G  +++ R    +                +F+G 
Sbjct: 53  --FAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPL---------PGAHKLFIGG 101

Query: 344 LPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           LP  + D+++ +L    G       ++A  +++     + KG A+  +   
Sbjct: 102 LPNYLNDDQVKELLTSFG------PLKAFNLVKDSATGLSKGYAFCEYVDI 146

>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 = 44.5 bits (106), Expect = 1e-05
 Identities = 17/93 (18%), Positives = 35/93 (37%), Gaps = 20/93 (21%)

Query: 228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADSVH 286
           +F+G LP  +    + +    FG + +  +    + D+     KG              +
Sbjct: 97  LFIGGLPNYLNDDQVKELLTSFGPLKAFNL----VKDSATGLSKG--------------Y 138

Query: 287 AYIVFKSEQSTEAALA-FNMAVIGGNHIRLDRA 318
           A+  +     T+ A+A  N   +G   + + RA
Sbjct: 139 AFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 88.9 bits (221), Expect = 6e-21
 Identities = 31/182 (17%), Positives = 71/182 (39%), Gaps = 35/182 (19%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRI-RSVPIIDTKIPR-KGAILQKQINENAD 283
           R ++VGN+P  + ++ ++  F     +  +      P++  +I + K             
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------------ 52

Query: 284 SVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLY---------- 333
              A++ F+S   T  A+AF+  +  G  +++ R    +      + P            
Sbjct: 53  --FAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVV 110

Query: 334 -DIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFK 390
            D    +F+G LP  + D+++ +L    G       ++A  +++     + KG A+  + 
Sbjct: 111 PDSAHKLFIGGLPNYLNDDQVKELLTSFG------PLKAFNLVKDSATGLSKGYAFCEYV 164

Query: 391 TR 392
             
Sbjct: 165 DI 166

>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 = 53.9 bits (130), Expect = 1e-08
 Identities = 20/134 (14%), Positives = 43/134 (32%), Gaps = 20/134 (14%)

Query: 192 KVGVGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGE 251
           K+      +     +E+  V+               +F+G LP  +    + +    FG 
Sbjct: 81  KIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGP 140

Query: 252 IDSVRIRSVPIIDTKIPR-KGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIG 309
           + +  +    + D+     KG              +A+  +     T+ A+   N   +G
Sbjct: 141 LKAFNL----VKDSATGLSKG--------------YAFCEYVDINVTDQAIAGLNGMQLG 182

Query: 310 GNHIRLDRACPPRK 323
              + + RA    K
Sbjct: 183 DKKLLVQRASVGAK 196

>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 = 79.2 bits (196), Expect = 1e-17
 Identities = 35/181 (19%), Positives = 66/181 (36%), Gaps = 38/181 (20%)

Query: 213 RKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KG 271
              EG +        +F+GNL        L     +    + + +     +D +    + 
Sbjct: 3   HMVEGSESTTP--FNLFIGNLNPNKSVAELKVAISELFAKNDLAV-----VDVRTGTNRK 55

Query: 272 AILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAP 331
                           Y+ F+S +  E AL      + GN I+L++    R   K   A 
Sbjct: 56  --------------FGYVDFESAEDLEKALELTGLKVFGNEIKLEKP-KGRDSKKVRAA- 99

Query: 332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
                +T+   NL F++ ++E+ ++F          +A+ +         KGIAY+ FK+
Sbjct: 100 -----RTLLAKNLSFNITEDELKEVFE---------DALEIRLVSQDGKSKGIAYIEFKS 145

Query: 392 R 392
            
Sbjct: 146 E 146

>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 = 43.4 bits (103), Expect = 3e-05
 Identities = 23/94 (24%), Positives = 29/94 (30%), Gaps = 23/94 (24%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           RT+   NL   + +  L + F    EI  V             + G              
Sbjct: 100 RTLLAKNLSFNITEDELKEVFEDALEIRLVS-------QDGKSK-G-------------- 137

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRA 318
            AYI FKSE   E  L     A I G  + L   
Sbjct: 138 IAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT 171

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 79.3 bits (196), Expect = 2e-17
 Identities = 30/172 (17%), Positives = 74/172 (43%), Gaps = 30/172 (17%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADS 284
             ++VG++  ++ + T+ + F  FG I S+ +      D+   + KG             
Sbjct: 29  SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDM----SWDSVTMKHKG------------- 71

Query: 285 VHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKT--VFV 341
             A++ ++  ++ + AL   N  ++GG +I++ R     +     D    + +    ++V
Sbjct: 72  -FAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYV 130

Query: 342 GNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
            ++  D+ D++I  +F   G       +++  + R P     KG  ++ ++ 
Sbjct: 131 ASVHQDLSDDDIKSVFEAFG------KIKSATLARDPTTGKHKGYGFIEYEK 176

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 48.8 bits (117), Expect = 7e-07
 Identities = 26/144 (18%), Positives = 54/144 (37%), Gaps = 27/144 (18%)

Query: 190 GKKVGVGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKF 249
           G+ + VG        +     +  +   F+        I+V ++   +    +   F  F
Sbjct: 97  GRNIKVGRPSNIGQAQPIIDQLAEEARAFN-------RIYVASVHQDLSDDDIKSVFEAF 149

Query: 250 GEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAV 307
           G+I S  +      D    + KG              + +I ++  QS++ A+ + N+  
Sbjct: 150 GKIKSATL----ARDPTTGKHKG--------------YGFIEYEKAQSSQDAVSSMNLFD 191

Query: 308 IGGNHIRLDRACPPRKKLKGEDAP 331
           +GG ++R+ +A  P   L     P
Sbjct: 192 LGGQYLRVGKAVTPPMPLLTPATP 215

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 77.2 bits (191), Expect = 4e-17
 Identities = 33/171 (19%), Positives = 64/171 (37%), Gaps = 36/171 (21%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           R ++VGNL   + +  L + F   G I ++          KI           ++N  +V
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANI----------KIMI---------DKNNKNV 41

Query: 286 -HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGN 343
            +A++ +        AL   N   I  N ++++ A   ++    +          +FVG+
Sbjct: 42  NYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQSSSDDTF-------NLFVGD 94

Query: 344 LPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           L  +V DE +   F          S  +  V+        +G  +V F ++
Sbjct: 95  LNVNVDDETLRNAFKDFP------SYLSGHVMWDMQTGSSRGYGFVSFTSQ 139

>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 = 40.6 bits (96), Expect = 2e-04
 Identities = 18/94 (19%), Positives = 37/94 (39%), Gaps = 20/94 (21%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADSV 285
            +FVG+L + V  +TL   F  F    S  +    + D +    +G              
Sbjct: 89  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHV----MWDMQTGSSRG-------------- 130

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRA 318
           + ++ F S+   + A+ +     + G  +R++ A
Sbjct: 131 YGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164

>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 = 73.4 bits (181), Expect = 9e-16
 Identities = 34/171 (19%), Positives = 66/171 (38%), Gaps = 37/171 (21%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADS 284
             + V  LP  +  + L   F   G I++ RI    + D K     G             
Sbjct: 4   TNLIVNYLPQDMTDRELYALFRAIGPINTCRI----MRDYKTGYSYG------------- 46

Query: 285 VHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGN 343
            +A++ F SE  ++ A+   N   +    +++  A P  + +K            ++V N
Sbjct: 47  -YAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGESIKD---------TNLYVTN 96

Query: 344 LPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           LP  + D+++  +F   G      S+    ++R       +G+A+V +  R
Sbjct: 97  LPRTITDDQLDTIFGKYG------SIVQKNILRDKLTGRPRGVAFVRYNKR 141

>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 = 44.9 bits (107), Expect = 7e-06
 Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 8/59 (13%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
              + V  LP D+ D E+Y LF   G       +   R++R        G A+V F + 
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIG------PINTCRIMRDYKTGYSYGYAFVDFTSE 55

>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 = 72.7 bits (179), Expect = 4e-15
 Identities = 35/168 (20%), Positives = 68/168 (40%), Gaps = 31/168 (18%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
            +++VG+L   V +  L ++F   G I S+R+      D        I ++ +       
Sbjct: 16  ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRV----CRD-------MITRRSLG------ 58

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNL 344
           +AY+ F+     E AL   N  VI G  +R+  +       K            +F+ NL
Sbjct: 59  YAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVG-------NIFIKNL 111

Query: 345 PFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
              + ++ +Y  F        ++ + +V+   +    KG  +V F+T+
Sbjct: 112 DKSIDNKALYDTFSAF----GNILSCKVVCDENG--SKGYGFVHFETQ 153

>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 = 45.0 bits (107), Expect = 1e-05
 Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 8/59 (13%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
             +++VG+L  DV +  +Y+ F   G       + ++RV R    R   G AYV F+  
Sbjct: 15  MASLYVGDLHPDVTEAMLYEKFSPAG------PILSIRVCRDMITRRSLGYAYVNFQQP 67

>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 = 72.3 bits (178), Expect = 4e-15
 Identities = 29/169 (17%), Positives = 61/169 (36%), Gaps = 28/169 (16%)

Query: 225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADS 284
           LR +F+G L  +   ++L   F ++G +    +   P  +TK  R               
Sbjct: 13  LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDP--NTKRSRG-------------- 56

Query: 285 VHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNL 344
              ++ + + +  +AA+      + G  +   RA       +      +   K +FVG +
Sbjct: 57  -FGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGA---HLTVKKIFVGGI 112

Query: 345 PFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
             D ++  +   F   G       +E + ++        +G A+V F  
Sbjct: 113 KEDTEEHHLRDYFEQYG------KIEVIEIMTDRGSGKKRGFAFVTFDD 155

>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 = 49.2 bits (118), Expect = 4e-07
 Identities = 17/108 (15%), Positives = 40/108 (37%), Gaps = 17/108 (15%)

Query: 213 RKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGA 272
           R++         ++ IFVG +    ++  L   F ++G+I+ + I    + D    +K  
Sbjct: 92  REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEI----MTDRGSGKKRG 147

Query: 273 ILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACP 320
                         A++ F    S +  +      + G++  + +A  
Sbjct: 148 F-------------AFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALS 182

>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 = 73.5 bits (181), Expect = 7e-15
 Identities = 27/173 (15%), Positives = 59/173 (34%), Gaps = 32/173 (18%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEI-DSVRIRSVPIIDTKIPRKGAILQKQINENADS 284
            T+++ N P    ++ +         +  S+R+ S          +              
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPS----LRFNTSRR------------- 160

Query: 285 VHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGN 343
             AYI   S++     +   N   I G  +    + P  K  K  D+   +  + + + N
Sbjct: 161 -FAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKS-KRTDSATLE-GREIMIRN 217

Query: 344 LPFDVKDEE-IYQLF--CGLNDLESSVEAVRVIRH-PHMRVGKGIAYVLFKTR 392
           L  ++ DE  + + F   G      S+E + +             A+++F+ +
Sbjct: 218 LSTELLDENLLRESFEGFG------SIEKINIPAGQKEHSFNNCCAFMVFENK 264

>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 = 71.9 bits (177), Expect = 2e-14
 Identities = 34/199 (17%), Positives = 60/199 (30%), Gaps = 43/199 (21%)

Query: 196 GEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSV 255
            ++     +     L  +K        + L T+ V NLP    +  + K F   G I  V
Sbjct: 12  SKRPLDEGSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHV 71

Query: 256 RIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRL 315
            +                     +   +   A I F       AA+     V+G N I +
Sbjct: 72  DVAD-------------------SLKKNFRFARIEFARYDGALAAITKTHKVVGQNEIIV 112

Query: 316 DRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRH 375
                               + T+++ N P       I  L   +N +  S+      R 
Sbjct: 113 SHL----------------TECTLWMTNFPPSYTQRNIRDLLQDINVVALSI------RL 150

Query: 376 PHMRVG--KGIAYVLFKTR 392
           P +R    +  AY+   ++
Sbjct: 151 PSLRFNTSRRFAYIDVTSK 169

>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 = 51.5 bits (124), Expect = 2e-07
 Identities = 27/134 (20%), Positives = 48/134 (35%), Gaps = 28/134 (20%)

Query: 186 KEEEGKKVGVGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKE 245
            + EG  +          ++  D       EG        R I + NL  ++  + L++E
Sbjct: 182 LKIEGYTLVTKVSNPLEKSKRTDS---ATLEG--------REIMIRNLSTELLDENLLRE 230

Query: 246 -FIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN 304
            F  FG I+ + I                             A++VF+++ S E AL  N
Sbjct: 231 SFEGFGSIEKINI--PAGQKEHSFNNC--------------CAFMVFENKDSAERALQMN 274

Query: 305 MAVIGGNHIRLDRA 318
            +++G   I +  A
Sbjct: 275 RSLLGNREISVSLA 288

>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 = 69.9 bits (172), Expect = 2e-14
 Identities = 30/168 (17%), Positives = 61/168 (36%), Gaps = 35/168 (20%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             +F+G L     +  L + F K+G +  ++I   P   T   R G              
Sbjct: 4   CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDP--ATGRSR-G-------------- 46

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLP 345
             ++ F+   S +  +     ++ G  I   RA P  ++ K            +FVG + 
Sbjct: 47  FGFLSFEKPSSVDEVVK-TQHILDGKVIDPKRAIPRDEQDK---------TGKIFVGGIG 96

Query: 346 FDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
            DV+ +E  + F   G      ++   +++        +G  +V + +
Sbjct: 97  PDVRPKEFEEFFSQWG------TIIDAQLMLDKDTGQSRGFGFVTYDS 138

>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 = 47.9 bits (115), Expect = 7e-07
 Identities = 15/95 (15%), Positives = 30/95 (31%), Gaps = 17/95 (17%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             IFVG +   V+ K   + F ++G I   ++    +       +G              
Sbjct: 88  GKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQL---MLDKDTGQSRG-------------- 130

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACP 320
             ++ + S  + +              I + RA P
Sbjct: 131 FGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEP 165

>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 = 67.7 bits (166), Expect = 6e-13
 Identities = 23/170 (13%), Positives = 50/170 (29%), Gaps = 48/170 (28%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           R I +  LP  V  + +      +  +    +            KG              
Sbjct: 23  RKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV---------DKYKG-------------- 58

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNL 344
            A++   + +  EAA+ AF+ + +    + +                       + V NL
Sbjct: 59  TAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDA---------------LLCVANL 103

Query: 345 PFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           P  +  ++  +L    G      S+E   ++        KG  +  +  +
Sbjct: 104 PPSLTQQQFEELVRPFG------SLERCFLVYSERTGQSKGYGFAEYMKK 147

>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 = 67.7 bits (166), Expect = 6e-13
 Identities = 21/171 (12%), Positives = 51/171 (29%), Gaps = 36/171 (21%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADSV 285
            + V NLP  + ++   +    FG ++   +    +   +  + KG              
Sbjct: 97  LLCVANLPPSLTQQQFEELVRPFGSLERCFL----VYSERTGQSKG-------------- 138

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNL 344
           + +  +  + S   A        +G   + +        +L           + + V  L
Sbjct: 139 YGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT--DAGQLTPALLH----SRCLCVDRL 192

Query: 345 PFDVKDEE-IYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           P    D + + +            S    ++      +  KG A + ++T 
Sbjct: 193 PPGFNDVDALCRALSAVH------SPTFCQLACGQDGQ-LKGFAVLEYETA 236

>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 = 42.7 bits (101), Expect = 1e-04
 Identities = 13/74 (17%), Positives = 26/74 (35%), Gaps = 15/74 (20%)

Query: 321 PRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHM 378
             +K        +  ++ + +  LP DV ++E++ L     L           V ++   
Sbjct: 7   EIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYELKY-------CFVDKY--- 56

Query: 379 RVGKGIAYVLFKTR 392
              KG A+V     
Sbjct: 57  ---KGTAFVTLLNG 67

>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 = 64.9 bits (159), Expect = 8e-13
 Identities = 29/170 (17%), Positives = 61/170 (35%), Gaps = 37/170 (21%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADSV 285
            + V  LP  + ++     F   GEI+S ++    + D    +  G              
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKL----VRDKITGQSLG-------------- 45

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNL 344
           + ++ +   +  E A+   N   +    I++  A P    ++            ++V  L
Sbjct: 46  YGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRD---------ANLYVSGL 96

Query: 345 PFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           P  +  +E+ QLF   G       +   R++      V +G+ ++ F  R
Sbjct: 97  PKTMTQKELEQLFSQYG------RIITSRILVDQVTGVSRGVGFIRFDKR 140

>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 = 61.1 bits (149), Expect = 2e-11
 Identities = 30/170 (17%), Positives = 62/170 (36%), Gaps = 30/170 (17%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             +FVG +P    +K L + F ++G +  + +               +  +  N      
Sbjct: 4   IKMFVGQVPRTWSEKDLRELFEQYGAVYEINV---------------LRDRSQNPPQSKG 48

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNL 344
             ++ F + ++   A  A +   +        +     K    E     + +K +F+G +
Sbjct: 49  CCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQM----KPADSEKNNAVEDRK-LFIGMI 103

Query: 345 PFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
                + +I  +F   G       +E  R++R P     +G A+V F TR
Sbjct: 104 SKKCTENDIRVMFSSFG------QIEECRILRGPDGL-SRGCAFVTFTTR 146

>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 = 41.4 bits (98), Expect = 1e-04
 Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 17/72 (23%)

Query: 190 GKKVGVGE----KRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKE 245
             KV  G     + K AD+E  + +  RK             +F+G +  K  +  +   
Sbjct: 69  NMKVLPGMHHPIQMKPADSEKNNAVEDRK-------------LFIGMISKKCTENDIRVM 115

Query: 246 FIKFGEIDSVRI 257
           F  FG+I+  RI
Sbjct: 116 FSSFGQIEECRI 127

>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 = 58.1 bits (141), Expect = 7e-11
 Identities = 27/134 (20%), Positives = 47/134 (35%), Gaps = 26/134 (19%)

Query: 196 GEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSV 255
           G       +   + + +   E  D      RT+F   L  +++ + L   F   G++  V
Sbjct: 1   GSSGSSGKSPVREPVDNLSPEERDA-----RTVFCMQLAARIRPRDLEDFFSAVGKVRDV 55

Query: 256 RIRSVPIID--TKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHI 313
           RI    I D  ++   KG               AY+ F   QS   A+      + G  I
Sbjct: 56  RI----ISDRNSRRS-KG--------------IAYVEFCEIQSVPLAIGLTGQRLLGVPI 96

Query: 314 RLDRACPPRKKLKG 327
            +  +   + +L G
Sbjct: 97  IVQASQAEKNRLSG 110

>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 = 54.6 bits (132), Expect = 1e-09
 Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 8/74 (10%)

Query: 320 PPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPH 377
            P ++     +P     +TVF   L   ++  ++   F   G       V  VR+I   +
Sbjct: 9   SPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVG------KVRDVRIISDRN 62

Query: 378 MRVGKGIAYVLFKT 391
            R  KGIAYV F  
Sbjct: 63  SRRSKGIAYVEFCE 76

>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 = 55.7 bits (135), Expect = 5e-10
 Identities = 24/128 (18%), Positives = 46/128 (35%), Gaps = 25/128 (19%)

Query: 228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHA 287
           IF+ NL   +  K L   F  FG I S ++    + D     KG              + 
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKV----VCDENGS-KG--------------YG 48

Query: 288 YIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACP--PRKKLKGEDAPLYDIKKTVFVGNL 344
           ++ F+++++ E A+   N  ++    + + R      R+   G  A  +     V++ N 
Sbjct: 49  FVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEF---TNVYIKNF 105

Query: 345 PFDVKDEE 352
                   
Sbjct: 106 GPGSTRAA 113

>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 = 57.8 bits (140), Expect = 9e-10
 Identities = 33/169 (19%), Positives = 54/169 (31%), Gaps = 48/169 (28%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVH 286
            +FVGNLP  + ++   + F ++GE   V I            +G               
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFI---------NRDRG--------------F 60

Query: 287 AYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLP 345
            +I  +S    E A    +  ++    +R+  A                    + V NL 
Sbjct: 61  GFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGAA---------------LTVKNLS 105

Query: 346 FDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
             V +E + Q F   G       VE   V+     R   G  +V F  +
Sbjct: 106 PVVSNELLEQAFSQFG------PVEKAVVVVDDRGR-ATGKGFVEFAAK 147

>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 = 40.4 bits (95), Expect = 5e-04
 Identities = 19/85 (22%), Positives = 33/85 (38%), Gaps = 21/85 (24%)

Query: 310 GNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSV 367
           G  I +     P +K   +          +FVGNLP D+ +E+  +LF   G        
Sbjct: 3   GFTIDIKSFLKPGEKTYTQRC-------RLFVGNLPTDITEEDFKRLFERYG------EP 49

Query: 368 EAVRVIRHPHMRVGKGIAYVLFKTR 392
             V + R       +G  ++  ++R
Sbjct: 50  SEVFINR------DRGFGFIRLESR 68

>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 = 54.4 bits (131), Expect = 1e-09
 Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 6/66 (9%)

Query: 327 GEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAY 386
           G+  P+      V V  +PF   + ++   F GL      V+AV +++    R   G   
Sbjct: 7   GKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLR-----VDAVHLLKDHVGR-NNGNGL 60

Query: 387 VLFKTR 392
           V F + 
Sbjct: 61  VKFLSP 66

>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 = 44.7 bits (106), Expect = 3e-06
 Identities = 15/95 (15%), Positives = 32/95 (33%), Gaps = 19/95 (20%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             + V  +P    +   +++F     +D+V +    + D      G              
Sbjct: 17  LYVSVHGMPFSAMEND-VRDFFHGLRVDAVHL----LKDHVGRNNG-------------- 57

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACP 320
           +  + F S Q T  AL  N  ++   ++ +  A  
Sbjct: 58  NGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPATE 92

>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 = 53.3 bits (129), Expect = 2e-09
 Identities = 24/99 (24%), Positives = 40/99 (40%), Gaps = 21/99 (21%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIID--TKIPRKGAILQKQINENAD 283
           R+I+VGN+      + L   F   G ++ V I    + D  +  P KG            
Sbjct: 7   RSIYVGNVDYGATAEELEAHFHGCGSVNRVTI----LCDKFSGHP-KGF----------- 50

Query: 284 SVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPR 322
              AYI F  ++S   +LA + ++  G  I++      R
Sbjct: 51  ---AYIEFSDKESVRTSLALDESLFRGRQIKVIPKRTNR 86

>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 = 50.2 bits (121), Expect = 2e-08
 Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 8/58 (13%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
            ++++VGN+ +    EE+   F  CG      SV  V ++        KG AY+ F  
Sbjct: 6   ARSIYVGNVDYGATAEELEAHFHGCG------SVNRVTILCDKFSGHPKGFAYIEFSD 57

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 54.1 bits (130), Expect = 2e-09
 Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 1/56 (1%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
           +  V +  LPF    EE+   F     +    E +  + +P  R   G A+VLF  
Sbjct: 23  QVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRP-TGDAFVLFAC 77

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 39.1 bits (91), Expect = 4e-04
 Identities = 15/95 (15%), Positives = 34/95 (35%), Gaps = 16/95 (16%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADSV 285
            + +  LP     + ++  F +   I   +   +  +     R  G              
Sbjct: 25  IVRMRGLPFTATAEEVVAFFGQHCPITGGK-EGILFVTYPDGRPTG-------------- 69

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACP 320
            A+++F  E+  + AL  +  ++G  +I L R+  
Sbjct: 70  DAFVLFACEEYAQNALRKHKDLLGKRYIELFRSTA 104

>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 = 52.7 bits (127), Expect = 4e-09
 Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 6/57 (10%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
             TV +   PF+V ++ + +    L        A+R++R+ H     G  +V F   
Sbjct: 10  CHTVKLRGAPFNVTEKNVMEFLAPLK-----PVAIRIVRNAHGN-KTGYIFVDFSNE 60

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 46.1 bits (110), Expect = 6e-07
 Identities = 19/101 (18%), Positives = 39/101 (38%), Gaps = 19/101 (18%)

Query: 221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINE 280
            G    T+ +   P  V +K  + EF+   +  ++RI    + +    + G         
Sbjct: 6   SGTTCHTVKLRGAPFNVTEKN-VMEFLAPLKPVAIRI----VRNAHGNKTG--------- 51

Query: 281 NADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPP 321
                + ++ F +E+  + AL  N   +GG +I + R    
Sbjct: 52  -----YIFVDFSNEEEVKQALKCNREYMGGRYIEVFREKSG 87

>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 = 52.3 bits (126), Expect = 6e-09
 Identities = 23/105 (21%), Positives = 45/105 (42%), Gaps = 20/105 (19%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADS 284
            T++VG L  KV +  L + F++ G + +  +      D    + +G             
Sbjct: 16  ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHM----PKDRVTGQHQG------------- 58

Query: 285 VHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGE 328
            + ++ F SE+  + A+   +M  + G  IR+++A    K L G 
Sbjct: 59  -YGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGP 102

>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 = 38.8 bits (91), Expect = 3e-04
 Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 8/58 (13%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
             TV+VG L   V +  +++LF   G       V    + +       +G  +V F +
Sbjct: 15  DATVYVGGLDEKVSEPLLWELFLQAG------PVVNTHMPKDRVTGQHQGYGFVEFLS 66

>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 = 52.3 bits (126), Expect = 6e-09
 Identities = 22/105 (20%), Positives = 41/105 (39%), Gaps = 20/105 (19%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           RT++VGNL   V +  +++ F + G   S ++    I +                     
Sbjct: 16  RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKM----ITE-HTSNDP-------------- 56

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGED 329
           + ++ F   +   AAL A N   I G  ++++ A  P  +  G  
Sbjct: 57  YCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKSGPS 101

>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 = 42.2 bits (100), Expect = 2e-05
 Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 10/59 (16%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
            +T++VGNL  DV +  I QLF   G        ++ ++I            +V F   
Sbjct: 15  PRTLYVGNLSRDVTEVLILQLFSQIG------PCKSCKMIT--EHTSNDPYCFVEFYEH 65

>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 = 52.5 bits (126), Expect = 7e-09
 Identities = 12/72 (16%), Positives = 33/72 (45%), Gaps = 4/72 (5%)

Query: 321 PRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRV 380
           P  + +      ++    V++  LPF+ +++ +   F  L+ +E   +++ +   P+ + 
Sbjct: 10  PSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVE---DSIYIAYGPNGK- 65

Query: 381 GKGIAYVLFKTR 392
             G  +V F+  
Sbjct: 66  ATGEGFVEFRNE 77

>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 = 41.7 bits (98), Expect = 5e-05
 Identities = 16/108 (14%), Positives = 36/108 (33%), Gaps = 17/108 (15%)

Query: 213 RKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGA 272
           +K        +    +++  LP + + K  + +F  F ++D V               G 
Sbjct: 13  QKRSRSRSPHEAGFCVYLKGLPFEAENKH-VIDF--FKKLDIVEDSIYIAYGPNGKATG- 68

Query: 273 ILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACP 320
                          ++ F++E   +AAL  +   +G   I++     
Sbjct: 69  -------------EGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITK 103

>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 = 51.5 bits (124), Expect = 9e-09
 Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 10/74 (13%)

Query: 320 PPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMR 379
               + +   +P Y    T F+GNLP+DV +E I + F GLN     + AVR+ R P   
Sbjct: 7   HHHHRSRLPKSPPY----TAFLGNLPYDVTEESIKEFFRGLN-----ISAVRLPREPSNP 57

Query: 380 VG-KGIAYVLFKTR 392
              KG  Y  F+  
Sbjct: 58  ERLKGFGYAEFEDL 71

>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 = 46.8 bits (112), Expect = 4e-07
 Identities = 24/97 (24%), Positives = 38/97 (39%), Gaps = 17/97 (17%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
            T F+GNLP  V ++++ + F     I +VR+            KG              
Sbjct: 20  YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRL--PREPSNPERLKG-------------- 62

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPR 322
             Y  F+   S  +AL+ N   +G   IR+D A   +
Sbjct: 63  FGYAEFEDLDSLLSALSLNEESLGNRRIRVDVADQAQ 99

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 51.5 bits (124), Expect = 9e-09
 Identities = 17/92 (18%), Positives = 29/92 (31%), Gaps = 24/92 (26%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
            T ++GN+P    +  LI  F  FG I   +           P KG              
Sbjct: 28  TTAYIGNIPHFATEADLIPLFQNFGFILDFKH---------YPEKG-------------- 64

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLD 316
             +I + + +     + A       G ++R  
Sbjct: 65  CCFIKYDTHEQAAVCIVALANFPFQGRNLRTG 96

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 10/57 (17%), Positives = 21/57 (36%), Gaps = 14/57 (24%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           T ++GN+P    + ++  LF   G       +   +          KG  ++ + T 
Sbjct: 29  TAYIGNIPHFATEADLIPLFQNFG------FILDFKHYP------EKGCCFIKYDTH 73

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 5/56 (8%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
            T +VGNLPF+    +I  +F  L+     + +VR++R       KG  YV F   
Sbjct: 16  YTAYVGNLPFNTVQGDIDAIFKDLS-----IRSVRLVRDKDTDKFKGFCYVEFDEV 66

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 24/99 (24%), Positives = 40/99 (40%), Gaps = 20/99 (20%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADS 284
            T +VGNLP    +  +   F     I SVR+    + D    + KG             
Sbjct: 16  YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRL----VRDKDTDKFKG------------- 57

Query: 285 VHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRK 323
              Y+ F    S + AL ++ A++G   +R+D A   ++
Sbjct: 58  -FCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRKQ 95

>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 = 50.7 bits (122), Expect = 1e-08
 Identities = 20/92 (21%), Positives = 38/92 (41%), Gaps = 25/92 (27%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
            T++VG L   + +  L   F +FGEI ++ +         + R+               
Sbjct: 13  TTLYVGGLGDTITETDLRNHFYQFGEIRTITV---------VQRQQ-------------- 49

Query: 286 HAYIVFKSEQSTEAAL--AFNMAVIGGNHIRL 315
            A+I F + Q+ E A   +FN  ++ G  + +
Sbjct: 50  CAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV 81

>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 = 41.5 bits (98), Expect = 3e-05
 Identities = 10/56 (17%), Positives = 25/56 (44%), Gaps = 10/56 (17%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
            T++VG L   + + ++   F    ++ +    + V++       +  A++ F TR
Sbjct: 13  TTLYVGGLGDTITETDLRNHFYQFGEIRT----ITVVQ------RQQCAFIQFATR 58

>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 = 51.1 bits (123), Expect = 2e-08
 Identities = 23/57 (40%), Positives = 30/57 (52%), Gaps = 6/57 (10%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVG-KGIAYVLFKTR 392
            T F+GNLP+DV +E I + F GLN     + AVR+ R P      KG  Y  F+  
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLN-----ISAVRLPREPSNPERLKGFGYAEFEDL 67

>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 = 46.5 bits (111), Expect = 7e-07
 Identities = 27/104 (25%), Positives = 42/104 (40%), Gaps = 21/104 (20%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR--KGAILQKQINENAD 283
            T F+GNLP  V ++++ + F     I +VR+      +   P   KG            
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRL----PREPSNPERLKG------------ 58

Query: 284 SVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKG 327
               Y  F+   S  +AL+ N   +G   IR+D A   + K  G
Sbjct: 59  --FGYAEFEDLDSLLSALSLNEESLGNKRIRVDVADQAQDKDSG 100

>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 = 50.9 bits (122), Expect = 2e-08
 Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 4/57 (7%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           K    + N+PF +   ++ Q   G+   E    AV V+   + + G G A V FK  
Sbjct: 15  KVCAHITNIPFSITKMDVLQFLEGIPVDE---NAVHVLVDNNGQ-GLGQALVQFKNE 67

>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 = 47.0 bits (112), Expect = 6e-07
 Identities = 13/114 (11%), Positives = 33/114 (28%), Gaps = 19/114 (16%)

Query: 219 DDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEI-DSVRIRSVPIIDTKIPRKGAILQKQ 277
            D         + N+P  + K  +++         ++V +    ++D      G      
Sbjct: 9   GDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHV----LVDNNGQGLG------ 58

Query: 278 INENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAP 331
                    A + FK+E     +   +   + G    +        +   ++ P
Sbjct: 59  --------QALVQFKNEDDARKSERLHRKKLNGREAFVHVVTLEDMREIEKNPP 104

>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 = 50.8 bits (122), Expect = 2e-08
 Identities = 19/130 (14%), Positives = 46/130 (35%), Gaps = 24/130 (18%)

Query: 202 ADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVP 261
           +   + +    R E+  +       T++ G +   +  + + + F  FG+I  +R+    
Sbjct: 2   SSGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRV---- 57

Query: 262 IIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACP 320
                 P KG              ++++ F + +S   A+ + N   I G+ ++      
Sbjct: 58  -----FPEKG--------------YSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE 98

Query: 321 PRKKLKGEDA 330
                 G  +
Sbjct: 99  SPDMTSGPSS 108

>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 = 43.5 bits (103), Expect = 8e-06
 Identities = 13/55 (23%), Positives = 22/55 (40%), Gaps = 10/55 (18%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           TV+ G +   + D+ + Q F     +      +RV         KG ++V F T 
Sbjct: 27  TVYCGGIASGLTDQLMRQTFSPFGQIME----IRVFP------EKGYSFVRFSTH 71

>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 = 50.3 bits (121), Expect = 3e-08
 Identities = 21/101 (20%), Positives = 35/101 (34%), Gaps = 19/101 (18%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVH 286
            +F+GNL        L     +    + + +  V    T   RK                
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV---RTGTNRK---------------F 60

Query: 287 AYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKG 327
            Y+ F+S +  E AL      + GN I+L++    R   +G
Sbjct: 61  GYVDFESAEDLEKALELTGLKVFGNEIKLEKP-KGRDGTRG 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 = 41.1 bits (97), Expect = 4e-05
 Identities = 9/56 (16%), Positives = 19/56 (33%), Gaps = 9/56 (16%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
            +F+GNL  +    E+              +   + V+        +   YV F++
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELF------AKNDLAVVDVRTGT-NRKFGYVDFES 67

>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 = 53.1 bits (127), Expect = 3e-08
 Identities = 29/194 (14%), Positives = 61/194 (31%), Gaps = 58/194 (29%)

Query: 226 RTIFVGNL-PLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADS 284
             + V NL P +V  ++L   F  +G++  V+I           +K              
Sbjct: 35  SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF--------NKKE------------- 73

Query: 285 VHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKK------ 337
            +A +        + A+   N   + G  IR+  +     +L  E      + K      
Sbjct: 74  -NALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSP 132

Query: 338 --------------------TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPH 377
                               T+ + N+P  V +E++  LF   +     V+  +  +   
Sbjct: 133 LHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLF---SSNGGVVKGFKFFQK-- 187

Query: 378 MRVGKGIAYVLFKT 391
               + +A +   +
Sbjct: 188 ---DRKMALIQMGS 198

>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 = 50.1 bits (120), Expect = 4e-08
 Identities = 17/56 (30%), Positives = 22/56 (39%), Gaps = 6/56 (10%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
             V +  LP+   + +IY  F  LN        V +   P  RV  G A V F T 
Sbjct: 16  HCVHMRGLPYRATENDIYNFFSPLN-----PMRVHIEIGPDGRV-TGEADVEFATH 65

>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 = 42.0 bits (99), Expect = 2e-05
 Identities = 16/107 (14%), Positives = 34/107 (31%), Gaps = 19/107 (17%)

Query: 215 EEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAIL 274
             G   +      + +  LP +  +   I  F  F  ++ +R+      D +    G   
Sbjct: 5   SSGSSFQSTTGHCVHMRGLPYRATEND-IYNF--FSPLNPMRVHIEIGPDGR--VTG--- 56

Query: 275 QKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPP 321
                       A + F + +   AA+A + A +   ++ L      
Sbjct: 57  -----------EADVEFATHEDAVAAMAKDKANMQHRYVELFLNSTA 92

>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 = 50.5 bits (121), Expect = 5e-08
 Identities = 24/123 (19%), Positives = 41/123 (33%), Gaps = 19/123 (15%)

Query: 197 EKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVR 256
               K           +     + +    R+++VGN+      + L   F   G I+ + 
Sbjct: 8   TTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRIT 67

Query: 257 IRSVPIIDTKIPR-KGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRL 315
           I    + D      KG              +AYI F    S +AA+A +  V  G  I++
Sbjct: 68  I----LCDKFSGHPKG--------------YAYIEFAERNSVDAAVAMDETVFRGRTIKV 109

Query: 316 DRA 318
              
Sbjct: 110 LPK 112

>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 = 47.0 bits (112), Expect = 6e-07
 Identities = 14/58 (24%), Positives = 27/58 (46%), Gaps = 8/58 (13%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
           K++V+VGN+ +    +++   F  CG      S+  + ++        KG AY+ F  
Sbjct: 36  KRSVYVGNVDYGSTAQDLEAHFSSCG------SINRITILCDKFSGHPKGYAYIEFAE 87

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 49.7 bits (119), Expect = 5e-08
 Identities = 16/58 (27%), Positives = 25/58 (43%), Gaps = 8/58 (13%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
            K V    L  +V++  +  +    G       VE V ++ HP  R   G+A VLF +
Sbjct: 6   LKEVTFARLNDNVRETFLKDMCRKYG------EVEEVEILLHPRTRKHLGLARVLFTS 57

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 47.4 bits (113), Expect = 3e-07
 Identities = 18/102 (17%), Positives = 38/102 (37%), Gaps = 18/102 (17%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           + +    L   V++  L     K+GE++ V I   P   T+    G              
Sbjct: 7   KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHP--RTRKHL-G-------------- 49

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLK 326
            A ++F S +  +  +   ++  + GN I        ++++K
Sbjct: 50  LARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIKGQQRMK 91

>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 = 50.6 bits (121), Expect = 5e-08
 Identities = 19/73 (26%), Positives = 24/73 (32%), Gaps = 6/73 (8%)

Query: 320 PPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMR 379
             R     E          V +  LP+   + +IY  F  LN        V +   P  R
Sbjct: 30  MGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-----PVRVHIEIGPDGR 84

Query: 380 VGKGIAYVLFKTR 392
           V  G A V F T 
Sbjct: 85  V-TGEADVEFATH 96

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 44.1 bits (104), Expect = 9e-06
 Identities = 18/106 (16%), Positives = 35/106 (33%), Gaps = 19/106 (17%)

Query: 213 RKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGA 272
             +  F  +      + +  LP K  +   I  F  F  ++ VR+      D +    G 
Sbjct: 34  SGDSEFTVQSTTGHCVHMRGLPYKATEND-IYNF--FSPLNPVRVHIEIGPDGR--VTG- 87

Query: 273 ILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRA 318
                         A + F + +   AA++ + A +   +I L   
Sbjct: 88  -------------EADVEFATHEEAVAAMSKDRANMQHRYIELFLN 120

>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 = 49.4 bits (118), Expect = 7e-08
 Identities = 17/65 (26%), Positives = 25/65 (38%), Gaps = 4/65 (6%)

Query: 327 GEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAY 386
             ++P       V +  LPF    EEI Q F GL  +      + +      R   G A+
Sbjct: 6   SGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVP---NGMTLPVDFQGR-STGEAF 61

Query: 387 VLFKT 391
           V F +
Sbjct: 62  VQFAS 66

>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 = 44.0 bits (104), Expect = 5e-06
 Identities = 14/95 (14%), Positives = 33/95 (34%), Gaps = 17/95 (17%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             + +  LP    K+ +++ F     + +     + +      R                
Sbjct: 16  GFVRLRGLPFGCSKEEIVQFFSGLEIVPN----GMTLPVDFQGRSTGE------------ 59

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACP 320
            A++ F S++  E AL  +   IG  +I + ++  
Sbjct: 60  -AFVQFASQEIAEKALKKHKERIGHRYIEIFKSSR 93

>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 = 49.9 bits (119), Expect = 8e-08
 Identities = 17/67 (25%), Positives = 28/67 (41%), Gaps = 4/67 (5%)

Query: 326 KGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIA 385
           +G ++        V +  LPF    EEI Q F GL  +      + +   P  +   G A
Sbjct: 32  RGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVP---NGITLPVDPEGK-ITGEA 87

Query: 386 YVLFKTR 392
           +V F ++
Sbjct: 88  FVQFASQ 94

>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 = 43.3 bits (102), Expect = 1e-05
 Identities = 18/95 (18%), Positives = 35/95 (36%), Gaps = 17/95 (17%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             + +  LP    K+  I +F  F  ++ V       +D +    G              
Sbjct: 43  GFVRLRGLPFGCTKEE-IVQF--FSGLEIVPNGITLPVDPEGKITG-------------- 85

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACP 320
            A++ F S++  E AL  +   IG  +I + ++  
Sbjct: 86  EAFVQFASQELAEKALGKHKERIGHRYIEVFKSSQ 120

>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 = 48.4 bits (116), Expect = 1e-07
 Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 4/55 (7%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
            + V N+PF V  +EI   F G   +  S   V +  +       G A V F++R
Sbjct: 17  IIKVQNMPFTVSIDEILDFFYGYQVIPGS---VCLKYNEKGM-PTGEAMVAFESR 67

>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 = 41.5 bits (98), Expect = 3e-05
 Identities = 21/97 (21%), Positives = 33/97 (34%), Gaps = 20/97 (20%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEI-DSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
            I V N+P  V    ++  F  +  I  SV +      +  +P  G              
Sbjct: 17  IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCL---KYNEKGMPT-G-------------- 58

Query: 286 HAYIVFKSEQSTEAALA-FNMAVIGGNHIRLDRACPP 321
            A + F+S     AA+   N   IG   ++L     P
Sbjct: 59  EAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGP 95

>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 = 50.7 bits (121), Expect = 1e-07
 Identities = 30/194 (15%), Positives = 59/194 (30%), Gaps = 58/194 (29%)

Query: 226 RTIFVGNL-PLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADS 284
             + V NL P +V  ++L   F  +G++  V+I           +K              
Sbjct: 4   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN--------KKE------------- 42

Query: 285 VHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRA---CPPRKKLKGEDAPL-------- 332
            +A +        + A+   N   + G  IR+  +        +   ED  L        
Sbjct: 43  -NALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSP 101

Query: 333 ---------------YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPH 377
                          +    T+ + N+P  V +E++  LF        S     V     
Sbjct: 102 LHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLF--------SSNGGVVKGFKF 153

Query: 378 MRVGKGIAYVLFKT 391
            +  + +A +   +
Sbjct: 154 FQKDRKMALIQMGS 167

>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 = 47.7 bits (114), Expect = 2e-07
 Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 4/54 (7%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
            + V N+PF V  +EI   F G   +  S   V +  +       G A V F++
Sbjct: 17  VIKVQNMPFTVSIDEILDFFYGYQVIPGS---VCLKYNEKGM-PTGEAMVAFES 66

>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 = 37.3 bits (87), Expect = 9e-04
 Identities = 20/94 (21%), Positives = 32/94 (34%), Gaps = 20/94 (21%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEI-DSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
            I V N+P  V    ++  F  +  I  SV +      +  +P  G              
Sbjct: 17  VIKVQNMPFTVSIDEILDFFYGYQVIPGSVCL---KYNEKGMP-TG-------------- 58

Query: 286 HAYIVFKSEQSTEAALA-FNMAVIGGNHIRLDRA 318
            A + F+S     AA+   N   IG   ++L   
Sbjct: 59  EAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP 92

>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 = 47.4 bits (113), Expect = 2e-07
 Identities = 20/92 (21%), Positives = 41/92 (44%), Gaps = 12/92 (13%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           R ++VGN+P  + ++ ++  F     +  +                 +L  QIN+  D  
Sbjct: 7   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAP----------GNPVLAVQINQ--DKN 54

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDR 317
            A++ F+S   T  A+AF+  +  G  +++ R
Sbjct: 55  FAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR 86

>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 = 44.0 bits (104), Expect = 4e-06
 Identities = 10/57 (17%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCG-LNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           + ++VGN+PF + +E +   F   +     +      +    +   K  A++ F++ 
Sbjct: 7   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 63

>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 = 48.4 bits (115), Expect = 2e-07
 Identities = 11/54 (20%), Positives = 19/54 (35%), Gaps = 2/54 (3%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
            V +  LP+    E++          +  V  V  I     R   G A+V  ++
Sbjct: 19  VVKLRGLPWSCSIEDVQNFLSDCTIHD-GVAGVHFIYTREGR-QSGEAFVELES 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 = 38.0 bits (88), Expect = 8e-04
 Identities = 18/102 (17%), Positives = 33/102 (32%), Gaps = 17/102 (16%)

Query: 220 DEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQI 278
            EG     + +  LP     + +          D V    V  I T+  R  G       
Sbjct: 12  PEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVA--GVHFIYTREGRQSG------- 62

Query: 279 NENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACP 320
                   A++  +SE   + AL  +   +G  +I + ++  
Sbjct: 63  -------EAFVELESEDDVKLALKKDRESMGHRYIEVFKSHR 97

>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 = 48.1 bits (115), Expect = 2e-07
 Identities = 18/107 (16%), Positives = 40/107 (37%), Gaps = 20/107 (18%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADS 284
           + +++ NL  +V ++ L+  F +F E     I           R +G             
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPI----QFRMMTGRMRG------------- 68

Query: 285 VHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGEDA 330
             A+I F +++    AL   N   + G  + ++     +++  G  +
Sbjct: 69  -QAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQRSSGPSS 114

>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 = 47.2 bits (113), Expect = 3e-07
 Identities = 19/91 (20%), Positives = 31/91 (34%), Gaps = 24/91 (26%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             ++VG L        L +EF +FG I ++           +                  
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDH---------VKGDS-------------- 54

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRL 315
            AYI ++S  + +AA        +GG   RL
Sbjct: 55  FAYIQYESLDAAQAACAKMRGFPLGGPDRRL 85

>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 = 38.0 bits (89), Expect = 5e-04
 Identities = 9/58 (15%), Positives = 22/58 (37%), Gaps = 14/58 (24%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFC--GLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
             ++VG L  +     + + F   G      S+  +  ++      G   AY+ +++ 
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFG------SIRTIDHVK------GDSFAYIQYESL 63

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 47.3 bits (113), Expect = 3e-07
 Identities = 16/100 (16%), Positives = 34/100 (34%), Gaps = 19/100 (19%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             +F+  LP    K+ L +     G +  +R+    + +     KG              
Sbjct: 18  HKLFISGLPFSCTKEELEEICKAHGTVKDLRL----VTNRAGKPKG-------------- 59

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKK 324
            AY+ +++E     A+   +   I  N I++  +      
Sbjct: 60  LAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPSS 99

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 13/60 (21%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVG--KGIAYVLFKT 391
           K  +F+  LPF    EE+ ++    G      +V+ +R++ +   R G  KG+AYV ++ 
Sbjct: 17  KHKLFISGLPFSCTKEELEEICKAHG------TVKDLRLVTN---RAGKPKGLAYVEYEN 67

>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 = 48.3 bits (115), Expect = 4e-07
 Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 8/58 (13%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
            T++VGNL F   +E+IY+LF   G       ++ + +      +   G  +V + +R
Sbjct: 40  CTLYVGNLSFYTTEEQIYELFSKSG------DIKKIIMGLDKMKKTACGFCFVEYYSR 91

>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 = 45.9 bits (109), Expect = 2e-06
 Identities = 21/110 (19%), Positives = 38/110 (34%), Gaps = 22/110 (20%)

Query: 216 EGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIID--TKIPRKGAI 273
           E  +   K   T++VGNL     ++ + + F K G+I  + +     +D   K    G  
Sbjct: 30  EEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIM----GLDKMKKTAC-G-- 82

Query: 274 LQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPR 322
                         ++ + S    E A+   N   +    IR D     +
Sbjct: 83  ------------FCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK 120

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 46.5 bits (111), Expect = 4e-07
 Identities = 10/55 (18%), Positives = 21/55 (38%), Gaps = 2/55 (3%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
            T+ + N+      + I         L   V  +R+I+    +  +G A+V   +
Sbjct: 10  DTIILRNIAPHTVVDSIMTALSPYASLA--VNNIRLIKDKQTQQNRGFAFVQLSS 62

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 16/98 (16%), Positives = 28/98 (28%), Gaps = 20/98 (20%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
            TI + N+       +++     +  +    IR +    T+  R G              
Sbjct: 10  DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNR-G-------------- 54

Query: 286 HAYIVFKSEQSTEAAL-----AFNMAVIGGNHIRLDRA 318
            A++   S       L           I G  I +D A
Sbjct: 55  FAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92

>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 = 46.8 bits (112), Expect = 5e-07
 Identities = 24/101 (23%), Positives = 40/101 (39%), Gaps = 22/101 (21%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIID--TKIPRKGAILQKQINENADS 284
           T+ V NL  +    +L + F K+G +  V I      +  TK PR G             
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYI----PREPHTKAPR-G------------- 56

Query: 285 VHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKK 324
             A++ F   +  + A  A + A + G  +R+  A   R+ 
Sbjct: 57  -FAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRD 96

>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 = 40.3 bits (95), Expect = 9e-05
 Identities = 19/69 (27%), Positives = 29/69 (42%), Gaps = 8/69 (11%)

Query: 326 KGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKG 383
            G   P  D   T+ V NL +    + + ++F   G       V  V + R PH +  +G
Sbjct: 3   SGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYG------RVGDVYIPREPHTKAPRG 56

Query: 384 IAYVLFKTR 392
            A+V F  R
Sbjct: 57  FAFVRFHDR 65

>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 = 46.5 bits (111), Expect = 6e-07
 Identities = 11/58 (18%), Positives = 28/58 (48%), Gaps = 3/58 (5%)

Query: 334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
            +  ++++G+L   + +  I + F     +  +V +V++IR+    +  G  +V F  
Sbjct: 7   GMAASLWMGDLEPYMDENFISRAF---ATMGETVMSVKIIRNRLTGIPAGYCFVEFAD 61

>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 = 46.4 bits (111), Expect = 7e-07
 Identities = 28/104 (26%), Positives = 47/104 (45%), Gaps = 20/104 (19%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADS 284
           R ++VG L  +V  K L   FI FG+I  ++I     +D +  + +G             
Sbjct: 13  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI----PLDYETEKHRG------------- 55

Query: 285 VHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKG 327
             A++ F+  +   AA+   N + + G  IR++ A P R K  G
Sbjct: 56  -FAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKESG 98

>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 = 46.1 bits (110), Expect = 8e-07
 Identities = 22/117 (18%), Positives = 43/117 (36%), Gaps = 24/117 (20%)

Query: 212 HRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKG 271
                G +D    ++ ++V NL L   ++ + KEF         R++ +         + 
Sbjct: 2   SSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI---------RD 52

Query: 272 AILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKG 327
                         +A++ F + +    A+ A N  V+ G+ I +  A P  K   G
Sbjct: 53  --------------YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSG 95

>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 = 37.6 bits (88), Expect = 7e-04
 Identities = 13/56 (23%), Positives = 21/56 (37%), Gaps = 10/56 (17%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           K ++V NL     +E I + F  +          RV +       +  A+V F  R
Sbjct: 16  KILYVRNLMLSTSEEMIEKEFNNIKPGAV----ERVKKI------RDYAFVHFSNR 61

>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 = 45.7 bits (109), Expect = 9e-07
 Identities = 22/102 (21%), Positives = 36/102 (35%), Gaps = 24/102 (23%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVH 286
            +FVGNLP  + ++ + K F K+G+   V I            KG               
Sbjct: 17  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFI---------HKDKG--------------F 53

Query: 287 AYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKG 327
            +I  ++    E A    +   + G  +R+  AC       G
Sbjct: 54  GFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTSG 95

>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 = 39.5 bits (93), Expect = 1e-04
 Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 14/57 (24%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
            +FVGNLP D+ +EE+ +LF   G          V + +       KG  ++  +TR
Sbjct: 17  RLFVGNLPPDITEEEMRKLFEKYG------KAGEVFIHK------DKGFGFIRLETR 61

>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 = 47.1 bits (112), Expect = 1e-06
 Identities = 30/144 (20%), Positives = 52/144 (36%), Gaps = 22/144 (15%)

Query: 184 IAKEEEGKKVGVGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLI 243
           + K+        GE       +T  +           + + + ++ V NL  +    TL 
Sbjct: 29  VFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLR 88

Query: 244 KEFIKFGEIDSVRIRSVPIID--TKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL 301
           + F K+G +  V I      D  TK  R G               A++ F  ++  E A+
Sbjct: 89  RVFEKYGRVGDVYI----PRDRYTKESR-G--------------FAFVRFHDKRDAEDAM 129

Query: 302 -AFNMAVIGGNHIRLDRACPPRKK 324
            A + AV+ G  +R+  A   R  
Sbjct: 130 DAMDGAVLDGRELRVQMARYGRPP 153

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 39.8 bits (93), Expect = 3e-04
 Identities = 14/107 (13%), Positives = 31/107 (28%), Gaps = 12/107 (11%)

Query: 291 FKSEQSTEAALAFNMAVIGGNHIRLDRACP----PRKKLKGEDAPLYDIKKTVFVGNLPF 346
             +  + +    +            D A                   +   ++ V NL +
Sbjct: 21  VDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTY 80

Query: 347 DVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
               + + ++F   G       V  V + R  + +  +G A+V F  
Sbjct: 81  RTSPDTLRRVFEKYG------RVGDVYIPRDRYTKESRGFAFVRFHD 121

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 49.9 bits (118), Expect = 1e-06
 Identities = 63/458 (13%), Positives = 125/458 (27%), Gaps = 149/458 (32%)

Query: 8   EDNNISAPSSIFTTLFGGIPNESTVA----SSLFSD----SNPFKRQHRESQSAENESIF 59
             + +S    +F TL      E  V       L  +     +P K + R  Q +    ++
Sbjct: 57  SKDAVSGTLRLFWTLLS--KQEEMVQKFVEEVLRINYKFLMSPIKTEQR--QPSMMTRMY 112

Query: 60  NPMNSDSLDSNNSELKKIKKTRQE------------KPNPDLP-DAEGAATKT----LSL 102
                D L ++N    K   +R +            +P  ++  D    + KT       
Sbjct: 113 IEQR-DRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVC 171

Query: 103 SNKSTKLIYPRSI----LG--FEPNGTIEN------EIKKEHSSNVGSESYLNRQKQNSN 150
            +   +      I    L     P   +E       +I    +S      + +  K   +
Sbjct: 172 LSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSR---SDHSSNIKLRIH 228

Query: 151 FSVEGKKRSENKKTKKRKR-----DDVEKDYVEKKYGV---------------IAKEEEG 190
            S++ + R    K+K  +       +V+       + +                      
Sbjct: 229 -SIQAELR-RLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATT 286

Query: 191 KKVGVGEKRKK-ADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKV------------ 237
             + +         +E + +L+   +    D    L    +   P ++            
Sbjct: 287 THISLDHHSMTLTPDEVKSLLLKYLDCRPQD----LPREVLTTNPRRLSIIAESIRDGLA 342

Query: 238 -----------KKKTLIKEFIKFGEIDSVR--IRSVPII--DTKIP-------------- 268
                      K  T+I+  +   E    R     + +      IP              
Sbjct: 343 TWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKS 402

Query: 269 ---------RKGAILQKQINENADSVHA-YIVFKSEQSTEAALAFNMAVIGGNHIRL-DR 317
                     K ++++KQ  E+  S+ + Y+  K +   E AL          H  + D 
Sbjct: 403 DVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYAL----------HRSIVDH 452

Query: 318 ACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQ 355
                          Y+I KT    +L     D+  Y 
Sbjct: 453 ---------------YNIPKTFDSDDLIPPYLDQYFYS 475

>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 = 45.8 bits (109), Expect = 1e-06
 Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 8/57 (14%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
           KTVF+ NL FD ++E + ++    G       ++ VRV+ HP     KG A+  F T
Sbjct: 16  KTVFIRNLSFDSEEEALGEVLQQFG------DLKYVRVVLHPDTEHSKGCAFAQFMT 66

>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 = 45.4 bits (108), Expect = 2e-06
 Identities = 19/114 (16%), Positives = 46/114 (40%), Gaps = 28/114 (24%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIID--TKIPRKGAILQKQINENAD 283
           +T+F+ NL    +++ L +   +FG++  VR+    ++   T+  + G            
Sbjct: 16  KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRV----VLHPDTEHSK-G------------ 58

Query: 284 SVHAYIVFKSEQSTEAALA-------FNMAVIGGNHIRLDRACPPRKKLKGEDA 330
              A+  F ++++ +  LA            + G  +++D A    +   G  +
Sbjct: 59  --CAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPSS 110

>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 = 45.8 bits (109), Expect = 2e-06
 Identities = 18/104 (17%), Positives = 39/104 (37%), Gaps = 21/104 (20%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           R +++ NLP K+  + +   F K+G I  +R+      +T   R                
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG-----NTPETR---------------G 48

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGE 328
            AY+V++     + A+   +   +   ++ +      R   K +
Sbjct: 49  TAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRAFQKMD 92

>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 = 41.2 bits (97), Expect = 7e-05
 Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 11/56 (19%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFC--GLNDLESSVEAVRVIRHPHMRVGKGIAYVLFK 390
           + +++ NLP+ +  EE+Y +F   G       +  +RV   P  R   G AYV+++
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYG------PIRQIRVGNTPETR---GTAYVVYE 55

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 45.9 bits (109), Expect = 2e-06
 Identities = 24/95 (25%), Positives = 43/95 (45%), Gaps = 20/95 (21%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADS 284
           R ++VG L  +V  K L   FI FG+I  ++I     +D +  + +G             
Sbjct: 64  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI----PLDYETEKHRG------------- 106

Query: 285 VHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRA 318
             A++ F+  +   AA+   N + + G  IR++ A
Sbjct: 107 -FAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 40.5 bits (95), Expect = 2e-04
 Identities = 19/110 (17%), Positives = 38/110 (34%), Gaps = 8/110 (7%)

Query: 285 VHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNL 344
           VH+     S++  E       +V        +R         G        K+ ++VG L
Sbjct: 12  VHSKCENLSDEMYEILSNLPESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGL 71

Query: 345 PFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
             +V D+ ++  F   G       +  +++         +G A+V F+  
Sbjct: 72  AEEVDDKVLHAAFIPFG------DITDIQIPLDYETEKHRGFAFVEFELA 115

>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 = 45.0 bits (107), Expect = 2e-06
 Identities = 20/107 (18%), Positives = 39/107 (36%), Gaps = 24/107 (22%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             I V N+P +  ++ + + F  FGE+ +VR          +P+K               
Sbjct: 16  SKILVRNIPFQANQREIRELFSTFGELKTVR----------LPKKMTGTGA--------- 56

Query: 286 H---AYIVFKSEQSTEAALA--FNMAVIGGNHIRLDRACPPRKKLKG 327
           H    ++ F ++Q  + A     +   + G  + L+ A        G
Sbjct: 57  HRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSG 103

>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 = 38.4 bits (90), Expect = 5e-04
 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 11/61 (18%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVG--KGIAYVLFKT 391
              + V N+PF     EI +LF   G       ++ VR+ +      G  +G  +V F T
Sbjct: 15  TSKILVRNIPFQANQREIRELFSTFG------ELKTVRLPKKMT-GTGAHRGFGFVDFIT 67

Query: 392 R 392
           +
Sbjct: 68  K 68

>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 = 45.8 bits (108), Expect = 2e-06
 Identities = 10/55 (18%), Positives = 17/55 (30%), Gaps = 2/55 (3%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
            V +  LP+    E++         +      V  I     R   G A+V   + 
Sbjct: 46  VVKLRGLPWSCSVEDVQNFLSDCT-IHDGAAGVHFIYTREGR-QSGEAFVELGSE 98

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 44.7 bits (106), Expect = 3e-06
 Identities = 20/110 (18%), Positives = 37/110 (33%), Gaps = 28/110 (25%)

Query: 212 HRKEEGFDDEGKLL--RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR 269
           H   E +DD  K      + +  L   V +  L++   +FG I  V +         +P+
Sbjct: 6   HHHMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVV---------MPK 56

Query: 270 KGAILQKQINENADSVHAYIVFKSEQSTEAALAF---NMAVIGGNHIRLD 316
           K                A + F+       A+ +   N   I G+   ++
Sbjct: 57  KR--------------QALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN 92

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 44.8 bits (106), Expect = 3e-06
 Identities = 6/54 (11%), Positives = 20/54 (37%), Gaps = 2/54 (3%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
            +    LP+    E++   F     + +    +  + +   +  +G A +  ++
Sbjct: 13  LIRAQGLPWSCTMEDVLNFFSDCR-IRNGENGIHFLLNRDGKR-RGDALIEMES 64

>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 = 37.9 bits (88), Expect = 7e-04
 Identities = 17/118 (14%), Positives = 38/118 (32%), Gaps = 20/118 (16%)

Query: 219 DDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQI 278
           ++E   +  I    LP     +  +  F     I +     +  +  +  ++        
Sbjct: 5   EEEVDDVFLIRAQGLPWSCTMED-VLNFFSDCRIRNG-ENGIHFLLNRDGKRRGD----- 57

Query: 279 NENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACP-----PRKKLKGEDAP 331
                   A I  +SEQ  + AL  +   +G  ++ +            K L+ + +P
Sbjct: 58  --------ALIEMESEQDVQKALEKHRMYMGQRYVEVYEINNEDVDALMKSLQVKSSP 107

>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 = 44.2 bits (105), Expect = 3e-06
 Identities = 14/103 (13%), Positives = 32/103 (31%), Gaps = 26/103 (25%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
            T++V      +    L   F  FG I  + +          P +               
Sbjct: 16  NTLYVYGE--DMTPTLLRGAFSPFGNIIDLSM---------DPPRN-------------- 50

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKG 327
            A++ ++  +S + A+   N   +    ++++ A        G
Sbjct: 51  CAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDSG 93

>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 = 44.2 bits (105), Expect = 3e-06
 Identities = 22/94 (23%), Positives = 38/94 (40%), Gaps = 19/94 (20%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           RT+FVGNL  +V+++ L + F++ G +  V I      D +   K               
Sbjct: 17  RTVFVGNLEARVREEILYELFLQAGPLTKVTI----CKDREGKPKS-------------- 58

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRA 318
             ++ FK  +S   A+   N   + G  I +   
Sbjct: 59  FGFVCFKHPESVSYAIALLNGIRLYGRPINVSGP 92

>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 = 40.7 bits (96), Expect = 6e-05
 Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 9/57 (15%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
           +TVFVGNL   V++E +Y+LF   G       +  V + +    +  K   +V FK 
Sbjct: 17  RTVFVGNLEARVREEILYELFLQAG------PLTKVTICKDREGK-PKSFGFVCFKH 66

>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 = 44.1 bits (105), Expect = 4e-06
 Identities = 20/101 (19%), Positives = 37/101 (36%), Gaps = 21/101 (20%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR--KGAILQKQINENADS 284
            + +G L   V K  +++ F  +G+I  + +     ++   P   KG             
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDM----PVERMHPHLSKG------------- 48

Query: 285 VHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKK 324
            +AY+ F++    E AL   +   I G  I       P  +
Sbjct: 49  -YAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAPWPR 88

>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 = 37.9 bits (89), Expect = 4e-04
 Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 9/58 (15%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIR-HPHMRVGKGIAYVLFKTR 392
            V +G L  +V  + I ++F   G       ++ + +     H  + KG AYV F+  
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYG------KIKMIDMPVERMHPHLSKGYAYVEFENP 57

>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 = 45.6 bits (108), Expect = 4e-06
 Identities = 30/166 (18%), Positives = 54/166 (32%), Gaps = 26/166 (15%)

Query: 161 NKKTKKRKRDDVEKD--YVEKKYGVIAKEEEGKKVGVGEKRKKADNETEDMLVHRKEEGF 218
           N KT K +      D    EK +   A +         +   K    T +   H      
Sbjct: 8   NGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVT-EGSHHHHHHMH 66

Query: 219 DDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQI 278
            D   L   ++VGNL     K  L + F  +G + SV +   P         G       
Sbjct: 67  RDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP--------PG------- 111

Query: 279 NENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRK 323
                   A++ F+  +    A+   +   + G  +R++ +   ++
Sbjct: 112 -------FAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEKR 150

>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 = 45.1 bits (107), Expect = 4e-06
 Identities = 22/100 (22%), Positives = 38/100 (38%), Gaps = 22/100 (22%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIID--TKIPRKGAILQKQINENAD 283
             + V  L L   ++ L + F K+G I  V I    + D  ++  R G            
Sbjct: 47  CCLGVFGLSLYTTERDLREVFSKYGPIADVSI----VYDQQSRRSR-G------------ 89

Query: 284 SVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPR 322
              A++ F++    + A    N   + G  IR+D +   R
Sbjct: 90  --FAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKR 127

>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 = 40.5 bits (95), Expect = 1e-04
 Identities = 12/74 (16%), Positives = 25/74 (33%), Gaps = 8/74 (10%)

Query: 320 PPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPH 377
             R      +    D    + V  L     + ++ ++F   G       +  V ++    
Sbjct: 30  MGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYG------PIADVSIVYDQQ 83

Query: 378 MRVGKGIAYVLFKT 391
            R  +G A+V F+ 
Sbjct: 84  SRRSRGFAFVYFEN 97

>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 = 45.6 bits (108), Expect = 4e-06
 Identities = 32/166 (19%), Positives = 69/166 (41%), Gaps = 26/166 (15%)

Query: 170 DDVEKDYVEKKYGVIAKEEEGKKVGVGEKRKKADNETEDMLVHRKEEGFDDEGKLL--RT 227
           +D ++  V  K    AK  +G+  G     ++A +  E +     +E      + +    
Sbjct: 17  EDGDQGIVRLKEK--AKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWI 74

Query: 228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADSVH 286
           +FV ++  + ++  + ++F  +GEI ++ +     +D +    KG              +
Sbjct: 75  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHL----NLDRRTGFSKG--------------Y 116

Query: 287 AYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACP--PRKKLKGED 329
           A + +++ +   AA  A N A I G  I++D      P++  K E 
Sbjct: 117 ALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKKSEK 162

>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 = 43.8 bits (104), Expect = 4e-06
 Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 8/69 (11%)

Query: 326 KGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKG 383
            G    L   K TV+V NLPF + + ++Y++F   G       V  V +++    R  KG
Sbjct: 6   SGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYG------KVVKVTIMKDKDTRKSKG 59

Query: 384 IAYVLFKTR 392
           +A++LF  +
Sbjct: 60  VAFILFLDK 68

>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 = 39.9 bits (94), Expect = 1e-04
 Identities = 23/96 (23%), Positives = 39/96 (40%), Gaps = 22/96 (22%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIID--TKIPRKGAILQKQINENAD 283
            T++V NLP  +    L + F K+G++  V I    + D  T+  + G            
Sbjct: 17  STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTI----MKDKDTRKSK-G------------ 59

Query: 284 SVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRA 318
              A+I+F  + S +    A N   + G  I+   A
Sbjct: 60  --VAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 44.2 bits (105), Expect = 5e-06
 Identities = 19/133 (14%), Positives = 41/133 (30%), Gaps = 26/133 (19%)

Query: 195 VGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDS 254
           +G       + +  +          +       +FV   PL V++  L + F  FG +  
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKE 60

Query: 255 VRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHI 313
           V+I             G               A++ F+  +S   A+   +        +
Sbjct: 61  VKIL-----------NG--------------FAFVEFEEAESAAKAIEEVHGKSFANQPL 95

Query: 314 RLDRACPPRKKLK 326
            +  +  P K+ +
Sbjct: 96  EVVYSKLPAKRYR 108

>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 = 45.9 bits (108), Expect = 5e-06
 Identities = 17/181 (9%), Positives = 41/181 (22%), Gaps = 24/181 (13%)

Query: 226 RTIFVGNL-PLKVKKKTLIKEFIKFGEIDSVRI----RSVPIIDTKIPR---------KG 271
             + V  L   K+    +   F  +G ++ V+         +++                
Sbjct: 5   PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNN 64

Query: 272 AILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAP 331
             +  Q      S    I+       E                  R        +     
Sbjct: 65  NFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYK------DFSESRNNRFSTPEQAAKNR 118

Query: 332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
           +      +   N P +V +E  +++   L           V              + + +
Sbjct: 119 IQHPSNVLHFFNAPLEVTEENFFEICDELG----VKRPTSVKVFSGKSERSSSGLLEWDS 174

Query: 392 R 392
           +
Sbjct: 175 K 175

>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 = 43.8 bits (104), Expect = 5e-06
 Identities = 15/97 (15%), Positives = 42/97 (43%), Gaps = 20/97 (20%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADS 284
           R +++G++P    ++ ++      G + ++++    + D +  R KG             
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKM----MFDPQTGRSKG------------- 45

Query: 285 VHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACP 320
            +A+I F+  +S+ +A+   N   +G   ++   +  
Sbjct: 46  -YAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN 81

>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 = 38.0 bits (89), Expect = 6e-04
 Identities = 14/57 (24%), Positives = 29/57 (50%), Gaps = 8/57 (14%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
           + V++G++P+D  +E+I  L    G       V  ++++  P     KG A++ F+ 
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVG------PVINLKMMFDPQTGRSKGYAFIEFRD 53

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 43.7 bits (103), Expect = 5e-06
 Identities = 16/114 (14%), Positives = 34/114 (29%), Gaps = 23/114 (20%)

Query: 212 HRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKG 271
                   +   L   ++VGNLP   +   L +   + G +        P        + 
Sbjct: 6   SGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGP--------RR 57

Query: 272 AILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKK 324
                          A++ +    + + A+       +G + +R+  A   R K
Sbjct: 58  --------------RAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRDK 97

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 43.8 bits (104), Expect = 6e-06
 Identities = 20/103 (19%), Positives = 38/103 (36%), Gaps = 21/103 (20%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             I+VGNLP  ++ K +   F K+G      IR + + + +                   
Sbjct: 23  CRIYVGNLPPDIRTKDIEDVFYKYG-----AIRDIDLKNRRGGPP--------------- 62

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKG 327
            A++ F+  +  E A+   +     G  +R++     R    G
Sbjct: 63  FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGSG 105

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 11/57 (19%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
            ++VGNLP D++ ++I  +F   G         A+R I   + R G   A+V F+  
Sbjct: 24  RIYVGNLPPDIRTKDIEDVFYKYG---------AIRDIDLKNRRGGPPFAFVEFEDP 71

>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 = 44.2 bits (105), Expect = 6e-06
 Identities = 29/115 (25%), Positives = 44/115 (38%), Gaps = 25/115 (21%)

Query: 219 DDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIID-TKIPRKGAILQKQ 277
           D  GK    +F+G L  +  +K L   F K G I  V +    I D T   R G      
Sbjct: 5   DHPGK----LFIGGLNRETNEKMLKAVFGKHGPISEVLL----IKDRTSKSR-G------ 49

Query: 278 INENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGEDAP 331
                    A+I F++    + A    N   + G  I++++A  P  +  G   P
Sbjct: 50  --------FAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRP 96

>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 = 43.4 bits (103), Expect = 6e-06
 Identities = 25/102 (24%), Positives = 31/102 (30%), Gaps = 27/102 (26%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVR--IRSVPIIDTKIPRKGAILQKQINENAD 283
           RT+   NL   + +  L + F    EI  V    +S          KG            
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKS----------KG------------ 54

Query: 284 SVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKK 324
              AYI FKSE   E  L     A I G  + L         
Sbjct: 55  --IAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGT 94

>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 = 38.0 bits (89), Expect = 5e-04
 Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 13/58 (22%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVG--KGIAYVLFKTR 392
           +T+   NL F++ ++E+ ++F            +R++     + G  KGIAY+ FK+ 
Sbjct: 17  RTLLAKNLSFNITEDELKEVF-------EDALEIRLVS----QDGKSKGIAYIEFKSE 63

>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 = 43.4 bits (103), Expect = 6e-06
 Identities = 23/101 (22%), Positives = 37/101 (36%), Gaps = 24/101 (23%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-------KGAILQKQI 278
            TIFV  L   V  +++   F + G I + +    P+I   +         KG       
Sbjct: 14  NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMI--NLYTDRETGKLKG------- 64

Query: 279 NENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRA 318
                   A + F    S +AA+  F+     GN I++  A
Sbjct: 65  -------EATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>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 = 39.2 bits (92), Expect = 2e-04
 Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 4/57 (7%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGL--NDLESSVEAVRVIRHPHMRVGKGIAYVLF 389
            T+FV  L  +V  E +   F   G+   + ++    + +         KG A V F
Sbjct: 14  NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSF 70

>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 = 43.9 bits (104), Expect = 7e-06
 Identities = 22/104 (21%), Positives = 40/104 (38%), Gaps = 27/104 (25%)

Query: 226 RTIFVGNLPL-KVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADS 284
             +F+GNL    VKK  +   F K+G +    +            KG             
Sbjct: 28  SRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH-----------KG------------- 63

Query: 285 VHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKG 327
            +A++ + +E+   AA+   N  V+ G  + ++ A  P+    G
Sbjct: 64  -YAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDRSG 106

>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 = 42.9 bits (102), Expect = 7e-06
 Identities = 24/95 (25%), Positives = 43/95 (45%), Gaps = 20/95 (21%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADS 284
           R ++VG L  +V  K L   FI FG+I  ++I     +D +  + +G             
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI----PLDYETEKHRG------------- 50

Query: 285 VHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRA 318
             A++ F+  +   AA+   N + + G  IR++ A
Sbjct: 51  -FAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 84

>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 = 45.5 bits (107), Expect = 8e-06
 Identities = 12/74 (16%), Positives = 27/74 (36%), Gaps = 6/74 (8%)

Query: 320 PPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPH 377
             +             +  +++GNL +   DE++ +     G+ND+      ++   +  
Sbjct: 52  VGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILE----IKFFENRA 107

Query: 378 MRVGKGIAYVLFKT 391
               KG A V   +
Sbjct: 108 NGQSKGFALVGVGS 121

>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 = 42.6 bits (101), Expect = 1e-05
 Identities = 24/113 (21%), Positives = 48/113 (42%), Gaps = 24/113 (21%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADS 284
           R++FVGN+P +  ++ L   F + G + S R+    + D +  + KG             
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRL----VYDRETGKPKG------------- 51

Query: 285 VHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACP----PRKKLKGEDAPL 332
            + +  ++ +++  +A+   N     G  +R+D A         K  G  AP+
Sbjct: 52  -YGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAPV 103

>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 = 42.9 bits (101), Expect = 1e-05
 Identities = 18/102 (17%), Positives = 41/102 (40%), Gaps = 18/102 (17%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             +F+G +P   K++ +++E  K  E          ++D  +    A      ++  +  
Sbjct: 9   CRLFIGGIPKMKKREEILEEIAKVTEG---------VLDVIVYASAA------DKMKNRG 53

Query: 286 HAYIVFKSEQSTEAA---LAFNMAVIGGNHIRLDRACPPRKK 324
            A++ ++S ++   A   L      + G+ I +D A P    
Sbjct: 54  FAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDV 95

>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 = 42.1 bits (99), Expect = 2e-05
 Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 4/58 (6%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP-HMRVGKGIAYVLFKTR 392
              +F+G +P   K EEI +    + +    V  V V          +G A+V +++ 
Sbjct: 8   NCRLFIGGIPKMKKREEILEEIAKVTE---GVLDVIVYASAADKMKNRGFAFVEYESH 62

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 23/107 (21%), Positives = 39/107 (36%), Gaps = 22/107 (20%)

Query: 225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADS 284
           LR++FV   P  V    L + F+ FG + SV +            KG             
Sbjct: 8   LRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMD---------KDKG------------- 45

Query: 285 VHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAP 331
           V A +      + EA L+ +   +GG+ +R+        +     +P
Sbjct: 46  VFAIVEMGDVGAREAVLSQSQHSLGGHRLRVRPREQKEFQSPASKSP 92

>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 = 42.7 bits (101), Expect = 2e-05
 Identities = 19/103 (18%), Positives = 39/103 (37%), Gaps = 20/103 (19%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           + + V N+P + +   L + F +FG+I  V I    I + +  + G              
Sbjct: 16  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEI----IFNERGSK-G-------------- 56

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKG 327
             ++ F++    + A    +  V+ G  I ++ A        G
Sbjct: 57  FGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSG 99

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 20/109 (18%), Positives = 32/109 (29%), Gaps = 26/109 (23%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             + V  L   V +  L++   KFG I  V +          P K               
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMM---------PFKR-------------- 52

Query: 286 HAYIVFKSEQSTEAALAF---NMAVIGGNHIRLDRACPPRKKLKGEDAP 331
            A + F++  S +  + F       I G     + +   R    G   P
Sbjct: 53  QALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGP 101

>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 = 42.4 bits (100), Expect = 2e-05
 Identities = 25/127 (19%), Positives = 41/127 (32%), Gaps = 27/127 (21%)

Query: 213 RKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR--- 269
               G  DE      I+V  L   V    L   F + G +   +    P+I   I     
Sbjct: 3   SGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMI--HIYLDKE 60

Query: 270 ----KGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKK 324
               KG               A + ++   + +AA+  F+     G+ +++  A   RKK
Sbjct: 61  TGKPKGD--------------ATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA---RKK 103

Query: 325 LKGEDAP 331
                 P
Sbjct: 104 PPMNSGP 110

>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 = 38.9 bits (91), Expect = 4e-04
 Identities = 10/58 (17%), Positives = 22/58 (37%), Gaps = 4/58 (6%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGL--NDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
            ++V  L   V  +++   F  CG+   +  +    + +         KG A V ++ 
Sbjct: 17  AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 74

>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 = 41.8 bits (99), Expect = 2e-05
 Identities = 13/57 (22%), Positives = 23/57 (40%), Gaps = 8/57 (14%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
             +FV NL +   +E++ +LF   G       +  +        +  KG A+V F  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYG------PLSELHYPIDSLTKKPKGFAFVTFMF 59

>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 = 41.8 bits (99), Expect = 3e-05
 Identities = 17/100 (17%), Positives = 34/100 (34%), Gaps = 20/100 (20%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADSV 285
            +FV NL     ++ L K F  +G +  +       ID+   + KG              
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHY----PIDSLTKKPKG-------------- 51

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKK 324
            A++ F   +    A    +  V  G  + +  +   ++ 
Sbjct: 52  FAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEA 91

>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 = 42.3 bits (100), Expect = 3e-05
 Identities = 25/131 (19%), Positives = 56/131 (42%), Gaps = 30/131 (22%)

Query: 197 EKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVR 256
           E+ +  D++  +    R  EG+         +FV ++  + ++  + ++F  +GEI ++ 
Sbjct: 6   ERVRNEDDDELEPGPQRSVEGW--------ILFVTSIHEEAQEDEIQEKFCDYGEIKNIH 57

Query: 257 IRSVPIIDTKIPR-KGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIR 314
           +     +D +    KG              +A + +++ +   AA  A N A I G  I+
Sbjct: 58  L----NLDRRTGFSKG--------------YALVEYETHKQALAAKEALNGAEIMGQTIQ 99

Query: 315 LDRACP--PRK 323
           +D      P++
Sbjct: 100 VDWCFVKGPKR 110

>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 = 41.8 bits (99), Expect = 3e-05
 Identities = 20/95 (21%), Positives = 35/95 (36%), Gaps = 20/95 (21%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADS 284
             + V  L L   ++ L + F K+G I  V I    + D +  R +G             
Sbjct: 16  CCLGVFGLSLYTTERDLREVFSKYGPIADVSI----VYDQQSRRSRG------------- 58

Query: 285 VHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRA 318
             A++ F++    + A    N   + G  IR+   
Sbjct: 59  -FAFVYFENVDDAKEAKERANGMELDGRRIRVSGP 92

>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 = 41.8 bits (99), Expect = 3e-05
 Identities = 28/109 (25%), Positives = 46/109 (42%), Gaps = 26/109 (23%)

Query: 219 DDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIID--TKIPRKGAILQK 276
            DEGKL    FVG L     +++L + F K+G+I  V +    + D  T+  R G     
Sbjct: 10  SDEGKL----FVGGLSFDTNEQSLEQVFSKYGQISEVVV----VKDRETQRSR-G----- 55

Query: 277 QINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKK 324
                      ++ F++    + A+ A N   + G  IR+D+A      
Sbjct: 56  ---------FGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDN 95

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 42.0 bits (99), Expect = 3e-05
 Identities = 24/110 (21%), Positives = 39/110 (35%), Gaps = 24/110 (21%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-------KGAILQKQI 278
            TIFV  L   V  +++   F + G I + +    P+I   +         KG       
Sbjct: 8   NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMI--NLYTDRETGKLKGE------ 59

Query: 279 NENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKG 327
                   A + F    S +AA+  F+     GN I++  A       +G
Sbjct: 60  --------ATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRG 101

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 4/57 (7%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGL--NDLESSVEAVRVIRHPHMRVGKGIAYVLF 389
            T+FV  L  +V  E +   F   G+   + ++    + +         KG A V F
Sbjct: 8   NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSF 64

>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 = 44.1 bits (103), Expect = 3e-05
 Identities = 22/98 (22%), Positives = 37/98 (37%), Gaps = 25/98 (25%)

Query: 226 RTIFVGNLPLKVKKKTLIKE----FIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINEN 281
            TI++ NL  K+KK  L K     F +FG+I  +       +   +  +G          
Sbjct: 10  HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDIL------VSRSLKMRG---------- 53

Query: 282 ADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRA 318
                A+++FK   S   AL +          +R+  A
Sbjct: 54  ----QAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 87

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 42.2 bits (98), Expect = 1e-04
 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 3/56 (5%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
            T+++ NL   +K +E+ +    +      +  + V R   MR   G A+V+FK  
Sbjct: 10  HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVIFKEV 62

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 42.0 bits (99), Expect = 4e-05
 Identities = 29/133 (21%), Positives = 44/133 (33%), Gaps = 26/133 (19%)

Query: 195 VGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDS 254
           +             M   R     +    L     V NL  +    TL + F K+G +  
Sbjct: 21  MASMTGGQQMGRGSMSYGRPPPDVEGMTSL----KVDNLTYRTSPDTLRRVFEKYGRVGD 76

Query: 255 VRIRSVPIID--TKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGN 311
           V I      D  TK  R G               A++ F  ++  E A+ A + AV+ G 
Sbjct: 77  VYI----PRDRYTKESR-G--------------FAFVRFHDKRDAEDAMDAMDGAVLDGR 117

Query: 312 HIRLDRACPPRKK 324
            +R+  A   R  
Sbjct: 118 ELRVQMARYGRPP 130

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 39.0 bits (91), Expect = 5e-04
 Identities = 14/75 (18%), Positives = 28/75 (37%), Gaps = 8/75 (10%)

Query: 320 PPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPH 377
                  G   P  +   ++ V NL +    + + ++F   G       V  V + R  +
Sbjct: 31  GRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYG------RVGDVYIPRDRY 84

Query: 378 MRVGKGIAYVLFKTR 392
            +  +G A+V F  +
Sbjct: 85  TKESRGFAFVRFHDK 99

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 41.1 bits (97), Expect = 4e-05
 Identities = 21/105 (20%), Positives = 42/105 (40%), Gaps = 23/105 (21%)

Query: 228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHA 287
           ++VGNL     K  L + F  +G + +V I   P         G               A
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP--------PG--------------FA 40

Query: 288 YIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGEDAP 331
           ++ F+  +  E A+   +  VI G+ +R++ +    ++ + +  P
Sbjct: 41  FVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRSRFDRPP 85

>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 = 41.1 bits (97), Expect = 4e-05
 Identities = 22/98 (22%), Positives = 37/98 (37%), Gaps = 25/98 (25%)

Query: 226 RTIFVGNLPLKVKKKTLIKE----FIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINEN 281
            TI++ NL  K+KK  L K     F +FG+I  + +         +  +G          
Sbjct: 9   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV------SRSLKMRG---------- 52

Query: 282 ADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRA 318
                A+++FK   S   AL +          +R+  A
Sbjct: 53  ----QAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 86

>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 = 41.1 bits (97), Expect = 5e-05
 Identities = 23/100 (23%), Positives = 39/100 (39%), Gaps = 26/100 (26%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           + +FV NL   V ++ L K F +FG+++ V+             K               
Sbjct: 12  KVLFVRNLANTVTEEILEKAFSQFGKLERVKK-----------LKD-------------- 46

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKK 324
           +A+I F        A+   N   + G +I +  A PP +K
Sbjct: 47  YAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQK 86

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 40.8 bits (96), Expect = 6e-05
 Identities = 22/127 (17%), Positives = 46/127 (36%), Gaps = 22/127 (17%)

Query: 195 VGEKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDS 254
           +G       + +   LV R      +     + + V N+P + +   L + F +FG+I  
Sbjct: 1   MGSSHHHHHHSSG--LVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILD 58

Query: 255 VRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHI 313
           V I    I + +  + G                ++ F++    + A    +  V+ G  I
Sbjct: 59  VEI----IFNERGSK-G--------------FGFVTFENSADADRAREKLHGTVVEGRKI 99

Query: 314 RLDRACP 320
            ++ A  
Sbjct: 100 EVNNATA 106

>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 = 40.6 bits (96), Expect = 7e-05
 Identities = 20/96 (20%), Positives = 37/96 (38%), Gaps = 20/96 (20%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADSV 285
            ++VG+L   + +  L   F  FG+ID++ +    + D+   R KG              
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVL----MKDSDTGRSKG-------------- 48

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACP 320
           + +I F   +    AL   N   + G  +R+     
Sbjct: 49  YGFITFSDSECARRALEQLNGFELAGRPMRVGHVTE 84

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 37.9 bits (89), Expect = 6e-04
 Identities = 9/57 (15%), Positives = 26/57 (45%), Gaps = 8/57 (14%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
             ++VG+L F++ ++ +  +F   G       ++ + +++       KG  ++ F  
Sbjct: 6   SGLYVGSLHFNITEDMLRGIFEPFG------KIDNIVLMKDSDTGRSKGYGFITFSD 56

>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 = 40.6 bits (96), Expect = 7e-05
 Identities = 28/102 (27%), Positives = 41/102 (40%), Gaps = 21/102 (20%)

Query: 221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIID--TKIPRKGAILQKQI 278
            G     IFVG +P    +  L + F KFG +  V +    I D   + PR G       
Sbjct: 6   SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVM----IYDAEKQRPR-G------- 53

Query: 279 NENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACP 320
                    +I F+ EQS + A+  +   I G  + + RA P
Sbjct: 54  -------FGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRAEP 88

>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 = 40.2 bits (95), Expect = 8e-05
 Identities = 13/54 (24%), Positives = 21/54 (38%), Gaps = 4/54 (7%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           VFVG+L  ++    I   F         +   RV++       KG  +V F  +
Sbjct: 9   VFVGDLSPEITTAAIAAAFAPF----GRISDARVVKDMATGKSKGYGFVSFFNK 58

>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 = 39.5 bits (93), Expect = 1e-04
 Identities = 20/95 (21%), Positives = 36/95 (37%), Gaps = 20/95 (21%)

Query: 228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADSVH 286
           +FVG+L  ++    +   F  FG I   R+    + D    + KG              +
Sbjct: 9   VFVGDLSPEITTAAIAAAFAPFGRISDARV----VKDMATGKSKG--------------Y 50

Query: 287 AYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACP 320
            ++ F ++   E A+       +GG  IR + A  
Sbjct: 51  GFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATR 85

>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 = 8e-05
 Identities = 19/109 (17%), Positives = 42/109 (38%), Gaps = 28/109 (25%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           R I +  LP+ V +  +I   + FG++ ++ +         +  K               
Sbjct: 17  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLM---------LKGKN-------------- 53

Query: 286 HAYIVFKSEQSTEAALAF---NMAVIGGNHIRLDRACPPRKKLKGEDAP 331
            A+I   +E++    + +      V+ G  I +  +    K+LK + +P
Sbjct: 54  QAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFS--NHKELKTDSSP 100

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 15/61 (24%), Positives = 27/61 (44%), Gaps = 8/61 (13%)

Query: 334 DIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
           D   T+ V NL  D ++ ++ +LF   G      S+  + + +       KG A++ F  
Sbjct: 13  DDNATIRVTNLSEDTRETDLQELFRPFG------SISRIYLAKDKTTGQSKGFAFISFHR 66

Query: 392 R 392
           R
Sbjct: 67  R 67

>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 = 41.0 bits (96), Expect = 1e-04
 Identities = 31/129 (24%), Positives = 54/129 (41%), Gaps = 17/129 (13%)

Query: 197 EKRKKADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVR 256
           EK + +  E E + V R  E     G+    I+V NL   V++K L   F ++ +  S  
Sbjct: 21  EKGRISREEMETLSVFRSYE----PGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSET 76

Query: 257 IRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRL 315
            R   + D ++ ++G +             A+I   +E++   AL   N  V+ G  + +
Sbjct: 77  QR--IMFDIRLMKEGRMKG----------QAFIGLPNEKAAAKALKEANGYVLFGKPMVV 124

Query: 316 DRACPPRKK 324
             A   R K
Sbjct: 125 QFARSARPK 133

>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 = 39.9 bits (94), Expect = 1e-04
 Identities = 18/100 (18%), Positives = 34/100 (34%), Gaps = 26/100 (26%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             IFVGN+      + L   F + G +    +            K               
Sbjct: 10  WKIFVGNVSAACTSQELRSLFERRGRVIECDVV-----------KD-------------- 44

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKK 324
           +A++  + E   +AA+   N   + G  I ++ +   +KK
Sbjct: 45  YAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQKK 84

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 40.3 bits (94), Expect = 1e-04
 Identities = 16/91 (17%), Positives = 34/91 (37%), Gaps = 15/91 (16%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           R +FVG LP  + +  +   F +FG +               P+                
Sbjct: 9   RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKG--------------- 53

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLD 316
           +A+++F+ E S +A +   +   G  ++ + 
Sbjct: 54  YAFLLFQEESSVQALIDACLEEDGKLYLCVS 84

>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 = 39.4 bits (93), Expect = 1e-04
 Identities = 18/95 (18%), Positives = 37/95 (38%), Gaps = 20/95 (21%)

Query: 228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADSVH 286
           +FVG+L + V  +TL   F  F    S  +    + D +    +G              +
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHV----MWDMQTGSSRG--------------Y 45

Query: 287 AYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACP 320
            ++ F S+   + A+ +     + G  +R++ A  
Sbjct: 46  GFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 80

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 40.3 bits (94), Expect = 1e-04
 Identities = 19/109 (17%), Positives = 42/109 (38%), Gaps = 28/109 (25%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           R I +  LP+ V +  +I   + FG++ ++ +         +  K               
Sbjct: 32  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLM---------LKGKN-------------- 68

Query: 286 HAYIVFKSEQSTEAALAF---NMAVIGGNHIRLDRACPPRKKLKGEDAP 331
            A+I   +E++    + +      V+ G  I +  +    K+LK + +P
Sbjct: 69  QAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFS--NHKELKTDSSP 115

>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 = 38.4 bits (89), Expect = 6e-04
 Identities = 14/73 (19%), Positives = 24/73 (32%), Gaps = 10/73 (13%)

Query: 320 PPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMR 379
            PR    G+        + + +  LP DV + E+  L                + +  M 
Sbjct: 15  VPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLG----------LPFGKVTNLLML 64

Query: 380 VGKGIAYVLFKTR 392
            GK  A++   T 
Sbjct: 65  KGKNQAFIEMNTE 77

>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 = 40.0 bits (94), Expect = 1e-04
 Identities = 24/114 (21%), Positives = 39/114 (34%), Gaps = 24/114 (21%)

Query: 213 RKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KG 271
               G        +T+ + NL     ++TL + F K   I         +   +  + KG
Sbjct: 3   SGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIK--------VPQNQNGKSKG 54

Query: 272 AILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKK 324
                         +A+I F S +  + AL + N   I G  IRL+   P    
Sbjct: 55  --------------YAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSP 94

>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 = 38.8 bits (91), Expect = 3e-04
 Identities = 11/55 (20%), Positives = 27/55 (49%), Gaps = 8/55 (14%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
           KT+ + NL +   +E + ++F            ++V ++ + +  KG A++ F +
Sbjct: 16  KTLVLSNLSYSATEETLQEVF-------EKATFIKVPQNQNGK-SKGYAFIEFAS 62

>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 = 39.8 bits (93), Expect = 1e-04
 Identities = 14/104 (13%), Positives = 37/104 (35%), Gaps = 28/104 (26%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           R + +  LP +V +  +I   + FG++ ++ +         +  K               
Sbjct: 16  RVLHIRKLPGEVTETEVIALGLPFGKVTNILM---------LKGKN-------------- 52

Query: 286 HAYIVFKSEQSTEAALAF---NMAVIGGNHIRLDRACPPRKKLK 326
            A++   +E++    + +       +    I +  +    K+LK
Sbjct: 53  QAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYS--NHKELK 94

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 15/96 (15%), Positives = 39/96 (40%), Gaps = 20/96 (20%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADSV 285
            +FV  +  +  ++ +  +F ++GEI ++ +     +D +    KG              
Sbjct: 25  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHL----NLDRRTGYLKG-------------- 66

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACP 320
           +  + +++ +  +AA+   N   + G  I +D    
Sbjct: 67  YTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFV 102

>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 = 39.6 bits (93), Expect = 2e-04
 Identities = 11/56 (19%), Positives = 28/56 (50%), Gaps = 8/56 (14%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           +F+G +P ++ ++++  LF   G       +  + V++     + KG A++ +  R
Sbjct: 16  LFIGQIPRNLDEKDLKPLFEEFG------KIYELTVLKDRFTGMHKGCAFLTYCER 65

>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 = 40.0 bits (94), Expect = 2e-04
 Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 9/57 (15%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           TVFV NL + V  +++ ++F   G       V    ++     +  +GI  V F+  
Sbjct: 17  TVFVANLDYKVGWKKLKEVFSMAG------VVVRADILEDKDGK-SRGIGTVTFEQS 66

>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 = 40.0 bits (94), Expect = 2e-04
 Identities = 26/126 (20%), Positives = 38/126 (30%), Gaps = 33/126 (26%)

Query: 225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIID--TKIPRKGAILQKQINENA 282
              IFVG LP      +L K F  FG+I+   +    I D  T   R G           
Sbjct: 17  FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVV----ITDRQTGKSR-G----------- 60

Query: 283 DSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACP---PRKKLKGEDAPLYDIKKTV 339
              + ++      + E A      +I G    ++ A     PR    G           +
Sbjct: 61  ---YGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSLQTG---------FAI 108

Query: 340 FVGNLP 345
            V    
Sbjct: 109 GVSGPS 114

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 21/100 (21%), Positives = 37/100 (37%), Gaps = 27/100 (27%)

Query: 227 TIFVGNLPLK-VKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
            +F+GNLPLK V K+ L + F  +G I  + I           +                
Sbjct: 12  RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-----------KNA-------------- 46

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKK 324
             +I F + QS   A+   +  +  G  + L+ +    + 
Sbjct: 47  FGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNARP 86

>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 = 38.7 bits (91), Expect = 2e-04
 Identities = 25/94 (26%), Positives = 33/94 (35%), Gaps = 17/94 (18%)

Query: 225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADS 284
              +FVG L     KK L   F KFGE+    I+  P  +T   R               
Sbjct: 11  AGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDP--NTGRSR--------------- 53

Query: 285 VHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRA 318
              +I+FK   S E  L      + G  I   +A
Sbjct: 54  GFGFILFKDAASVEKVLDQKEHRLDGRVIDPKKA 87

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 20/108 (18%), Positives = 35/108 (32%), Gaps = 21/108 (19%)

Query: 213 RKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGA 272
           R         K+    F+G L  +  ++ L + F +FGE+    +   P   TK  R   
Sbjct: 17  RGSHMGSSGCKM----FIGGLSWQTTQEGLREYFGQFGEVKECLVMRDP--LTKRSR--- 67

Query: 273 ILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACP 320
                          ++ F  +   +  LA +   +    I    A P
Sbjct: 68  ------------GFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFP 103

>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 = 39.1 bits (92), Expect = 2e-04
 Identities = 24/108 (22%), Positives = 34/108 (31%), Gaps = 21/108 (19%)

Query: 213 RKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGA 272
               G D+ GKL    FVG L     ++TL   F ++GE+    I       T   R   
Sbjct: 8   MNNSGADEIGKL----FVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDK--TTNQSR--- 58

Query: 273 ILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACP 320
                          ++ FK        LA     + G +I      P
Sbjct: 59  ------------GFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPCTP 94

>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 = 39.2 bits (92), Expect = 3e-04
 Identities = 13/55 (23%), Positives = 21/55 (38%), Gaps = 7/55 (12%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
           KT+FV  L  D  +E + + F             R++        KG  +V F +
Sbjct: 16  KTLFVKGLSEDTTEETLKESF-------DGSVRARIVTDRETGSSKGFGFVDFNS 63

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 40.9 bits (95), Expect = 3e-04
 Identities = 20/139 (14%), Positives = 41/139 (29%), Gaps = 35/139 (25%)

Query: 200 KKADNETEDMLVHRKEE--GFDDEGKLLRTIFVGNLPLKVKKKT---------LIKEFIK 248
           +  D    +     +E+  G     K  +T++VG +   +  K          +   F +
Sbjct: 107 EVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSR 166

Query: 249 FGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAV 307
            G+ID +R          +  K                 ++ FK + + E A  A +   
Sbjct: 167 LGDIDRIRY---------VESKN--------------CGFVKFKYQANAEFAKEAMSNQT 203

Query: 308 IGGNHIRLDRACPPRKKLK 326
           +     +          L 
Sbjct: 204 LLLPSDKEWDDRREGTGLL 222

>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 = 39.3 bits (92), Expect = 3e-04
 Identities = 20/96 (20%), Positives = 37/96 (38%), Gaps = 20/96 (20%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADSV 285
            +FVG+L  ++  + +   F  FG I   R+    + D    + KG              
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARV----VKDMATGKSKG-------------- 58

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACP 320
           + ++ F ++   E A+       +GG  IR + A  
Sbjct: 59  YGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATR 94

>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 = 38.1 bits (89), Expect = 6e-04
 Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 8/57 (14%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
            VFVG+L  ++  E+I   F   G       +   RV++       KG  +V F  +
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFG------RISDARVVKDMATGKSKGYGFVSFFNK 67

>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 = 38.3 bits (90), Expect = 3e-04
 Identities = 15/103 (14%), Positives = 38/103 (36%), Gaps = 26/103 (25%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             +F+GNLP +  ++ +   F ++G++    I            K               
Sbjct: 9   VKLFIGNLPREATEQEIRSLFEQYGKVLECDI-----------IKN-------------- 43

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKG 327
           + ++  + + + E A+   +   + G +I ++ +    K   G
Sbjct: 44  YGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKASSG 86

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 38.6 bits (90), Expect = 3e-04
 Identities = 12/103 (11%), Positives = 32/103 (31%), Gaps = 18/103 (17%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           R++++   P       + +     G++ ++++R           KG+             
Sbjct: 12  RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRR----TLHKAFKGS------------- 54

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGE 328
             ++VF S +S +  +           + +        K   E
Sbjct: 55  -IFVVFDSIESAKKFVETPGQKYKETDLLILFKDDYFAKKNEE 96

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 12/103 (11%), Positives = 30/103 (29%), Gaps = 26/103 (25%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             + VGN+      + L  +F ++G +    I            K               
Sbjct: 11  TKLHVGNISPTCTNQELRAKFEEYGPVIECDI-----------VKD-------------- 45

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKG 327
           +A++  +  +    A+   +     G  + +  +    +   G
Sbjct: 46  YAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTASG 88

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 38.3 bits (90), Expect = 4e-04
 Identities = 22/101 (21%), Positives = 42/101 (41%), Gaps = 19/101 (18%)

Query: 225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENAD 283
           +R I+VGNL      + + + F +FG++ +V++    I D +  + KG            
Sbjct: 1   MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKL----IYDRETKKPKG------------ 44

Query: 284 SVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKK 324
               ++  + E  +EA    +     G  IR+  A P +  
Sbjct: 45  --FGFVEMQEESVSEAIAKLDNTDFMGRTIRVTEANPKKSL 83

>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 = 38.4 bits (90), Expect = 4e-04
 Identities = 16/105 (15%), Positives = 33/105 (31%), Gaps = 18/105 (17%)

Query: 216 EGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQ 275
            G     +    + V  LP K  ++ L + F  FGE+  V+++      T   + G    
Sbjct: 6   SGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDL--KTGHSK-G---- 58

Query: 276 KQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACP 320
                       ++ F   ++    ++    +I G          
Sbjct: 59  ----------FGFVRFTEYETQVKVMS-QRHMIDGRWCDCKLPNS 92

>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 = 38.4 bits (90), Expect = 4e-04
 Identities = 18/106 (16%), Positives = 34/106 (32%), Gaps = 18/106 (16%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVH 286
            +F+ NL     ++TL   F K G I S  I         +   G               
Sbjct: 7   GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMG--------------F 52

Query: 287 AYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGEDAP 331
            ++ +K  +  + AL       + G+ + +  +    +  K    P
Sbjct: 53  GFVEYKKPEQAQKALKQLQGHTVDGHKLEVRIS---ERATKPASGP 95

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 39.1 bits (91), Expect = 4e-04
 Identities = 18/98 (18%), Positives = 35/98 (35%), Gaps = 25/98 (25%)

Query: 226 RTIFVGNLPLKVK----KKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINEN 281
           + + + N+  +V     +  L       G+I  +       +D      G          
Sbjct: 30  QVVLITNINPEVPKEKLQALLYALASSQGDILDIV------VDLSDDNSG---------- 73

Query: 282 ADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRA 318
                AYIVF +++S +A + AF      GN + +  +
Sbjct: 74  ----KAYIVFATQESAQAFVEAFQGYPFQGNPLVITFS 107

>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 = 37.9 bits (89), Expect = 5e-04
 Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 6/55 (10%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
           +++GNL +   DE++ +     G+ND+      ++   +      KG A V   +
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILE----IKFFENRANGQSKGFALVGVGS 54

>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 = 38.4 bits (90), Expect = 5e-04
 Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 9/56 (16%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           +FVG L     +E++ +LF   G       ++   V+R P     KG A+V F + 
Sbjct: 18  LFVGMLNKQQSEEDVLRLFQPFG------VIDECTVLRGPDGS-SKGCAFVKFSSH 66

>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 = 37.6 bits (88), Expect = 8e-04
 Identities = 12/41 (29%), Positives = 21/41 (51%)

Query: 217 GFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRI 257
           G +  G   R +FVG L  +  ++ +++ F  FG ID   +
Sbjct: 7   GSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTV 47

>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 = 38.5 bits (90), Expect = 5e-04
 Identities = 15/100 (15%), Positives = 39/100 (39%), Gaps = 20/100 (20%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPR-KGAILQKQINENADSV 285
            +FV  +  +  ++ +  +F ++GEI ++ +     +D +    KG              
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHL----NLDRRTGYLKG-------------- 65

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKK 324
           +  + +++ +  +AA+   N   + G  I +D        
Sbjct: 66  YTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPP 105

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 38.4 bits (90), Expect = 5e-04
 Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 9/57 (15%)

Query: 338 TVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
            + V NL F V D +I +LF   G      +++   V      R   G A V F+ +
Sbjct: 31  KLLVSNLDFGVSDADIQELFAEFG------TLKKAAVHYDRSGR-SLGTADVHFERK 80

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 39.1 bits (91), Expect = 6e-04
 Identities = 11/60 (18%), Positives = 27/60 (45%), Gaps = 6/60 (10%)

Query: 334 DIKKTVFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
           + +  V+VG+  +   D+++ Q+    G+ D+      ++   +      KG A V+  +
Sbjct: 53  NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVE----LKFAENRANGQSKGYAEVVVAS 108

>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 = 37.2 bits (87), Expect = 7e-04
 Identities = 17/104 (16%), Positives = 34/104 (32%), Gaps = 27/104 (25%)

Query: 217 GFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQK 276
           G          +FVG     + +  L + F ++G++  V I          P +      
Sbjct: 1   GSSGSSG----VFVGRCTGDMTEDELREFFSQYGDVMDVFI--------PKPFRA----- 43

Query: 277 QINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACP 320
                     A++ F  +Q  ++       +I G  + +  A P
Sbjct: 44  ---------FAFVTFADDQIAQSLCG-EDLIIKGISVHISNAEP 77

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 37.7 bits (88), Expect = 9e-04
 Identities = 11/55 (20%), Positives = 22/55 (40%), Gaps = 8/55 (14%)

Query: 339 VFVGNLPFDVKDEEIYQLF--CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
           +F+ +LP +  D ++   F   G      +V + +V       + K   +V F  
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFG------NVISAKVFIDKQTSLSKCFGFVSFDN 91

>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 = 37.9 bits (88), Expect = 9e-04
 Identities = 19/97 (19%), Positives = 34/97 (35%), Gaps = 20/97 (20%)

Query: 227 TIFVGNLPLKVKKKTLIKE---FIKFGEIDSVRI-RSVPIIDTKIPRKGAILQKQINENA 282
            +FV  L  ++    ++K    F KFG+I  V I  S     ++ P              
Sbjct: 17  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSAS----------- 65

Query: 283 DSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRA 318
               AY+ +   +    A+   N  V+ G  ++    
Sbjct: 66  ----AYVTYIRSEDALRAIQCVNNVVVDGRTLKASLG 98

>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 = 37.9 bits (88), Expect = 9e-04
 Identities = 15/94 (15%), Positives = 24/94 (25%), Gaps = 24/94 (25%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             I   NLP       + + F +FG +  V           +P  G              
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRV----------LLPEGGIT------------ 48

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRA 318
            A + F        A      +      + L+ A
Sbjct: 49  -AIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA 81

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	393
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.96
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.96
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.95
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.95
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.95
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.95
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.94
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.94
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.94
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.94
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.93
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.93
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.93
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.93
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.92
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.92
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.92
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.91
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.9
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.9
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.85
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.75
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.72
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.71
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.71
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.7
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.69
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.69
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.69
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.69
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.68
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.68
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.68
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.68
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.68
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.68
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.67
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.67
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.67
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.67
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.67
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.67
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.67
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.66
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.66
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.66
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.66
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.66
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.66
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.66
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.66
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.65
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.65
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.65
2div_A	99	TRNA selenocysteine associated protein; structural	99.65
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.65
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.65
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.65
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.65
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.65
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.64
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.64
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.64
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.64
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.64
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.64
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.64
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.64
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.64
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.64
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.64
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.64
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.64
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.64
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.64
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.64
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.64
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.63
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.63
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.63
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.63
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.63
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.63
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.63
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.62
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.62
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.62
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.62
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.62
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.62
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.62
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.62
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.62
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.62
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.62
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.62
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.62
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.62
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.61
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.61
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.61
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.61
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.61
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.61
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.61
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.61
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.61
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.61
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.61
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.61
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.6
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.6
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.6
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.6
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.6
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.6
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.6
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.6
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.6
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.6
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.6
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.6
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.6
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.6
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.6
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.6
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.59
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.59
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.59
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.59
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.59
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.59
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.59
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.58
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.58
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.58
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.58
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.58
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.58
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.58
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.58
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.58
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.58
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.57
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.57
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.57
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.57
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.57
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.57
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.56
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.56
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.56
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.56
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.56
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.56
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.56
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.56
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.55
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.55
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.54
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.54
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.54
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.54
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.54
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.53
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.53
1x5p_A	97	Negative elongation factor E; structure genomics,	99.51
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.26
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.5
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.49
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.49
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.49
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.49
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.48
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.48
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.48
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.47
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.46
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.46
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.46
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.45
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.45
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.45
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.45
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.45
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.43
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.43
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.41
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.41
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.4
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.4
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.39
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.36
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.36
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.35
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.34
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.33
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.32
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.32
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.3
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.3
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.29
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.29
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.29
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.28
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.27
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.27
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.26
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.26
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.25
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.25
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.24
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.24
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.23
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.23
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.23
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.23
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.23
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.23
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.22
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.22
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.22
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.22
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.22
2div_A	99	TRNA selenocysteine associated protein; structural	99.22
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.22
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.22
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.22
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.21
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.21
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.21
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.21
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.2
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.2
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.2
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.2
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.2
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.19
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.19
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.19
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.19
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.19
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.19
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.19
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.19
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.19
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.19
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.18
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.18
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.18
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.18
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.17
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.17
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.17
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.17
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.17
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.17
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.16
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.16
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.16
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.16
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.16
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.16
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.16
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.15
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.15
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.15
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.14
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.14
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.14
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.13
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.13
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.12
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.12
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.12
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.12
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.11
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.11
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.11
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.11
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.11
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.11
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.11
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.1
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.1
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.1
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.1
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.1
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.1
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.09
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.09
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.08
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.08
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.08
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.08
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.07
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.07
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.07
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.07
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.07
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.06
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.06
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.06
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.05
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.05
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.05
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.04
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.04
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.03
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.01
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.0
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.99
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	98.99
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	98.99
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	98.98
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	98.97
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	98.51
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	98.96
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	98.93
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	98.93
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	98.92
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	98.92
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	98.91
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	98.91
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	98.91
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.91
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	98.9
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	98.9
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	98.9
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	98.89
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	98.89
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	98.88
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	98.87
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	98.87
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	98.87
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.86
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	98.86
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	98.81
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	98.81
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	98.81
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	98.8
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	98.8
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	98.8
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	98.79
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	98.79
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	98.79
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	98.77
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	98.76
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	98.76
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	98.76
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	98.75
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	98.73
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.72
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	98.71
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	98.7
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.65
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	98.64
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	98.63
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	98.62
1x5p_A	97	Negative elongation factor E; structure genomics,	98.58
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	98.57
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.52
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.52
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	98.5
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	98.5
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	98.48
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	98.44
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	98.4
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.32
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	98.15
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	98.1
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.1
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.07
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	98.07
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.01
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.85
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	97.84
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	97.19
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.74
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.51
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.42
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.36
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	95.9
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	95.53
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	95.08
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	94.6
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	94.46
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	93.43
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	93.25
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	93.21
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	90.83
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	90.08
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	88.92
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	84.57
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	82.21

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.96  E-value=6.3e-29  Score=223.38  Aligned_cols=147  Identities=18%  Similarity=0.357  Sum_probs=124.5

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+++|+++|+.+|+.||.|.+|+|++++.  +               +.++|||||+|.+.++|..||
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~--~---------------g~~~g~afV~f~~~~~A~~A~   72 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN--T---------------KRSRGFGFVTYATVEEVDAAM   72 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT--T---------------CCEEEEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCC--C---------------CCccceEEEEeCCHHHHHHHH
Confidence            44579999999999999999999999999999999977652  2               236699999999999999999


Q ss_pred             HhcCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCC
Q 016231          302 AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVG  381 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~  381 (393)
                      .+++..|.|+.|.|.++.+.......   ....+.++|||+|||+++++++|+++|+.|    |.|..|+|++++.+|.+
T Consensus        73 ~~~~~~~~g~~l~v~~~~~~~~~~~~---~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~g~~  145 (196)
T 1l3k_A           73 NARPHKVDGRVVEPKRAVSREDSQRP---GAHLTVKKIFVGGIKEDTEEHHLRDYFEQY----GKIEVIEIMTDRGSGKK  145 (196)
T ss_dssp             HTCSCEETTEECEEEECCC--------------CCSEEEEECCTTTCCHHHHHHHHTTT----SCEEEEEEEECTTTCCE
T ss_pred             hcCCCEECCEEeeeecccCccccccc---ccCCCcceEEEeCCCCCCCHHHHHHHHhcC----CCeEEEEEeecCCCCCc
Confidence            88999999999999998754322211   123356899999999999999999999999    99999999999989999


Q ss_pred             ccEEEEEeeec
Q 016231          382 KGIAYVLFKTR  392 (393)
Q Consensus       382 kGfaFVeF~t~  392 (393)
                      +|||||+|.+.
T Consensus       146 ~g~afV~F~~~  156 (196)
T 1l3k_A          146 RGFAFVTFDDH  156 (196)
T ss_dssp             EEEEEEEESSH
T ss_pred             cceEEEEECCH
Confidence            99999999874

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.96  E-value=3e-28  Score=212.35  Aligned_cols=138  Identities=23%  Similarity=0.361  Sum_probs=123.8

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hhc
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~ln  304 (393)
                      |+|||+|||+++|+++|+.+|+.||.|.+|+|++++.                  +.++|||||+|.+.++|..|+ .+|
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~------------------~~~~g~afV~f~~~~~a~~A~~~l~   62 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN------------------NKNVNYAFVEYHQSHDANIALQTLN   62 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-------------------CCEEEEEEEESSHHHHHHHHHHHT
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCC------------------CCCCCEEEEEeCCHHHHHHHHHHcC
Confidence            6899999999999999999999999999999976541                  236699999999999999999 899


Q ss_pred             CceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccE
Q 016231          305 MAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGI  384 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGf  384 (393)
                      +..+.|+.|.|.++.+...       ....+..+|||+|||+.+++++|+++|+.|    |.|..|+|++++.+|.++||
T Consensus        63 ~~~~~g~~i~v~~~~~~~~-------~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~----G~i~~~~i~~~~~~~~~~g~  131 (166)
T 3md3_A           63 GKQIENNIVKINWAFQSQQ-------SSSDDTFNLFVGDLNVNVDDETLRNAFKDF----PSYLSGHVMWDMQTGSSRGY  131 (166)
T ss_dssp             TCEETTEECEEEECCCCCC-------CCCTTCEEEEEESCCTTCCHHHHHHHHTTS----TTEEEEEEEECTTTCCEEEE
T ss_pred             CCccCCCeeEEEEcCCCCC-------CCCCCCceEEECCCCCCCCHHHHHHHHhcc----CCeeEEEEEecCCCCCcceE
Confidence            9999999999999865432       224457899999999999999999999999    99999999999999999999


Q ss_pred             EEEEeeec
Q 016231          385 AYVLFKTR  392 (393)
Q Consensus       385 aFVeF~t~  392 (393)
                      |||+|.+.
T Consensus       132 afV~f~~~  139 (166)
T 3md3_A          132 GFVSFTSQ  139 (166)
T ss_dssp             EEEEESCH
T ss_pred             EEEEeCCH
Confidence            99999874

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.95  E-value=8.8e-28  Score=209.58  Aligned_cols=138  Identities=20%  Similarity=0.357  Sum_probs=123.8

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      +++|||+|||+++++++|+.+|+.||.|.+|++++++.  +               +.++|||||+|.+.++|..|+ .|
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~--~---------------~~~~g~afV~f~~~~~A~~a~~~l   64 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKI--T---------------GQSLGYGFVNYIDPKDAEKAINTL   64 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTT--T---------------CCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCC--C---------------CcceeEEEEEECCHHHHHHHHHHc
Confidence            58999999999999999999999999999999977541  2               346699999999999999999 59


Q ss_pred             cCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCcc
Q 016231          304 NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKG  383 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kG  383 (393)
                      |+..+.|+.|.|.++.+...         .....+|||+|||..+++++|+++|+.|    |.|..|+|++++.+|.++|
T Consensus        65 ~~~~~~g~~l~v~~~~~~~~---------~~~~~~l~v~nl~~~~t~~~l~~~f~~~----G~i~~~~i~~~~~~g~~~g  131 (167)
T 1fxl_A           65 NGLRLQTKTIKVSYARPSSA---------SIRDANLYVSGLPKTMTQKELEQLFSQY----GRIITSRILVDQVTGVSRG  131 (167)
T ss_dssp             TTCEETTEECEEEECCCCCG---------GGTTCEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTCCEEE
T ss_pred             CCCccCCceEEEEecCCCcc---------cCCCCcEEECCCCCcCCHHHHHHHHHhc----CCEeEEEEEecCCCCCccc
Confidence            99999999999999875432         2345789999999999999999999999    9999999999988999999


Q ss_pred             EEEEEeeec
Q 016231          384 IAYVLFKTR  392 (393)
Q Consensus       384 faFVeF~t~  392 (393)
                      ||||+|.+.
T Consensus       132 ~afV~f~~~  140 (167)
T 1fxl_A          132 VGFIRFDKR  140 (167)
T ss_dssp             EEEEEESSH
T ss_pred             eEEEEeCCH
Confidence            999999874

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.95  E-value=8.6e-28  Score=210.52  Aligned_cols=139  Identities=21%  Similarity=0.343  Sum_probs=124.3

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      +.++|||+|||+++++++|+.+|+.||.|.+|+|++++.                 ++.++|||||+|.+.++|..|+ .
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~-----------------~~~~~g~afV~f~~~~~A~~a~~~   64 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYK-----------------TGYSYGYAFVDFTSEMDSQRAIKV   64 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETT-----------------TTEECSEEEEEESSHHHHHHHHHH
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCC-----------------CCccceEEEEEECCHHHHHHHHHh
Confidence            368999999999999999999999999999999977541                 2236699999999999999999 5


Q ss_pred             hcCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCc
Q 016231          303 FNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGK  382 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~k  382 (393)
                      +|+..+.|+.|.|.++.+...         ..+..+|||+|||..+++++|+++|+.|    |.|..|+|+++..+|.++
T Consensus        65 l~~~~~~g~~l~v~~~~~~~~---------~~~~~~l~v~nl~~~~t~~~l~~~f~~~----G~i~~~~i~~~~~~~~~~  131 (168)
T 1b7f_A           65 LNGITVRNKRLKVSYARPGGE---------SIKDTNLYVTNLPRTITDDQLDTIFGKY----GSIVQKNILRDKLTGRPR  131 (168)
T ss_dssp             HTTCEETTEECEEEECCCCSS---------TTTTCEEEEESCCTTCCHHHHHHHHTSS----SCEEEEEEEECTTTCCEE
T ss_pred             cCCCEeCCcEEEEEecCCCcc---------cCCCCCEEEeCCCCCCCHHHHHHhhhcC----CcEEEEEEEEcCCCCCcc
Confidence            999999999999999875432         2346799999999999999999999999    999999999998899999


Q ss_pred             cEEEEEeeec
Q 016231          383 GIAYVLFKTR  392 (393)
Q Consensus       383 GfaFVeF~t~  392 (393)
                      |||||+|.+.
T Consensus       132 g~afV~f~~~  141 (168)
T 1b7f_A          132 GVAFVRYNKR  141 (168)
T ss_dssp             EEEEEEESSH
T ss_pred             eEEEEEECCH
Confidence            9999999874

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.95  E-value=2.1e-28  Score=214.52  Aligned_cols=138  Identities=19%  Similarity=0.391  Sum_probs=121.8

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHh
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~l  303 (393)
                      ++++|||+|||+++|+++|+.+|+.||.|.+|+|++++.                 ++.++|||||+|.+.++|..||. 
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----------------~g~~~g~afV~f~~~~~a~~A~~-   63 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPA-----------------TGRSRGFGFLSFEKPSSVDEVVK-   63 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTT-----------------TSSCCSCEEEEESSTHHHHHHHH-
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCC-----------------CCCccceEEEEEccHHHHHHHHh-
Confidence            478999999999999999999999999999999966541                 23467999999999999999997 


Q ss_pred             cCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCcc
Q 016231          304 NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKG  383 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kG  383 (393)
                      ++..+.|+.|.|.++.+...         ..+..+|||+|||+++++++|+++|+.|    |.|..|+|++++.+|.++|
T Consensus        64 ~~~~~~g~~i~v~~~~~~~~---------~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~~~i~~~~~~g~~~g  130 (167)
T 2cjk_A           64 TQHILDGKVIDPKRAIPRDE---------QDKTGKIFVGGIGPDVRPKEFEEFFSQW----GTIIDAQLMLDKDTGQSRG  130 (167)
T ss_dssp             SCCEETTEECCCEECCCHHH---------HHHCEEEEEEEECTTCCHHHHHHHHHTT----SCCSEEECCCSSSSSTTSE
T ss_pred             cccccCCeEcccccccchhh---------ccCCCeEEECCCCCCCCHHHHHHHHHhC----ccEEEEEEEEcCCCCccce
Confidence            36789999999999865432         2345799999999999999999999999    9999999999998999999


Q ss_pred             EEEEEeeec
Q 016231          384 IAYVLFKTR  392 (393)
Q Consensus       384 faFVeF~t~  392 (393)
                      ||||+|.+.
T Consensus       131 ~afV~f~~~  139 (167)
T 2cjk_A          131 FGFVTYDSA  139 (167)
T ss_dssp             EEEEEESSH
T ss_pred             EEEEEECCH
Confidence            999999864

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.95  E-value=1.2e-27  Score=220.94  Aligned_cols=139  Identities=24%  Similarity=0.391  Sum_probs=120.6

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      +.+||||||||+++|+++|+++|+.||.|.+|+|++++.  +               +.++|||||+|.+.++|..|| .
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~--t---------------g~~~G~afV~F~~~~~A~~Ai~~   76 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMI--T---------------RRSLGYAYVNFQQPADAERALDT   76 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT--T---------------CCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccC--C---------------CCccccccceeCCHHHHHHHHHH
Confidence            468999999999999999999999999999999987652  2               346799999999999999999 7


Q ss_pred             hcCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCc
Q 016231          303 FNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGK  382 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~k  382 (393)
                      +|+..+.|+.|+|.++.......       .....+|||+|||+++++++|+++|+.|    |.|..|+|++|.  +.++
T Consensus        77 ~~~~~~~g~~i~~~~~~~~~~~~-------~~~~~~l~v~nl~~~~t~~~l~~~F~~~----G~i~~~~i~~d~--~~~~  143 (213)
T 4f02_A           77 MNFDVIKGKPVRIMWSQRDPSLR-------KSGVGNIFIKNLDKSIDNKALYDTFSAF----GNILSCKVVCDE--NGSK  143 (213)
T ss_dssp             HTTCEETTEECEEEECCCCTHHH-------HHCTTEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEEET--TEEE
T ss_pred             hhhhhcCCccccccccccccccc-------ccccccceECCcccccHHHHHHHHHhhc----CCeEEEEeeccC--CCCc
Confidence            99999999999999986432211       2235689999999999999999999999    999999999985  4579


Q ss_pred             cEEEEEeeec
Q 016231          383 GIAYVLFKTR  392 (393)
Q Consensus       383 GfaFVeF~t~  392 (393)
                      |||||+|.+.
T Consensus       144 g~~fV~f~~~  153 (213)
T 4f02_A          144 GYGFVHFETQ  153 (213)
T ss_dssp             EEEEEEESSH
T ss_pred             eEEEEEeCCH
Confidence            9999999874

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.94  E-value=7.9e-27  Score=205.38  Aligned_cols=140  Identities=19%  Similarity=0.351  Sum_probs=120.1

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      .++|||+|||+++|+++|+++|+.||.|.+|+|++++..  +.             +.++|||||+|.+.++|..|+ .|
T Consensus         3 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~--~~-------------~~~~g~afV~f~~~~~A~~A~~~l   67 (175)
T 3nmr_A            3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQ--NP-------------PQSKGCCFVTFYTRKAALEAQNAL   67 (175)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSS--SS-------------CEEEEEEEEEESSHHHHHHHHHHH
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCC--CC-------------CCcceEEEEEECCHHHHHHHHHHh
Confidence            689999999999999999999999999999999887632  11             136799999999999999999 69


Q ss_pred             cCceeC---CeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCC
Q 016231          304 NMAVIG---GNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRV  380 (393)
Q Consensus       304 ng~~~~---Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~  380 (393)
                      |+..+.   ++.|.+.++.+...        .....++|||+|||+++|+++|+++|+.|    |.|..|+|++++ +|.
T Consensus        68 ~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~l~v~nl~~~~t~~~l~~~F~~~----G~i~~v~~~~~~-~g~  134 (175)
T 3nmr_A           68 HNMKVLPGMHHPIQMKPADSEKN--------NAVEDRKLFIGMISKKCTENDIRVMFSSF----GQIEECRILRGP-DGL  134 (175)
T ss_dssp             TTTCCCTTCSSCCEEEECGGGCC--------SCGGGSEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECT-TSC
T ss_pred             cCcEEccCCccceEEcccccccc--------ccCCCCeEEEcCCCCcCCHHHHHHHHHhC----CCEEEEEEEECC-CCC
Confidence            998776   67888887754321        13356899999999999999999999999    999999999996 699


Q ss_pred             CccEEEEEeeec
Q 016231          381 GKGIAYVLFKTR  392 (393)
Q Consensus       381 ~kGfaFVeF~t~  392 (393)
                      ++|||||+|.+.
T Consensus       135 ~~g~afV~f~~~  146 (175)
T 3nmr_A          135 SRGCAFVTFTTR  146 (175)
T ss_dssp             EEEEEEEEESSH
T ss_pred             EEEEEEEEECCH
Confidence            999999999874

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.94  E-value=1.3e-26  Score=204.00  Aligned_cols=133  Identities=22%  Similarity=0.467  Sum_probs=118.1

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhccc----C-------CeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeC
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKF----G-------EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFK  292 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~----G-------~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~  292 (393)
                      +.++|||+|||+++|+++|+++|+.|    |       .|.++.+.                       .++|||||+|.
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~-----------------------~~~g~afV~f~   59 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-----------------------QDKNFAFLEFR   59 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE-----------------------TTTTEEEEEES
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec-----------------------CCCCEEEEEeC
Confidence            47899999999999999999999999    6       66666652                       14589999999


Q ss_pred             CHHHHHHHHHhcCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEE
Q 016231          293 SEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRV  372 (393)
Q Consensus       293 s~e~A~~Al~lng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI  372 (393)
                      +.++|..||.+|+..|.|+.|.|.++.....         .....+|||+|||+.+++++|+++|+.|    |.|..|+|
T Consensus        60 ~~~~A~~A~~~~~~~~~g~~i~v~~~~~~~~---------~~~~~~l~v~nlp~~~t~~~l~~~f~~~----G~v~~v~i  126 (172)
T 2g4b_A           60 SVDETTQAMAFDGIIFQGQSLKIRRPHDYQP---------LPGAHKLFIGGLPNYLNDDQVKELLTSF----GPLKAFNL  126 (172)
T ss_dssp             SHHHHHHHGGGTTCEETTEECEEECCSSCCC---------CTTTTCEEEECCCTTCCHHHHHHHHHTT----SCEEEEEE
T ss_pred             CHHHHHHHHHhCCcEecCceeeecCCcccCC---------CCCCCEEEEEcCCCcCCHHHHHHHHHhc----CCceEEEE
Confidence            9999999999999999999999998754321         2346899999999999999999999999    99999999


Q ss_pred             eecCCCCCCccEEEEEeeec
Q 016231          373 IRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       373 ~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ++++.+|.++|||||+|.+.
T Consensus       127 ~~~~~~g~~~g~afV~f~~~  146 (172)
T 2g4b_A          127 VKDSATGLSKGYAFCEYVDI  146 (172)
T ss_dssp             EECTTTCSEEEEEEEEESST
T ss_pred             EecCCCCCcceEEEEEeCCH
Confidence            99998999999999999875

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.94  E-value=2.7e-27  Score=215.86  Aligned_cols=147  Identities=18%  Similarity=0.374  Sum_probs=122.3

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH-h
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-F  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~-l  303 (393)
                      .++|||+|||+++|+++|+.+|+.||.|.+|+|++++.  +               +.++|||||+|.+.++|..||. |
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~--~---------------g~~~g~afV~f~~~~~A~~A~~~l   90 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSV--T---------------MKHKGFAFVEYEVPEAAQLALEQM   90 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-C--C----------------CCCSEEEEEESSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCC--C---------------CccCceEEEEeCCHHHHHHHHHHc
Confidence            68999999999999999999999999999999966541  2               2366999999999999999994 9


Q ss_pred             cCceeCCeEEEEeecCCCcccCCCC--CCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCC
Q 016231          304 NMAVIGGNHIRLDRACPPRKKLKGE--DAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVG  381 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~~~~~~~--~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~  381 (393)
                      |+..|.|+.|.|.++..........  ........++|||+|||.++++++|+++|+.|    |.|..|+|++++.+|.+
T Consensus        91 ~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~----G~v~~v~i~~~~~~g~~  166 (216)
T 2qfj_A           91 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAF----GKIKSATLARDPTTGKH  166 (216)
T ss_dssp             SSCCCC-CCCEEECCSCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTS----SCEEEEEEEECTTTCCE
T ss_pred             cCCeeCCeeEEEecCCCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhcc----CCeeEEEEEecCCCCCc
Confidence            9999999999999876542111000  00012356899999999999999999999999    99999999999999999


Q ss_pred             ccEEEEEeeec
Q 016231          382 KGIAYVLFKTR  392 (393)
Q Consensus       382 kGfaFVeF~t~  392 (393)
                      +|||||+|.+.
T Consensus       167 ~g~afV~F~~~  177 (216)
T 2qfj_A          167 KGYGFIEYEKA  177 (216)
T ss_dssp             EEEEEEEESSH
T ss_pred             CceEEEEecCH
Confidence            99999999864

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.94  E-value=3.4e-26  Score=205.86  Aligned_cols=142  Identities=22%  Similarity=0.451  Sum_probs=118.7

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhccc----C-------CeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeC
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKF----G-------EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFK  292 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~----G-------~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~  292 (393)
                      .+++|||+|||+++|+++|+++|+.|    |       .|.++.+                       +.++|||||+|.
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~-----------------------~~~~g~afV~F~   59 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-----------------------NQDKNFAFLEFR   59 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE-----------------------ETTTTEEEEEES
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe-----------------------cCCCCEEEEEeC
Confidence            47999999999999999999999999    4       4555544                       125699999999


Q ss_pred             CHHHHHHHHHhcCceeCCeEEEEeecCCCcccCCCC-----------CCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCC
Q 016231          293 SEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGE-----------DAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLN  361 (393)
Q Consensus       293 s~e~A~~Al~lng~~~~Gr~I~V~~a~~~~~~~~~~-----------~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~  361 (393)
                      +.++|..||.||+..|.|+.|.|.++..........           ......+.++|||+|||+.+++++|+++|+.| 
T Consensus        60 ~~~~A~~Al~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~-  138 (198)
T 2yh0_A           60 SVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSF-  138 (198)
T ss_dssp             CSHHHHHHGGGTTEEETTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTB-
T ss_pred             CHHHHHHHHHhcCCEEcCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHc-
Confidence            999999999999999999999999986542211100           01112467899999999999999999999999 


Q ss_pred             CCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          362 DLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       362 ~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                         |.|..|+|++++.+|.++|||||+|.+.
T Consensus       139 ---G~v~~~~~~~~~~~~~~~g~afV~f~~~  166 (198)
T 2yh0_A          139 ---GPLKAFNLVKDSATGLSKGYAFCEYVDI  166 (198)
T ss_dssp             ---SCEEEEEEEECTTTCSEEEEEEEEESSS
T ss_pred             ---CCccEEEEeecCCCCCcceEEEEEECCH
Confidence               9999999999988999999999999874

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.93  E-value=1.1e-25  Score=208.02  Aligned_cols=141  Identities=13%  Similarity=0.206  Sum_probs=116.8

Q ss_pred             cccEEEEeCCC-ccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          224 LLRTIFVGNLP-LKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       224 ~~rtVFVgNLp-~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      +.++|||+||| +.+|+++|+.+|+.||.|.+|+|+++                      ++|||||+|.+.++|+.|| 
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~----------------------~~g~afV~f~~~~~A~~Ai~   60 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----------------------KPGAAMVEMADGYAVDRAIT   60 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT----------------------STTCEEEEESSHHHHHHHHH
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC----------------------CCCEEEEEECCHHHHHHHHH
Confidence            46899999999 89999999999999999999998432                      2489999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCCcccCCC-----C-----------------------CCCCcCCcceeeeCCCCCCCCHHHH
Q 016231          302 AFNMAVIGGNHIRLDRACPPRKKLKG-----E-----------------------DAPLYDIKKTVFVGNLPFDVKDEEI  353 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~~~~~~-----~-----------------------~~~~~~~~~tLfVgNLp~~~teedL  353 (393)
                      .|||..|.|+.|.|.++.........     .                       ......+.++|||+|||+++|+++|
T Consensus        61 ~lng~~~~g~~l~v~~s~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L  140 (205)
T 3tyt_A           61 HLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENF  140 (205)
T ss_dssp             HHTTCEETTEECEEEECSCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHH
T ss_pred             HhCCCEECCceEEEEEccCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHH
Confidence            69999999999999998643210000     0                       0001245678999999999999999


Q ss_pred             HHHhhcCCCCCCCe--EEEEEeecCCCCCCccEEEEEeeec
Q 016231          354 YQLFCGLNDLESSV--EAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       354 ~e~F~~~~~~~G~I--~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +++|+.|    |.|  ..|+|+.+.  |.++|||||+|.+.
T Consensus       141 ~~~F~~~----G~v~~~~v~~~~~~--~~~~g~gfV~f~~~  175 (205)
T 3tyt_A          141 FEICDEL----GVKRPTSVKVFSGK--SERSSSGLLEWDSK  175 (205)
T ss_dssp             HHHHHHH----TCCCCSEEEECSCC--SSSSEEEEEECSSH
T ss_pred             HHHHHhc----CCcceEEEEEEcCC--CCCceEEEEEeCCH
Confidence            9999999    888  899998874  56789999999863

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.93  E-value=1.2e-25  Score=215.49  Aligned_cols=131  Identities=21%  Similarity=0.294  Sum_probs=111.3

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      .+..++|||+|||+++|+++|+.+|+.||.|.+|+|++++.                   .++|||||+|.+.++|..||
T Consensus        38 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-------------------~~~g~afV~f~~~~~A~~A~   98 (292)
T 2ghp_A           38 NRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK-------------------KNFRFARIEFARYDGALAAI   98 (292)
T ss_dssp             ----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT-------------------SSSEEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC-------------------CCcEEEEEEECCHHHHHHHH
Confidence            34579999999999999999999999999999999977541                   13589999999999999999


Q ss_pred             HhcCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCC-CeEEEEEeecCCCCC
Q 016231          302 AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLES-SVEAVRVIRHPHMRV  380 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G-~I~~VrI~~d~~tg~  380 (393)
                      .+|+..|.|+.|.|.++.                .++|||+|||+.+++++|+++|..|    | .|..|+|++++. |.
T Consensus        99 ~~~~~~~~g~~i~v~~~~----------------~~~l~v~nlp~~~t~~~l~~~f~~~----G~~i~~v~i~~~~~-~~  157 (292)
T 2ghp_A           99 TKTHKVVGQNEIIVSHLT----------------ECTLWMTNFPPSYTQRNIRDLLQDI----NVVALSIRLPSLRF-NT  157 (292)
T ss_dssp             TTTTCEETTEECEEEECC----------------SCEEEEECCCTTCCHHHHHHHHHHT----TCCCCEEECC-------
T ss_pred             HhCCcEeCCcEEEEEECC----------------CCEEEEECCCCCCCHHHHHHHHHHh----CCCeEEEEEEeCCC-CC
Confidence            999999999999999863                4799999999999999999999999    9 999999999965 88


Q ss_pred             CccEEEEEeeec
Q 016231          381 GKGIAYVLFKTR  392 (393)
Q Consensus       381 ~kGfaFVeF~t~  392 (393)
                      ++|||||+|.+.
T Consensus       158 ~~g~afV~f~~~  169 (292)
T 2ghp_A          158 SRRFAYIDVTSK  169 (292)
T ss_dssp             -CCEEEEECSSH
T ss_pred             cceEEEEEECCH
Confidence            999999999864

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.93  E-value=3.2e-25  Score=210.83  Aligned_cols=127  Identities=24%  Similarity=0.353  Sum_probs=117.1

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+++|+++|+.+|+.||.|..|+|.+                       ++|||||+|.+.++|..|+ 
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~-----------------------~kg~afV~f~~~~~A~~A~~   76 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR-----------------------DRGFGFIRLESRTLAEIAKA   76 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET-----------------------TTTEEEEECSSHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC-----------------------CCcEEEEEECCHHHHHHHHH
Confidence            4568999999999999999999999999999998832                       3489999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCC
Q 016231          302 AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVG  381 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~  381 (393)
                      .+|+..|.|+.|.|.++.+               ..+|||+|||+.+|+++|+++|+.|    |.|..|+|+++ .+|.+
T Consensus        77 ~l~g~~i~g~~l~v~~a~~---------------~~~l~v~nl~~~~t~~~l~~~F~~~----G~i~~v~i~~~-~~g~~  136 (261)
T 3sde_A           77 ELDGTILKSRPLRIRFATH---------------GAALTVKNLSPVVSNELLEQAFSQF----GPVEKAVVVVD-DRGRA  136 (261)
T ss_dssp             HHTTCEETTEECEEEECCC---------------SSEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEEE-TTSCE
T ss_pred             HcCCcEECCceeEeeeccc---------------CCcccccCCCCCCCHHHHHHHHHhc----CCeEEEEeeeC-CCCCc
Confidence            5999999999999999853               4689999999999999999999999    99999999999 58999


Q ss_pred             ccEEEEEeeec
Q 016231          382 KGIAYVLFKTR  392 (393)
Q Consensus       382 kGfaFVeF~t~  392 (393)
                      +|||||+|.+.
T Consensus       137 ~g~afV~f~~~  147 (261)
T 3sde_A          137 TGKGFVEFAAK  147 (261)
T ss_dssp             EEEEEEEESSH
T ss_pred             CcEEEEEeCCH
Confidence            99999999864

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.93  E-value=9.2e-26  Score=199.79  Aligned_cols=138  Identities=22%  Similarity=0.334  Sum_probs=115.0

Q ss_pred             CCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       221 ~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      .....++|||+|||+++|+++|+.+|..||.|..+.+ .+.                 ..+.++|||||+|.+.++|..|
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~-~~~-----------------~~~~~~g~afV~f~~~~~a~~A   70 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDV-----------------RTGTNRKFGYVDFESAEDLEKA   70 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCC-CEE-----------------EEETTTTEEEEEESSHHHHHHH
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEE-EEC-----------------CCCccccEEEEEECCHHHHHHH
Confidence            3455799999999999999999999999998765322 111                 1234679999999999999999


Q ss_pred             HHhcCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCC
Q 016231          301 LAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRV  380 (393)
Q Consensus       301 l~lng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~  380 (393)
                      |+||+..|.|+.|.|.++.+...       ....+.++|||+|||+++++++|+++|+.|    |.|..+     ..+|.
T Consensus        71 ~~l~g~~~~g~~l~v~~~~~~~~-------~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~----g~v~~~-----~~~~~  134 (175)
T 1fje_B           71 LELTGLKVFGNEIKLEKPKGRDS-------KKVRAARTLLAKNLSFNITEDELKEVFEDA----LEIRLV-----SQDGK  134 (175)
T ss_dssp             HHGGGEEETTEEEEEECCCCSSC-------STTGGGGEEEEESCCSSCCHHHHHHHCTTC----SEEEEE-----CSSSS
T ss_pred             HhcCCCEeCCeEEEEecCCCccc-------cccccCCEEEEeCCCCCCCHHHHHHHHHhc----CeEEEe-----cCCCC
Confidence            99999999999999999875432       123457899999999999999999999999    877765     46789


Q ss_pred             CccEEEEEeeec
Q 016231          381 GKGIAYVLFKTR  392 (393)
Q Consensus       381 ~kGfaFVeF~t~  392 (393)
                      ++|||||+|.+.
T Consensus       135 ~~g~afV~f~~~  146 (175)
T 1fje_B          135 SKGIAYIEFKSE  146 (175)
T ss_dssp             CCSEEEEECSSH
T ss_pred             CceEEEEEECCH
Confidence            999999999864

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.92  E-value=1.6e-24  Score=206.84  Aligned_cols=125  Identities=16%  Similarity=0.274  Sum_probs=115.3

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      +++|||+|||+++|+++|+.+|+.|| |.+|.+.                       .++|||||+|.+.++|..|+ .|
T Consensus        22 ~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~~-----------------------~~~g~afV~f~~~~~A~~A~~~l   77 (284)
T 3smz_A           22 RRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD-----------------------KYKGTAFVTLLNGEQAEAAINAF   77 (284)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEEE-----------------------TTTTEEEEEESSHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEEe-----------------------cCCCEEEEEeCCHHHHHHHHHHc
Confidence            68999999999999999999999999 8888871                       15589999999999999999 69


Q ss_pred             cCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCcc
Q 016231          304 NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKG  383 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kG  383 (393)
                      |+..|.|+.|.|.++.               ...+|||+|||+++++++|+++|+.|    |.|..|+|++++.+|.++|
T Consensus        78 ~~~~~~g~~i~v~~~~---------------~~~~l~v~nlp~~~t~~~l~~~f~~~----G~i~~~~i~~~~~~g~~~g  138 (284)
T 3smz_A           78 HQSRLRERELSVQLQP---------------TDALLCVANLPPSLTQQQFEELVRPF----GSLERCFLVYSERTGQSKG  138 (284)
T ss_dssp             TTCEETTEECEEEECC---------------CSCEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTCCEEE
T ss_pred             CCCeeCCeEEEEEecC---------------CCCEEEEcCCCCcCCHHHHHHHHHhc----CCeeEEEEEeeCCCCccce
Confidence            9999999999999863               23699999999999999999999999    9999999999999999999


Q ss_pred             EEEEEeeec
Q 016231          384 IAYVLFKTR  392 (393)
Q Consensus       384 faFVeF~t~  392 (393)
                      ||||+|.+.
T Consensus       139 ~afV~f~~~  147 (284)
T 3smz_A          139 YGFAEYMKK  147 (284)
T ss_dssp             EEEEEESSH
T ss_pred             EEEEEECCH
Confidence            999999863

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.92  E-value=2e-24  Score=206.19  Aligned_cols=141  Identities=13%  Similarity=0.139  Sum_probs=123.7

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|||+|||+.+|+++|+.+|+.||.|..|+++.++.  +               +.++|||||+|.+.++|..|+ .
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~--~---------------g~~~g~afV~f~~~~~a~~A~~~  156 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER--T---------------GQSKGYGFAEYMKKDSAARAKSD  156 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT--T---------------CCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCC--C---------------CccceEEEEEECCHHHHHHHHHH
Confidence            357999999999999999999999999999999976541  2               346699999999999999999 7


Q ss_pred             hcCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCC-CHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCC
Q 016231          303 FNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDV-KDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVG  381 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~-teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~  381 (393)
                      ||+..|.|+.|.|.++.+....      .......+|||+|||+++ ++++|+++|+.|    |.|..|+|++++ +|.+
T Consensus       157 l~~~~~~g~~i~v~~a~~~~~~------~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~----G~i~~v~i~~~~-~g~~  225 (284)
T 3smz_A          157 LLGKPLGPRTLYVHWTDAGQLT------PALLHSRCLCVDRLPPGFNDVDALCRALSAV----HSPTFCQLACGQ-DGQL  225 (284)
T ss_dssp             HTTCEETTEECEEEECCGGGCC------TTTTSCSEEEEECCCTTCCCHHHHHHHTCSS----SCCSEEEEEECS-SCCE
T ss_pred             hCCCEeCCcEEEEEECCCCCCC------cccCCccEEEEecCCcccCCHHHHHHHhhCC----CCeEEEEEEECC-CCCc
Confidence            9999999999999999765322      123456899999999995 999999999999    999999999996 7999


Q ss_pred             ccEEEEEeeec
Q 016231          382 KGIAYVLFKTR  392 (393)
Q Consensus       382 kGfaFVeF~t~  392 (393)
                      +|||||+|.+.
T Consensus       226 ~g~afV~f~~~  236 (284)
T 3smz_A          226 KGFAVLEYETA  236 (284)
T ss_dssp             EEEEEEECSSH
T ss_pred             ccEEEEEeCCH
Confidence            99999999874

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.92  E-value=8.6e-25  Score=209.51  Aligned_cols=145  Identities=17%  Similarity=0.267  Sum_probs=118.7

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccC-CeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFG-EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G-~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      ..++|||+|||+.+++++|+.+|+.|| .|..|+|++++.                  +.++|||||+|.+.++|..|+.
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~------------------~~~~g~afV~f~~~~~a~~A~~  177 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF------------------NTSRRFAYIDVTSKEDARYCVE  177 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------------------------CCEEEEECSSHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC------------------CCcceEEEEEECCHHHHHHHHH
Confidence            368999999999999999999999999 999999966541                  2356999999999999999995


Q ss_pred             -hcCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCC-CCHHHHHHHhhcCCCCCCCeEEEEEeecCC-CC
Q 016231          303 -FNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFD-VKDEEIYQLFCGLNDLESSVEAVRVIRHPH-MR  379 (393)
Q Consensus       303 -lng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~-~teedL~e~F~~~~~~~G~I~~VrI~~d~~-tg  379 (393)
                       ||+..|.|+.|.|.++.+.......  .....+..+|||+|||+. +++++|+++|+.|    |.|..|+|++++. ||
T Consensus       178 ~l~g~~~~g~~l~v~~a~~~~~~~~~--~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~----G~v~~v~i~~~~~~tg  251 (292)
T 2ghp_A          178 KLNGLKIEGYTLVTKVSNPLEKSKRT--DSATLEGREIMIRNLSTELLDENLLRESFEGF----GSIEKINIPAGQKEHS  251 (292)
T ss_dssp             HHTTCEETTEECEEEECCCC-----------CCTTTEEEEEEECTTTCCHHHHHHHHGGG----SCEEEEECCSCCC---
T ss_pred             HhCCCEeCCcEEEEEECCCCcccccc--cccCCCCceEEEECCCcccCCHHHHHHHHhcc----CCeeEEEEEecCCcCC
Confidence             9999999999999999765433221  122446789999999999 9999999999999    9999999999976 59


Q ss_pred             CCccEEEEEeeec
Q 016231          380 VGKGIAYVLFKTR  392 (393)
Q Consensus       380 ~~kGfaFVeF~t~  392 (393)
                      .++|||||+|.+.
T Consensus       252 ~~~g~afV~F~~~  264 (292)
T 2ghp_A          252 FNNCCAFMVFENK  264 (292)
T ss_dssp             CCCEEEEEEESSH
T ss_pred             CCceEEEEEeCCH
Confidence            9999999999874

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.91  E-value=9.6e-24  Score=201.24  Aligned_cols=142  Identities=23%  Similarity=0.342  Sum_probs=116.3

Q ss_pred             CCcccEEEEeCCCccCCHHHHH----HHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLI----KEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQST  297 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~----~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A  297 (393)
                      ....++|||+|||+++|+++|+    .+|+.||.|.+|+|++     +               +.++|||||+|.+.++|
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~-----~---------------~~~~g~afV~f~~~~~a   65 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR-----S---------------LKMRGQAFVIFKEVSSA   65 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC-----C---------------CCcceEEEEEECCHHHH
Confidence            4568999999999999999966    8999999999998843     1               23669999999999999


Q ss_pred             HHHH-HhcCceeCCeEEEEeecCCCcccCC---C----------------------------------------------
Q 016231          298 EAAL-AFNMAVIGGNHIRLDRACPPRKKLK---G----------------------------------------------  327 (393)
Q Consensus       298 ~~Al-~lng~~~~Gr~I~V~~a~~~~~~~~---~----------------------------------------------  327 (393)
                      ..|| .||+..|.|+.|.|.++........   +                                              
T Consensus        66 ~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  145 (282)
T 3pgw_A           66 TNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMP  145 (282)
T ss_pred             HHHHHHhcCCeeCCcEEEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCC
Confidence            9999 7999999999999999854321000   0                                              


Q ss_pred             -----------------------------------------------------CCCCCcCCcceeeeCCCCCCCCHHHHH
Q 016231          328 -----------------------------------------------------EDAPLYDIKKTVFVGNLPFDVKDEEIY  354 (393)
Q Consensus       328 -----------------------------------------------------~~~~~~~~~~tLfVgNLp~~~teedL~  354 (393)
                                                                           .......+.++|||+|||..+++++|+
T Consensus       146 ~~~~~~~~~~~~~g~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~  225 (282)
T 3pgw_A          146 PMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLS  225 (282)
T ss_pred             cccccccccccCCCCCCCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHH
Confidence                                                                 000112246789999999999999999


Q ss_pred             HHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          355 QLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       355 e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ++|+.|    |.|..|+|+.+.     +|||||+|.+.
T Consensus       226 ~~F~~~----G~i~~v~~~~~~-----~g~afV~f~~~  254 (282)
T 3pgw_A          226 MLFNQF----PGFKEVRLVPGR-----HDIAFVEFDNE  254 (282)
T ss_pred             HHHHhc----CCeEEEEEecCC-----CcEEEEEeCCH
Confidence            999999    999999998663     68999999874

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.90  E-value=3e-23  Score=193.35  Aligned_cols=139  Identities=18%  Similarity=0.283  Sum_probs=115.3

Q ss_pred             CcccEEEEeCCCc-cCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          223 KLLRTIFVGNLPL-KVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~-~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ..+++|||+|||+ ++++++|+.+|+.||.|.+|+|++++                      +|||||+|.+.++|..||
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~----------------------~g~afV~F~~~~~A~~Ai   89 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----------------------KENALVQMADGNQAQLAM   89 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----------------------SCCEEEEESCHHHHHHHH
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC----------------------CCEEEEEECCHHHHHHHH
Confidence            4579999999999 99999999999999999999995432                      389999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCCcccCCC------------------CC--------CCCcCCcceeeeCCCCCCCCHHHHH
Q 016231          302 -AFNMAVIGGNHIRLDRACPPRKKLKG------------------ED--------APLYDIKKTVFVGNLPFDVKDEEIY  354 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~~~~~~~------------------~~--------~~~~~~~~tLfVgNLp~~~teedL~  354 (393)
                       .||+..|.|+.|.|.++.+.......                  ..        .....+..+|||+|||+.+++++|+
T Consensus        90 ~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~  169 (229)
T 2adc_A           90 SHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLK  169 (229)
T ss_dssp             HHHTTCBCSSSBCEEECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHH
T ss_pred             HHhCCCeECCeEEEEEEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHH
Confidence             59999999999999998643110000                  00        0113456899999999999999999


Q ss_pred             HHhhcCCCCCC-CeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          355 QLFCGLNDLES-SVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       355 e~F~~~~~~~G-~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ++|+.|    | .|..|+|+.+     .+|||||+|.+.
T Consensus       170 ~~f~~~----G~~i~~v~i~~~-----~~g~afV~f~~~  199 (229)
T 2adc_A          170 VLFSSN----GGVVKGFKFFQK-----DRKMALIQMGSV  199 (229)
T ss_dssp             HHHHTT----SCCEEEEEECSS-----STTCEEEEESSH
T ss_pred             HHHHHc----CCCeeEEEEEEC-----CCcEEEEEECCH
Confidence            999999    9 9999999754     378999999874

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.90  E-value=1.6e-23  Score=189.41  Aligned_cols=137  Identities=18%  Similarity=0.300  Sum_probs=114.3

Q ss_pred             ccEEEEeCCCc-cCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          225 LRTIFVGNLPL-KVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       225 ~rtVFVgNLp~-~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      +++|||+|||+ .+++++|+.+|+.||.|.+|+|++++                      +|||||+|.+.++|..|+ .
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~----------------------~g~afV~f~~~~~a~~A~~~   60 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----------------------KENALVQMADGNQAQLAMSH   60 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC----------------------SSCCEEECTTTHHHHHHHHH
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC----------------------CCEEEEEECCHHHHHHHHHH
Confidence            58999999999 99999999999999999999984421                      389999999999999999 5


Q ss_pred             hcCceeCCeEEEEeecCCCcccCCC--------------------------CCCCCcCCcceeeeCCCCCCCCHHHHHHH
Q 016231          303 FNMAVIGGNHIRLDRACPPRKKLKG--------------------------EDAPLYDIKKTVFVGNLPFDVKDEEIYQL  356 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~~~~~~~--------------------------~~~~~~~~~~tLfVgNLp~~~teedL~e~  356 (393)
                      ||+..|.|+.|.|.++.+.......                          .......+..+|||+|||..+++++|+++
T Consensus        61 l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~  140 (198)
T 1qm9_A           61 LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVL  140 (198)
T ss_dssp             HTTCCCSSCCCEEEECCCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHH
T ss_pred             hCCCeecCeEEEEEEecCCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHH
Confidence            9999999999999998643211000                          00011345789999999999999999999


Q ss_pred             hhcCCCCCC-CeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          357 FCGLNDLES-SVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       357 F~~~~~~~G-~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      |+.|    | .|..|+|+.+     .+|||||+|.+.
T Consensus       141 f~~~----G~~v~~v~i~~~-----~~g~afV~f~~~  168 (198)
T 1qm9_A          141 FSSN----GGVVKGFKFFQK-----DRKMALIQMGSV  168 (198)
T ss_dssp             HHHT----TSCCCEEEESST-----TSSCEEEECSSH
T ss_pred             HHHc----CCCceEEEEEeC-----CCcEEEEEeCCH
Confidence            9999    9 9999999765     379999999864

>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=99.85  E-value=3.3e-21  Score=161.73  Aligned_cols=108  Identities=17%  Similarity=0.262  Sum_probs=71.5

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      ..+|||+|||+++|+++|+++|+.||.|.+|+|+++.    +               .++|||||+|.+.++|+.|| .|
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~----~---------------~~kg~afV~f~~~~~A~~Ai~~l   65 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE----N---------------GSKGYGFVHFETQEAAERAIEKM   65 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET----T---------------EEEEEEEEEESCHHHHHHHHHHH
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC----C---------------CCCceEEEEECCHHHHHHHHHHc
Confidence            5689999999999999999999999999999997754    1               15699999999999999999 69


Q ss_pred             cCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHH
Q 016231          304 NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEE  352 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teed  352 (393)
                      |+..|.|+.|.|.++.+........ ........+|||+|||+++|++.
T Consensus        66 ~~~~~~g~~i~V~~a~~~~~~~~~~-~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           66 NGMLLNDRKVFVGRFKSRKEREAEL-GARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             TTCEETTEECEEEESSCCCC-----------------------------
T ss_pred             CCCEECCEEEEEEECCCcccccccc-ccccCCCCceEeCCCCCCccccc
Confidence            9999999999999987543222111 11123446899999999999863

>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=99.75  E-value=4.7e-18  Score=139.26  Aligned_cols=79  Identities=18%  Similarity=0.319  Sum_probs=71.5

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      ..+|||+|||+++|+++|+.+|+.||.|.+|+|++++.  +               +.++|||||+|.+.++|..|+ .|
T Consensus        19 gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~--t---------------g~~kG~afV~f~~~~~A~~Ai~~l   81 (99)
T 4fxv_A           19 GTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKV--A---------------GHSLGYGFVNYVTAKDAERAINTL   81 (99)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSS--S---------------CCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCC--C---------------CcccccEEEEECCHHHHHHHHHHh
Confidence            57899999999999999999999999999999987652  2               346699999999999999999 69


Q ss_pred             cCceeCCeEEEEeecCC
Q 016231          304 NMAVIGGNHIRLDRACP  320 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~  320 (393)
                      ||..|.|+.|.|.+|.|
T Consensus        82 ng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           82 NGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             TTCEETTEECEEEECCB
T ss_pred             CCCEECCEEEEEEEeeC
Confidence            99999999999999864

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.72  E-value=1.6e-17  Score=135.24  Aligned_cols=98  Identities=21%  Similarity=0.368  Sum_probs=81.1

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hhc
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~ln  304 (393)
                      ++|||+|||+++|+++|+.+|+.||.|.+|.|+.+                      ++|||||+|.+.++|..|+ .||
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~----------------------~~g~afV~f~~~~~a~~A~~~l~   58 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----------------------PPGFAFVEFEDPRDAEDAVRGLD   58 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS----------------------SSSEEEEECSSHHHHHHHHHHHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC----------------------CCCEEEEEECCHHHHHHHHHHHC
Confidence            47999999999999999999999999999998543                      2389999999999999999 599


Q ss_pred             CceeCCeEEEEeecCCCcccCCCCCC-CCcCCcceeeeCCCC
Q 016231          305 MAVIGGNHIRLDRACPPRKKLKGEDA-PLYDIKKTVFVGNLP  345 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~~~~~~~~~~~-~~~~~~~tLfVgNLp  345 (393)
                      +..|.|+.|.|.++.+.......... .......+||||||+
T Consensus        59 g~~~~g~~l~V~~a~~~~~~~~~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           59 GKVICGSRVRVELSTGMPRRSRFDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             HSCSSSCCCEEEESSSCCCSSCCCSCCCSCCCCSCCCSCCCC
T ss_pred             CCeECCcEEEEEEccCCCCcccCCCCCccccCCCceecCCCC
Confidence            99999999999999875543322221 122346789999996

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.71  E-value=1.1e-17  Score=139.27  Aligned_cols=101  Identities=19%  Similarity=0.302  Sum_probs=88.2

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+.+|+++|+.+|+.||.|.+|+|+++.                    .++|||||+|.+.++|..|+ 
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~--------------------~~~g~afV~f~~~~~A~~A~~   65 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP--------------------ETRGTAYVVYEDIFDAKNAVD   65 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECST--------------------TTTTCEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCC--------------------CCCcEEEEEECCHHHHHHHHH
Confidence            347899999999999999999999999999999996432                    24589999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcC
Q 016231          302 AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGL  360 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~  360 (393)
                      .|||..|.|+.|.|.++.+....                 ++++...++++|.++|+.|
T Consensus        66 ~l~g~~~~g~~l~v~~a~~~~~~-----------------~~~~~~~~~~~l~~~~~~~  107 (115)
T 3lqv_A           66 HLSGFNVSNRYLVVLYYNANRAF-----------------QKMDTKKKEEQLKLLKEKY  107 (115)
T ss_dssp             HHTTCBSSSCBCEEEECCHHHHT-----------------TTSCHHHHHHHHHHHHHHH
T ss_pred             HcCCCEECCeEEEEEEecCChhh-----------------hhhhHhHhHHHHHHHHHHh
Confidence            59999999999999999754321                 5678888999999999999

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.71  E-value=5.9e-17  Score=135.36  Aligned_cols=82  Identities=21%  Similarity=0.267  Sum_probs=73.5

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      .+.++|||+|||+++++++|+++|+.||.|.+|+|++++.  +               +.++|||||+|.+.++|..|| 
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~--t---------------g~~rG~aFV~f~~~~~A~~Ai~   66 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPR--T---------------RKHLGLARVLFTSTRGAKETVK   66 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTT--T---------------CCEEEEEEEEESSHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCC--C---------------CceeeEEEEEECCHHHHHHHHH
Confidence            4578999999999999999999999999999999988652  2               346799999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCC
Q 016231          302 AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~  321 (393)
                      .||+..|.|+.|.|.++...
T Consensus        67 ~lng~~~~gr~i~V~~a~~~   86 (110)
T 3s8s_A           67 NLHLTSVMGNIIHAQLDIKG   86 (110)
T ss_dssp             HHTTCEETTEECEEEECSTT
T ss_pred             HhCCCEECCeEEEEEECCCC
Confidence            69999999999999998643

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.70  E-value=9.5e-17  Score=126.92  Aligned_cols=80  Identities=30%  Similarity=0.408  Sum_probs=71.2

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+++++++|+.+|+.||.|..|+|++++.  +               +.++|||||+|.+.++|..||
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~---------------g~~~g~afV~f~~~~~a~~A~   70 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPN--T---------------GRSRGFGFILFKDAASVEKVL   70 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTT--T---------------CCEEEEEEEEESSTHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCC--C---------------CccccEEEEEECCHHHHHHHH
Confidence            34579999999999999999999999999999999977642  2               236699999999999999999


Q ss_pred             HhcCceeCCeEEEEeec
Q 016231          302 AFNMAVIGGNHIRLDRA  318 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a  318 (393)
                      .+++..|.|+.|.|.+|
T Consensus        71 ~~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A           71 DQKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             HSSCEEETTEEEEEEEC
T ss_pred             HhCCCEECCEEEEEEeC
Confidence            88999999999999875

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.69  E-value=1.4e-16  Score=124.45  Aligned_cols=79  Identities=22%  Similarity=0.318  Sum_probs=71.0

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hhc
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~ln  304 (393)
                      .+|||+|||+++++++|+.+|+.||.|.+|+|++++.  +               +.++|||||+|.+.++|..|+ .||
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~--~---------------~~~~g~afV~f~~~~~a~~a~~~l~   64 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQ--T---------------GSSRGYGFVSFTSQDDAQNAMDSMQ   64 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTT--T---------------CCEEEEEEEEESCHHHHHHHHHHHT
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCC--C---------------CCccceEEEEECCHHHHHHHHHHhc
Confidence            6899999999999999999999999999999977642  2               236699999999999999999 599


Q ss_pred             CceeCCeEEEEeecCCC
Q 016231          305 MAVIGGNHIRLDRACPP  321 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~~  321 (393)
                      +..|.|+.|.|.++.+.
T Consensus        65 g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A           65 GQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             TCEETTEECEEEECCCC
T ss_pred             CCeeCCcEEEEEecCcC
Confidence            99999999999999754

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=4.7e-17  Score=134.51  Aligned_cols=80  Identities=13%  Similarity=0.123  Sum_probs=71.8

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      ...++|||+|||+++|+++|+.+|+.||.|.+|+|++++.   +               .++|||||+|.+.++|..||.
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~---g---------------~~rG~aFV~F~~~e~a~~Ai~   70 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH---K---------------AFKGSIFVVFDSIESAKKFVE   70 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT---T---------------SCCCEEEEEESSHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC---C---------------CCccEEEEEECCHHHHHHHHH
Confidence            4468999999999999999999999999999999977641   2               366999999999999999999


Q ss_pred             hcCceeCCeEEEEeecCC
Q 016231          303 FNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~  320 (393)
                      +|+..|.|+.|.|.++..
T Consensus        71 ~~~~~~~gr~l~V~~~~~   88 (103)
T 1s79_A           71 TPGQKYKETDLLILFKDD   88 (103)
T ss_dssp             SSCCCCTTTTCEEEEHHH
T ss_pred             cCCCEECCEEEEEEEchH
Confidence            999999999999998753

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.69  E-value=1.6e-16  Score=133.51  Aligned_cols=83  Identities=24%  Similarity=0.338  Sum_probs=73.7

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|||+|||+++|+++|+.+|+.||.|..|.|+.+.   +               +.++|||||+|.+.++|+.|+ .
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~---------------g~~~g~afV~F~~~~~A~~Ai~~   67 (116)
T 2fy1_A            6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR---T---------------SKSRGFAFITFENPADAKNAAKD   67 (116)
T ss_dssp             SCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST---T---------------TTCCCEEEEECSSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC---C---------------CCcccEEEEEECCHHHHHHHHHH
Confidence            46899999999999999999999999999999996653   2               236699999999999999999 6


Q ss_pred             hcCceeCCeEEEEeecCCCccc
Q 016231          303 FNMAVIGGNHIRLDRACPPRKK  324 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~~~~  324 (393)
                      ||+..|.|+.|.|.++.++...
T Consensus        68 l~g~~~~g~~l~V~~a~~~~~~   89 (116)
T 2fy1_A           68 MNGKSLHGKAIKVEQAKKPSFQ   89 (116)
T ss_dssp             CSSCBCSSSBCEEEECCCSSCS
T ss_pred             hCCCEECCEEEEEEECCCCCCC
Confidence            9999999999999999866543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.69  E-value=3.3e-17  Score=131.96  Aligned_cols=81  Identities=14%  Similarity=0.209  Sum_probs=69.7

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccC-CeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH-
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFG-EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-  302 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G-~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~-  302 (393)
                      +++|||+|||+++|+++|+.+|+.|| .|.+|+|++++  .+               +.++|||||+|.+.++|..||. 
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~--~t---------------~~~rg~aFV~F~~~~~A~~Ai~~   63 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNK--SS---------------GQSRGFAFVEFSHLQDATRWMEA   63 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCS--SS---------------CCCSSEEEEECSSHHHHHHHHHT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecC--CC---------------CCcCceEEEEecCHHHHHHHHHh
Confidence            47899999999999999999999999 79999986654  22               3466999999999999999994 


Q ss_pred             h-cCceeCCeEEEEeecCCCc
Q 016231          303 F-NMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       303 l-ng~~~~Gr~I~V~~a~~~~  322 (393)
                      + |+..|.|+.|.|.++.+..
T Consensus        64 ~~~~~~~~gr~i~V~~a~~~~   84 (91)
T 2lxi_A           64 NQHSLNILGQKVSMHYSDPKP   84 (91)
T ss_dssp             TTTEEEETTEEEEEECCCSCC
T ss_pred             cCCCeEECCEEEEEEEcCCCC
Confidence            5 4668999999999997653

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.68  E-value=1.6e-16  Score=125.22  Aligned_cols=80  Identities=23%  Similarity=0.367  Sum_probs=70.7

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|||+|||+++++++|+.+|+.||.|.+|+|++++.  +               +.++|||||+|.+.++|..|+ .
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~---------------~~~~g~afV~f~~~~~A~~A~~~   67 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMA--T---------------GKSKGYGFVSFFNKWDAENAIQQ   67 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT--T---------------CCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCC--C---------------CccceEEEEEECCHHHHHHHHHH
Confidence            468999999999999999999999999999999977541  2               236699999999999999999 5


Q ss_pred             hcCceeCCeEEEEeecCC
Q 016231          303 FNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~  320 (393)
                      ||+..|.|+.|.|.++.+
T Consensus        68 l~g~~~~g~~l~v~~a~~   85 (87)
T 3bs9_A           68 MGGQWLGGRQIRTNWATR   85 (87)
T ss_dssp             HTTCEETTEECEEEEEC-
T ss_pred             cCCCEECCeEEEEEecCC
Confidence            999999999999999864

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.68  E-value=9.5e-17  Score=140.69  Aligned_cols=107  Identities=13%  Similarity=0.109  Sum_probs=79.5

Q ss_pred             CCceEEEEeeCCHHHHHHHH-HhcCceeCCeEEEEeecCCCccc----CCCCCCCCcCCcceeeeCCCCCCCCHHHHHHH
Q 016231          282 ADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKK----LKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQL  356 (393)
Q Consensus       282 ~srG~AFVeF~s~e~A~~Al-~lng~~~~Gr~I~V~~a~~~~~~----~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~  356 (393)
                      .++|||||+|.+.++|+.|+ .+++....+..+.+.........    .............+|||+|||+++++++|+++
T Consensus        11 ~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~   90 (158)
T 2kn4_A           11 TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRV   90 (158)
T ss_dssp             SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCCTTCCHHHHHHH
T ss_pred             cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHH
Confidence            47799999999999999999 56654333333333322111000    00011122345789999999999999999999


Q ss_pred             hhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          357 FCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       357 F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      |+.|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus        91 F~~~----G~v~~~~i~~~~~~g~~~g~afV~f~~~  122 (158)
T 2kn4_A           91 FEKY----GRVGDVYIPRDRYTKESRGFAFVRFHDK  122 (158)
T ss_dssp             HHHH----SCEEEEECCCCSSCTTSCCEEEEEESBH
T ss_pred             HHhc----CCeEEEEEeecCCCCccceEEEEEECCH
Confidence            9999    9999999999999999999999999874

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=2.5e-16  Score=128.46  Aligned_cols=84  Identities=20%  Similarity=0.221  Sum_probs=74.1

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+++++++|+.+|+.||.|..|+|++++.  +               +.++|||||+|.+.++|..||
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~--~---------------~~~~g~afV~f~~~~~A~~A~   74 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKT--T---------------GQSKGFAFISFHRREDAARAI   74 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSS--S---------------CSEEEEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCC--C---------------CceeeEEEEEECCHHHHHHHH
Confidence            34579999999999999999999999999999999977542  2               236699999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCCc
Q 016231          302 -AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~~  322 (393)
                       .||+..|.|+.|.|.++.+..
T Consensus        75 ~~l~g~~~~g~~l~v~~a~~~~   96 (103)
T 2cq0_A           75 AGVSGFGYDHLILNVEWAKPST   96 (103)
T ss_dssp             HHTTTCEETTEECEEEESSCCC
T ss_pred             HHcCCCeeCCcEEEEEECCCCC
Confidence             599999999999999997653

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.68  E-value=1.9e-16  Score=124.36  Aligned_cols=79  Identities=29%  Similarity=0.439  Sum_probs=70.9

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+++++++|+.+|+.||.|..|+|++++.  +               +.++|||||+|.+.++|..|+ 
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~--~---------------~~~~g~afV~f~~~~~a~~A~~   67 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE--T---------------EKHRGFAFVEFELAEDAAAAID   67 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETT--T---------------TEECSEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCC--C---------------CccccEEEEEECCHHHHHHHHH
Confidence            3579999999999999999999999999999999977642  2               235699999999999999999 


Q ss_pred             HhcCceeCCeEEEEeec
Q 016231          302 AFNMAVIGGNHIRLDRA  318 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a  318 (393)
                      .||+..|.|+.|.|.++
T Consensus        68 ~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A           68 NMNESELFGRTIRVNLA   84 (85)
T ss_dssp             HHTTCEETTEECEEEEC
T ss_pred             HhCCCEECCcEEEEEEc
Confidence            79999999999999987

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=2.9e-16  Score=127.40  Aligned_cols=83  Identities=17%  Similarity=0.270  Sum_probs=73.6

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+.+|+++|+.+|+.||.|..|+|+.++   +               +.++|||||+|.+.++|..||
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~---------------g~~~g~afV~f~~~~~a~~A~   75 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR---A---------------GKPKGLAYVEYENESQASQAV   75 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT---T---------------SCEEEEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC---C---------------CCEEeEEEEEECCHHHHHHHH
Confidence            3457899999999999999999999999999999997754   2               236699999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCCc
Q 016231          302 -AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~~  322 (393)
                       .||+..|.|+.|.|.++.++.
T Consensus        76 ~~l~g~~~~g~~l~v~~a~~~~   97 (100)
T 2do4_A           76 MKMDGMTIKENIIKVAISNSGP   97 (100)
T ss_dssp             HHHTTEESSSCEEEEEECCCCS
T ss_pred             HHhCCCEECCEEEEEEECCCCC
Confidence             799999999999999997653

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.68  E-value=7.1e-17  Score=131.74  Aligned_cols=79  Identities=16%  Similarity=0.277  Sum_probs=68.5

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCC--eeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGE--IDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~--I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      .-.||||+|||+.+|+++|+++|+.||.  |.+|+|++++.  +               +.++|||||+|.+.++|..||
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~--t---------------g~srG~aFV~f~~~~~A~~Ai   70 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQ--T---------------QQNRGFAFVQLSSAMDASQLL   70 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSS--S---------------SSCSSEEEEECSSSHHHHHHH
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCC--C---------------CCCceEeEEEECCHHHHHHHH
Confidence            3578999999999999999999999995  56888876552  2               346799999999999999999


Q ss_pred             -HhcCc----eeCCeEEEEeecC
Q 016231          302 -AFNMA----VIGGNHIRLDRAC  319 (393)
Q Consensus       302 -~lng~----~~~Gr~I~V~~a~  319 (393)
                       .||+.    .+.||.|.|.+|.
T Consensus        71 ~~lng~~~~~~i~Gr~i~V~~Ak   93 (95)
T 2lkz_A           71 QILQSLHPPLKIDGKTIGVDFAK   93 (95)
T ss_dssp             HHHHSSSSCEEETTEEEEEEECC
T ss_pred             HHhcCCCCCceECCEEEEEEEcc
Confidence             68986    5899999999985

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.67  E-value=6.4e-16  Score=128.51  Aligned_cols=84  Identities=21%  Similarity=0.335  Sum_probs=74.2

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+.+++++|+.+|+.||.|..|+|++++.  +               +.++|||||+|.+.++|+.||
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~---------------~~~~g~afV~f~~~~~a~~A~   74 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMA--T---------------GKSKGYGFVSFFNKWDAENAI   74 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT--T---------------CCEEEEEEEEESSHHHHHHHH
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCC--C---------------CCcceEEEEEECCHHHHHHHH
Confidence            34579999999999999999999999999999999977542  2               236699999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCCc
Q 016231          302 -AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~~  322 (393)
                       .||+..|.|+.|.|.++.+..
T Consensus        75 ~~l~g~~~~g~~l~V~~a~~~~   96 (115)
T 2dgo_A           75 QQMGGQWLGGRQIRTNWATRKP   96 (115)
T ss_dssp             HHTTTCEETTEECEEEESSCCC
T ss_pred             HHhCCCEECCEEEEEEEccCCC
Confidence             699999999999999997653

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.67  E-value=2.3e-16  Score=124.83  Aligned_cols=80  Identities=24%  Similarity=0.383  Sum_probs=72.0

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhc
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~ln  304 (393)
                      .++|||+|||+++++++|+.+|+.||.|.+|+|++++.  +               +.++|||||+|.+.++|..|+.+|
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~---------------~~~~g~afV~f~~~~~a~~a~~~~   68 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKF--S---------------GHPKGFAYIEFSDKESVRTSLALD   68 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCS--S---------------SSCCEEEEEEESSTHHHHHHGGGT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCC--C---------------CCcceEEEEEECCHHHHHHHHhcC
Confidence            68999999999999999999999999999999977542  2               236699999999999999999999


Q ss_pred             CceeCCeEEEEeecCCC
Q 016231          305 MAVIGGNHIRLDRACPP  321 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~~  321 (393)
                      +..|.|+.|.|.++.++
T Consensus        69 g~~~~g~~l~V~~a~~~   85 (89)
T 3ucg_A           69 ESLFRGRQIKVIPKRTN   85 (89)
T ss_dssp             TCEETTEECEEEETTTT
T ss_pred             CCEECCcEEEEEEccCC
Confidence            99999999999998653

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.67  E-value=5.5e-17  Score=129.73  Aligned_cols=79  Identities=14%  Similarity=0.191  Sum_probs=67.0

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccC--CeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFG--EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G--~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      .+|||+|||+++|+++|+.+|+.||  .|.+|+|++++.  +               +.++|||||+|.+.++|..|| .
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~--~---------------g~~kG~afV~f~~~~~a~~Ai~~   64 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRA--N---------------GQSKGFALVGVGSEASSKKLMDL   64 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTT--T---------------CCEEEEEEECC-CHHHHHHHHHH
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCC--C---------------CccCcEEEEEECCHHHHHHHHHH
Confidence            5799999999999999999999999  999999977642  2               346799999999999999999 7


Q ss_pred             hcCceeCCeEEEEeecCCC
Q 016231          303 FNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~  321 (393)
                      |||..|.|+.|.|.++.++
T Consensus        65 l~g~~~~gr~i~V~~~~~~   83 (90)
T 3p5t_L           65 LPKRELHGQNPVVTPSNKL   83 (90)
T ss_dssp             GGGSCSSSCCCEECCC---
T ss_pred             cCCCeeCCEEEEEEECCCC
Confidence            9999999999999999764

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=4.7e-16  Score=126.85  Aligned_cols=82  Identities=24%  Similarity=0.405  Sum_probs=72.9

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+.+++++|+.+|+.||.|.+|+|++++.                   .++|||||+|.+.++|..||
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-------------------~~~g~afV~f~~~~~a~~A~   72 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT-------------------SNDPYCFVEFYEHRDAAAAL   72 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC-------------------SSCCEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC-------------------CCCCEEEEEECCHHHHHHHH
Confidence            34579999999999999999999999999999999976531                   14589999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCCc
Q 016231          302 -AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~~  322 (393)
                       .||+..|.|+.|.|.++.++.
T Consensus        73 ~~l~g~~~~g~~l~V~~a~~~~   94 (103)
T 2cqi_A           73 AAMNGRKILGKEVKVNWATTPS   94 (103)
T ss_dssp             HHHTTEEETTEEEEEEECCCTT
T ss_pred             HHhCCCCcCCCeEEEEECCCCc
Confidence             599999999999999998654

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=3.4e-16  Score=126.82  Aligned_cols=84  Identities=27%  Similarity=0.421  Sum_probs=74.3

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+.+++++|+.+|+.||.|..|+|++++.  +               +.++|||||+|.+.++|..||
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~---------------~~~~g~afV~f~~~~~a~~A~   69 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAE--K---------------QRPRGFGFITFEDEQSVDQAV   69 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTT--T---------------CSCCSEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCC--C---------------CCCCceEEEEECCHHHHHHHH
Confidence            34579999999999999999999999999999999966542  2               236699999999999999999


Q ss_pred             HhcCceeCCeEEEEeecCCCc
Q 016231          302 AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      .+|+..|.|+.|.|.++.++.
T Consensus        70 ~~~~~~~~g~~l~V~~a~~~~   90 (99)
T 2dgs_A           70 NMHFHDIMGKKVEVKRAEPRD   90 (99)
T ss_dssp             HHCCCBSSSCBCEEEECCCCC
T ss_pred             HhCCCEECCeEEEEEECCCCc
Confidence            999999999999999997654

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.67  E-value=4.8e-16  Score=126.97  Aligned_cols=83  Identities=27%  Similarity=0.359  Sum_probs=73.2

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+.+++++|+.+|+.|| |..|+|++++.  +               +.++|||||+|.+.++|..||
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~--~---------------g~~~g~afV~f~~~~~a~~A~   73 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKD--T---------------DKFKGFCYVEFDEVDSLKEAL   73 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSS--S---------------CSEEEEEEEEESSHHHHHHHG
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCC--C---------------CccceEEEEEECCHHHHHHHH
Confidence            34579999999999999999999999997 99999977642  2               236699999999999999999


Q ss_pred             HhcCceeCCeEEEEeecCCCc
Q 016231          302 AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      .||+..|.|+.|.|.++.+..
T Consensus        74 ~l~g~~~~g~~l~V~~a~~~~   94 (103)
T 2dng_A           74 TYDGALLGDRSLRVDIAEGRK   94 (103)
T ss_dssp             GGTTCEETTEECEEEECCCCC
T ss_pred             hhCCCeECCeEEEEEEecCCC
Confidence            999999999999999997653

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.67  E-value=3.9e-16  Score=126.09  Aligned_cols=85  Identities=18%  Similarity=0.232  Sum_probs=73.6

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      +.++|||+|||+++++++|+.+|+.||.|..|+|++++.. .+             ++.++|||||+|.+.++|..|| .
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~g-------------t~~~~g~afV~f~~~~~a~~A~~~   69 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNK-AG-------------VLLSMGFGFVEYKKPEQAQKALKQ   69 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECT-TC-------------CEEEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC-CC-------------CcCcccEEEEEECCHHHHHHHHHH
Confidence            4789999999999999999999999999999999876521 01             1136699999999999999999 5


Q ss_pred             hcCceeCCeEEEEeecCCCc
Q 016231          303 FNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~~  322 (393)
                      ||+..|.|+.|.|.++.+..
T Consensus        70 l~g~~~~g~~l~V~~a~~~~   89 (98)
T 2cpf_A           70 LQGHTVDGHKLEVRISERAT   89 (98)
T ss_dssp             STTCEETTEECEEECSSCSS
T ss_pred             hCCCeeCCeEEEEEEccCCC
Confidence            99999999999999997654

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.66  E-value=4.5e-16  Score=127.23  Aligned_cols=82  Identities=22%  Similarity=0.315  Sum_probs=72.9

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+.+++++|+.+|+.||.|..|+|+.++   +               +.++|||||+|.+.++|..|| 
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~---------------g~~~g~afV~f~~~~~A~~Ai~   74 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP---D---------------GSSKGCAFVKFSSHTEAQAAIH   74 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS---S---------------SCEEEEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC---C---------------CCcCcEEEEEeCCHHHHHHHHH
Confidence            347999999999999999999999999999999997754   1               236699999999999999999 


Q ss_pred             HhcCceeCC---eEEEEeecCCCc
Q 016231          302 AFNMAVIGG---NHIRLDRACPPR  322 (393)
Q Consensus       302 ~lng~~~~G---r~I~V~~a~~~~  322 (393)
                      .||+..|.|   +.|.|.++.+..
T Consensus        75 ~l~g~~~~gg~~~~l~V~~a~~~~   98 (105)
T 2dnh_A           75 ALHGSQTMPGASSSLVVKFADTDK   98 (105)
T ss_dssp             HHSSCCCCTTCSSCCEEEESCSSC
T ss_pred             HHcCCccCCCCCccEEEEECccCc
Confidence            699999998   999999997654

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.66  E-value=3.7e-16  Score=125.36  Aligned_cols=79  Identities=25%  Similarity=0.384  Sum_probs=71.1

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+.+++++|+.+|+.||.|.+|+|++++.                  +.++|||||+|.+.++|..|| 
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~------------------g~~~g~afV~f~~~~~a~~A~~   75 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE------------------GKPKSFGFVCFKHPESVSYAIA   75 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT------------------SCEEEEEEEEESSTHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC------------------CCCceEEEEEECCHHHHHHHHH
Confidence            4578999999999999999999999999999999977541                  235699999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecC
Q 016231          302 AFNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~  319 (393)
                      .||+..|.|+.|.|.++.
T Consensus        76 ~l~g~~~~g~~l~V~~a~   93 (95)
T 2ywk_A           76 LLNGIRLYGRPINVSGPS   93 (95)
T ss_dssp             HHTTCEETTEECEEECCC
T ss_pred             HhCCCEECCCEEEEEEcC
Confidence            599999999999999975

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.66  E-value=5.3e-16  Score=125.52  Aligned_cols=84  Identities=17%  Similarity=0.205  Sum_probs=74.0

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+.+|+++|+.+|+.||.|..|+|++++  .+               +.++|||||+|.+.++|..|| 
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~--~~---------------~~~~g~afV~f~~~~~a~~A~~   68 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDS--LT---------------KKPKGFAFVTFMFPEHAVKAYA   68 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCT--TT---------------CCCCSEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecC--CC---------------CCcCeEEEEEECCHHHHHHHHH
Confidence            457899999999999999999999999999999986643  12               346699999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCCcc
Q 016231          302 AFNMAVIGGNHIRLDRACPPRK  323 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~~  323 (393)
                      .||+..|.|+.|.|.++.+...
T Consensus        69 ~l~g~~~~g~~l~V~~a~~~~~   90 (99)
T 1whw_A           69 EVDGQVFQGRMLHVLPSTIKKE   90 (99)
T ss_dssp             HTTTEESSSCEEEEEECCCCST
T ss_pred             HhCCCEECCcEEEEEEcCCCcc
Confidence            7999999999999999986543

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=9.4e-16  Score=125.06  Aligned_cols=83  Identities=19%  Similarity=0.360  Sum_probs=73.3

Q ss_pred             CCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       221 ~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      .....++|||+|||+++|+++|+.+|+.||.|..|+|+.++    .               .++|||||+|.+.++|..|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~----~---------------~~~g~afV~f~~~~~a~~A   71 (103)
T 2cq3_A           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE----R---------------GSKGFGFVTFENSADADRA   71 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT----T---------------TTCCEEEEEESCHHHHHHH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC----C---------------CCcEEEEEEECCHHHHHHH
Confidence            34557999999999999999999999999999999996643    1               1458999999999999999


Q ss_pred             H-HhcCceeCCeEEEEeecCCCc
Q 016231          301 L-AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       301 l-~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      | .||+..|.|+.|.|.++.+..
T Consensus        72 ~~~l~g~~~~g~~l~v~~a~~~~   94 (103)
T 2cq3_A           72 REKLHGTVVEGRKIEVNNATARV   94 (103)
T ss_dssp             HHHHTTCEETTEECEEEECCSSC
T ss_pred             HHHhCCCEECCEEEEEEEcccCC
Confidence            9 699999999999999997653

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.66  E-value=4.6e-16  Score=129.53  Aligned_cols=83  Identities=19%  Similarity=0.335  Sum_probs=73.7

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+++++++|+.+|+.||.|..|+|++++.  +               +.++|||||+|.+.++|..|| 
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~---------------g~~~g~afV~f~~~~~a~~A~~   85 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQ--T---------------NLSKCFGFVSYDNPVSAQAAIQ   85 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSS--S---------------CSEEEEEEEECSSHHHHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC--C---------------CCcCccEEEEECCHHHHHHHHH
Confidence            3468999999999999999999999999999999977542  2               236699999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCCc
Q 016231          302 AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      .||+..|.|+.|.|.++.+..
T Consensus        86 ~l~g~~~~g~~l~V~~a~~~~  106 (115)
T 2cpz_A           86 SMNGFQIGMKRLKVQLKRSKN  106 (115)
T ss_dssp             HHTTCEETTEECEEECCCCSC
T ss_pred             HcCCCEECCEEEEEEEcCCCC
Confidence            799999999999999997654

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=4.3e-16  Score=127.46  Aligned_cols=84  Identities=27%  Similarity=0.390  Sum_probs=73.2

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      ...++|||+|||+.+++++|+.+|+.|| |..|+|++++.  +              .+.++|||||+|.+.++|..||.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~--~--------------~g~~~g~afV~f~~~~~a~~A~~   75 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPS--N--------------PERLKGFGYAEFEDLDSLLSALS   75 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSS--C--------------TTSBCSCEEEEESSHHHHHHHHG
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCC--C--------------CCCcCeEEEEEECCHHHHHHHHh
Confidence            3468999999999999999999999999 99999966542  1              02366999999999999999999


Q ss_pred             hcCceeCCeEEEEeecCCCcc
Q 016231          303 FNMAVIGGNHIRLDRACPPRK  323 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~~~  323 (393)
                      ||+..|.|+.|.|.++.+...
T Consensus        76 l~g~~~~g~~l~V~~a~~~~~   96 (104)
T 1wi8_A           76 LNEESLGNKRIRVDVADQAQD   96 (104)
T ss_dssp             GGTCEETTEECEEEECCCCCC
T ss_pred             cCCCEeCCcEEEEEEccCCCC
Confidence            999999999999999976543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=3.2e-16  Score=127.83  Aligned_cols=84  Identities=26%  Similarity=0.352  Sum_probs=73.5

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+++++++|+.+|+.||.|..|.|+.++.  +               +.++|||||+|.+.++|..||
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~--~---------------~~~~g~afV~f~~~~~A~~A~   72 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPH--T---------------KAPRGFAFVRFHDRRDAQDAE   72 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSS--S---------------CSBCSCEEEEESSSSHHHHHH
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCC--C---------------CCCCeEEEEEECCHHHHHHHH
Confidence            34579999999999999999999999999999999966541  2               236699999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCCc
Q 016231          302 -AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~~  322 (393)
                       .||+..|.|+.|.|.++.+..
T Consensus        73 ~~l~g~~~~g~~l~V~~a~~~~   94 (103)
T 2dnm_A           73 AAMDGAELDGRELRVQVARYGR   94 (103)
T ss_dssp             HHHSSCCBTTBCCEEEECSSCC
T ss_pred             HHcCCCEECCcEEEEEECCcCC
Confidence             599999999999999997543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=6.8e-16  Score=123.61  Aligned_cols=81  Identities=21%  Similarity=0.225  Sum_probs=72.2

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+.+++++|+.+|+.||.|..|.|++++.  +               +.++|||||+|.+.++|..||
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~---------------~~~~g~afV~f~~~~~A~~A~   74 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQ--S---------------RRSRGFAFVYFENVDDAKEAK   74 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSS--S---------------SSEEEEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCC--C---------------CCcccEEEEEECCHHHHHHHH
Confidence            44579999999999999999999999999999999977542  2               236699999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecC
Q 016231          302 -AFNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~  319 (393)
                       .||+..|.|+.|.|.++.
T Consensus        75 ~~l~g~~~~g~~l~v~~a~   93 (95)
T 2cqc_A           75 ERANGMELDGRRIRVSGPS   93 (95)
T ss_dssp             HHHTTEEETTEEEEEECCS
T ss_pred             HHhCCCEECCEEEEEEecC
Confidence             599999999999999985

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=6.3e-16  Score=125.73  Aligned_cols=85  Identities=29%  Similarity=0.430  Sum_probs=74.3

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+.+++++|+.+|+.||.|..|+|+.++.  +               +.++|||||+|.+.++|..||
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~--~---------------~~~~g~afV~f~~~~~A~~A~   71 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE--T---------------EKHRGFAFVEFELAEDAAAAI   71 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSS--S---------------CCCSSEEEECCSSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCC--C---------------CCcceEEEEEECCHHHHHHHH
Confidence            34579999999999999999999999999999999866541  2               236699999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCCcc
Q 016231          302 -AFNMAVIGGNHIRLDRACPPRK  323 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~~~  323 (393)
                       .||+..|.|+.|.|.++.+...
T Consensus        72 ~~l~g~~~~g~~l~V~~a~~~~~   94 (102)
T 2cqb_A           72 DNMNESELFGRTIRVNLAKPMRI   94 (102)
T ss_dssp             HHHTTEEETTEEEEEEECCCCCC
T ss_pred             HHhCCCEECCcEEEEEeCCCCCC
Confidence             6999999999999999976543

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.65  E-value=5.4e-16  Score=125.07  Aligned_cols=81  Identities=16%  Similarity=0.336  Sum_probs=72.2

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      +++|||+|||+.+++++|+.+|+.||.|.+|+|+.++.  +               +.++|||||+|.+.++|..|+ .|
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~---------------g~~~g~afV~f~~~~~A~~Ai~~l   64 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQ--T---------------GRSKGYAFIEFRDLESSASAVRNL   64 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTT--T---------------CCBCSEEEEEESSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCC--C---------------CccceEEEEEECCHHHHHHHHHHh
Confidence            68999999999999999999999999999999966541  2               236699999999999999999 69


Q ss_pred             cCceeCCeEEEEeecCCCc
Q 016231          304 NMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~  322 (393)
                      ||..|.|+.|.|.++.++.
T Consensus        65 ~g~~~~g~~l~V~~a~~~~   83 (96)
T 2x1f_A           65 NGYQLGSRFLKCGYSSNSD   83 (96)
T ss_dssp             TTCEETTEECEEEECSCSS
T ss_pred             CCCeECCeEEEEEEcCCCC
Confidence            9999999999999997653

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.65  E-value=7.5e-16  Score=123.53  Aligned_cols=82  Identities=21%  Similarity=0.323  Sum_probs=73.0

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|||+|||+.+++++|+.+|+.||.|..|+|++++.  +               +.++|||||+|.+.++|..|| .
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~---------------~~~~g~afV~f~~~~~a~~A~~~   66 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSD--T---------------GRSKGYGFITFSDSECARRALEQ   66 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSS--S---------------CCCCSEEEEEESCHHHHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCC--C---------------CceeeEEEEEECCHHHHHHHHHH
Confidence            478999999999999999999999999999999976542  2               236699999999999999999 5


Q ss_pred             hcCceeCCeEEEEeecCCCc
Q 016231          303 FNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~~  322 (393)
                      ||+..|.|+.|.|.++.+..
T Consensus        67 l~g~~~~g~~l~V~~a~~~~   86 (95)
T 2dnz_A           67 LNGFELAGRPMRVGHVTERL   86 (95)
T ss_dssp             HTTCCSSSSCCEEEESSCCC
T ss_pred             hCCCeeCCcEEEEEEccccc
Confidence            99999999999999997653

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=4.2e-16  Score=126.11  Aligned_cols=83  Identities=19%  Similarity=0.315  Sum_probs=73.2

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCee-EEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEID-SVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~-sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      ....++|||+|||+++++++|+.+|+.||.|. +|+|++++.  +               +.++|||||+|.+.++|+.|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~--~---------------g~~~g~afV~f~~~~~a~~A   68 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRL--T---------------GIPAGYCFVEFADLATAEKC   68 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSS--S---------------CCEEEEEEEECSCHHHHHHH
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCC--C---------------CCcCCEEEEEeCCHHHHHHH
Confidence            34579999999999999999999999999999 999977642  2               23669999999999999999


Q ss_pred             H-HhcCceeCCeE----EEEeecCCC
Q 016231          301 L-AFNMAVIGGNH----IRLDRACPP  321 (393)
Q Consensus       301 l-~lng~~~~Gr~----I~V~~a~~~  321 (393)
                      + .||+..|.|+.    |.|.++.+.
T Consensus        69 ~~~l~g~~~~g~~~~~~l~v~~a~~~   94 (99)
T 2div_A           69 LHKINGKPLPGATPAKRFKLNYATYS   94 (99)
T ss_dssp             HHTTTTSEESSCSSCEECCEEETTCC
T ss_pred             HHHHcCCccCCCCcceeEEEeecCCC
Confidence            9 59999999999    999999754

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=4.4e-16  Score=127.55  Aligned_cols=81  Identities=16%  Similarity=0.222  Sum_probs=72.2

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+.+++++|+.+|+.||.|..|.|+.++.  +               +.++|||||+|.+.++|..|| 
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~--~---------------~~~~g~afV~f~~~~~a~~A~~   83 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR--T---------------GYLKGYTLVEYETYKEAQAAME   83 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT--T---------------SSEEEEEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCC--C---------------CceeeEEEEEECCHHHHHHHHH
Confidence            3468999999999999999999999999999999977542  2               236699999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCC
Q 016231          302 AFNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~  320 (393)
                      .||+..|.|+.|.|.++.+
T Consensus        84 ~l~g~~~~g~~l~V~~a~~  102 (106)
T 1p27_B           84 GLNGQDLMGQPISVDWCFV  102 (106)
T ss_dssp             HHTTCBSSSSBCEEEESEE
T ss_pred             HhcCCEECCcEEEEEeecC
Confidence            5999999999999999864

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=7.7e-16  Score=125.86  Aligned_cols=86  Identities=24%  Similarity=0.379  Sum_probs=74.6

Q ss_pred             CCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       221 ~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      .....++|||+|||+.+|+++|+.+|+.||.|..|+|+.++.  +               +.++|||||+|.+.++|..|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~---------------~~~~g~afV~f~~~~~a~~A   73 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRV--T---------------GQHQGYGFVEFLSEEDADYA   73 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSS--S---------------CSBCSCEEEEESSHHHHHHH
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--C---------------CcCCcEEEEEECCHHHHHHH
Confidence            344579999999999999999999999999999999866541  2               23669999999999999999


Q ss_pred             H-HhcCceeCCeEEEEeecCCCcc
Q 016231          301 L-AFNMAVIGGNHIRLDRACPPRK  323 (393)
Q Consensus       301 l-~lng~~~~Gr~I~V~~a~~~~~  323 (393)
                      | .||+..|.|+.|.|.++.+...
T Consensus        74 ~~~l~g~~~~g~~l~v~~a~~~~~   97 (105)
T 1x5u_A           74 IKIMDMIKLYGKPIRVNKASAHNK   97 (105)
T ss_dssp             HHHSSSCBCSSCBCEEEETTTTSC
T ss_pred             HHHhCCCeECCeEEEEEECCCCCc
Confidence            9 5999999999999999976543

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.65  E-value=2.2e-16  Score=129.04  Aligned_cols=81  Identities=17%  Similarity=0.149  Sum_probs=72.6

Q ss_pred             CcccEEEEeCCCc------cCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHH
Q 016231          223 KLLRTIFVGNLPL------KVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQS  296 (393)
Q Consensus       223 ~~~rtVFVgNLp~------~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~  296 (393)
                      ...++|||+|||+      .+++++|+.+|+.||.|.+|+|++++.  +               +.++|||||+|.+.++
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~--t---------------g~~kG~afV~f~~~~~   66 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEA--T---------------GKTKGFLFVECGSMND   66 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETT--T---------------TEECSEEEEEESSHHH
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCC--C---------------CccceEEEEEECCHHH
Confidence            4478999999999      999999999999999999999987652  2               2366999999999999


Q ss_pred             HHHHH-HhcCceeCC-eEEEEeecCC
Q 016231          297 TEAAL-AFNMAVIGG-NHIRLDRACP  320 (393)
Q Consensus       297 A~~Al-~lng~~~~G-r~I~V~~a~~  320 (393)
                      |..|| .|||..|.| +.|.|.++.+
T Consensus        67 A~~Ai~~lng~~~~g~r~l~V~~a~~   92 (100)
T 3ns6_A           67 AKKIIKSFHGKRLDLKHRLFLYTMKD   92 (100)
T ss_dssp             HHHHHHHHTTCBSSSSCBCEEEESHH
T ss_pred             HHHHHHHhCCcccCCCeEEEEEECch
Confidence            99999 699999999 9999999864

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.65  E-value=9.2e-16  Score=126.45  Aligned_cols=84  Identities=21%  Similarity=0.344  Sum_probs=73.8

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+++|+++|+.+|+.||.|..|+|++++.  +               +.++|||||+|.+.++|..||
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~---------------g~~~g~afV~f~~~~~A~~A~   74 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPD--T---------------EHSKGCAFAQFMTQEAAQKCL   74 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSS--S---------------CCBCSEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--C---------------CCCccEEEEEECCHHHHHHHH
Confidence            34578999999999999999999999999999999976542  2               235699999999999999999


Q ss_pred             -Hhc------CceeCCeEEEEeecCCCc
Q 016231          302 -AFN------MAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 -~ln------g~~~~Gr~I~V~~a~~~~  322 (393)
                       .||      +..|.|+.|.|.++.+..
T Consensus        75 ~~~~~~~~~~~~~~~g~~l~v~~a~~~~  102 (111)
T 1x4h_A           75 AAASLEAEGGGLKLDGRQLKVDLAVTRD  102 (111)
T ss_dssp             HHHCTTTTTCCEESSSCEEEEECCCCCC
T ss_pred             HHhccccccCCcEEcCEEEEEEECCCCc
Confidence             699      999999999999997654

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=3.4e-16  Score=130.73  Aligned_cols=82  Identities=11%  Similarity=0.134  Sum_probs=72.3

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCe-eEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEI-DSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I-~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      ....++|||+|||+++|+++|+.+|+.||.| ..|+|++++   +               +.++|||||+|.+.++|..|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~---~---------------g~~~G~afV~F~~~~~a~~A   73 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN---N---------------GQGLGQALVQFKNEDDARKS   73 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT---T---------------SSCSSCEEEECSSHHHHHHH
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC---C---------------CCcceEEEEEECCHHHHHHH
Confidence            3457999999999999999999999999999 889986654   2               23669999999999999999


Q ss_pred             HHhcCceeCCeEEEEeecCCC
Q 016231          301 LAFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       301 l~lng~~~~Gr~I~V~~a~~~  321 (393)
                      |.+|+..|.|+.|.|.++.+.
T Consensus        74 l~~~~~~~~gr~i~v~~a~~~   94 (114)
T 2cpy_A           74 ERLHRKKLNGREAFVHVVTLE   94 (114)
T ss_dssp             GGGCSEEETTEEEEEEEECHH
T ss_pred             HHhCCCccCCeEEEEEECCHH
Confidence            977999999999999998653

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.64  E-value=6.8e-16  Score=123.06  Aligned_cols=81  Identities=22%  Similarity=0.241  Sum_probs=72.0

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+++++++|+.+|+.||.|..|+|+++    ++               .++|||||+|.+.++|..|+ 
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~----~g---------------~~~g~afV~f~~~~~a~~a~~   66 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME----NG---------------KSKGCGVVKFESPEVAERACR   66 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES----SS---------------CEEEEEEEEESSHHHHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc----CC---------------CcceEEEEEECCHHHHHHHHH
Confidence            45789999999999999999999999999999999652    22               35699999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCCc
Q 016231          302 AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      .||+..|.|+.|.|.++.+..
T Consensus        67 ~l~g~~~~g~~l~v~~a~~~~   87 (92)
T 2dgv_A           67 MMNGMKLSGREIDVRIDRNAS   87 (92)
T ss_dssp             HHTTCCBTTBCCCCEECSCCS
T ss_pred             HhCCCEECCcEEEEEEcCCCC
Confidence            599999999999999997653

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=4.5e-16  Score=127.42  Aligned_cols=84  Identities=23%  Similarity=0.341  Sum_probs=74.0

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+.+++++|+.+|+.||.|..|+|++++.  +               +.++|||||+|.+.++|..||
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~--~---------------g~~~g~afV~f~~~~~a~~a~   75 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKT--T---------------NQSRGFGFVKFKDPNCVGTVL   75 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSS--S---------------CCEEEEEEEEESSTTHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCC--C---------------CCcceEEEEEECCHHHHHHHH
Confidence            34579999999999999999999999999999999977542  2               236699999999999999999


Q ss_pred             HhcCceeCCeEEEEeecCCCc
Q 016231          302 AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      ..|+..|.|+.|.|.++.+..
T Consensus        76 ~~~~~~~~g~~l~V~~a~~~~   96 (105)
T 2dh8_A           76 ASRPHTLDGRNIDPKPCTPRG   96 (105)
T ss_dssp             HHCSEEETTEEEBCCCSCCSS
T ss_pred             HhCCCeECCEEEEEEEccCCC
Confidence            669999999999999997654

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=2.5e-16  Score=128.35  Aligned_cols=83  Identities=23%  Similarity=0.414  Sum_probs=73.5

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+.+++++|+.+|+.||.|..|+|++++.  +               +.++|||||+|.+.++|..|+ 
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~--~---------------g~~~g~afV~f~~~~~a~~A~~   68 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRE--T---------------GKPKGYGFCEYQDQETALSAMR   68 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETT--T---------------TEEEEEEEEECSCHHHHHHHHH
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCC--C---------------CccceEEEEEECCHHHHHHHHH
Confidence            3468999999999999999999999999999999977642  2               236699999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCCc
Q 016231          302 AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      .||+..|.|+.|.|.++.+..
T Consensus        69 ~l~g~~~~g~~l~v~~a~~~~   89 (104)
T 1p1t_A           69 NLNGREFSGRALRVDNAASEK   89 (104)
T ss_dssp             HSSSBSCSSSCBEEEETTCTT
T ss_pred             HhCCCeeCCcEEEEEeCCCcc
Confidence            699999999999999997643

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=7e-16  Score=125.90  Aligned_cols=83  Identities=24%  Similarity=0.334  Sum_probs=73.4

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcc-cCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIK-FGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~-~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      ....++|||+|||+++|+++|+.+|+. ||.|.+|+|++++   ++               .++|||||+|.+.++|..|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~---~g---------------~~~g~afV~f~~~~~a~~A   67 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ---TG---------------VSKGYGFVKFTDELEQKRA   67 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT---TC---------------CEEEEEEEEESCHHHHHHH
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC---CC---------------CccceEEEEECCHHHHHHH
Confidence            345789999999999999999999999 9999999997754   22               3669999999999999999


Q ss_pred             H-HhcCce-eCCeEEEEeecCCCc
Q 016231          301 L-AFNMAV-IGGNHIRLDRACPPR  322 (393)
Q Consensus       301 l-~lng~~-~~Gr~I~V~~a~~~~  322 (393)
                      | .||+.. |.|+.|.|.++.+..
T Consensus        68 ~~~l~g~~~~~g~~l~v~~a~~~~   91 (104)
T 2dhg_A           68 LTECQGAVGLGSKPVRLSVAIPKA   91 (104)
T ss_dssp             HHHTTTCCSSSSSCCCCCBCCCCC
T ss_pred             HHHccCCcccCCEeEEEEEccCCC
Confidence            9 599999 999999999997654

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=9.2e-16  Score=122.76  Aligned_cols=80  Identities=26%  Similarity=0.367  Sum_probs=71.1

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+.+++++|+.+|+.||.|..|+|+.++.  +               +.++|||||+|.+.++|..|+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~---------------~~~~g~afV~f~~~~~A~~A~   75 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKD--T---------------RKSKGVAFILFLDKDSAQNCT   75 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSS--S---------------CCCTTCEEEEESCHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCC--C---------------CCcccEEEEEECCHHHHHHHH
Confidence            34578999999999999999999999999999999966542  2               236699999999999999999


Q ss_pred             -HhcCceeCCeEEEEeec
Q 016231          302 -AFNMAVIGGNHIRLDRA  318 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a  318 (393)
                       .||+..|.|+.|.|.++
T Consensus        76 ~~l~g~~~~g~~l~v~~a   93 (94)
T 2e5h_A           76 RAINNKQLFGRVIKASIA   93 (94)
T ss_dssp             HHTTTEEETTEEEEEEEC
T ss_pred             HHcCCCeeCCcEEEEEec
Confidence             69999999999999987

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=1.9e-15  Score=125.36  Aligned_cols=82  Identities=22%  Similarity=0.220  Sum_probs=72.7

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+.+++++|+.+|..||.|..|+|+.++   ++               .++|||||+|.+.++|..||
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~---~g---------------~~~g~afV~f~~~~~a~~A~   73 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK---DG---------------KSRGIGTVTFEQSIEAVQAI   73 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT---TC---------------SEEEEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC---CC---------------CeeeEEEEEECCHHHHHHHH
Confidence            3457899999999999999999999999999999997754   12               36699999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCC
Q 016231          302 -AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~  321 (393)
                       .||+..|.|+.|.|.++...
T Consensus        74 ~~l~g~~~~g~~l~v~~a~~~   94 (114)
T 2do0_A           74 SMFNGQLLFDRPMHVKMDERA   94 (114)
T ss_dssp             HHHTTCEETTEECEEEECSCC
T ss_pred             HHhCCCEeCCCEEEEEEcccC
Confidence             59999999999999998643

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.64  E-value=6.8e-16  Score=127.38  Aligned_cols=82  Identities=20%  Similarity=0.261  Sum_probs=72.1

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+.+|+++|+.+|+.||.|..|+|+.++  .               ++.++|||||+|.+.++|..|| 
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~--~---------------~~~~~g~afV~f~~~~~A~~Ai~   86 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDR--R---------------TGFSKGYALVEYETHKQALAAKE   86 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCT--T---------------TSSBCSEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC--C---------------CCCcceEEEEEECCHHHHHHHHH
Confidence            446899999999999999999999999999999986643  1               2346699999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCC
Q 016231          302 AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~  321 (393)
                      .|||..|.|+.|.|.++.+.
T Consensus        87 ~l~g~~~~g~~l~V~~a~~~  106 (110)
T 1oo0_B           87 ALNGAEIMGQTIQVDWCFVK  106 (110)
T ss_dssp             HHTTCEETTEECEEEESEES
T ss_pred             HcCCCEECCcEEEEEEcccC
Confidence            59999999999999998643

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=8.1e-16  Score=123.56  Aligned_cols=82  Identities=28%  Similarity=0.338  Sum_probs=72.5

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEE-EEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSV-RIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sV-ri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      ..++|||+|||+.+++++|+.+|+.||.|..| +|++++.  +               +.++|||||+|.+.++|..||.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~--~---------------g~~~g~afV~f~~~~~A~~A~~   66 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPD--T---------------GNSKGYAFINFASFDASDAAIE   66 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTT--T---------------CSCCSEEEEEBSSHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCC--C---------------CCcCeEEEEEECCHHHHHHHHH
Confidence            47899999999999999999999999999999 8866531  2               2366999999999999999995


Q ss_pred             -hcCceeCCeEEEEeecCCCc
Q 016231          303 -FNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       303 -lng~~~~Gr~I~V~~a~~~~  322 (393)
                       ||+..|.|+.|.|.++.+..
T Consensus        67 ~l~g~~~~g~~l~v~~a~~~~   87 (96)
T 1x5t_A           67 AMNGQYLCNRPITVSYAFKKD   87 (96)
T ss_dssp             TTTTCEETTEECEEEESCCCC
T ss_pred             HcCCCEECCEEEEEEEecccC
Confidence             99999999999999997654

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=1.4e-15  Score=121.31  Aligned_cols=80  Identities=19%  Similarity=0.274  Sum_probs=71.5

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      ...++|||+|||+++++++|+.+|+.| .|..|+|+++.   +               +.++|||||+|.+.++|..||.
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~---~---------------g~~~g~afV~f~~~~~a~~A~~   68 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNA---H---------------GNKTGYIFVDFSNEEEVKQALK   68 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECT---T---------------SCEEEEEEEECSSHHHHHHHHH
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECC---C---------------CCCceEEEEEECCHHHHHHHHH
Confidence            457899999999999999999999999 89999997652   2               2366999999999999999999


Q ss_pred             hcCceeCCeEEEEeecCCC
Q 016231          303 FNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~  321 (393)
                      +|+..|.|+.|.|.++.+.
T Consensus        69 ~~g~~~~gr~i~v~~a~~~   87 (91)
T 2dgw_A           69 CNREYMGGRYIEVFREKSG   87 (91)
T ss_dssp             SCSEEETTEEEEEEEESSC
T ss_pred             hCCceeCCcEEEEEECCcC
Confidence            9999999999999998754

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=2.2e-15  Score=122.85  Aligned_cols=83  Identities=17%  Similarity=0.241  Sum_probs=72.3

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+.+++++|+.+|+.||.|..|+|+.++.  +               +.++|||||+|.+.++|..||
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~---------------g~~~g~afV~f~~~~~a~~A~   74 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLK--T---------------GHSKGFGFVRFTEYETQVKVM   74 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSS--S---------------CSEEEEEEEEESSHHHHHHHH
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCC--C---------------CCccceEEEEECCHHHHHHHH
Confidence            34578999999999999999999999999999999977542  2               236699999999999999999


Q ss_pred             HhcCceeCCeEEEEeecCCCc
Q 016231          302 AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      . ++..|.|+.|.|.++.+..
T Consensus        75 ~-~~~~~~g~~l~v~~a~~~~   94 (103)
T 2cqg_A           75 S-QRHMIDGRWCDCKLPNSKQ   94 (103)
T ss_dssp             H-SCEEETTEEEEEECCCTTC
T ss_pred             H-cCCeeCCeEEEEEecCCCC
Confidence            7 5789999999999997653

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=1.2e-15  Score=124.34  Aligned_cols=82  Identities=18%  Similarity=0.273  Sum_probs=72.9

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+.+|+++|+.+|+.||.|..|+|+.+    ++               .++|||||+|.+.++|..||
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~----~g---------------~~~g~afV~f~~~~~A~~A~   72 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME----GG---------------RSKGFGFVCFSSPEEATKAV   72 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC----SS---------------SEEEEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC----CC---------------CcCEEEEEEECCHHHHHHHH
Confidence            345799999999999999999999999999999999664    22               35699999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCCc
Q 016231          302 -AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~~  322 (393)
                       .||+..|.|+.|.|.++.+..
T Consensus        73 ~~l~g~~~~g~~l~V~~a~~~~   94 (103)
T 2d9p_A           73 TEMNGRIVATKPLYVALAQRKE   94 (103)
T ss_dssp             HHHTTCBSSSSBCEEEECSSCC
T ss_pred             HHhCCCEeCCcEEEEEEecccc
Confidence             599999999999999997654

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=6.7e-16  Score=125.59  Aligned_cols=84  Identities=24%  Similarity=0.428  Sum_probs=73.7

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+++++++|+.+|+.||.|..|+|++++  .+               +.++|||||+|.+.++|..||
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~--~~---------------~~~~g~afV~f~~~~~A~~A~   71 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDR--ET---------------QRSRGFGFVTFENIDDAKDAM   71 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCS--SS---------------CSCCSEEEEECSSHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCC--CC---------------CCcccEEEEEECCHHHHHHHH
Confidence            3457999999999999999999999999999999996654  12               236699999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCCc
Q 016231          302 -AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~~  322 (393)
                       .||+..|.|+.|.|.++.+..
T Consensus        72 ~~l~g~~~~g~~l~v~~a~~~~   93 (102)
T 1x5s_A           72 MAMNGKSVDGRQIRVDQAGKSS   93 (102)
T ss_dssp             HHHTTCCTTSCCCEEEEEECCC
T ss_pred             HHhCCCEECCeEEEEEECCCCC
Confidence             799999999999999997653

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=1.2e-15  Score=125.80  Aligned_cols=81  Identities=23%  Similarity=0.424  Sum_probs=71.6

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+++|+++|+.+|+.||.|..|+|+.+.                    .++|||||+|.+.++|..||
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--------------------~~~g~afV~f~~~~~A~~A~   78 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR--------------------GGPPFAFVEFEDPRDAEDAV   78 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSS--------------------SSSCCEEEEESCHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC--------------------CCCcEEEEEECCHHHHHHHH
Confidence            3457899999999999999999999999999999984321                    25699999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCCc
Q 016231          302 -AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~~  322 (393)
                       .||+..|.|+.|.|.++.+..
T Consensus        79 ~~l~g~~~~g~~l~V~~a~~~~  100 (109)
T 1x4a_A           79 YGRDGYDYDGYRLRVEFPRSGR  100 (109)
T ss_dssp             HHHTTCEETTEECEEECCCCCC
T ss_pred             HHcCCCEECCeEEEEEEcccCC
Confidence             799999999999999997654

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.64  E-value=7e-16  Score=121.65  Aligned_cols=82  Identities=21%  Similarity=0.362  Sum_probs=71.9

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|||+|||+++|+++|+.+|+.||.|.+|.|+.++..  +              +.++|||||+|.+.++|..|+ .
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~--------------~~~~g~afV~f~~~~~a~~A~~~   66 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMH--P--------------HLSKGYAYVEFENPDEAEKALKH   66 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTE--E--------------EEECSEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCC--C--------------CCCCcEEEEEEecHHHHHHHHHH
Confidence            3689999999999999999999999999999999776521  1              125689999999999999999 5


Q ss_pred             hcCceeCCeEEEEeecCCC
Q 016231          303 FNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~  321 (393)
                      |||..|.|+.|.|.++.++
T Consensus        67 l~g~~~~g~~l~v~~a~~~   85 (88)
T 4a8x_A           67 MDGGQIDGQEITATAVLAP   85 (88)
T ss_dssp             HTTCEETTEECEEEEECCC
T ss_pred             cCCCeECCeEEEEEECCCC
Confidence            9999999999999999754

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.64  E-value=1.1e-15  Score=125.29  Aligned_cols=79  Identities=15%  Similarity=0.259  Sum_probs=71.1

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+.+|+++|+.+|+.||.|.+|.|++++   +               +.++|||||+|.+.++|..|| 
T Consensus        27 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~---------------g~~~g~afV~f~~~~~a~~A~~   88 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR---S---------------GRSLGTADVHFERKADALKAMK   88 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT---T---------------SCEEEEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC---C---------------CCcceEEEEEECCHHHHHHHHH
Confidence            447899999999999999999999999999999997754   2               235699999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecC
Q 016231          302 AFNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~  319 (393)
                      .||+..|.|+.|.|.++.
T Consensus        89 ~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           89 QYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             HHTTCEETTEECEEEEEC
T ss_pred             HhCCCEeCCcEEEEEEeC
Confidence            599999999999999874

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=1.4e-15  Score=123.10  Aligned_cols=80  Identities=19%  Similarity=0.256  Sum_probs=70.9

Q ss_pred             CcccEEEEeCCCccCCHHHHH----HHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLI----KEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE  298 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~----~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~  298 (393)
                      ...++|||+|||+++++++|+    .+|+.||.|.+|+|++++.                    .+|||||+|.+.++|.
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~--------------------~rg~afV~f~~~~~A~   66 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTD--------------------YQLKAVVQMENLQDAI   66 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCS--------------------TTCCEEEEESSHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCC--------------------CCeEEEEEECCHHHHH
Confidence            346899999999999999999    9999999999999966541                    1489999999999999


Q ss_pred             HHH-HhcCceeCCeEEEEeecCCCc
Q 016231          299 AAL-AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       299 ~Al-~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      .|| .||+..|.|+.|.|.++.+..
T Consensus        67 ~Ai~~l~g~~~~gr~l~V~~a~~~~   91 (96)
T 2dgx_A           67 GAVNSLHRYKIGSKKILVSLATGAS   91 (96)
T ss_dssp             HHHHHHTTEEETTEEEEEEECCCSS
T ss_pred             HHHHHhCCCEECCeEEEEEEcCCCC
Confidence            999 599999999999999997543

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=4.8e-16  Score=127.88  Aligned_cols=82  Identities=16%  Similarity=0.188  Sum_probs=71.5

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+++|+++|+++|+.||.| .|+|++++   +               ++++|||||+|.+.++|+.||
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~---~---------------g~~~G~afV~F~~~~~a~~Al   72 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP---D---------------GRVTGEADVEFATHEDAVAAM   72 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS---S---------------SCEEEEEEEECSSSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC---C---------------CCEeeEEEEEECCHHHHHHHH
Confidence            3456899999999999999999999999954 89997754   2               236699999999999999999


Q ss_pred             HhcCceeCCeEEEEeecCCCc
Q 016231          302 AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      .+|+..|.||.|.|.++.+..
T Consensus        73 ~~~~~~~~gr~i~V~~~~~~~   93 (102)
T 1wez_A           73 AKDKANMQHRYVELFLNSTAG   93 (102)
T ss_dssp             TTSSCCSSSSCCEEEEECCCC
T ss_pred             HhCCCeECCcEEEEEECCCCC
Confidence            999999999999999987543

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.63  E-value=6.5e-16  Score=130.16  Aligned_cols=80  Identities=14%  Similarity=0.105  Sum_probs=71.8

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCC---eeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGE---IDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~---I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~  299 (393)
                      ...++|||+|||+++|+++|+.+|+.||.   |..|+|+.++.                  ++++|||||+|.+.++|..
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~------------------g~~~G~afV~F~~~~~a~~   76 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE------------------GRQSGEAFVELESEDDVKL   76 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS------------------SCEEEEEEEEBSSHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC------------------CCCCeEEEEEECCHHHHHH
Confidence            44789999999999999999999999999   88999977541                  2367999999999999999


Q ss_pred             HHHhcCceeCCeEEEEeecCC
Q 016231          300 ALAFNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       300 Al~lng~~~~Gr~I~V~~a~~  320 (393)
                      ||.+|+..|.|+.|.|.++..
T Consensus        77 Al~~~g~~~~gr~i~V~~a~~   97 (118)
T 2db1_A           77 ALKKDRESMGHRYIEVFKSHR   97 (118)
T ss_dssp             HGGGTTEEETTEEEEEEEECH
T ss_pred             HHhcCCCeECCeEEEEEECCH
Confidence            999999999999999999854

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.63  E-value=3.1e-16  Score=120.52  Aligned_cols=75  Identities=23%  Similarity=0.385  Sum_probs=67.3

Q ss_pred             EEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhcCc
Q 016231          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMA  306 (393)
Q Consensus       227 tVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~lng~  306 (393)
                      +|||+|||+++++++|+.+|+.||.|..|+|++++.  +               +.++|||||+|.+.++|+.|+.+|+.
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~---------------~~~~g~afV~f~~~~~a~~a~~~~~~   63 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKT--T---------------NRHRGFGFVTFESEDIVEKVCEIHFH   63 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSS--S---------------TTSCBEEEEECSCHHHHHHHHSSSCC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCC--C---------------CCcCcEEEEEECCHHHHHHHHHCCCC
Confidence            499999999999999999999999999999866541  2               34669999999999999999999999


Q ss_pred             eeCCeEEEEeec
Q 016231          307 VIGGNHIRLDRA  318 (393)
Q Consensus       307 ~~~Gr~I~V~~a  318 (393)
                      .|.|+.|.|.+|
T Consensus        64 ~~~g~~l~v~~A   75 (75)
T 2mss_A           64 EINNKMVECKKA   75 (75)
T ss_dssp             CSSSCCCEEECC
T ss_pred             EECCEEEEEEeC
Confidence            999999999875

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.63  E-value=1.3e-15  Score=124.82  Aligned_cols=84  Identities=23%  Similarity=0.398  Sum_probs=73.3

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeee-cccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSV-PIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~-~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      ....++|||+|||+.+|+++|+.+|+.||.|..|+|+++ +  .+               +.++|||||+|.+.++|..|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~---------------~~~~g~afV~f~~~~~a~~A   74 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMT--GT---------------GAHRGFGFVDFITKQDAKKA   74 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCS--SS---------------CSSCSEEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCC--CC---------------CCcCceEEEEECCHHHHHHH
Confidence            445799999999999999999999999999999998654 2  12               34669999999999999999


Q ss_pred             H-Hh-cCceeCCeEEEEeecCCCc
Q 016231          301 L-AF-NMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       301 l-~l-ng~~~~Gr~I~V~~a~~~~  322 (393)
                      | .| |+..|.|+.|.|.++.+..
T Consensus        75 ~~~l~~~~~~~g~~l~v~~a~~~~   98 (107)
T 2cph_A           75 FNALCHSTHLYGRRLVLEWADSEV   98 (107)
T ss_dssp             HHHHHTCCBSSSCBCEEEECCCCC
T ss_pred             HHHhccCCeECCCEEEEEeCCCCC
Confidence            9 68 8999999999999997653

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=9.7e-16  Score=125.92  Aligned_cols=81  Identities=16%  Similarity=0.201  Sum_probs=70.4

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeE-EEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDS-VRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~s-Vri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ...++|||+|||+++|+++|+++|+.||.|.. |+|+.+.   +               +.++|||||+|.+.++|..||
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~---~---------------g~~~G~afV~F~~~~~a~~A~   74 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDF---Q---------------GRSTGEAFVQFASQEIAEKAL   74 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCS---S---------------SCBCSEEEEEESSHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECC---C---------------CCcceEEEEEECCHHHHHHHH
Confidence            45689999999999999999999999999987 7775431   2               346699999999999999999


Q ss_pred             HhcCceeCCeEEEEeecCCC
Q 016231          302 AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~  321 (393)
                      ..|+..|.||.|.|.++.+.
T Consensus        75 ~~~~~~~~gr~i~v~~~~~~   94 (104)
T 1wg5_A           75 KKHKERIGHRYIEIFKSSRA   94 (104)
T ss_dssp             TTTTCCSSSSCCEEEEECTT
T ss_pred             HhCcchhCCcEEEEEECCHH
Confidence            77999999999999998654

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.63  E-value=1.3e-15  Score=126.40  Aligned_cols=84  Identities=21%  Similarity=0.339  Sum_probs=70.8

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+++|+++|+.+|+.||.|.+|+|++++  .+               +.++|||||+|.+.++|..||
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~--~t---------------g~~kg~afV~f~~~~~A~~Ai   84 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDP--LT---------------KRSRGFGFVTFMDQAGVDKVL   84 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCT--TT---------------CCCTTCEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECC--CC---------------CCcCcEEEEEECCHHHHHHHH
Confidence            4457899999999999999999999999999999996654  12               346699999999999999999


Q ss_pred             HhcCceeCCeEEEEeecCCCc
Q 016231          302 AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      ..++..|.|+.|.|.++.+..
T Consensus        85 ~~~~~~l~g~~l~V~~a~~~~  105 (109)
T 2rs2_A           85 AQSRHELDSKTIDPKVAFPRR  105 (109)
T ss_dssp             HSSCEEETTEEEEEEECCCCC
T ss_pred             HHCCCcCCCEEEEEEEccCCC
Confidence            766799999999999997543

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.63  E-value=8.2e-16  Score=128.44  Aligned_cols=80  Identities=20%  Similarity=0.380  Sum_probs=71.1

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+++++++|+.+|+.||.|..|+|++++  .+               +.++|||||+|.+.++|..||
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~--~~---------------g~~~g~afV~f~~~~~A~~A~   99 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDK--QT---------------SLSKCFGFVSFDNPDSAQVAI   99 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCS--SS---------------SCCCCEEEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCC--CC---------------CCcCcEEEEEECCHHHHHHHH
Confidence            4457999999999999999999999999999999996653  12               346699999999999999999


Q ss_pred             -HhcCceeCCeEEEEeec
Q 016231          302 -AFNMAVIGGNHIRLDRA  318 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a  318 (393)
                       .||+..|.|+.|.|.++
T Consensus       100 ~~l~g~~~~g~~l~V~~a  117 (118)
T 2khc_A          100 KAMNGFQVGTKRLKVQLK  117 (118)
T ss_dssp             HHCCCCEETTEECCEEEC
T ss_pred             HHcCCCEECCEEEEEEec
Confidence             69999999999999986

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.63  E-value=1.2e-15  Score=128.49  Aligned_cols=80  Identities=25%  Similarity=0.372  Sum_probs=72.4

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhc
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~ln  304 (393)
                      .++|||+|||+++|+++|+.+|+.||.|..|+|++++.  +               +.++|||||+|.+.++|..||.||
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~---------------~~~~g~afV~f~~~~~a~~A~~l~   98 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKF--S---------------GHPKGYAYIEFAERNSVDAAVAMD   98 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECT--T---------------SSCEEEEEEEESSHHHHHHHHTTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCC--C---------------CCcccEEEEEECCHHHHHHHHhcC
Confidence            58999999999999999999999999999999987642  2               236699999999999999999999


Q ss_pred             CceeCCeEEEEeecCCC
Q 016231          305 MAVIGGNHIRLDRACPP  321 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~~  321 (393)
                      +..|.|+.|.|.++.+.
T Consensus        99 g~~~~g~~l~V~~a~~~  115 (124)
T 2jwn_A           99 ETVFRGRTIKVLPKRTN  115 (124)
T ss_dssp             TCEETTEECEEEESSCC
T ss_pred             CCeECCeEEEEEECCCC
Confidence            99999999999998754

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=8e-16  Score=128.12  Aligned_cols=78  Identities=19%  Similarity=0.366  Sum_probs=68.7

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      +...++|||+|||+++|+++|+.+|+.||.|.+|+|+++                       +|||||+|.+.++|..|+
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-----------------------kGfaFVeF~~~~~A~~Ai   69 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----------------------KNQAFIEMNTEEAANTMV   69 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-----------------------TTEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-----------------------CCEEEEEECCHHHHHHHH
Confidence            345799999999999999999999999999999998542                       389999999999999999


Q ss_pred             H-hc--CceeCCeEEEEeecCCCc
Q 016231          302 A-FN--MAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 ~-ln--g~~~~Gr~I~V~~a~~~~  322 (393)
                      . ++  +..|.|+.|.|.++.+..
T Consensus        70 ~~l~~~~~~l~Gr~l~V~~A~~~~   93 (105)
T 1sjq_A           70 NYYTSVTPVLRGQPIYIQFSNHKE   93 (105)
T ss_dssp             HHHTTSCCEETTEECCBCCCSSSS
T ss_pred             HHhccCCceECCEEEEEEEcCCCC
Confidence            4 65  478999999999997643

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.62  E-value=8.4e-16  Score=127.73  Aligned_cols=85  Identities=20%  Similarity=0.305  Sum_probs=73.1

Q ss_pred             cccEEEEeCCCccCCHHHHH---HHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          224 LLRTIFVGNLPLKVKKKTLI---KEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~---~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      ..++|||+|||+.+++++|+   .+|+.||.|..|+|+++..  ++..            +.++|||||+|.+.++|+.|
T Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~--~~~~------------~~~~G~afV~f~~~~~A~~A   79 (111)
T 2cpi_A           14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTS--YAGS------------QGPSASAYVTYIRSEDALRA   79 (111)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSS--CCSS------------SCCCEEEEEEESSHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCC--cCcc------------CCCCeEEEEEECcHHHHHHH
Confidence            46899999999999999999   9999999999999966542  2211            23679999999999999999


Q ss_pred             H-HhcCceeCCeEEEEeecCCCc
Q 016231          301 L-AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       301 l-~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      | .||+..|.|+.|.|.++.+..
T Consensus        80 i~~lng~~~~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           80 IQCVNNVVVDGRTLKASLGTTKY  102 (111)
T ss_dssp             HHHHTTEEETTEEEEEESCCCCS
T ss_pred             HHHhCCCEECCEEEEEEeccccc
Confidence            9 589999999999999997653

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.62  E-value=9.4e-16  Score=123.80  Aligned_cols=82  Identities=21%  Similarity=0.271  Sum_probs=71.6

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+++++++|+.+|..||.|..+.++.++  .+               +.++|||||+|.+.++|+.|| 
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~--~~---------------g~~~g~afV~f~~~~~a~~Ai~   75 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN--EK---------------GMPTGEAMVAFESRDEATAAVI   75 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC--SS---------------SCEEEEEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEEC--CC---------------CCeeeEEEEEECCHHHHHHHHH
Confidence            346899999999999999999999999999877776654  22               236699999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCC
Q 016231          302 AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~  321 (393)
                      .||+..|.|+.|.|.++..+
T Consensus        76 ~l~g~~~~g~~l~V~~a~~~   95 (98)
T 2cqp_A           76 DLNDRPIGSRKVKLVLGSGP   95 (98)
T ss_dssp             HTTTCEETTEECEEEESSCS
T ss_pred             HhCCCeeCCeEEEEEEcCCC
Confidence            79999999999999998654

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.62  E-value=1.2e-15  Score=124.89  Aligned_cols=85  Identities=19%  Similarity=0.269  Sum_probs=73.7

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+++|+++|+.+|+.||.|..|+|+.++.  +               +.++|||||+|.+.++|..||
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~---------------g~~~g~afV~f~~~~~A~~A~   72 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRF--T---------------GMHKGCAFLTYCERESALKAQ   72 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSS--S---------------CSCCSEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC--C---------------CCcceEEEEEECCHHHHHHHH
Confidence            44579999999999999999999999999999999966542  2               236699999999999999999


Q ss_pred             -HhcCcee---CCeEEEEeecCCCcc
Q 016231          302 -AFNMAVI---GGNHIRLDRACPPRK  323 (393)
Q Consensus       302 -~lng~~~---~Gr~I~V~~a~~~~~  323 (393)
                       .||+..+   .|+.|.|.++.+...
T Consensus        73 ~~l~g~~~~~~~g~~l~v~~a~~~~~   98 (106)
T 2dgp_A           73 SALHEQKTLPGMNRPIQVKPADSESR   98 (106)
T ss_dssp             HHHTTTCCCTTCSSCCEEEECCCCSC
T ss_pred             HHhcCCcccCCCCceEEEEECCcccc
Confidence             6999987   899999999976543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=2.4e-15  Score=125.35  Aligned_cols=83  Identities=23%  Similarity=0.344  Sum_probs=72.1

Q ss_pred             CCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       221 ~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      .+...++|||+|||+.+|+++|+.+|+.||.|..|+|++++.  +               +.++|||||+|.+.++|+.|
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~---------------~~~~g~afV~f~~~~~a~~A   75 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQ--T---------------GKSRGYGFVTMADRAAAERA   75 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSS--S---------------CCCCSEEEEEESSHHHHHHH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCC--C---------------CccceEEEEEECCHHHHHHH
Confidence            345679999999999999999999999999999999966541  2               23669999999999999999


Q ss_pred             H-HhcCceeCCeEEEEeecCCC
Q 016231          301 L-AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       301 l-~lng~~~~Gr~I~V~~a~~~  321 (393)
                      | .+|+ .|.|+.|.|.++.+.
T Consensus        76 i~~~~~-~~~g~~l~V~~a~~~   96 (116)
T 2cqd_A           76 CKDPNP-IIDGRKANVNLAYLG   96 (116)
T ss_dssp             HTCSSC-EETTEECEEEESTTT
T ss_pred             HHhCCC-cCCCEEEEEEEcccC
Confidence            9 5777 899999999999754

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.62  E-value=1.4e-15  Score=126.06  Aligned_cols=83  Identities=19%  Similarity=0.327  Sum_probs=73.6

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+.+++++|+.+|+.||.|..|+|++++.  +               +.++|||||+|.+.++|..|+
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~--~---------------g~~~g~afV~F~~~~~A~~Ai   85 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSE--T---------------GRSKGYGFITFSDSECAKKAL   85 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETT--T---------------TEEEEEEEEEESCHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCC--C---------------CccceEEEEEECCHHHHHHHH
Confidence            44579999999999999999999999999999999987652  2               236699999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCC
Q 016231          302 -AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~  321 (393)
                       .|||..|.|+.|.|.++.+.
T Consensus        86 ~~l~g~~i~g~~l~V~~a~~k  106 (108)
T 2jrs_A           86 EQLNGFELAGRPMKVGHVTER  106 (108)
T ss_dssp             HHHTTCCSSSSCCEEECSCSS
T ss_pred             HHcCCCEECCEEEEEEEcccC
Confidence             69999999999999998653

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.62  E-value=1.3e-15  Score=134.84  Aligned_cols=80  Identities=18%  Similarity=0.258  Sum_probs=70.9

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccC--CeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFG--EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G--~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ..++|||+|||+++|+++|+.+|+.||  .|.+|+|++++.  +               +.++|||||+|.+.++|..||
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~--t---------------g~skGfaFV~f~~~~~A~~Ai  116 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRA--N---------------GQSKGYAEVVVASENSVHKLL  116 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTT--T---------------CCEEEEEEEEESCHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCC--C---------------CccceEEEEEECCHHHHHHHH
Confidence            468999999999999999999999999  999999987652  2               346699999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCC
Q 016231          302 -AFNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~  320 (393)
                       .|||..|.|+.|.|.++.+
T Consensus       117 ~~lng~~~~Gr~l~V~~a~~  136 (156)
T 3n9u_C          117 ELLPGKVLNGEKVDVRPATR  136 (156)
T ss_dssp             HHSTTCEETTEECEEEECCH
T ss_pred             HHcCCCEECCeEeEEEEcCC
Confidence             6899999999999999864

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.62  E-value=6.9e-16  Score=123.72  Aligned_cols=79  Identities=20%  Similarity=0.280  Sum_probs=69.6

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|||+|||+++|+++|+.+|..||.|..+.++.++  .+               +.++|||||+|.+.++|..|| .
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~--~~---------------g~~~g~afV~f~~~~~a~~Ai~~   76 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN--EK---------------GMPTGEAMVAFESRDEATAAVID   76 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEEC--TT---------------SCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeC--CC---------------CCEeeEEEEEECCHHHHHHHHHH
Confidence            35899999999999999999999999999888886654  22               236699999999999999999 5


Q ss_pred             hcCceeCCeEEEEeecC
Q 016231          303 FNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~  319 (393)
                      ||+..|.|+.|.|.++.
T Consensus        77 l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           77 LNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             HTTCEETTEECEEECCC
T ss_pred             hCCCeECCcEEEEEecc
Confidence            99999999999999875

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.62  E-value=2.2e-15  Score=129.39  Aligned_cols=86  Identities=24%  Similarity=0.358  Sum_probs=75.3

Q ss_pred             cCCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHH
Q 016231          220 DEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (393)
Q Consensus       220 ~~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~  299 (393)
                      ......++|||+|||+++++++|+.+|+.||.|.+|+|++++.  +               +.++|||||+|.+.++|..
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~--~---------------~~~~g~afV~f~~~~~a~~   99 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRE--T---------------RQSRGYGFVKFQSGSSAQQ   99 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETT--T---------------TEEEEEEEEEESSHHHHHH
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCC--C---------------CCcceEEEEEECCHHHHHH
Confidence            3445579999999999999999999999999999999987652  2               2356999999999999999


Q ss_pred             HH-HhcCceeCCeEEEEeecCCCc
Q 016231          300 AL-AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       300 Al-~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      || .||+..|.|+.|.|.++.+..
T Consensus       100 A~~~l~g~~~~g~~l~v~~a~~~~  123 (139)
T 1u6f_A          100 AIAGLNGFNILNKRLKVALAASGH  123 (139)
T ss_dssp             HHHHTTTEECSSCEEEEEESSCCC
T ss_pred             HHHHhCCCEECCeEEEEEECCCCC
Confidence            99 599999999999999997653

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=2e-15  Score=125.13  Aligned_cols=85  Identities=19%  Similarity=0.212  Sum_probs=73.2

Q ss_pred             CCCcccEEEEeCCCccCCHHHHHHHhcccCCee--------EEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeC
Q 016231          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEID--------SVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFK  292 (393)
Q Consensus       221 ~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~--------sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~  292 (393)
                      +....++|||+|||+.+|+++|+.+|+.||.|.        .|+|+.++  .+               +.++|||||+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~--~~---------------g~~~g~afV~f~   73 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDK--ET---------------GKPKGDATVSYE   73 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCT--TT---------------CSBCSEEEEEBS
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeC--CC---------------CCeeeEEEEEEC
Confidence            344579999999999999999999999999998        58886543  12               336699999999


Q ss_pred             CHHHHHHHH-HhcCceeCCeEEEEeecCCCc
Q 016231          293 SEQSTEAAL-AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       293 s~e~A~~Al-~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      +.++|..|| .||+..|.|+.|.|.++.+..
T Consensus        74 ~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  104 (113)
T 2cpe_A           74 DPPTAKAAVEWFDGKDFQGSKLKVSLARKKP  104 (113)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEECSSCCC
T ss_pred             CHHHHHHHHHHcCCCccCCCEEEEEECCCCC
Confidence            999999999 599999999999999997653

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.62  E-value=1.5e-15  Score=123.11  Aligned_cols=81  Identities=25%  Similarity=0.286  Sum_probs=71.6

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeE--------EEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCC
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDS--------VRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKS  293 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~s--------Vri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s  293 (393)
                      ....++|||+|||+++++++|+.+|+.||.|..        |+|++++  .+               +.++|||||+|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~--~~---------------g~~~G~afV~f~~   72 (99)
T 2la6_A           10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDR--ET---------------GKLKGEATVSFDD   72 (99)
T ss_dssp             CCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECT--TT---------------CSEEEEEEEEBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecC--CC---------------CCeeeEEEEEECC
Confidence            445799999999999999999999999999999        9987754  22               2366999999999


Q ss_pred             HHHHHHHH-HhcCceeCCeEEEEeecC
Q 016231          294 EQSTEAAL-AFNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       294 ~e~A~~Al-~lng~~~~Gr~I~V~~a~  319 (393)
                      .++|..|+ .|||..|.|+.|.|.+|.
T Consensus        73 ~~~a~~Ai~~l~g~~~~g~~l~V~~A~   99 (99)
T 2la6_A           73 PPSAKAAIDWFDGKEFSGNPIKVSFAT   99 (99)
T ss_dssp             HHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHhCCCEeCCcEEEEEecC
Confidence            99999999 699999999999999873

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=1.4e-15  Score=126.79  Aligned_cols=82  Identities=20%  Similarity=0.397  Sum_probs=72.7

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHh
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~l  303 (393)
                      ..++|||+|||+++|+++|+.+|..||.|..|+|++++  .+               +.++|||||+|.+.++|..||..
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~---------------g~~~g~afV~f~~~~~a~~Ai~~   88 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDP--AS---------------KRSRGFGFVTFSSMAEVDAAMAA   88 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCT--TT---------------SSCCSEEEEECSSHHHHHHHHTS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC--CC---------------CCcCceEEEEeCCHHHHHHHHHh
Confidence            36899999999999999999999999999999997654  22               23669999999999999999977


Q ss_pred             cCceeCCeEEEEeecCCCc
Q 016231          304 NMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~  322 (393)
                      |+..|.|+.|.|.++.+..
T Consensus        89 ~~~~~~g~~l~V~~a~~~~  107 (116)
T 1x4b_A           89 RPHSIDGRVVEPKRAVARE  107 (116)
T ss_dssp             CSEEETTEEEEEECCSSCC
T ss_pred             CCcEECCEEEEEEECCCCc
Confidence            9999999999999997654

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.62  E-value=1.1e-15  Score=126.41  Aligned_cols=75  Identities=19%  Similarity=0.256  Sum_probs=67.0

Q ss_pred             cccEEEEeCCCc-cCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          224 LLRTIFVGNLPL-KVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       224 ~~rtVFVgNLp~-~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ++++|||+|||+ .+|+++|+.+|+.||.|.+|+|++                       .+|||||+|.+.++|..|+ 
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~-----------------------~kg~aFVef~~~~~A~~Ai~   70 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN-----------------------KINEAFIEMATTEDAQAAVD   70 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECS-----------------------SSSCEEEEESSHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEc-----------------------CCCEEEEEECCHHHHHHHHH
Confidence            578999999999 999999999999999999999843                       2379999999999999999 


Q ss_pred             HhcC--ceeCCeEEEEeecCCC
Q 016231          302 AFNM--AVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 ~lng--~~~~Gr~I~V~~a~~~  321 (393)
                      .||+  ..|.|++|.|.++...
T Consensus        71 ~l~~~~~~~~Gr~l~V~~a~~~   92 (102)
T 1x4d_A           71 YYTTTPALVFGKPVRVHLSQKY   92 (102)
T ss_dssp             HHHHSCCEETTEECEEEEECCC
T ss_pred             HHcCCCceECCcEEEEEECCCC
Confidence            5775  4699999999999754

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=8.5e-16  Score=127.73  Aligned_cols=82  Identities=23%  Similarity=0.261  Sum_probs=72.5

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      ...++|||+|||+++++++|+.+|+.||.|..|+|++++.  +               +.++|||||+|.+.++|..||.
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~---------------g~~~g~afV~f~~~~~a~~A~~   85 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRN--S---------------RRSKGIAYVEFCEIQSVPLAIG   85 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCC--S---------------SSCCCCEEEEESCGGGHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCC--C---------------CccCcEEEEEeCcHHHHHHHHH
Confidence            3468999999999999999999999999999999966541  2               2366999999999999999999


Q ss_pred             hcCceeCCeEEEEeecCCC
Q 016231          303 FNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~  321 (393)
                      ||+..|.|+.|.|.++.+.
T Consensus        86 l~g~~~~g~~l~V~~a~~~  104 (114)
T 2cq4_A           86 LTGQRLLGVPIIVQASQAE  104 (114)
T ss_dssp             HTTEEETTEEEEEEEHHHH
T ss_pred             cCCCEeCCeEEEEEecCCC
Confidence            9999999999999998643

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=3.2e-15  Score=119.08  Aligned_cols=76  Identities=20%  Similarity=0.294  Sum_probs=69.3

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+++|+++|+.+|+.||.|..|+|+                         +|||||+|.+.++|..|+
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~-------------------------~~~afV~f~~~~~a~~A~   60 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-------------------------KDYAFVHMEKEADAKAAI   60 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC-------------------------SSCEEEEESCHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE-------------------------CCEEEEEECCHHHHHHHH
Confidence            4457899999999999999999999999999999983                         269999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCCc
Q 016231          302 -AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~~  322 (393)
                       .||+..|.|+.|.|.++.+..
T Consensus        61 ~~l~g~~~~g~~l~v~~a~~~~   82 (90)
T 2dnp_A           61 AQLNGKEVKGKRINVELSTKGQ   82 (90)
T ss_dssp             HHHTTCEETTEECEEEESCCCC
T ss_pred             HHhCCCEECCcEEEEEECCCCC
Confidence             599999999999999997653

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=6.2e-15  Score=119.48  Aligned_cols=76  Identities=25%  Similarity=0.393  Sum_probs=68.9

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhccc--CCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKF--GEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~--G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~  299 (393)
                      ....++|||+|||+.+|+++|+.+|+.|  |.|..|.+                         .+|||||+|.+.++|..
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~-------------------------~~g~afV~f~~~~~A~~   66 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-------------------------IRDYAFVHFSNREDAVE   66 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE-------------------------CSSEEEEEESSHHHHHH
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEE-------------------------eCCeEEEEeCCHHHHHH
Confidence            3457999999999999999999999999  89988876                         23799999999999999


Q ss_pred             HH-HhcCceeCCeEEEEeecCCCc
Q 016231          300 AL-AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       300 Al-~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      || .||+..|.|+.|.|.++.+..
T Consensus        67 A~~~l~g~~~~g~~l~v~~a~~~~   90 (99)
T 2cpd_A           67 AMKALNGKVLDGSPIEVTLAKPVD   90 (99)
T ss_dssp             HHHHHSSEEETTEEEEEECCCCCC
T ss_pred             HHHHhCCCEeCCcEEEEEECCCCC
Confidence            99 599999999999999997654

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.61  E-value=2.1e-15  Score=124.51  Aligned_cols=76  Identities=16%  Similarity=0.173  Sum_probs=68.0

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      .++++|||+|||+.+|+++|+.+|++||.|.+|+|++                       ++|||||+|.+.++|..|+ 
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~-----------------------~kg~AFVef~~~~~A~~Av~   75 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP-----------------------KKRQALVEFEDVLGACNAVN   75 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET-----------------------TTTEEEEEESSHHHHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc-----------------------CCCEEEEEECCHHHHHHHHH
Confidence            4689999999999999999999999999999999843                       3489999999999999999 


Q ss_pred             HhcCce--eCCeEEEEeecCCC
Q 016231          302 AFNMAV--IGGNHIRLDRACPP  321 (393)
Q Consensus       302 ~lng~~--~~Gr~I~V~~a~~~  321 (393)
                      .||+..  |.|+.|.|.++.+.
T Consensus        76 ~ln~~~~~i~Gr~i~V~~S~~k   97 (100)
T 3r27_A           76 YAADNQIYIAGHPAFVNYSTSQ   97 (100)
T ss_dssp             HHHHSCEEETTEEEEEEECSCS
T ss_pred             HhcCCCceeCCcEEEEEecccc
Confidence            688764  78999999999753

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=4.4e-15  Score=118.74  Aligned_cols=76  Identities=16%  Similarity=0.306  Sum_probs=69.5

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+.+++++|+.+|+.||.|..|+|+                         +|||||+|.+.++|..|+
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~-------------------------~~~afV~f~~~~~a~~A~   61 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-------------------------KDYAFVHMERAEDAVEAI   61 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC-------------------------SSEEEEEESCHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE-------------------------CCEEEEEECCHHHHHHHH
Confidence            4557999999999999999999999999999999983                         269999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCCc
Q 016231          302 -AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~~  322 (393)
                       .||+..|.|+.|.|.++.+..
T Consensus        62 ~~l~g~~~~g~~l~V~~a~~~~   83 (92)
T 2dgt_A           62 RGLDNTEFQGKRMHVQLSTSRL   83 (92)
T ss_dssp             HHHTTEEETTEEEEEEESSCCC
T ss_pred             HHhCCCeeCCcEEEEEEccCCC
Confidence             699999999999999997654

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.61  E-value=3.2e-16  Score=120.33  Aligned_cols=75  Identities=23%  Similarity=0.364  Sum_probs=66.7

Q ss_pred             EEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhcCc
Q 016231          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMA  306 (393)
Q Consensus       227 tVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~lng~  306 (393)
                      +|||+|||+++++++|+.+|+.||.|.+|.|++++.                 ++.++|||||+|.+.++|..|+.+++.
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----------------~~~~~g~afV~f~~~~~a~~Ai~~~~~   63 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNK-----------------TNKRRGFCFITFKEEEPVKKIMEKKYH   63 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCC-----------------CSSSCCCEEEECSSSHHHHHHHTTSSC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC-----------------CCCcCCEEEEEECCHHHHHHHHHhCCC
Confidence            599999999999999999999999999999865431                 234669999999999999999988999


Q ss_pred             eeCCeEEEEeec
Q 016231          307 VIGGNHIRLDRA  318 (393)
Q Consensus       307 ~~~Gr~I~V~~a  318 (393)
                      .+.|+.|.|.++
T Consensus        64 ~~~g~~l~v~~a   75 (75)
T 1iqt_A           64 NVGLSKCEIKVA   75 (75)
T ss_dssp             CBTTBCCCEEEC
T ss_pred             eECCEEEEEEEC
Confidence            999999999875

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.61  E-value=1.5e-15  Score=122.53  Aligned_cols=73  Identities=16%  Similarity=0.166  Sum_probs=67.1

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      .+..||||||++.+|+++|+++|.+||+|.++++..                       ++|||||+|.+.++|..|+ .
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~-----------------------~kGfaFVey~~~~eA~~Ai~~   62 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL-----------------------NQGIALCKYTTREEANKAQMA   62 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET-----------------------TTTEEEEEESSHHHHHHHHHH
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC-----------------------CCcEEEEEECCHHHHHHHHHH
Confidence            367899999999999999999999999999999832                       4599999999999999999 7


Q ss_pred             hcCceeCCeEEEEeecC
Q 016231          303 FNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~  319 (393)
                      ||+..+.|+.|+|..+.
T Consensus        63 Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A           63 LNNCVLANTTIFAESPS   79 (89)
T ss_dssp             HTTEEETTEEEEEECCC
T ss_pred             hcCCEECCcEEEEEECC
Confidence            99999999999999873

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.61  E-value=1.2e-15  Score=132.48  Aligned_cols=81  Identities=15%  Similarity=0.103  Sum_probs=72.2

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCC---eeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGE---IDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE  298 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~---I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~  298 (393)
                      ....++|||+|||+++|+++|+++|+.||.   |..|+|++++.                  ++++|||||+|.+.++|+
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~------------------g~srG~aFV~F~~~e~a~  102 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE------------------GRQSGEAFVELGSEDDVK  102 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS------------------SCEEEEEEEECSSHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC------------------CCCCeEEEEEECCHHHHH
Confidence            345789999999999999999999999999   88999977641                  236799999999999999


Q ss_pred             HHHHhcCceeCCeEEEEeecCC
Q 016231          299 AALAFNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       299 ~Al~lng~~~~Gr~I~V~~a~~  320 (393)
                      .||.+|+..|.||.|.|.++.+
T Consensus       103 ~Al~~~g~~l~gr~i~V~~a~~  124 (136)
T 2hgl_A          103 MALKKDRESMGHRYIEVFKSHR  124 (136)
T ss_dssp             HHHTTTEEESSSSEEEEEECCH
T ss_pred             HHHhcCCCEECCEEEEEEECCh
Confidence            9999999999999999999853

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=1.8e-15  Score=122.43  Aligned_cols=77  Identities=18%  Similarity=0.381  Sum_probs=68.5

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+++|+++|+.+|+.||.|. +++++.                     .++|||||+|.+.++|..|+ 
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~---------------------~~~g~afV~f~~~~~a~~A~~   74 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ---------------------GPRRRAFLHYPDSAAAQQAVS   74 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE---------------------TTTTEEEEECSSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC---------------------CCCcEEEEEECCHHHHHHHHH
Confidence            4478999999999999999999999999996 666442                     15689999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCC
Q 016231          302 AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~  321 (393)
                      .||+..|.|+.|.|.++.++
T Consensus        75 ~l~g~~~~g~~l~V~~a~~~   94 (97)
T 2e5j_A           75 CLQGLRLGTDTLRVALARQQ   94 (97)
T ss_dssp             HHTTCCSSSSCCEEEECCCC
T ss_pred             HhCCCEECCcEEEEEEcCCC
Confidence            79999999999999999754

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.61  E-value=5.6e-16  Score=119.38  Aligned_cols=75  Identities=20%  Similarity=0.336  Sum_probs=66.4

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH-hc
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA-FN  304 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~-ln  304 (393)
                      ++|||+|||+++++++|+.+|+.||.|..|+|++++  .+               +.++|||||+|.+.++|..|+. ++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~--~~---------------~~~~g~afV~f~~~~~a~~a~~~~~   63 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDP--LT---------------KRSRGFGFVTFMDQAGVDKVLAQSR   63 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCC--CS---------------SSCSSEEEECCCCTTHHHHHHHTTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCC--CC---------------CCcCceEEEEEcCHHHHHHHHHhCC
Confidence            479999999999999999999999999999997654  12               2366999999999999999995 66


Q ss_pred             CceeCCeEEEEeec
Q 016231          305 MAVIGGNHIRLDRA  318 (393)
Q Consensus       305 g~~~~Gr~I~V~~a  318 (393)
                       ..+.|+.|.|.++
T Consensus        64 -~~~~g~~l~v~~a   76 (77)
T 1uaw_A           64 -HELDSKTIDPKVA   76 (77)
T ss_dssp             -CCCSSCCCEEEEC
T ss_pred             -CccCCEEEEEEec
Confidence             9999999999886

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.61  E-value=3.9e-15  Score=120.99  Aligned_cols=75  Identities=27%  Similarity=0.488  Sum_probs=68.5

Q ss_pred             CCcccEEEEeCCCc-cCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          222 GKLLRTIFVGNLPL-KVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       222 ~~~~rtVFVgNLp~-~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      ....++|||+|||+ ++++++|+.+|+.||.|..|+|                         ++|||||+|.+.++|..|
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i-------------------------~~g~afV~f~~~~~A~~A   73 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------------------------KNAFGFIQFDNPQSVRDA   73 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEE-------------------------CSSEEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE-------------------------eCCEEEEEECCHHHHHHH
Confidence            34579999999999 9999999999999999999988                         238999999999999999


Q ss_pred             H-HhcCceeCCeEEEEeecCCC
Q 016231          301 L-AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       301 l-~lng~~~~Gr~I~V~~a~~~  321 (393)
                      + .||+..|.|+.|.|.++.+.
T Consensus        74 i~~l~g~~~~g~~l~V~~a~~~   95 (97)
T 2xnq_A           74 IEXESQEMNFGKKLILEVSSSN   95 (97)
T ss_dssp             HHHHTTSEETTEECEEEECCCC
T ss_pred             HHHcCCCEECCEEEEEEecCCC
Confidence            9 59999999999999998643

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=2.2e-15  Score=125.96  Aligned_cols=77  Identities=17%  Similarity=0.166  Sum_probs=69.0

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhc
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~ln  304 (393)
                      .++|||+|||+++|+++|+++|+.| .|.+|+|+.++   .               ++++|||||+|.+.++|+.||.+|
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~---~---------------g~~~G~afV~F~~~~~a~~Al~~~   76 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH---V---------------GRNNGNGLVKFLSPQDTFEALKRN   76 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT---T---------------CCCCSEEEEECSSHHHHHHHHHTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC---C---------------CCCCeEEEEEECCHHHHHHHHhcC
Confidence            5789999999999999999999999 78999996653   1               236699999999999999999999


Q ss_pred             CceeCCeEEEEeecCC
Q 016231          305 MAVIGGNHIRLDRACP  320 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~  320 (393)
                      +..|.||.|.|..+.+
T Consensus        77 ~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           77 RMLMIQRYVEVSPATE   92 (109)
T ss_dssp             TEEETTEEEEEEECCH
T ss_pred             CCeECCeEEEEEECCc
Confidence            9999999999988854

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=3.3e-15  Score=119.04  Aligned_cols=77  Identities=17%  Similarity=0.347  Sum_probs=69.9

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+++++++|+.+|+.||.|..|+|+                         +|||||+|.+.++|..|+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-------------------------~g~afV~f~~~~~A~~A~   59 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------------------------KNYGFVHIEDKTAAEDAI   59 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-------------------------TTEEEEEESSHHHHHHHH
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-------------------------CCEEEEEECCHHHHHHHH
Confidence            3457999999999999999999999999999999983                         279999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCCcc
Q 016231          302 -AFNMAVIGGNHIRLDRACPPRK  323 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~~~  323 (393)
                       .||+..|.|+.|.|.++.+...
T Consensus        60 ~~l~g~~~~g~~l~v~~a~~~~~   82 (90)
T 2dnq_A           60 RNLHHYKLHGVNINVEASKNKSK   82 (90)
T ss_dssp             HHHTTCBCSSCBCEEECSSCCCC
T ss_pred             HHhcCCccCCcEEEEEECCCCCC
Confidence             7999999999999999976543

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.60  E-value=6.4e-16  Score=126.01  Aligned_cols=82  Identities=28%  Similarity=0.396  Sum_probs=70.1

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      ...++|||+|||+++++++|+.+|+.|| |.+|+|++++. .               ++.++|||||+|.+.++|..||.
T Consensus        17 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~-~---------------~g~~~g~afV~f~~~~~a~~Ai~   79 (100)
T 2j76_E           17 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPS-N---------------PERLKGFGYAEFEDLDSLLSALS   79 (100)
T ss_dssp             ---CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTT-T---------------TCCCCSCEEEEECCHHHHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCC-c---------------CCccCeEEEEEECCHHHHHHHHh
Confidence            3479999999999999999999999999 99999865431 1               23467999999999999999999


Q ss_pred             hcCceeCCeEEEEeecCCC
Q 016231          303 FNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~  321 (393)
                      ||+..|.|+.|.|.++.+.
T Consensus        80 l~g~~~~g~~l~V~~a~~~   98 (100)
T 2j76_E           80 LNEESLGNRRIRVDVADQA   98 (100)
T ss_dssp             TTTCCBTTBCCCCEECCCS
T ss_pred             cCCCEECCeEEEEEeccCC
Confidence            9999999999999998653

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=2.7e-15  Score=117.80  Aligned_cols=74  Identities=26%  Similarity=0.484  Sum_probs=67.5

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      +...++|||+|||+.+++++|+.+|+.||.|..|++++                       ++|||||+|.+.++|..|+
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~-----------------------~kg~afV~f~~~~~A~~a~   65 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ-----------------------RQQCAFIQFATRQAAEVAA   65 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG-----------------------GGTEEEEEESSHHHHHHHH
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC-----------------------CCCEEEEEECCHHHHHHHH
Confidence            34578999999999999999999999999999999853                       2489999999999999999


Q ss_pred             H-h-cCceeCCeEEEEeec
Q 016231          302 A-F-NMAVIGGNHIRLDRA  318 (393)
Q Consensus       302 ~-l-ng~~~~Gr~I~V~~a  318 (393)
                      . | |+..|.|+.|.|.++
T Consensus        66 ~~l~~~~~~~g~~l~v~~a   84 (85)
T 2ytc_A           66 EKSFNKLIVNGRRLNVKWG   84 (85)
T ss_dssp             HTTTTTCEETTEECCEEEC
T ss_pred             HHhcCCeeECCCEEEEEec
Confidence            5 8 999999999999987

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=4.3e-15  Score=122.54  Aligned_cols=77  Identities=13%  Similarity=0.250  Sum_probs=67.9

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      .++++|||+|||+.+|+++|+.+|+.||.|..|+|++                       .+|||||+|.+.++|..|+ 
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~-----------------------~kg~aFVef~~~~~A~~Ai~   69 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK-----------------------GKNQAFLELATEEAAITMVN   69 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEET-----------------------TTTEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC-----------------------CCCEEEEEECCHHHHHHHHH
Confidence            4578999999999999999999999999999998843                       2389999999999999999 


Q ss_pred             Hh--cCceeCCeEEEEeecCCCc
Q 016231          302 AF--NMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 ~l--ng~~~~Gr~I~V~~a~~~~  322 (393)
                      .|  ++..|.|+.|.|.++.+..
T Consensus        70 ~l~~~~~~~~Gr~l~V~~a~~~~   92 (101)
T 2cq1_A           70 YYSAVTPHLRNQPIYIQYSNHKE   92 (101)
T ss_dssp             HHHHSCCEETTEECEEEECSCSS
T ss_pred             HhccCCceECCcEEEEEEcCccc
Confidence            45  5678999999999997643

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.60  E-value=3.4e-15  Score=123.69  Aligned_cols=78  Identities=19%  Similarity=0.206  Sum_probs=68.0

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ..++++|||+|||+.+++++|+.+|+.||.|..|+|++                       .+|||||+|.+.++|..|+
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~-----------------------~kg~aFVef~~~~~A~~Ai   68 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-----------------------FKRQALVEFENIDSAKECV   68 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET-----------------------TTTEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEC-----------------------CCCEEEEEECCHHHHHHHH
Confidence            34579999999999999999999999999999998843                       2389999999999999999


Q ss_pred             -HhcCc--eeCCeEEEEeecCCCc
Q 016231          302 -AFNMA--VIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 -~lng~--~~~Gr~I~V~~a~~~~  322 (393)
                       .|++.  .|.|+.|.|.++.+..
T Consensus        69 ~~l~~~~~~i~Gr~l~V~~a~~~~   92 (104)
T 1wex_A           69 TFAADVPVYIAGQQAFFNYSTSKR   92 (104)
T ss_dssp             HHHHHSCCBSSSSBCEEEECSSSS
T ss_pred             HHhccCCceECCEEEEEEEccCcc
Confidence             57654  5999999999997654

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=7.8e-16  Score=121.09  Aligned_cols=79  Identities=15%  Similarity=0.183  Sum_probs=69.8

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|||+|||+++++++|+.+|+.||.|..|+|+.++.  +               +.++|||||+|.+.++|..|+ .
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~--~---------------~~~~g~afV~f~~~~~a~~A~~~   66 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKT--T---------------NKCKGYGFVDFDSPSAAQKAVTA   66 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSS--S---------------CSCCSEEEEEESCHHHHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--C---------------CCcCcEEEEEECCHHHHHHHHHH
Confidence            478999999999999999999999999999999976542  2               236699999999999999999 5


Q ss_pred             hcCceeCCeEEEEeecC
Q 016231          303 FNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~  319 (393)
                      ||+..|.|+.|+|.++.
T Consensus        67 l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A           67 LKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             HHHHTCCEESCCSSCCC
T ss_pred             hcCCeEeeEEEeecCCC
Confidence            99999999999887754

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=3.5e-15  Score=126.90  Aligned_cols=78  Identities=19%  Similarity=0.358  Sum_probs=68.7

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ..++++|||+|||+++|+++|+.+|+.||.|.+|+|+++                       +|||||+|.+.++|..|+
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-----------------------kG~AFVeF~~~e~A~~Ai   84 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----------------------KNQAFIEMNTEEAANTMV   84 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-----------------------GTEEEEECSCHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----------------------CCEEEEEECCHHHHHHHH
Confidence            345789999999999999999999999999999998542                       389999999999999999


Q ss_pred             -Hhc--CceeCCeEEEEeecCCCc
Q 016231          302 -AFN--MAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 -~ln--g~~~~Gr~I~V~~a~~~~  322 (393)
                       .++  +..|.|+.|.|.++.+..
T Consensus        85 ~~l~~~~~~l~Gr~l~V~~a~~k~  108 (119)
T 2ad9_A           85 NYYTSVTPVLRGQPIYIQFSNHKE  108 (119)
T ss_dssp             HHHHHHCCCBTTBCCEEEECSSSS
T ss_pred             HHhccCCceECCeEEEEEEccCCC
Confidence             576  468999999999997654

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.60  E-value=1.9e-15  Score=127.69  Aligned_cols=83  Identities=16%  Similarity=0.215  Sum_probs=72.7

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+.+|+++|+.+|+.||.|..|.|+.++.  +               +.++|||||+|.+.++|..||
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~---------------~~~~g~afV~f~~~~~a~~A~   81 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR--T---------------GYLKGYTLVEYETYKEAQAAM   81 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTT--T---------------SSBCSCEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--C---------------CccceEEEEEECCHHHHHHHH
Confidence            34478999999999999999999999999999999966541  2               236699999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCC
Q 016231          302 -AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~  321 (393)
                       .||+..|.|+.|.|.++.+.
T Consensus        82 ~~l~g~~~~g~~l~v~~a~~~  102 (126)
T 3ex7_B           82 EGLNGQDLMGQPISVDWCFVR  102 (126)
T ss_dssp             HHHTTCBSSSSBCEEEESEES
T ss_pred             HHhCCCeeCCeEEEEEEecCC
Confidence             69999999999999998643

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.60  E-value=6.3e-16  Score=127.70  Aligned_cols=81  Identities=16%  Similarity=0.113  Sum_probs=71.6

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCC---eeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGE---IDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE  298 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~---I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~  298 (393)
                      ....++|||+|||+++|+++|+.+|+.||.   |..|+|++++  .                +.++|||||+|.+.++|.
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~--~----------------g~~~G~afV~F~~~~~a~   69 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNR--D----------------GKRRGDALIEMESEQDVQ   69 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCT--T----------------STTCSEEEEEBSSHHHHH
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECC--C----------------CCEeeEEEEEECCHHHHH
Confidence            345789999999999999999999999998   8899986643  1                236799999999999999


Q ss_pred             HHHHhcCceeCCeEEEEeecCC
Q 016231          299 AALAFNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       299 ~Al~lng~~~~Gr~I~V~~a~~  320 (393)
                      .||.+|+..|.|+.|.|.++.+
T Consensus        70 ~Al~~~~~~~~gr~i~V~~a~~   91 (107)
T 2lmi_A           70 KALEKHRMYMGQRYVEVYEINN   91 (107)
T ss_dssp             HHHTTTTCCSSSSCCCCEECCH
T ss_pred             HHHHhCcceeCCeEEEEEECCH
Confidence            9999999999999999999864

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=4.7e-15  Score=120.47  Aligned_cols=80  Identities=26%  Similarity=0.312  Sum_probs=68.2

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+++|+++|+.+|+.||.|   +++.+   .               .+.++|||||+|.+.++|+.||
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~---~---------------~g~~~g~afV~f~~~~~A~~A~   70 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN---Q---------------NGKSKGYAFIEFASFEDAKEAL   70 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC---S---------------SSCBCSEEEEECSSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC---C---------------CCCEeeEEEEEECCHHHHHHHH
Confidence            4457999999999999999999999999976   44332   1               2346699999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCCc
Q 016231          302 -AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~~  322 (393)
                       .||+..|.|+.|.|.++.++.
T Consensus        71 ~~l~g~~~~g~~l~v~~a~~~~   92 (101)
T 2fc9_A           71 NSCNKREIEGRAIRLELQGPRG   92 (101)
T ss_dssp             HHTSSEEETTEEEEEEECSSCC
T ss_pred             HHhCCCEeCCeEEEEEEcCCCC
Confidence             599999999999999997654

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.60  E-value=1.7e-15  Score=127.19  Aligned_cols=79  Identities=20%  Similarity=0.118  Sum_probs=69.0

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccC-CeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFG-EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G-~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      ....++|||+|||+++++++|+++|+.|| .|..|.|+..                     .++|||||+|.+.++|+.|
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~---------------------~~rGfaFV~F~~~e~A~~A   83 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR---------------------DFDGTGALEFPSEEILVEA   83 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC---------------------SSSCCEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC---------------------CCCCEEEEEECCHHHHHHH
Confidence            34468999999999999999999999999 8998887321                     1559999999999999999


Q ss_pred             H-HhcCceeCCeEEEEeecCCC
Q 016231          301 L-AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       301 l-~lng~~~~Gr~I~V~~a~~~  321 (393)
                      | .|||..|.|+.|.|.++..+
T Consensus        84 i~~lng~~l~Gr~i~V~~a~~~  105 (111)
T 2jvr_A           84 LERLNNIEFRGSVITVERDDNP  105 (111)
T ss_dssp             HHHTTTEEETTEEEEEEESCC-
T ss_pred             HHHcCCCEECCeEEEEEECCCC
Confidence            9 69999999999999998643

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.60  E-value=1.2e-15  Score=132.97  Aligned_cols=101  Identities=19%  Similarity=0.197  Sum_probs=83.3

Q ss_pred             CCceEEEEeeCCHHHHHHHH-Hh-cCceeCCeEEEEeecCCCcccC-------CCCCCCCcCCcceeeeCCCCCCCCHHH
Q 016231          282 ADSVHAYIVFKSEQSTEAAL-AF-NMAVIGGNHIRLDRACPPRKKL-------KGEDAPLYDIKKTVFVGNLPFDVKDEE  352 (393)
Q Consensus       282 ~srG~AFVeF~s~e~A~~Al-~l-ng~~~~Gr~I~V~~a~~~~~~~-------~~~~~~~~~~~~tLfVgNLp~~~teed  352 (393)
                      ..+|+++|+|.+.+.|+.|+ .+ |+..+.| .|.+.++.......       .........+.++|||+|||+.+++++
T Consensus        11 ~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~~   89 (150)
T 2i2y_A           11 TLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTE   89 (150)
T ss_dssp             SSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSCHH
T ss_pred             cccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHHH
Confidence            46699999999999999999 78 9999999 99999886421110       011122345678999999999999999


Q ss_pred             HHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          353 IYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       353 L~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      |+++|+.|    |.|..|+|+++     ++|||||+|.+.
T Consensus        90 l~~~F~~~----G~i~~v~i~~~-----~~g~afV~f~~~  120 (150)
T 2i2y_A           90 LERAFGYY----GPLRSVWVARN-----PPGFAFVEFEDP  120 (150)
T ss_dssp             HHHHHHHH----SCEEEEEECSS-----SCSEEEEEESSH
T ss_pred             HHHHHHhh----CCEEEEEEeeC-----CCcEEEEEECCH
Confidence            99999999    99999999887     589999999864

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.60  E-value=2.1e-15  Score=122.54  Aligned_cols=74  Identities=19%  Similarity=0.331  Sum_probs=68.0

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|||+|||+++++++|+.+|+.||.|.+|+|+.                       ++|||||+|.+.++|..|+ .
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~-----------------------~~g~afV~f~~~~~A~~Ai~~   82 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP-----------------------EKGCCFIKYDTHEQAAVCIVA   82 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET-----------------------TTTEEEEECSSHHHHHHHHHH
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec-----------------------CCCEEEEEECCHHHHHHHHHH
Confidence            468999999999999999999999999999999841                       4589999999999999999 7


Q ss_pred             hcCceeCCeEEEEeecCC
Q 016231          303 FNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~  320 (393)
                      ||+..|.|+.|.|.++.+
T Consensus        83 l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           83 LANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             HTTCEETTEECCCCBCCC
T ss_pred             hCCCeECCeEEEEEeccC
Confidence            999999999999999864

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=4.5e-15  Score=123.17  Aligned_cols=81  Identities=21%  Similarity=0.320  Sum_probs=70.7

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+.+|+++|+.+|+.||.|..|+|++++   +               +.++|||||+|.+.++|..|| 
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~---~---------------g~~~g~afV~f~~~~~a~~A~~   84 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS---S---------------GTSRGVGFARMESTEKCEAVIG   84 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS---S---------------SCEEEEEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC---C---------------CCcceEEEEEECCHHHHHHHHH
Confidence            346899999999999999999999999999999997754   2               236699999999999999999 


Q ss_pred             HhcCcee--------CCeEEEEeecCCC
Q 016231          302 AFNMAVI--------GGNHIRLDRACPP  321 (393)
Q Consensus       302 ~lng~~~--------~Gr~I~V~~a~~~  321 (393)
                      .||+..|        .+++|.|.++.++
T Consensus        85 ~l~g~~~~~~~~~~~~~~~l~v~~a~p~  112 (114)
T 1x5o_A           85 HFNGKFIKTPPGVSAPTEPLLCKFSGPS  112 (114)
T ss_dssp             HHBTCCCCCCTTSCCCSSCBEEEECCCS
T ss_pred             HhCCCEEcCCccccCCCCceeEEccCCC
Confidence            5999999        5788999988643

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.60  E-value=3.6e-15  Score=130.60  Aligned_cols=82  Identities=26%  Similarity=0.377  Sum_probs=73.0

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+++|+++|+.+|+.||.|..|+|++++  .+               +.++|||||+|.+.++|..|| 
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~--~~---------------g~~~g~afV~f~~~~~a~~A~~  130 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDR--YT---------------KESRGFAFVRFHDKRDAEDAMD  130 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCS--SC---------------TTSCCEEEEEESBHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC--CC---------------CccceEEEEEECCHHHHHHHHH
Confidence            457899999999999999999999999999999996654  12               346699999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCC
Q 016231          302 AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~  321 (393)
                      .||+..|.|+.|.|.++.+.
T Consensus       131 ~l~g~~~~g~~l~v~~a~~~  150 (158)
T 2kn4_A          131 AMDGAVLDGRELRVQMARYG  150 (158)
T ss_dssp             HSTTEESSSSEEEEEEECCS
T ss_pred             HhCCCEECCeEEEEEECCCC
Confidence            69999999999999999764

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.60  E-value=3e-15  Score=123.19  Aligned_cols=81  Identities=17%  Similarity=0.165  Sum_probs=70.4

Q ss_pred             CCcccEEEEeCCCccC------CHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHH
Q 016231          222 GKLLRTIFVGNLPLKV------KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQ  295 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~------tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e  295 (393)
                      ....++|||+|||+.+      |+++|+.+|+.||.|.+|+|++    .++               .++|||||+|.+.+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~----~~g---------------~~~G~afV~f~~~~   72 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE----EDG---------------KTKGYIFLEYASPA   72 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCC----BTT---------------BSCCEEEEEECSSS
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeC----CCC---------------CeeeEEEEEECCHH
Confidence            3447899999999999      8899999999999999998852    222               36699999999999


Q ss_pred             HHHHHH-HhcCceeCCe-EEEEeecCCC
Q 016231          296 STEAAL-AFNMAVIGGN-HIRLDRACPP  321 (393)
Q Consensus       296 ~A~~Al-~lng~~~~Gr-~I~V~~a~~~  321 (393)
                      +|..|| .|||..|.|+ .|.|.++...
T Consensus        73 ~A~~Ai~~l~g~~~~g~~~l~V~~a~~~  100 (105)
T 2nlw_A           73 HAVDAVKNADGYKLDKQHTFRVNLFTDF  100 (105)
T ss_dssp             HHHHHHHHCSSEECSTTCEEEEECSCCC
T ss_pred             HHHHHHHHhCCcccCCCceEEEEEcchH
Confidence            999999 5999999998 9999998643

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=5e-15  Score=122.22  Aligned_cols=77  Identities=17%  Similarity=0.300  Sum_probs=70.0

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+.+++++|+.+|+.||.|..|+|+++                       +|||||+|.+.++|..|| 
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----------------------~g~afV~f~~~~~a~~A~~   79 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----------------------KGYSFVRFSTHESAAHAIV   79 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----------------------TTEEEEEESSHHHHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----------------------CCEEEEEECCHHHHHHHHH
Confidence            34789999999999999999999999999999998542                       389999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCCc
Q 016231          302 AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      .||+..|.|+.|.|.++.+..
T Consensus        80 ~l~g~~~~g~~l~v~~a~~~~  100 (109)
T 1x4g_A           80 SVNGTTIEGHVVKCYWGKESP  100 (109)
T ss_dssp             HHTTCEETTEECEEECCCCCC
T ss_pred             HcCCCEECCcEEEEEecCCCC
Confidence            799999999999999997653

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=3.7e-15  Score=123.53  Aligned_cols=81  Identities=20%  Similarity=0.374  Sum_probs=71.7

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+++|+++|+.+|+.||.|..|+|+++.    +               .++|||||+|.+.++|..|+
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~----~---------------~~kg~afV~f~~~~~A~~Ai   86 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE----R---------------GSKGFGFVTFENSADADRAR   86 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT----T---------------BCTTEEEEECCCSHHHHHHH
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC----C---------------CCceEEEEEECCHHHHHHHH
Confidence            3457999999999999999999999999999999996543    1               15589999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCC
Q 016231          302 -AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~  321 (393)
                       .||+..|.|+.|.|.++.+.
T Consensus        87 ~~l~g~~~~g~~l~V~~a~~~  107 (109)
T 2err_A           87 EKLHGTVVEGRKIEVNNATAR  107 (109)
T ss_dssp             HHHTTCEETTEECEEEECCCS
T ss_pred             HHcCCCEECCEEEEEEECCCC
Confidence             59999999999999998653

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.59  E-value=4.9e-15  Score=125.07  Aligned_cols=82  Identities=13%  Similarity=0.221  Sum_probs=72.8

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+.+++++|+.+|+.||.|..|+|++++   +               +.++|||||+|.+.++|..|+
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~---~---------------g~~~g~afV~f~~~~~A~~Ai   93 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR---S---------------GRSLGTADVHFERRADALKAM   93 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS---S---------------SSCCSEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC---C---------------CCEeeEEEEEECCHHHHHHHH
Confidence            3457899999999999999999999999999999996654   2               235699999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCC
Q 016231          302 -AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~  321 (393)
                       .||+..|.|+.|.|.++.+.
T Consensus        94 ~~l~g~~~~g~~l~V~~a~~~  114 (124)
T 2kt5_A           94 KQYKGVPLDGRPMDIQLVASQ  114 (124)
T ss_dssp             HHHTTEESSSCEEEEEEECCT
T ss_pred             HHcCCCEECCcEEEEEEeCCC
Confidence             59999999999999999754

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.59  E-value=2.6e-15  Score=128.64  Aligned_cols=84  Identities=21%  Similarity=0.225  Sum_probs=73.7

Q ss_pred             CCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       221 ~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      ...+.++|||+|||+++++++|+.+|+.||.|..|+|++++.  +               +.++|||||+|.+.++|..|
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~--t---------------g~~~G~afV~F~~~~~A~~A  104 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQ--S---------------RRSRGFAFVYFENVDDAKEA  104 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSS--S---------------SCCCCEEEEEESCHHHHHHH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--C---------------CccceEEEEEECCHHHHHHH
Confidence            344578999999999999999999999999999999976542  2               23569999999999999999


Q ss_pred             H-HhcCceeCCeEEEEeecCCC
Q 016231          301 L-AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       301 l-~lng~~~~Gr~I~V~~a~~~  321 (393)
                      | .||+..|.|+.|.|.++.+.
T Consensus       105 i~~lng~~i~g~~l~V~~a~~~  126 (129)
T 2kxn_B          105 KERANGMELDGRRIRVDFSITK  126 (129)
T ss_dssp             HHHHTTCCSSSSCCEESCCSSS
T ss_pred             HHHhCCCEECCEEEEEEEecCC
Confidence            9 59999999999999998754

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=1.1e-15  Score=129.38  Aligned_cols=81  Identities=16%  Similarity=0.277  Sum_probs=69.8

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      ...++|||+|||+++|+++|+.+|+.||.|..+.++.+.  .+               +.++|||||+|.+.++|..||.
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~--~~---------------g~~~G~afV~F~~~~~a~~Al~   85 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYG--PN---------------GKATGEGFVEFRNEADYKAALC   85 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEEC--TT---------------SSEEEEEEEEBSSSHHHHHHHT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEEC--CC---------------CCCCeEEEEEECCHHHHHHHHH
Confidence            346899999999999999999999999999875554432  12               3466999999999999999999


Q ss_pred             hcCceeCCeEEEEeecCC
Q 016231          303 FNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~  320 (393)
                      +|+..|.|+.|.|.++.+
T Consensus        86 ~~g~~~~gr~i~V~~a~~  103 (124)
T 1wel_A           86 RHKQYMGNRFIQVHPITK  103 (124)
T ss_dssp             SCSBCSTTSCBEEEEECH
T ss_pred             hCCCeECCcEEEEEECCH
Confidence            999999999999999864

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.59  E-value=4.1e-15  Score=120.55  Aligned_cols=77  Identities=26%  Similarity=0.433  Sum_probs=69.9

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+.+|+++|+.+|+.||.|..|+|++                       ++|||||+|.+.++|..|+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~-----------------------~kg~afV~f~~~~~a~~a~   68 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK-----------------------DKGFGFIRLETRTLAEIAK   68 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEET-----------------------TTTEEEEECSSSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEec-----------------------CCCEEEEEECCHHHHHHHH
Confidence            34578999999999999999999999999999999842                       3489999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCC
Q 016231          302 -AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~  321 (393)
                       .||+..|.|+.|.|.++.+.
T Consensus        69 ~~l~g~~~~g~~l~v~~a~~~   89 (99)
T 2cpj_A           69 VELDNMPLRGKQLRVRFACHS   89 (99)
T ss_dssp             HHHTTCCBTTBCCEEEESSCC
T ss_pred             HHhCCCEeCCceEEEEEcCCC
Confidence             79999999999999999764

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.59  E-value=7.8e-15  Score=128.60  Aligned_cols=82  Identities=21%  Similarity=0.289  Sum_probs=73.2

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+.+|+++|+.+|+.||.|..|.|+.++.  +               +.++|||||+|.+.++|..|| 
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~---------------~~~~g~afV~f~~~~~A~~Ai~   99 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM--K---------------KTACGFCFVEYYSRADAENAMR   99 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT--T---------------CCEEEEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--C---------------CccceEEEEEECCHHHHHHHHH
Confidence            3579999999999999999999999999999999977652  2               236699999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCC
Q 016231          302 AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~  321 (393)
                      .||+..|.|+.|.|.++.+.
T Consensus       100 ~l~g~~~~g~~l~V~~a~~~  119 (156)
T 1h2v_Z          100 YINGTRLDDRIIRTDWDAGF  119 (156)
T ss_dssp             HTTTSEETTEECEEEEESCC
T ss_pred             HhCCCEECCeEEEEEECCCC
Confidence            59999999999999999764

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.59  E-value=4.3e-15  Score=119.95  Aligned_cols=76  Identities=25%  Similarity=0.373  Sum_probs=68.8

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      .+.++|||+|||+++|+++|+.+|+.||.|.+|+|++                       .+|||||+|.+.++|+.|+ 
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~-----------------------~~g~afV~f~~~~~A~~A~~   71 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK-----------------------GDSFAYIQYESLDAAQAACA   71 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECS-----------------------SSCCEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeC-----------------------CCCEEEEEECCHHHHHHHHH
Confidence            4568999999999999999999999999999998843                       2379999999999999999 


Q ss_pred             HhcCceeC--CeEEEEeecCCC
Q 016231          302 AFNMAVIG--GNHIRLDRACPP  321 (393)
Q Consensus       302 ~lng~~~~--Gr~I~V~~a~~~  321 (393)
                      .||+..|.  |+.|.|.++.+.
T Consensus        72 ~l~g~~~~~~g~~l~V~~a~~~   93 (97)
T 1why_A           72 KMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             HHTTCBCSSSSCBCEEEECCCC
T ss_pred             HHCCCEeCCCCcEEEEEECCCC
Confidence            59999999  999999999754

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.58  E-value=8.7e-15  Score=119.57  Aligned_cols=76  Identities=28%  Similarity=0.447  Sum_probs=69.0

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+++|+++|+.+|+.||.|..|+|+                         +|||||+|.+.++|..|| 
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~-------------------------~~~afV~f~~~~~a~~A~~   63 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-------------------------KDYAFIHFDERDGAVKAME   63 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC-------------------------SSCEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-------------------------CCEEEEEeCCHHHHHHHHH
Confidence            346899999999999999999999999999999883                         269999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCCcc
Q 016231          302 AFNMAVIGGNHIRLDRACPPRK  323 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~~  323 (393)
                      .||+..|.|+.|.|.++.+...
T Consensus        64 ~l~g~~~~g~~l~v~~a~~~~~   85 (103)
T 2dgu_A           64 EMNGKDLEGENIEIVFAKPPDQ   85 (103)
T ss_dssp             HHTTEEETTEEEEEEECCCCCC
T ss_pred             HHCCCccCCCEEEEEEcCCCcc
Confidence            5999999999999999976543

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.58  E-value=4.2e-15  Score=127.57  Aligned_cols=80  Identities=24%  Similarity=0.330  Sum_probs=69.3

Q ss_pred             CCcccEEEEeCCCccCCHHHHH----HHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLI----KEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQST  297 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~----~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A  297 (393)
                      ..+.++|||+|||+.+++++|+    .+|+.||.|.+|.++.     +               +.++|||||+|.+.++|
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~-----~---------------~~~rG~aFV~F~~~~~A   85 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL-----S---------------DDNSGKAYIVFATQESA   85 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC-----C---------------CSSCCCEEEEESSHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc-----C---------------CCcCCEEEEEECCHHHH
Confidence            3457899999999999999876    6999999999988732     1               23569999999999999


Q ss_pred             HHHH-HhcCceeCCeEEEEeecCCC
Q 016231          298 EAAL-AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       298 ~~Al-~lng~~~~Gr~I~V~~a~~~  321 (393)
                      ..|+ .|||..|.|+.|.|.++...
T Consensus        86 ~~Ai~~lng~~l~gr~l~V~~a~~~  110 (127)
T 2a3j_A           86 QAFVEAFQGYPFQGNPLVITFSETP  110 (127)
T ss_dssp             HHHHHHSTTCCCTTSCCEEEECCCC
T ss_pred             HHHHHHHCCCEeCCCEEEEEEccCc
Confidence            9999 79999999999999999754

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.58  E-value=8.6e-16  Score=124.85  Aligned_cols=81  Identities=19%  Similarity=0.203  Sum_probs=69.7

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      ...++|||+|||+++|+++|+.+|+.||.|.. .++.+.                 .++.++|||||+|.+.++|..||.
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~-----------------~~g~~~g~afV~f~~~~~a~~A~~   76 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDV-----------------RTGTNRKFGYVDFESAEDLEKALE   76 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEE-----------------EEETTTTEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecC-----------------CCCCcCcEEEEEECCHHHHHHHHh
Confidence            35789999999999999999999999999876 443332                 123467999999999999999999


Q ss_pred             hcCceeCCeEEEEeecCCC
Q 016231          303 FNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~  321 (393)
                      ||+..|.|+.|.|.++.+.
T Consensus        77 l~g~~~~g~~l~V~~a~~~   95 (101)
T 1fj7_A           77 LTGLKVFGNEIKLEKPKGR   95 (101)
T ss_dssp             GGGCCBTTBCCEEECCSCC
T ss_pred             cCCcEECCcEEEEEEcCCC
Confidence            9999999999999999754

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.58  E-value=7.2e-15  Score=130.42  Aligned_cols=82  Identities=20%  Similarity=0.252  Sum_probs=72.2

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+.+++++|+.+|+.||.|..|.|+.++.                 ++.++|||||+|.+.++|..|| 
T Consensus        70 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~-----------------~g~~~g~afV~f~~~~~A~~Ai~  132 (165)
T 1rk8_A           70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR-----------------TGFSKGYALVEYETHKQALAAKE  132 (165)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----------------TSSEEEEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCC-----------------CCcEeeEEEEEECCHHHHHHHHH
Confidence            3468999999999999999999999999999999977542                 2346699999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCC
Q 016231          302 AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~  321 (393)
                      .||+..|.|+.|.|.++.+.
T Consensus       133 ~l~g~~~~g~~l~V~~a~~~  152 (165)
T 1rk8_A          133 ALNGAEIMGQTIQVDWCFVK  152 (165)
T ss_dssp             HHTTCEETTEECEEEESEEC
T ss_pred             HhCCCEECCEEEEEEEecCC
Confidence            69999999999999998643

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.58  E-value=7e-15  Score=125.67  Aligned_cols=81  Identities=28%  Similarity=0.432  Sum_probs=70.8

Q ss_pred             CCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       221 ~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      .....++|||+|||+.+++++|+.+|+.||.|..|+|++++.  +               +.++|||||+|.+.++|..|
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~--~---------------~~~~g~afV~f~~~~~a~~A  121 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE--T---------------EKHRGFAFVEFELAEDAAAA  121 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTT--T---------------CCCCSEEEEEESCHHHHHHH
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCC--C---------------CCcCcEEEEEECCHHHHHHH
Confidence            345679999999999999999999999999999999866541  2               23669999999999999999


Q ss_pred             H-HhcCceeCCeEEEEeec
Q 016231          301 L-AFNMAVIGGNHIRLDRA  318 (393)
Q Consensus       301 l-~lng~~~~Gr~I~V~~a  318 (393)
                      | .||+..|.|+.|.|.+|
T Consensus       122 ~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A          122 IDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             HHHSTEEEETTEEEEEEC-
T ss_pred             HHHhCCCEECCEEEEEEeC
Confidence            9 69999999999999875

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.58  E-value=2.1e-15  Score=121.88  Aligned_cols=75  Identities=27%  Similarity=0.470  Sum_probs=68.0

Q ss_pred             CcccEEEEeCCCc-cCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          223 KLLRTIFVGNLPL-KVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~-~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      .+.++|||+|||+ .+++++|+.+|+.||.|.+|+|.                         +|||||+|.+.++|..|+
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~-------------------------~g~afV~f~~~~~A~~A~   62 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------------------------NAFGFIQFDNPQSVRDAI   62 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-------------------------TTEEEEEESCHHHHHHHH
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------------------------CCEEEEEECCHHHHHHHH
Confidence            4578999999999 99999999999999999999982                         279999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCCc
Q 016231          302 -AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~~  322 (393)
                       .||+..|.|+.|.|.++.+..
T Consensus        63 ~~l~g~~~~g~~l~V~~a~~~~   84 (96)
T 2kvi_A           63 ECESQEMNFGKKLILEVSSSNA   84 (96)
T ss_dssp             HHHTCSSCBTTTBCEEEEECCC
T ss_pred             HHcCCCeeCCcEEEEEEcCcCC
Confidence             599999999999999986543

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.58  E-value=1.9e-15  Score=129.15  Aligned_cols=84  Identities=18%  Similarity=0.248  Sum_probs=72.8

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeE--EEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDS--VRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~s--Vri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~  299 (393)
                      ....++|||+|||+++|+++|+.+|+.||.|..  |+|++++.  +               +.++|||||+|.+. +|..
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~--t---------------g~~rG~aFV~f~~~-~a~~   81 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQ--T---------------QLNRGFAFIQLSTI-EAAQ   81 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSS--S---------------SSBCSCEEEECCHH-HHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCC--C---------------CCcceEEEEEECCH-HHHH
Confidence            355789999999999999999999999999977  89877542  2               34669999999999 9999


Q ss_pred             HH-HhcCc----eeCCeEEEEeecCCCcc
Q 016231          300 AL-AFNMA----VIGGNHIRLDRACPPRK  323 (393)
Q Consensus       300 Al-~lng~----~~~Gr~I~V~~a~~~~~  323 (393)
                      || .||+.    .|.|+.|.|.++.+...
T Consensus        82 Ai~~l~g~~~~~~~~gr~l~V~~a~~~~~  110 (131)
T 2m2b_A           82 LLQILQALHPPLTIDGKTINVEFAKGSKR  110 (131)
T ss_dssp             HHHHHTTCCCSCCGGGCCCCCEECCCSCC
T ss_pred             HHHHhcCCCCCccCCCEEEEEEECCCCCC
Confidence            99 79999    99999999999976543

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.58  E-value=3.4e-15  Score=120.14  Aligned_cols=79  Identities=25%  Similarity=0.333  Sum_probs=70.0

Q ss_pred             CcccEEEEeCCCccCCHHHHH----HHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLI----KEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE  298 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~----~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~  298 (393)
                      .+.++|||+|||+++++++|+    .+|+.||.|..|.|++.                    +.++|||||+|.+.++|.
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~--------------------~~~~g~afV~f~~~~~A~   65 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS--------------------LKMRGQAFVIFKEVSSAT   65 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHH--------------------HHHTTCEEEEESSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcC--------------------CCcCcEEEEEeCCHHHHH
Confidence            457899999999999999999    99999999999988421                    125689999999999999


Q ss_pred             HHH-HhcCceeCCeEEEEeecCCC
Q 016231          299 AAL-AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       299 ~Al-~lng~~~~Gr~I~V~~a~~~  321 (393)
                      .|+ .|||..|.|+.|.|.++.+.
T Consensus        66 ~A~~~l~g~~~~g~~l~v~~a~~~   89 (97)
T 1nu4_A           66 NALRSMQGFPFYDKPMRIQYAKTD   89 (97)
T ss_dssp             HHHHHHTTCEETTEECEEEECSSC
T ss_pred             HHHHHhCCCEECCcEEEEEEccCC
Confidence            999 69999999999999999754

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.58  E-value=2.2e-15  Score=122.67  Aligned_cols=80  Identities=16%  Similarity=0.357  Sum_probs=71.3

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      ...++|||+|||+++++++|+.+|+.||.|..|+|++++   ++               .++|||||+|.+.++|..|+.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~g---------------~~~g~afV~f~~~~~a~~Ai~   68 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR---TG---------------VSKGYGFVSFYNDVDVQKIVE   68 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TS---------------CEEEEEEEEESSCCCHHHHTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC---CC---------------CccceEEEEECCHHHHHHHHh
Confidence            346899999999999999999999999999999997754   22               366999999999999999999


Q ss_pred             hcCceeCCeEEEEeecCCC
Q 016231          303 FNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~  321 (393)
                       ++..|.|+.|.|.++.+.
T Consensus        69 -~~~~~~g~~l~v~~a~~~   86 (102)
T 2xs2_A           69 -SQINFHGKKLKLGPAIRK   86 (102)
T ss_dssp             -CCCEETTEECEEEEEEEC
T ss_pred             -CCCeECCEEEEEEECCcC
Confidence             999999999999998643

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.58  E-value=2.1e-15  Score=118.04  Aligned_cols=72  Identities=19%  Similarity=0.211  Sum_probs=63.3

Q ss_pred             ccEEEEeCCCccC------CHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHH
Q 016231          225 LRTIFVGNLPLKV------KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE  298 (393)
Q Consensus       225 ~rtVFVgNLp~~~------tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~  298 (393)
                      +++|||+|||+.+      |+++|+.+|+.||.|.+|+|++    .++               .++|||||+|.+.++|.
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~----~~g---------------~~~g~afV~f~~~~~A~   61 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE----EDG---------------KTKGYIFLEYASPAHAV   61 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC----BTT---------------BCCCEEEEEESSHHHHH
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC----CCC---------------cEeEEEEEEECCHHHHH
Confidence            3789999999999      7899999999999999998842    222               36699999999999999


Q ss_pred             HHH-HhcCceeCCe-EEEE
Q 016231          299 AAL-AFNMAVIGGN-HIRL  315 (393)
Q Consensus       299 ~Al-~lng~~~~Gr-~I~V  315 (393)
                      .|+ .|||..|.|+ .|.|
T Consensus        62 ~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A           62 DAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             HHHTTSSSCCCSSSSCCCC
T ss_pred             HHHHHhcCcccCCceeEEe
Confidence            999 6999999999 8876

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=9.5e-15  Score=120.11  Aligned_cols=82  Identities=22%  Similarity=0.331  Sum_probs=70.3

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCC-eeEEEEe-eecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGE-IDSVRIR-SVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~-I~sVri~-~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ..++|||+|||+++|+++|+.+|..||. |..|.|+ .+.  .               ++.++|||||+|.+.++|..|+
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~--~---------------~g~~~g~afV~f~~~~~A~~A~   69 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAA--D---------------KMKNRGFAFVEYESHRAAAMAR   69 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSC--T---------------TTTTCCEEEEEESSHHHHHHHH
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCC--C---------------CCCcCcEEEEEecCHHHHHHHH
Confidence            4689999999999999999999999998 9999885 322  1               2246799999999999999999


Q ss_pred             -Hhc--CceeCCeEEEEeecCCCc
Q 016231          302 -AFN--MAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 -~ln--g~~~~Gr~I~V~~a~~~~  322 (393)
                       .||  +..|.|+.|.|.++.+..
T Consensus        70 ~~l~~g~~~~~g~~l~V~~a~~~~   93 (109)
T 2dis_A           70 RKLMPGRIQLWGHQIAVDWAEPEI   93 (109)
T ss_dssp             TTTTTCCSCBTTBCCEEEESCSSC
T ss_pred             HHhhCCCceecCCeEEEEEcCCCC
Confidence             585  589999999999997643

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.57  E-value=3.7e-15  Score=125.47  Aligned_cols=77  Identities=18%  Similarity=0.246  Sum_probs=67.6

Q ss_pred             CCcccEEEEeCCCcc-CCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLK-VKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~-~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      ..++++|||+|||++ +|+++|+.+|+.||.|.+|+|++                       ++|||||+|.+.++|..|
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~-----------------------~kg~aFVef~~~~~A~~A   78 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR-----------------------MKSQAFIEMETREDAMAM   78 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET-----------------------TTTEEEEECSSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec-----------------------CCCEEEEEECCHHHHHHH
Confidence            445799999999998 99999999999999999999842                       348999999999999999


Q ss_pred             H-Hhc--CceeCCeEEEEeecCCC
Q 016231          301 L-AFN--MAVIGGNHIRLDRACPP  321 (393)
Q Consensus       301 l-~ln--g~~~~Gr~I~V~~a~~~  321 (393)
                      + .||  +..|.|+.|.|.++...
T Consensus        79 i~~l~~~~~~l~Gr~l~V~~a~~~  102 (112)
T 1x4f_A           79 VDHCLKKALWFQGRCVKVDLSEKY  102 (112)
T ss_dssp             HHHHHHSCCCSSSSCCEEEEECSC
T ss_pred             HHHhccCCceECCEEEEEEECccc
Confidence            9 565  45699999999999754

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.57  E-value=2.9e-15  Score=124.80  Aligned_cols=75  Identities=17%  Similarity=0.247  Sum_probs=67.9

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      +..++|||+|||+.+|+++|+.+|+.||.|..|+|+.                       ++|||||+|.+.++|..|| 
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~-----------------------~~g~afV~f~~~~~A~~Ai~   64 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----------------------GGITAIVEFLEPLEARKAFR   64 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----------------------SSSCEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-----------------------CCCEEEEEeCCHHHHHHHHH
Confidence            3468999999999999999999999999999988732                       3489999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCC
Q 016231          302 AFNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~  320 (393)
                      .||+..|.|+.|.|.++..
T Consensus        65 ~l~g~~~~g~~l~V~~a~~   83 (111)
T 1whx_A           65 HLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             HHTTCBSSSSBCEEEEEET
T ss_pred             HhCCCEECCeEEEEEECCC
Confidence            6999999999999999853

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.57  E-value=1.1e-15  Score=121.47  Aligned_cols=78  Identities=23%  Similarity=0.382  Sum_probs=67.7

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hhc
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~ln  304 (393)
                      ++|||+|||+++++++|+.+|+.||.|.+|+|++++.  +               +.++|||||+|.+.+ |..|+ .||
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~---------------~~~~g~afV~f~~~~-a~~a~~~l~   63 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRE--T---------------KKPKGFGFVEMQEES-VSEAIAKLD   63 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSS--S---------------CCCCEEEEEEECTTH-HHHHHHTSC
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCC--C---------------CCcceEEEEEECCHH-HHHHHHHhC
Confidence            6899999999999999999999999999999966541  2               236699999999999 99999 699


Q ss_pred             CceeCCeEEEEeecCCC
Q 016231          305 MAVIGGNHIRLDRACPP  321 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~~  321 (393)
                      +..|.|+.|.|.++.+.
T Consensus        64 g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A           64 NTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             SSCCSSSSCSEEEC---
T ss_pred             CCEECCeEEEEEEcCCC
Confidence            99999999999999754

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.57  E-value=1.1e-14  Score=120.19  Aligned_cols=76  Identities=13%  Similarity=0.152  Sum_probs=69.0

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+++|+++|+.+|+.||.|..|.|+.+                        |||||+|.+.++|+.|| 
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~------------------------g~afV~f~~~~~a~~Ai~   68 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------------------------GTGVVEFVRKEDMTYAVR   68 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT------------------------TEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC------------------------CEEEEEECCHHHHHHHHH
Confidence            45789999999999999999999999999999998431                        69999999999999999 


Q ss_pred             HhcCceeCC-----eEEEEeecCCCc
Q 016231          302 AFNMAVIGG-----NHIRLDRACPPR  322 (393)
Q Consensus       302 ~lng~~~~G-----r~I~V~~a~~~~  322 (393)
                      .||+..|.|     +.|.|.++.+..
T Consensus        69 ~l~g~~~~g~~~~~~~i~V~~a~~~~   94 (108)
T 1x4c_A           69 KLDNTKFRSHEGETAYIRVKVDGPRS   94 (108)
T ss_dssp             HSSSEEEECTTSCEEEEEEEESSCCS
T ss_pred             HHCcCCccCCcCcceEEEEEeCCCCC
Confidence            599999999     999999997643

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=3.1e-15  Score=127.75  Aligned_cols=78  Identities=18%  Similarity=0.295  Sum_probs=68.5

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCe----eEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEI----DSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I----~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      .++|||+|||+++|+++|++||+.||.|    ..|+|+.+.   ++               +++|||||+|.+.++|..|
T Consensus        23 ~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~---~g---------------r~~G~aFV~F~~~~~A~~A   84 (123)
T 2dha_A           23 QVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP---DG---------------RPTGDAFVLFACEEYAQNA   84 (123)
T ss_dssp             CCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT---TS---------------CEEEEEEECCSSHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC---CC---------------CEeeEEEEEECCHHHHHHH
Confidence            6899999999999999999999999975    688887652   22               3669999999999999999


Q ss_pred             HHhcCceeCCeEEEEeecCC
Q 016231          301 LAFNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       301 l~lng~~~~Gr~I~V~~a~~  320 (393)
                      |..|+..|.||.|.|..+.+
T Consensus        85 l~~~~~~l~gR~i~V~~a~~  104 (123)
T 2dha_A           85 LRKHKDLLGKRYIELFRSTA  104 (123)
T ss_dssp             HTTTTEESSSCEECCEEECH
T ss_pred             HHhCCCeeCCeEEEEEECCH
Confidence            97799999999999988753

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.56  E-value=1.1e-14  Score=120.38  Aligned_cols=74  Identities=26%  Similarity=0.479  Sum_probs=68.1

Q ss_pred             cccEEEEeCCCcc-CCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          224 LLRTIFVGNLPLK-VKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       224 ~~rtVFVgNLp~~-~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ..++|||+|||+. +++++|+.+|+.||.|..|.|                         ++|||||+|.+.++|..|| 
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-------------------------~~g~afV~f~~~~~A~~A~~   80 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------------------------HKGYAFVQYSNERHARAAVL   80 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-------------------------ETTEEEEECSSSHHHHHHHH
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-------------------------eCCEEEEEECCHHHHHHHHH
Confidence            4689999999999 999999999999999999988                         2379999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCCc
Q 016231          302 AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      .||+..|.|+.|.|.++.++.
T Consensus        81 ~l~g~~~~g~~l~V~~a~~~~  101 (110)
T 1wf1_A           81 GENGRVLAGQTLDINMAGEPK  101 (110)
T ss_dssp             HHTTCEETTEECCEEESCCCC
T ss_pred             HcCCCEECCeEEEEEECCCCC
Confidence            799999999999999997543

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.56  E-value=8.6e-15  Score=115.24  Aligned_cols=72  Identities=26%  Similarity=0.546  Sum_probs=65.8

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhccc----C-------CeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEee
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKF----G-------EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVF  291 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~----G-------~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF  291 (393)
                      +..++|||+|||+++++++|+.+|+.|    |       .|.+|++++                       ++|||||+|
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~-----------------------~kg~afV~f   60 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ-----------------------DKNFAFLEF   60 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECS-----------------------SSSEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecC-----------------------CCcEEEEEc
Confidence            457999999999999999999999999    8       899988832                       348999999


Q ss_pred             CCHHHHHHHHHhcCceeCCeEEEEee
Q 016231          292 KSEQSTEAALAFNMAVIGGNHIRLDR  317 (393)
Q Consensus       292 ~s~e~A~~Al~lng~~~~Gr~I~V~~  317 (393)
                      .+.++|..|+.||+..|.|+.|.|.+
T Consensus        61 ~~~~~a~~A~~l~g~~~~g~~l~V~r   86 (87)
T 2hzc_A           61 RSVDETTQAMAFDGIIFQGQSLKIRR   86 (87)
T ss_dssp             SSHHHHHHHGGGTTCEETTEECEEEC
T ss_pred             CCHHHHHHHHhcCCCEECCeEEEEeC
Confidence            99999999999999999999999975

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.56  E-value=1.1e-14  Score=120.78  Aligned_cols=76  Identities=21%  Similarity=0.326  Sum_probs=69.5

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+++|+++|+.+|+.||.|..|+|+                         +|||||+|.+.++|..|+
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-------------------------kg~afV~f~~~~~A~~Ai   82 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------------------------NGFAFVEFEEAESAAKAI   82 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-------------------------TTEEEEECSSHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-------------------------CCEEEEEECCHHHHHHHH
Confidence            4457999999999999999999999999999999984                         279999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCCc
Q 016231          302 -AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~~  322 (393)
                       .|||..|.|+.|.|.++.+..
T Consensus        83 ~~l~g~~~~g~~l~V~~a~~~~  104 (108)
T 2jvo_A           83 EEVHGKSFANQPLEVVYSKLPA  104 (108)
T ss_dssp             HHHTTCEETTEECEEESCSCCC
T ss_pred             HHcCCCEECCeEEEEEEecCCC
Confidence             699999999999999997643

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.56  E-value=9.4e-15  Score=117.45  Aligned_cols=78  Identities=29%  Similarity=0.305  Sum_probs=67.3

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+.+++++|+.+|+.||.|..+   .    .+               +.++|||||+|.+.++|..|+
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~---~----~~---------------~~~~g~afV~f~~~~~a~~A~   70 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV---S----QD---------------GKSKGIAYIEFKSEADAEKNL   70 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE---E----ET---------------TEEEEEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe---C----CC---------------CCcceEEEEEECCHHHHHHHH
Confidence            3457999999999999999999999999987655   1    11               236699999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCC
Q 016231          302 -AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~  321 (393)
                       .||+..|.|+.|.|.++.+.
T Consensus        71 ~~l~g~~~~g~~l~v~~a~~~   91 (96)
T 1fjc_A           71 EEKQGAEIDGRSVSLYYTGEK   91 (96)
T ss_dssp             HHTTEEEETTEEEEEEECSSS
T ss_pred             HHhCCCEECCeEEEEEEcCCC
Confidence             59999999999999999754

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=1e-14  Score=121.11  Aligned_cols=83  Identities=19%  Similarity=0.257  Sum_probs=68.7

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+++|+++|+.+|+.||.|..|.+.....  +               +.++|||||+|.+.++|..|| 
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~--~---------------g~~~g~afV~f~~~~~a~~Ai~   85 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM--T---------------GRMRGQAFITFPNKEIAWQALH   85 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE--C---------------SSSCSEEEEECSSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC--C---------------CccceEEEEEECCHHHHHHHHH
Confidence            4579999999999999999999999999984332222111  1               236699999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCCc
Q 016231          302 AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      .||+..|.|+.|.|.++.+..
T Consensus        86 ~l~g~~~~g~~l~v~~a~~~~  106 (115)
T 2cpx_A           86 LVNGYKLYGKILVIEFGKNKK  106 (115)
T ss_dssp             HSTTCBCSSCBCEEEECCCCS
T ss_pred             HhCCCEeCCcEEEEEEccCCC
Confidence            699999999999999997654

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=8e-15  Score=117.34  Aligned_cols=76  Identities=14%  Similarity=0.218  Sum_probs=66.8

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCC-eeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGE-IDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~-I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ...++|||+|||+++|+++|+.+|+.||. |..+.++                        ++|||||+|.+.++|..|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~------------------------~~g~afV~f~~~~~A~~A~   61 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------------------------KSGYAFVDYPDQNWAIRAI   61 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------------------------ETTEEEECCSCHHHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc------------------------CCCEEEEEECCHHHHHHHH
Confidence            34689999999999999999999999999 6655551                        3489999999999999999


Q ss_pred             -HhcC-ceeCCeEEEEeecCCCc
Q 016231          302 -AFNM-AVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 -~lng-~~~~Gr~I~V~~a~~~~  322 (393)
                       .||+ ..|.|+.|.|.++.+..
T Consensus        62 ~~l~g~~~~~g~~l~v~~a~~~~   84 (93)
T 2cqh_A           62 ETLSGKVELHGKIMEVDYSVSKK   84 (93)
T ss_dssp             HHHTTTCEETTEECEEEECCCCC
T ss_pred             HHccCCeeECCEEEEEEEccCcc
Confidence             6999 99999999999997653

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.56  E-value=7.4e-15  Score=127.95  Aligned_cols=79  Identities=20%  Similarity=0.313  Sum_probs=70.9

Q ss_pred             CCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       221 ~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      .....++|||+|||+.+|+++|+.+|+.||.|.+|+|+++                      ++|||||+|.+.++|..|
T Consensus        69 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~----------------------~~g~afV~f~~~~~a~~A  126 (150)
T 2i2y_A           69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----------------------PPGFAFVEFEDPRDAADA  126 (150)
T ss_dssp             SSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS----------------------SCSEEEEEESSHHHHHHH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC----------------------CCcEEEEEECCHHHHHHH
Confidence            3445799999999999999999999999999999999542                      248999999999999999


Q ss_pred             H-HhcCceeCCeEEEEeecCCC
Q 016231          301 L-AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       301 l-~lng~~~~Gr~I~V~~a~~~  321 (393)
                      | .||+..|.|+.|.|.++.++
T Consensus       127 ~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A          127 VRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             HHHHSSSCSSSSCCEEEECCCC
T ss_pred             HHHcCCCEECCeEEEEEEcCCC
Confidence            9 59999999999999999754

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=1.3e-14  Score=116.66  Aligned_cols=77  Identities=13%  Similarity=0.279  Sum_probs=68.6

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEE-EeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVR-IRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVr-i~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ..++|||+|||+++++++|+.+|+.||.|.+|+ |+.++                     ..|.|||+|.+.++|..|+ 
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~---------------------~~~~afV~f~~~~~a~~Ai~   72 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS---------------------ETAVVNVTYSSKDQARQALD   72 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSS---------------------SSEEEEEEESSHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---------------------CCCEEEEEECCHHHHHHHHH
Confidence            468999999999999999999999999999995 64433                     2367999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCC
Q 016231          302 AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~  321 (393)
                      .||+..|.|+.|.|.++.+.
T Consensus        73 ~l~g~~~~g~~l~V~~a~~~   92 (96)
T 2e44_A           73 KLNGFQLENFTLKVAYIPDE   92 (96)
T ss_dssp             HHTTCBCSSCBCEEEECCCC
T ss_pred             HhCCCEECCcEEEEEEcCcc
Confidence            69999999999999999765

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=3.2e-14  Score=115.53  Aligned_cols=82  Identities=28%  Similarity=0.360  Sum_probs=68.8

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+++|+++|+.+|+.|+   .|+++.++  .+               +.++|||||+|.+.++|..||
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~--~~---------------~~~~g~afV~f~~~~~A~~A~   71 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDR--ET---------------GSSKGFGFVDFNSEEDAKAAK   71 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECS--SS---------------CSEEEEEEEECSSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecC--CC---------------CCcCcEEEEEECCHHHHHHHH
Confidence            34579999999999999999999999885   46665543  12               236699999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCCcc
Q 016231          302 -AFNMAVIGGNHIRLDRACPPRK  323 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~~~  323 (393)
                       .||+..|.|+.|.|.++.+...
T Consensus        72 ~~l~g~~~~g~~l~V~~a~~~~~   94 (102)
T 2fc8_A           72 EAMEDGEIDGNKVTLDWAKPKGE   94 (102)
T ss_dssp             HHHTTCEETTEECEEEECCCCCS
T ss_pred             HHhCCCeECCeEEEEEEecCCCC
Confidence             5999999999999999976543

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.55  E-value=6e-15  Score=126.60  Aligned_cols=79  Identities=20%  Similarity=0.277  Sum_probs=68.3

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCee--EEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEID--SVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~--sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      ...++|||+|||+++|+++|+++|+.| .|.  +|+|++++  +                +.++|||||+|.+.++|+.|
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~--~----------------GrsrGfaFV~F~~~e~A~~A  100 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDP--E----------------GKITGEAFVQFASQELAEKA  100 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCS--S----------------SSSCSEEEEEESSTTHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECC--C----------------CCCceEEEEEECCHHHHHHH
Confidence            346889999999999999999999999 566  88886654  1                23669999999999999999


Q ss_pred             HHhcCceeCCeEEEEeecCC
Q 016231          301 LAFNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       301 l~lng~~~~Gr~I~V~~a~~  320 (393)
                      |.+++..|.||.|.|..+.+
T Consensus       101 l~~~~~~l~gR~I~V~~a~~  120 (126)
T 2hgm_A          101 LGKHKERIGHRYIEVFKSSQ  120 (126)
T ss_dssp             HTTTTCCBTTBCCCCEEECH
T ss_pred             HHHCCCEECCEEEEEEECCH
Confidence            98888999999999988753

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.54  E-value=8.8e-15  Score=126.24  Aligned_cols=83  Identities=27%  Similarity=0.400  Sum_probs=72.9

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+++|+++|+.+|+.||.|..|+|+.++.  +               +.++|||||+|.+.++|+.|| 
T Consensus        45 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~--~---------------g~~~G~afV~F~~~~~A~~Ai~  107 (135)
T 2lea_A           45 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY--T---------------KESRGFAFVRFHDKRDAEDAMD  107 (135)
T ss_dssp             GGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSS--S---------------SSCCSCCEEECSCHHHHHHHHT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCC--C---------------CccceEEEEEECCHHHHHHHHH
Confidence            4468999999999999999999999999999999866431  2               236699999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCCc
Q 016231          302 AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      .||+..|.|+.|.|.++.+..
T Consensus       108 ~l~g~~i~g~~l~V~~a~~~~  128 (135)
T 2lea_A          108 AMDGAVLDGRELRVQMARYGR  128 (135)
T ss_dssp             TTTTCCSSSSCCEEEECCCCC
T ss_pred             HcCCCEECCEEEEEEECCCCC
Confidence            699999999999999997543

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=3.5e-14  Score=114.08  Aligned_cols=77  Identities=26%  Similarity=0.387  Sum_probs=66.1

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHh
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~l  303 (393)
                      ..++|||+|||+++|+++|+.+|+.||.|.+|.  .++  .+                 .+ ||||+|.+.++|..||.|
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~--~~~--~~-----------------g~-~afV~f~~~~~a~~ai~l   64 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVV--MDK--DK-----------------GV-FAIVEMGDVGAREAVLSQ   64 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEE--ECS--SS-----------------CC-EEEEEESSHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEE--EcC--CC-----------------Cc-EEEEEECCHHHHHHHHhc
Confidence            468999999999999999999999999999872  222  00                 11 999999999999999999


Q ss_pred             cCceeCCeEEEEeecCCCc
Q 016231          304 NMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~  322 (393)
                      |+..|.|+.|.|.++.+..
T Consensus        65 ~g~~~~g~~l~V~~a~~~~   83 (94)
T 2e5g_A           65 SQHSLGGHRLRVRPREQKE   83 (94)
T ss_dssp             SCCEETTEECCCBCSCCSC
T ss_pred             CCeEECCEEEEEEECCcCC
Confidence            9999999999999886543

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.54  E-value=9.5e-15  Score=137.04  Aligned_cols=80  Identities=14%  Similarity=0.176  Sum_probs=70.9

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccC--CeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFG--EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G--~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ..++|||+|||+++|+++|+.+|+.||  .|.+|+|++++.  +               +.++|||||+|.+.++|..||
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~--t---------------g~skGfaFV~f~~~~~a~~Ai  129 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRA--N---------------GQSKGFALVGVGSEASSKKLM  129 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTT--T---------------CCEEEEEEEEESCTTHHHHHH
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCC--C---------------CccceEEEEEECCHHHHHHHH
Confidence            467899999999999999999999999  999999987642  2               346799999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCC
Q 016231          302 -AFNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~  320 (393)
                       .||+..|.|+.|.|.++.+
T Consensus       130 ~~lng~~~~Gr~l~V~~a~~  149 (229)
T 3q2s_C          130 DLLPKRELHGQNPVVTPVNK  149 (229)
T ss_dssp             TTSTTSCBTTBCCEEEECCH
T ss_pred             HHcCCCeECCEEeEEEECCC
Confidence             5999999999999999864

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.54  E-value=1.9e-14  Score=114.33  Aligned_cols=73  Identities=12%  Similarity=0.224  Sum_probs=66.6

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      +..++|||+|||+.+++++|+.+|+.| .|.+|+|.  .                     ++|||||+|.+.++|..|+ 
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~--~---------------------~~g~afV~f~~~~~a~~Ai~   58 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD--R---------------------NKRTAFVTLLNGEQAQNAIQ   58 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE--G---------------------GGTEEEECCSCHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe--C---------------------CCcEEEEEECCHHHHHHHHH
Confidence            346899999999999999999999999 99999882  1                     4589999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecC
Q 016231          302 AFNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~  319 (393)
                      .||+..+.|+.|.|.++.
T Consensus        59 ~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A           59 MFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             HHTTEEETTEEEEEEECC
T ss_pred             HhCCCeECCcEEEEEEcC
Confidence            599999999999999985

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.54  E-value=2.3e-15  Score=131.20  Aligned_cols=80  Identities=19%  Similarity=0.180  Sum_probs=70.1

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      ...++|||+|||+++|+++|+++|+.|| |..|+|++++  +                +.++|||||+|.+.++|+.||.
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~--~----------------g~srGfaFV~F~~~e~A~~Al~  104 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP--D----------------GRVTGEADVEFATHEEAVAAMS  104 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSS--S----------------SCSSCCCEEECSHHHHHHHHTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECC--C----------------CCCceEEEEEeCCHHHHHHHHh
Confidence            3468999999999999999999999999 6689886653  1                2367999999999999999999


Q ss_pred             hcCceeCCeEEEEeecCCC
Q 016231          303 FNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~  321 (393)
                      +|+..|.||.|.|..+.+.
T Consensus       105 ~~g~~l~gR~i~V~~a~~~  123 (139)
T 2hgn_A          105 KDRANMQHRYIELFLNSTT  123 (139)
T ss_dssp             CCSCSSSSCCCCCEECCCS
T ss_pred             hCCCEECCEEEEEEECCCC
Confidence            9999999999999998754

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.53  E-value=2.1e-14  Score=124.08  Aligned_cols=80  Identities=26%  Similarity=0.283  Sum_probs=68.8

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEE--------EEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCC
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSV--------RIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKS  293 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sV--------ri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s  293 (393)
                      ..+.++|||+|||+.+|+++|+.+|+.||.|..|        ++..                    ++.++|||||+|.+
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~--------------------~g~~~g~afV~f~~  101 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMK--------------------EGRMKGQAFIGLPN  101 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEE--------------------ETTTEEEEEEECSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEecc--------------------CCCcccEEEEEeCC
Confidence            3457899999999999999999999999998764        2211                    23467999999999


Q ss_pred             HHHHHHHH-HhcCceeCCeEEEEeecCCC
Q 016231          294 EQSTEAAL-AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       294 ~e~A~~Al-~lng~~~~Gr~I~V~~a~~~  321 (393)
                      .++|..|| .|||..|.|+.|.|.++.+.
T Consensus       102 ~~~A~~Ai~~lng~~~~g~~l~V~~a~~~  130 (143)
T 3egn_A          102 EKAAAKALKEANGYVLFGKPMVVQFARSA  130 (143)
T ss_dssp             HHHHHHHHHHHTTBEETTEECEEEECCCS
T ss_pred             HHHHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            99999999 59999999999999999754

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.53  E-value=2.1e-14  Score=115.09  Aligned_cols=75  Identities=20%  Similarity=0.340  Sum_probs=60.9

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      .....+|||+|||+++|+++|+.+|++||.|.+|+|+++                      ++|||||+|.+.++|.+  
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~----------------------srGfaFV~F~~~~~A~~--   63 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----------------------FRAFAFVTFADDKVAQS--   63 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS----------------------CCSEEEEEESCHHHHHH--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC----------------------CCCEEEEEECCHHHHHH--
Confidence            345789999999999999999999999999999998541                      45999999999999884  


Q ss_pred             HhcCc--eeCCeEEEEeecCCC
Q 016231          302 AFNMA--VIGGNHIRLDRACPP  321 (393)
Q Consensus       302 ~lng~--~~~Gr~I~V~~a~~~  321 (393)
                       +++.  .+.|+.|.|.++.+.
T Consensus        64 -~~~~~~~~~g~~v~v~~a~~k   84 (89)
T 3d2w_A           64 -LCGEDLIIKGISVHISNAEPK   84 (89)
T ss_dssp             -HTTCEEEETTEEEEEEECC--
T ss_pred             -HcCCCcccCCEEEEEEEcCCC
Confidence             3444  456999999999754

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=1.2e-13  Score=111.56  Aligned_cols=75  Identities=16%  Similarity=0.265  Sum_probs=67.1

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+||  ++|+++|+.+|+.||.|..|.|.                       .++|||||+|.+.++|..|| 
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~-----------------------~~~g~afV~f~~~~~a~~Ai~   67 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD-----------------------PPRNCAFVTYEKMESADQAVA   67 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE-----------------------TTTTEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec-----------------------CCCCEEEEEECCHHHHHHHHH
Confidence            34689999996  89999999999999999999882                       14589999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCCc
Q 016231          302 AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      .||+..|.|+.|.|.++.+..
T Consensus        68 ~l~g~~~~g~~l~v~~a~~~~   88 (97)
T 1x5p_A           68 ELNGTQVESVQLKVNIARKQP   88 (97)
T ss_dssp             HTTTEEETTEEEEEECCSSCC
T ss_pred             HhCCCeECCeEEEEEECCCCC
Confidence            799999999999999997643

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.26  E-value=1.2e-15  Score=127.40  Aligned_cols=85  Identities=22%  Similarity=0.241  Sum_probs=73.1

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeE--------EEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCC
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDS--------VRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKS  293 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~s--------Vri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s  293 (393)
                      ....++|||+|||+.+++++|+.+|+.||.|..        |+|++++.                 ++.++|||||+|.+
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~-----------------~g~~~g~afV~f~~   66 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRE-----------------TGKLKGEATVSFDD   66 (116)
Confidence            345789999999999999999999999999988        77765431                 23466999999999


Q ss_pred             HHHHHHHH-HhcCceeCCeEEEEeecCCCcc
Q 016231          294 EQSTEAAL-AFNMAVIGGNHIRLDRACPPRK  323 (393)
Q Consensus       294 ~e~A~~Al-~lng~~~~Gr~I~V~~a~~~~~  323 (393)
                      .++|..|| .||+..|.|+.|.|.++.+...
T Consensus        67 ~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           67 PPSAKAAIDWFDGKEFSGNPIKVSFATRRAD   97 (116)
Confidence            99999999 5999999999999999976543

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=3.1e-14  Score=112.88  Aligned_cols=76  Identities=20%  Similarity=0.293  Sum_probs=64.4

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHh
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~l  303 (393)
                      ..++|||+|||+++|+++|+.+|+.||.|.+|+|+++                      ++|||||+|.+.++|+.|+..
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~----------------------~~g~afV~f~~~~~a~~~~~~   61 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----------------------FRAFAFVTFADDQIAQSLCGE   61 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----------------------CCSCCEEECSCHHHHHHTTTC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC----------------------CCCEEEEEECCHHHHHHHhcC
Confidence            4689999999999999999999999999999998431                      348999999999999865432


Q ss_pred             cCceeCCeEEEEeecCCCc
Q 016231          304 NMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~  322 (393)
                       ...+.|+.|.|.++.+..
T Consensus        62 -~~~~~g~~l~v~~a~~~~   79 (88)
T 1wf0_A           62 -DLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             -EEEETTEEEEEECCCCCC
T ss_pred             -CceeCCEEEEEEecCCCC
Confidence             345699999999997654

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.49  E-value=1.6e-13  Score=118.85  Aligned_cols=80  Identities=21%  Similarity=0.318  Sum_probs=71.6

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+.+|+++|+.+|+.||.|..|+++.++  .+               +.++|||||+|.+.++|..|+ 
T Consensus        85 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~--~~---------------~~~~g~afV~f~~~~~A~~A~~  147 (166)
T 3md3_A           85 DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDM--QT---------------GSSRGYGFVSFTSQDDAQNAMD  147 (166)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECT--TT---------------CCEEEEEEEEESCHHHHHHHHH
T ss_pred             CCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecC--CC---------------CCcceEEEEEeCCHHHHHHHHH
Confidence            447899999999999999999999999999999997754  12               236699999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecC
Q 016231          302 AFNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~  319 (393)
                      .|||..|.|+.|.|.++.
T Consensus       148 ~l~g~~~~g~~i~v~~a~  165 (166)
T 3md3_A          148 SMQGQDLNGRPLRINWAA  165 (166)
T ss_dssp             HHTTCEETTEECEEEESC
T ss_pred             HhCCCccCCcEEEEEecC
Confidence            599999999999999985

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.49  E-value=7.7e-14  Score=127.49  Aligned_cols=78  Identities=12%  Similarity=0.140  Sum_probs=69.6

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhc
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~ln  304 (393)
                      .++|||+|||+++|+++|+.+|+.||.|.+|+|+++.   .               +.++|||||+|.+.++|..||.+.
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~---~---------------~~~kG~aFVeF~~~e~A~~A~~~~  170 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL---H---------------KAFKGSIFVVFDSIESAKKFVETP  170 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT---T---------------CCEEEEEEEEESSHHHHHHHHHCT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC---C---------------CCcccEEEEEECCHHHHHHHHHhC
Confidence            6899999999999999999999999999999997753   1               236799999999999999999766


Q ss_pred             CceeCCeEEEEeecCC
Q 016231          305 MAVIGGNHIRLDRACP  320 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~  320 (393)
                      +..|.|+.|.|.+...
T Consensus       171 ~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          171 GQKYKETDLLILFKDD  186 (193)
T ss_dssp             TCEETTEECEEEETTT
T ss_pred             CCeECCEEEEEEEhHH
Confidence            6799999999998754

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.49  E-value=4.9e-14  Score=127.19  Aligned_cols=82  Identities=13%  Similarity=0.221  Sum_probs=72.4

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+.+++++|+.+|+.||.|..|.|+.++   +               +.++|||||+|.+.++|..||
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~---~---------------g~~kG~afV~F~~~~~A~~Ai  146 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR---S---------------GRSLGTADVHFERRADALKAM  146 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT---T---------------SSCSCCEEEEESCHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC---C---------------CCEeeEEEEEeCCHHHHHHHH
Confidence            3457899999999999999999999999999999996543   2               236699999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCC
Q 016231          302 -AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~  321 (393)
                       .||+..|.|+.|.|.++...
T Consensus       147 ~~lng~~l~Gr~l~V~~a~~~  167 (177)
T 2f3j_A          147 KQYKGVPLDGRPMDIQLVASQ  167 (177)
T ss_dssp             HHSTTCBCSSSBCEEEEESSG
T ss_pred             HHhCCCEECCEEEEEEEecCC
Confidence             59999999999999998643

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.49  E-value=9.6e-14  Score=127.52  Aligned_cols=78  Identities=21%  Similarity=0.373  Sum_probs=70.6

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      ..+|||+|||+.+|+++|+.+|+.||.|..|+|+++.    +               .++|||||+|.+.++|..|| .|
T Consensus       103 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~----~---------------~~~g~~fV~f~~~~~a~~Ai~~l  163 (213)
T 4f02_A          103 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE----N---------------GSKGYGFVHFETQEAAERAIEKM  163 (213)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET----T---------------EEEEEEEEEESSHHHHHHHHHHH
T ss_pred             cccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC----C---------------CCceEEEEEeCCHHHHHHHHHHh
Confidence            4689999999999999999999999999999997754    1               14699999999999999999 69


Q ss_pred             cCceeCCeEEEEeecCCC
Q 016231          304 NMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~  321 (393)
                      ||..|.|+.|.|.++.+.
T Consensus       164 ng~~~~g~~i~V~~a~~~  181 (213)
T 4f02_A          164 NGMLLNDRKVFVGRFKSR  181 (213)
T ss_dssp             TTCEETTEECEEEECCCH
T ss_pred             CCCEECCEEEEEEEcCCC
Confidence            999999999999999754

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.48  E-value=1.6e-13  Score=124.47  Aligned_cols=81  Identities=23%  Similarity=0.463  Sum_probs=72.5

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      .++|||+|||+.+|+++|+.+|+.||.|..|+|++++.  +               +.++|||||+|.+.++|..|+ .|
T Consensus       125 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~---------------g~~~g~afV~F~~~~~A~~A~~~l  187 (216)
T 2qfj_A          125 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPT--T---------------GKHKGYGFIEYEKAQSSQDAVSSM  187 (216)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTT--T---------------CCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCC--C---------------CCcCceEEEEecCHHHHHHHHHHc
Confidence            58999999999999999999999999999999977542  2               236699999999999999999 59


Q ss_pred             cCceeCCeEEEEeecCCCc
Q 016231          304 NMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~  322 (393)
                      |+..|.|+.|.|.++.++.
T Consensus       188 ~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          188 NLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             TTCBCSSSBCEEEECSSCS
T ss_pred             cCCEeCCcEEEEEEecCCC
Confidence            9999999999999997653

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.48  E-value=5.4e-14  Score=122.53  Aligned_cols=80  Identities=20%  Similarity=0.321  Sum_probs=71.3

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhc
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~ln  304 (393)
                      .++|||+|||+.+|+++|+.+|+.||.|..|+++.++  .+               +.++|||||+|.+.++|..|+.++
T Consensus        87 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~--~~---------------g~~~g~afV~f~~~~~a~~A~~~~  149 (167)
T 2cjk_A           87 TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDK--DT---------------GQSRGFGFVTYDSADAVDRVCQNK  149 (167)
T ss_dssp             CEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSS--SS---------------STTSEEEEEEESSHHHHHHHHHCS
T ss_pred             CCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcC--CC---------------CccceEEEEEECCHHHHHHHHhCC
Confidence            4689999999999999999999999999999986643  12               346699999999999999999999


Q ss_pred             CceeCCeEEEEeecCCC
Q 016231          305 MAVIGGNHIRLDRACPP  321 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~~  321 (393)
                      +..|.|+.|.|.++.+.
T Consensus       150 ~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          150 FIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             EECSSSSCEEEEECCCC
T ss_pred             CEEeCCeEEEEeecCCC
Confidence            99999999999998753

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.48  E-value=9.1e-14  Score=142.14  Aligned_cols=81  Identities=19%  Similarity=0.301  Sum_probs=72.4

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|||+|||+.+|+++|..+|+.||.|..|.|+.++.  +               +.++|||||+|.+.++|..|| .
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~--t---------------g~~kG~aFV~F~~~e~A~~Ai~~  163 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKR--S---------------GKPRGYAFIEYEHERDMHSAYKH  163 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCC--C---------------CCccceEEEeeccHHHHHHHHHH
Confidence            468999999999999999999999999999999976542  2               336699999999999999999 7


Q ss_pred             hcCceeCCeEEEEeecCCC
Q 016231          303 FNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~  321 (393)
                      ||+..|.|+.|.|.++.+.
T Consensus       164 lng~~i~gr~i~V~~a~~~  182 (437)
T 3pgw_S          164 ADGKKIDGRRVLVDVERGR  182 (437)
T ss_pred             cCCCEECCEEEEEEEeCCC
Confidence            9999999999999999753

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.47  E-value=1.9e-13  Score=122.10  Aligned_cols=81  Identities=17%  Similarity=0.390  Sum_probs=70.8

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhc
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~ln  304 (393)
                      .++|||+|||+.+|+++|+.+|+.||.|..|+|++++  .+               +.++|||||+|.+.++|..||..+
T Consensus       104 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~--~~---------------g~~~g~afV~F~~~~~A~~A~~~~  166 (196)
T 1l3k_A          104 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR--GS---------------GKKRGFAFVTFDDHDSVDKIVIQK  166 (196)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECT--TT---------------CCEEEEEEEEESSHHHHHHHHHCS
T ss_pred             cceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecC--CC---------------CCccceEEEEECCHHHHHHHHHhC
Confidence            5899999999999999999999999999999997754  12               236699999999999999999879


Q ss_pred             CceeCCeEEEEeecCCCc
Q 016231          305 MAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~~~  322 (393)
                      +..|.|+.|.|.++.+..
T Consensus       167 ~~~~~G~~i~v~~a~~k~  184 (196)
T 1l3k_A          167 YHTVNGHNCEVRKALSKQ  184 (196)
T ss_dssp             CCEETTEECEEEECC---
T ss_pred             CcEECCEEEEEEecCChh
Confidence            999999999999997654

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=6.8e-14  Score=118.08  Aligned_cols=74  Identities=15%  Similarity=0.246  Sum_probs=65.5

Q ss_pred             CcccEEEE--eCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          223 KLLRTIFV--GNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       223 ~~~rtVFV--gNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      .+.++|||  ||||+++++++|+++|++||.|.+|.|+.                       ++|||||+|.+.++|+.|
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~-----------------------~rgfaFV~f~~~~~A~~A   79 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----------------------NKPYSFARYRTTEESKRA   79 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT-----------------------TCSCEEEEESSHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----------------------CCCEEEEEECCHHHHHHH
Confidence            34788999  77999999999999999999999988732                       248999999999999999


Q ss_pred             H-HhcCcee-----CCeEEEEeecC
Q 016231          301 L-AFNMAVI-----GGNHIRLDRAC  319 (393)
Q Consensus       301 l-~lng~~~-----~Gr~I~V~~a~  319 (393)
                      + .|||..|     .|+.|.|.++.
T Consensus        80 i~~lnG~~~~~~lg~g~~l~v~~a~  104 (114)
T 2cq2_A           80 YVTLNGKEVVDDLGQKITLYLNFVE  104 (114)
T ss_dssp             HHHTTTCEEECTTSCEEECEEEEES
T ss_pred             HHHhCCCEEccccCCCcEEEEEecc
Confidence            9 6999988     68999998875

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.46  E-value=1.6e-13  Score=120.10  Aligned_cols=78  Identities=18%  Similarity=0.341  Sum_probs=70.2

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      .++|||+|||+.+|+++|+.+|+.||.|..|++++++  .+               +.++|||||+|.+.++|..|+ .|
T Consensus        94 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~--~~---------------g~~~g~afV~f~~~~~A~~A~~~l  156 (172)
T 2g4b_A           94 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS--AT---------------GLSKGYAFCEYVDINVTDQAIAGL  156 (172)
T ss_dssp             TTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECT--TT---------------CSEEEEEEEEESSTTHHHHHHHHH
T ss_pred             CCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecC--CC---------------CCcceEEEEEeCCHHHHHHHHHHc
Confidence            6899999999999999999999999999999997754  12               236699999999999999999 59


Q ss_pred             cCceeCCeEEEEeecC
Q 016231          304 NMAVIGGNHIRLDRAC  319 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~  319 (393)
                      ||..|.|+.|.|.+|+
T Consensus       157 ~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          157 NGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             TTCEETTEECEEEECC
T ss_pred             CCCEECCeEEEEEeCC
Confidence            9999999999999873

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.46  E-value=1.3e-13  Score=114.87  Aligned_cols=80  Identities=23%  Similarity=0.289  Sum_probs=63.4

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+++|+++|+.+|+.||.|. +.++.+..  +.            ..+.++|||||+|.+.++|+.|| 
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~--~~------------~~g~~~G~aFV~f~~~~~a~~Ai~   70 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAE--SK------------SYFPPKGYAFLLFQEESSVQALID   70 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSS--SC------------CCSCTTSEEEECCSSHHHHHHHHH
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCC--CC------------CCCCcccEEEEEECCHHHHHHHHH
Confidence            3478999999999999999999999999999 77744331  10            01347799999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecC
Q 016231          302 AFNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~  319 (393)
                      .++  .++|+.|.+..+.
T Consensus        71 ~~~--~~~G~~~~~~~~~   86 (114)
T 2dnl_A           71 ACL--EEDGKLYLCVSSP   86 (114)
T ss_dssp             HSE--EETTEEEEEECCS
T ss_pred             hhh--hcCCcEEEeccCC
Confidence            564  4788888776543

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=99.45  E-value=7.7e-14  Score=116.75  Aligned_cols=74  Identities=14%  Similarity=0.163  Sum_probs=63.8

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|||+|||+++|+++|+.+|+.||.|..|.|+.+                        |||||+|.+.++|..|| .
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~------------------------g~afV~f~~~~~a~~Ai~~   70 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------------------------GTGVVEFVRKEDMTYAVRK   70 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------------------------SEEEEEESSHHHHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC------------------------CEEEEEECCHHHHHHHHHH
Confidence            4688999999999999999999999999999988321                        69999999999999999 5


Q ss_pred             hcCceeCCeE-----EEEeecCCC
Q 016231          303 FNMAVIGGNH-----IRLDRACPP  321 (393)
Q Consensus       303 lng~~~~Gr~-----I~V~~a~~~  321 (393)
                      ||+..|.|+.     |.|..+.+.
T Consensus        71 l~g~~~~gr~~~~~~i~v~~~~~~   94 (115)
T 3beg_B           71 LDNTKFRSHEGETAYIRVKVDGPR   94 (115)
T ss_dssp             HTTCBCCCTTSCCCBCEEEECC--
T ss_pred             hCCCEECCcEeeeEEEEeccCCCC
Confidence            9999999988     777776543

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.45  E-value=1.8e-13  Score=122.42  Aligned_cols=77  Identities=21%  Similarity=0.217  Sum_probs=68.0

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      -.+|||+|||+.+|+++|+.+|+.||.|.+|+|....                     ++|||||+|.+.++|..|+ .|
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~---------------------~rgfAFVeF~d~~~A~~Ai~~L  104 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---------------------NQFQALLQYADPVSAQHAKLSL  104 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS---------------------SCEEEEEEESCHHHHHHHHHHS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC---------------------CCCEEEEEECCHHHHHHHHHHh
Confidence            4679999999999999999999999999999984311                     3489999999999999999 69


Q ss_pred             cCceeCC--eEEEEeecCCCc
Q 016231          304 NMAVIGG--NHIRLDRACPPR  322 (393)
Q Consensus       304 ng~~~~G--r~I~V~~a~~~~  322 (393)
                      ||..|.|  +.|+|.++.+..
T Consensus       105 nG~~i~g~g~~L~V~~Ak~~~  125 (164)
T 1sjr_A          105 DGQNIYNACCTLRIDFSKLTS  125 (164)
T ss_dssp             TTBCSSSSCSCEEEEECSSSS
T ss_pred             CCCEecCCCcEEEEEEecCCc
Confidence            9999965  999999998653

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.45  E-value=4.3e-13  Score=115.69  Aligned_cols=76  Identities=21%  Similarity=0.214  Sum_probs=67.3

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceE-EEEeeCCHHHHHHHH-H
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVH-AYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~-AFVeF~s~e~A~~Al-~  302 (393)
                      -..|||+||++.+|+++|+.+|+.||.|.+|+|...                      ++|| |||+|.+.++|..|+ .
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~----------------------~~gfqAFVef~~~~~A~~Ai~~   85 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----------------------NNQFQALLQYADPVSAQHAKLS   85 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE----------------------TTEEEEEEEESCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC----------------------CCCcEEEEEECCHHHHHHHHHH
Confidence            456889999999999999999999999999988542                      2367 999999999999999 7


Q ss_pred             hcCceeCC--eEEEEeecCCCc
Q 016231          303 FNMAVIGG--NHIRLDRACPPR  322 (393)
Q Consensus       303 lng~~~~G--r~I~V~~a~~~~  322 (393)
                      |||..|.|  +.|+|+++.+..
T Consensus        86 LnG~~i~g~~~~LrI~~ak~~~  107 (130)
T 3zzy_A           86 LDGQNIYNACCTLRIDFSKLTS  107 (130)
T ss_dssp             HTTCEEETTEEEEEEEECSCSS
T ss_pred             cCCCeecCCCcEEEEEecCCCc
Confidence            99999988  999999997653

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.45  E-value=2.9e-13  Score=118.34  Aligned_cols=77  Identities=22%  Similarity=0.351  Sum_probs=68.0

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|||+|||+.+|+++|+.+|+.||.|.+|+|++++   .               +.++|||||+|.+.++|..|+ .
T Consensus        94 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~---~---------------g~~~g~afV~f~~~~~A~~A~~~  155 (175)
T 3nmr_A           94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP---D---------------GLSRGCAFVTFTTRAMAQTAIKA  155 (175)
T ss_dssp             GGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT---T---------------SCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC---C---------------CCEEEEEEEEECCHHHHHHHHHH
Confidence            46899999999999999999999999999999997753   1               235699999999999999999 7


Q ss_pred             hcCceeC---CeEEEEeec
Q 016231          303 FNMAVIG---GNHIRLDRA  318 (393)
Q Consensus       303 lng~~~~---Gr~I~V~~a  318 (393)
                      |||..+.   |++|.|.++
T Consensus       156 l~g~~~~~g~~~~l~V~~a  174 (175)
T 3nmr_A          156 MHQAQTMEGCSSPMVVKFA  174 (175)
T ss_dssp             HTTSCCCTTCSSCCEEEEC
T ss_pred             hcCCcccCCCCCCeEEEec
Confidence            9998776   499999987

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.45  E-value=3.4e-13  Score=120.61  Aligned_cols=83  Identities=17%  Similarity=0.298  Sum_probs=73.3

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+.+++++|+.+|+.||.|..|+|++++  .+               +.++|||||+|.+.++|..|+ 
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~--~~---------------~~~~g~afV~f~~~~~a~~A~~  174 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS--AT---------------GLSKGYAFCEYVDINVTDQAIA  174 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECT--TT---------------CSEEEEEEEEESSSSHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecC--CC---------------CCcceEEEEEECCHHHHHHHHH
Confidence            457999999999999999999999999999999997654  12               235699999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCCc
Q 016231          302 AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      .||+..|.|+.|.|.++.+..
T Consensus       175 ~l~g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          175 GLNGMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             HHTTCEETTEECEEEESCCCC
T ss_pred             HcCCCEECCEEEEEEECCCCC
Confidence            599999999999999997653

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.43  E-value=4.1e-13  Score=114.90  Aligned_cols=74  Identities=20%  Similarity=0.185  Sum_probs=64.8

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceE-EEEeeCCHHHHHHHH-Hh
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVH-AYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~-AFVeF~s~e~A~~Al-~l  303 (393)
                      ..|||+|||+.+|+++|+.+|+.||.|.+|+|...                       .|| |||+|.+.++|..|+ .|
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-----------------------~Gf~aFVef~~~~~A~~A~~~L   82 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-----------------------NGIQAMVEFESVLCAQKAKAAL   82 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-----------------------SSEEEEEEESSHHHHHHHHHHH
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-----------------------CCCEEEEEECCHHHHHHHHHHh
Confidence            34789999999999999999999999999998331                       166 999999999999999 69


Q ss_pred             cCceeCC--eEEEEeecCCCc
Q 016231          304 NMAVIGG--NHIRLDRACPPR  322 (393)
Q Consensus       304 ng~~~~G--r~I~V~~a~~~~  322 (393)
                      ||..|.|  +.|+|.++.+..
T Consensus        83 nG~~i~g~~~~l~V~~Ak~~~  103 (124)
T 2e5i_A           83 NGADIYAGCCTLKIEYARPTR  103 (124)
T ss_dssp             TTCCCBTTBSEEEEECCSCSC
T ss_pred             CCCEecCCCeEEEEEEecCCc
Confidence            9999987  699999997653

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.43  E-value=4.7e-13  Score=116.45  Aligned_cols=79  Identities=22%  Similarity=0.308  Sum_probs=69.5

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+.+++++|+.+|+.||.|..|++++++.  +               +.++|||||+|.+.++|..|+ 
T Consensus        87 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~--~---------------~~~~g~afV~f~~~~~A~~A~~  149 (168)
T 1b7f_A           87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKL--T---------------GRPRGVAFVRYNKREEAQEAIS  149 (168)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTT--T---------------CCEEEEEEEEESSHHHHHHHHH
T ss_pred             CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCC--C---------------CCcceEEEEEECCHHHHHHHHH
Confidence            3468999999999999999999999999999999976541  2               235699999999999999999 


Q ss_pred             HhcCceeCC--eEEEEeec
Q 016231          302 AFNMAVIGG--NHIRLDRA  318 (393)
Q Consensus       302 ~lng~~~~G--r~I~V~~a  318 (393)
                      .||+..|.|  +.|.|.+|
T Consensus       150 ~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          150 ALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHTTCCCTTCSSCCEEEEC
T ss_pred             HhcCCEecCCCeEEEEEeC
Confidence            599999988  99999875

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.41  E-value=6.6e-13  Score=114.97  Aligned_cols=78  Identities=24%  Similarity=0.335  Sum_probs=67.7

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|||+|||+.+++++|+.+|+.||.|..|+++.++.  +               +.++|||||+|.+.++|..|+ .
T Consensus        87 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~--~---------------g~~~g~afV~f~~~~~A~~A~~~  149 (167)
T 1fxl_A           87 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQV--T---------------GVSRGVGFIRFDKRIEAEEAIKG  149 (167)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT--T---------------CCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCC--C---------------CCccceEEEEeCCHHHHHHHHHH
Confidence            357899999999999999999999999999999976541  2               235699999999999999999 5


Q ss_pred             hcCceeCCeE--EEEeec
Q 016231          303 FNMAVIGGNH--IRLDRA  318 (393)
Q Consensus       303 lng~~~~Gr~--I~V~~a  318 (393)
                      |||..|.|+.  |.|.+|
T Consensus       150 l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          150 LNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             HTTCCCTTCSSCCEEEEC
T ss_pred             hcCCccCCCccceEEEeC
Confidence            9999999975  777765

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.40  E-value=4.6e-13  Score=115.24  Aligned_cols=77  Identities=17%  Similarity=0.140  Sum_probs=65.2

Q ss_pred             cEEEEeCC----CccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCC----HHH-
Q 016231          226 RTIFVGNL----PLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKS----EQS-  296 (393)
Q Consensus       226 rtVFVgNL----p~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s----~e~-  296 (393)
                      ..|||+||    |+.+++.+|+.+|+.||+|.+|.++.+|  .++.               ++|||||+|.+    ++. 
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp--~Tg~---------------slGfgfVef~d~~g~~d~a   65 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDP--NSAL---------------PLHVYLIKYASSDGKINDA   65 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECT--TTCC---------------EEEEEEEECC------CCH
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecC--CCCc---------------eeeEEEEEECCCCCCcchH
Confidence            57999999    9999999999999999999999999987  3444               55999999996    322 


Q ss_pred             ---HHHHHH---hcCceeCCeEEEEeecC
Q 016231          297 ---TEAALA---FNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       297 ---A~~Al~---lng~~~~Gr~I~V~~a~  319 (393)
                         |..|+.   +||..|.|+.|+|....
T Consensus        66 ~kAA~kAi~~~~lng~~I~Gr~irV~ln~   94 (136)
T 2j8a_A           66 AKAAFSAVRKHESSGCFIMGFKFEVILNK   94 (136)
T ss_dssp             HHHHHHHHHHTTTTCEEETTEEEEEEECC
T ss_pred             HHHHHHHHHHhhhcCCeecCcEEEEEECc
Confidence               667764   79999999999999864

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.40  E-value=3.9e-13  Score=109.60  Aligned_cols=71  Identities=24%  Similarity=0.231  Sum_probs=62.5

Q ss_pred             cccE-EEEeCCCccCCHHH----HHHHhccc-CCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHH
Q 016231          224 LLRT-IFVGNLPLKVKKKT----LIKEFIKF-GEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQST  297 (393)
Q Consensus       224 ~~rt-VFVgNLp~~~tee~----L~~~Fs~~-G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A  297 (393)
                      ++.| |||+|||+.+++++    |+.+|+.| |.|.+|.                           .|+|||.|.+.++|
T Consensus         7 p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~Vt---------------------------gG~AfV~F~~~esA   59 (96)
T 2diu_A            7 GCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSIT---------------------------GCSAILRFINQDSA   59 (96)
T ss_dssp             CSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEECC---------------------------TTCEEEEESSHHHH
T ss_pred             CcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEEe---------------------------cCEEEEEECCHHHH
Confidence            4666 99999999999988    55899999 5998771                           07999999999999


Q ss_pred             HHHH-HhcCceeCCeEEEEeecCCC
Q 016231          298 EAAL-AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       298 ~~Al-~lng~~~~Gr~I~V~~a~~~  321 (393)
                      ..|+ .|||..|.||+|+|.++...
T Consensus        60 ~~A~~~l~G~~l~gr~i~v~~A~~~   84 (96)
T 2diu_A           60 ERAQKRMENEDVFGNRIIVSFTPKN   84 (96)
T ss_dssp             HHHHHHHTTCCSSSSCCEEESSCCS
T ss_pred             HHHHHHhcCCccCCceEEEEecCCC
Confidence            9999 79999999999999999754

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.39  E-value=2.5e-12  Score=106.59  Aligned_cols=82  Identities=16%  Similarity=0.210  Sum_probs=68.8

Q ss_pred             CcccEEEEeCCCc-----cCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHH
Q 016231          223 KLLRTIFVGNLPL-----KVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQST  297 (393)
Q Consensus       223 ~~~rtVFVgNLp~-----~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A  297 (393)
                      .++++|+|+||..     +.++++|+.+|++||.|.+|.|++++.. +               +.++|||||+|.+.++|
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~-~---------------~~~~G~~FV~f~~~~~A   69 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGA-P---------------DDEAVRIFLEFERVESA   69 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSC-C---------------TTTSEEEEEEESSHHHH
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCC-C---------------CCCcEEEEEEECCHHHH
Confidence            3579999999963     2478999999999999999999775421 1               23669999999999999


Q ss_pred             HHHH-HhcCceeCCeEEEEeecCC
Q 016231          298 EAAL-AFNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       298 ~~Al-~lng~~~~Gr~I~V~~a~~  320 (393)
                      ..|+ .|||..|.||.|.|.++..
T Consensus        70 ~~Ai~~lnG~~~~Gr~i~v~~a~~   93 (105)
T 2pe8_A           70 IKAVVDLNGRYFGGRVVKACFYNL   93 (105)
T ss_dssp             HHHHHHHTTCEETTEECEEEECCH
T ss_pred             HHHHHHHCCCEECCcEEEEEEcCH
Confidence            9999 7999999999999999853

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.36  E-value=8.9e-13  Score=124.80  Aligned_cols=76  Identities=21%  Similarity=0.333  Sum_probs=68.7

Q ss_pred             CCcccEEEEeCCCccC---------CHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeC
Q 016231          222 GKLLRTIFVGNLPLKV---------KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFK  292 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~---------tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~  292 (393)
                      ....++|||||||+.+         ++++|+.+|+.||.|.+|+|+.                       ++|||||+|.
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~-----------------------~kG~AFV~F~  187 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE-----------------------SKNCGFVKFK  187 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG-----------------------GGTEEEEEES
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC-----------------------CCCEEEEEeC
Confidence            4568999999999998         7999999999999999999853                       3489999999


Q ss_pred             CHHHHHHHH-HhcCcee------------CCeEEEEeecCC
Q 016231          293 SEQSTEAAL-AFNMAVI------------GGNHIRLDRACP  320 (393)
Q Consensus       293 s~e~A~~Al-~lng~~~------------~Gr~I~V~~a~~  320 (393)
                      +.++|+.|+ .|++..|            .|+.|.|.|+..
T Consensus       188 ~~~~Ae~A~~am~g~~l~~~~~~e~~~~~~gr~L~V~wA~~  228 (240)
T 3u1l_A          188 YQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANE  228 (240)
T ss_dssp             SHHHHHHHHHHHTTCCCCCTTSTTGGGGGGSCCCEEEECC-
T ss_pred             CHHHHHHHHHHhCCCEEeccccccccccCCCCEEEEEEccC
Confidence            999999999 7999999            899999999964

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.36  E-value=2.3e-12  Score=113.35  Aligned_cols=76  Identities=29%  Similarity=0.322  Sum_probs=66.0

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+.+|+++|+.+|+.||.|..+     .  .+               +.++|||||+|.+.++|..|+ 
T Consensus        97 ~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~--~~---------------~~~~g~afV~f~~~~~A~~A~~  154 (175)
T 1fje_B           97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----S--QD---------------GKSKGIAYIEFKSEADAEKNLE  154 (175)
T ss_dssp             GGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----C--SS---------------SSCCSEEEEECSSHHHHHHHHH
T ss_pred             ccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----c--CC---------------CCCceEEEEEECCHHHHHHHHH
Confidence            347899999999999999999999999987644     1  12               236699999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCC
Q 016231          302 AFNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~  320 (393)
                      .|||..|.|+.|.|.++.+
T Consensus       155 ~l~g~~~~g~~i~v~~a~~  173 (175)
T 1fje_B          155 EKQGAEIDGRSVSLYYTGE  173 (175)
T ss_dssp             HHTEEEETTEEEEEEECSS
T ss_pred             HhCCCEECCeEEEEEecCC
Confidence            5999999999999999864

>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=99.35  E-value=8.9e-13  Score=107.67  Aligned_cols=56  Identities=25%  Similarity=0.437  Sum_probs=51.8

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ....++|||+|||+++|+++|+++|+.|    |.|.+|+|++|+.+|.++|||||+|.++
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~----G~I~~v~i~~d~~tg~~kG~afV~f~~~   71 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSI----GEVESAKLIRDKVAGHSLGYGFVNYVTA   71 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTT----SCEEEEEEEECSSSCCEEEEEEEEESSH
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEeEeeecCCCCcccccEEEEECCH
Confidence            3345789999999999999999999999    9999999999999999999999999874

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.34  E-value=6.7e-12  Score=104.29  Aligned_cols=81  Identities=16%  Similarity=0.203  Sum_probs=67.2

Q ss_pred             CCCcccEEEEeCCCccC-----------CHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEE
Q 016231          221 EGKLLRTIFVGNLPLKV-----------KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYI  289 (393)
Q Consensus       221 ~~~~~rtVFVgNLp~~~-----------tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFV  289 (393)
                      ...++++|+|.||....           ++++|+.+|++||.|.+|.| .+.                    .++|||||
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~--------------------~~~G~afV   69 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR--------------------HPDGVASV   69 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT--------------------CTTCEEEE
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC--------------------CCCEEEEE
Confidence            34568999999994332           26899999999999999966 221                    14599999


Q ss_pred             eeCCHHHHHHHH-HhcCceeCCeEEEEeecCCCc
Q 016231          290 VFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       290 eF~s~e~A~~Al-~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      +|.+.++|..|+ .|||..|.|+.|.|.++.+..
T Consensus        70 ~f~~~~~A~~Ai~~lng~~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           70 SFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTT  103 (112)
T ss_dssp             ECSCHHHHHHHHHHSTTCEETTEECEEEECCSCC
T ss_pred             EECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCC
Confidence            999999999999 799999999999999997643

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.33  E-value=2.8e-13  Score=108.81  Aligned_cols=53  Identities=21%  Similarity=0.358  Sum_probs=50.0

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCC-CeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLES-SVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G-~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +++|||+|||+++|+++|+++|+.|    | .|.+|+|++|+.+|.++|||||+|.++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~----G~~v~~v~i~~d~~t~~~rg~aFV~F~~~   54 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSH----GVQAREVRLMRNKSSGQSRGFAFVEFSHL   54 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHH----TCCCSBCCSSSCSSSCCCSSEEEEECSSH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHh----CCEeEEEEEEecCCCCCcCceEEEEecCH
Confidence            3689999999999999999999999    8 899999999999999999999999874

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.32  E-value=6.1e-13  Score=108.29  Aligned_cols=54  Identities=17%  Similarity=0.341  Sum_probs=49.7

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCC--CeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLES--SVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G--~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .-.||||+|||+++|+++|+++|+.|    |  .|..|+|++|+.+|.+||||||+|.++
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~----G~i~v~~v~i~~d~~tg~srG~aFV~f~~~   63 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPY----ASLAVNNIRLIKDKQTQQNRGFAFVQLSSA   63 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTT----CCCCGGGEECCCCSSSSSCSSEEEEECSSS
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhh----CCccEEEEEEEecCCCCCCceEeEEEECCH
Confidence            34799999999999999999999999    7  467999999999999999999999874

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.32  E-value=4.7e-12  Score=120.19  Aligned_cols=76  Identities=24%  Similarity=0.261  Sum_probs=68.4

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+.+|+++|+.+|+.||.|.+|+|+.+                      .+|||||+|.+.++|..||
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~----------------------~~g~afV~f~~~~~A~~A~  261 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG----------------------RHDIAFVEFDNEVQAGAAR  261 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecC----------------------CCcEEEEEeCCHHHHHHHH
Confidence            345789999999999999999999999999999998532                      1389999999999999999


Q ss_pred             -HhcCceeC-CeEEEEeecC
Q 016231          302 -AFNMAVIG-GNHIRLDRAC  319 (393)
Q Consensus       302 -~lng~~~~-Gr~I~V~~a~  319 (393)
                       .|||..|. |+.|.|.++.
T Consensus       262 ~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          262 DALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             HHcCCcEeCCCCEEEEEEec
Confidence             69999999 9999999974

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.30  E-value=1.1e-12  Score=113.03  Aligned_cols=94  Identities=16%  Similarity=0.216  Sum_probs=54.1

Q ss_pred             eEEEEeeCCHHHHHHHH-HhcCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCC
Q 016231          285 VHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDL  363 (393)
Q Consensus       285 G~AFVeF~s~e~A~~Al-~lng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~  363 (393)
                      -|+|++|.+...+..|| .+++....|+. .+.+..+         .+...+.++|||+|||+.+++++|+++|+.|   
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~g~~-~~~~~~~---------~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~---   71 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQMGRG-SMSYGRP---------PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKY---   71 (135)
T ss_dssp             -------------------------------CCSCCS---------CSSGGGCCCEEEECCCSSCHHHHHHHHHGGG---
T ss_pred             ccccccccCCCchhhhhhhccCCCCCCCC-CCCcCCC---------CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhc---
Confidence            47888888888888888 57776655543 1112211         2234467899999999999999999999999   


Q ss_pred             CCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          364 ESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       364 ~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                       |.|..|+|++++.+|.++|||||+|.+.
T Consensus        72 -G~i~~v~i~~~~~~g~~~G~afV~F~~~   99 (135)
T 2lea_A           72 -GRVGDVYIPRDRYTKESRGFAFVRFHDK   99 (135)
T ss_dssp             -SCCSEEECCCCSSSSSCCSCCEEECSCH
T ss_pred             -CCEEEEEEEecCCCCccceEEEEEECCH
Confidence             9999999999998999999999999874

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.30  E-value=3.8e-12  Score=100.22  Aligned_cols=56  Identities=21%  Similarity=0.474  Sum_probs=52.3

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.++
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~g~~~g~afV~f~~~   63 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKF----GEVVDCTIKMDPNTGRSRGFGFILFKDA   63 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTT----SCEEEEEEEECTTTCCEEEEEEEEESST
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhC----CCEEEEEEeecCCCCccccEEEEEECCH
Confidence            3456899999999999999999999999    9999999999999999999999999874

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.29  E-value=3e-12  Score=115.14  Aligned_cols=76  Identities=21%  Similarity=0.267  Sum_probs=68.3

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccC-CeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFG-EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G-~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      .+.++|||+|||+.+++++|+.+|+.|| .|..|+|+..                      ++|||||+|.+.++|..|+
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~----------------------~~g~afV~f~~~~~A~~A~  175 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----------------------DRKMALIQMGSVEEAVQAL  175 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST----------------------TSSCEEEECSSHHHHHHHH
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC----------------------CCcEEEEEeCCHHHHHHHH
Confidence            3479999999999999999999999999 9999998331                      2489999999999999999


Q ss_pred             -HhcCceeC-CeEEEEeecCC
Q 016231          302 -AFNMAVIG-GNHIRLDRACP  320 (393)
Q Consensus       302 -~lng~~~~-Gr~I~V~~a~~  320 (393)
                       .|||..|. |+.|.|.++.+
T Consensus       176 ~~l~g~~~~~g~~l~v~~a~~  196 (198)
T 1qm9_A          176 IDLHNHDLGENHHLRVSFSKS  196 (198)
T ss_dssp             HHHTSSCCSSCCSCCEEEECC
T ss_pred             HHhcCCccCCCCeEEEEeecc
Confidence             69999999 99999999864

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.29  E-value=3.9e-12  Score=104.81  Aligned_cols=54  Identities=20%  Similarity=0.365  Sum_probs=50.3

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...++|||+|||+++|+++|+++|+.|    |.|.+|+|++++. |.++|||||+|.++
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~----G~v~~v~i~~d~~-g~~rG~aFV~F~~~   62 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDK----GQVLNIQMRRTLH-KAFKGSIFVVFDSI   62 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTS----SCEEEEEEECCCT-TSCCCEEEEEESSH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhc----CCEEEEEEEECCC-CCCccEEEEEECCH
Confidence            346899999999999999999999999    9999999999987 99999999999874

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.29  E-value=3.3e-12  Score=106.40  Aligned_cols=55  Identities=27%  Similarity=0.344  Sum_probs=51.8

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+.++|||+|||+.+++++|+++|+.|    |.|..|+|++|+.+|.++|||||+|.+.
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~----G~i~~v~i~~d~~tg~~rG~aFV~f~~~   58 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKY----GEVEEVEILLHPRTRKHLGLARVLFTST   58 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTT----SCEEEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhc----CCeeEEEEEECCCCCceeeEEEEEECCH
Confidence            356899999999999999999999999    9999999999999999999999999874

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.28  E-value=7.6e-12  Score=116.03  Aligned_cols=75  Identities=21%  Similarity=0.273  Sum_probs=67.9

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccC-CeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFG-EIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G-~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      +.++|||+|||+.+++++|+.+|+.|| .|..|+|+..                      ++|||||+|.+.++|..|+ 
T Consensus       150 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~----------------------~~g~afV~f~~~~~A~~Ai~  207 (229)
T 2adc_A          150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----------------------DRKMALIQMGSVEEAVQALI  207 (229)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS----------------------STTCEEEEESSHHHHHHHHH
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC----------------------CCcEEEEEECCHHHHHHHHH
Confidence            468999999999999999999999999 9999998321                      3489999999999999999 


Q ss_pred             HhcCceeC-CeEEEEeecCC
Q 016231          302 AFNMAVIG-GNHIRLDRACP  320 (393)
Q Consensus       302 ~lng~~~~-Gr~I~V~~a~~  320 (393)
                      .|||..|. |+.|.|.++.+
T Consensus       208 ~l~g~~~~~g~~l~v~~a~~  227 (229)
T 2adc_A          208 DLHNHDLGENHHLRVSFSKS  227 (229)
T ss_dssp             HHTTCBSSSSCBCEEEECSS
T ss_pred             HHCCCccCCCCeEEEEEecC
Confidence            59999999 99999999864

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.27  E-value=4.1e-12  Score=112.56  Aligned_cols=100  Identities=14%  Similarity=0.206  Sum_probs=52.0

Q ss_pred             EeeCCHHHHHHHH-HhcCceeC--CeEEEEeecCCCcccC-----------CCCCCCCcCCcceeeeCCCCCCCCHHHHH
Q 016231          289 IVFKSEQSTEAAL-AFNMAVIG--GNHIRLDRACPPRKKL-----------KGEDAPLYDIKKTVFVGNLPFDVKDEEIY  354 (393)
Q Consensus       289 VeF~s~e~A~~Al-~lng~~~~--Gr~I~V~~a~~~~~~~-----------~~~~~~~~~~~~tLfVgNLp~~~teedL~  354 (393)
                      .+|.+.+++..|+ .+++....  |+.+.+.++.......           .........+.++|||+|||+.+++++|+
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~   90 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQ   90 (165)
T ss_dssp             -------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHH
Confidence            7889999999998 67776654  6666665532211000           00011123456789999999999999999


Q ss_pred             HHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          355 QLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       355 e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+|..|    |.|..|.|+.++.+|.++|||||+|.+.
T Consensus        91 ~~F~~~----G~i~~v~i~~~~~~g~~~g~afV~f~~~  124 (165)
T 1rk8_A           91 EKFCDY----GEIKNIHLNLDRRTGFSKGYALVEYETH  124 (165)
T ss_dssp             HHHGGG----SCEEEEEEEECTTTSSEEEEEEEEESSH
T ss_pred             HHhhcC----CCEEEEEEEecCCCCcEeeEEEEEECCH
Confidence            999999    9999999999999999999999999863

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.27  E-value=8.7e-12  Score=100.61  Aligned_cols=56  Identities=20%  Similarity=0.436  Sum_probs=52.3

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~   62 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKF----GVVTEVVMIYDAEKQRPRGFGFITFEDE   62 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSS----SCEEEEEECCCTTTCSCCSEEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEeCCCCCCCCceEEEEECCH
Confidence            4467899999999999999999999999    9999999999999999999999999864

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.26  E-value=1.8e-11  Score=115.74  Aligned_cols=79  Identities=15%  Similarity=0.185  Sum_probs=68.5

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      .++|||+|||+.+|+++|+.+|+.||.|..|+|+.+.   +               +.++|||||+|.+.++|..|| .|
T Consensus        96 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~---~---------------g~~~g~afV~f~~~~~A~~A~~~l  157 (261)
T 3sde_A           96 GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD---R---------------GRATGKGFVEFAAKPPARKALERC  157 (261)
T ss_dssp             SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET---T---------------SCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCC---C---------------CCcCcEEEEEeCCHHHHHHHHHHh
Confidence            5789999999999999999999999999999997763   2               236699999999999999999 67


Q ss_pred             -cCceeC---CeEEEEeecCCC
Q 016231          304 -NMAVIG---GNHIRLDRACPP  321 (393)
Q Consensus       304 -ng~~~~---Gr~I~V~~a~~~  321 (393)
                       ++..+.   |+.|.|.++.+.
T Consensus       158 ~~~~~~~~~~~r~i~v~~~~~~  179 (261)
T 3sde_A          158 GDGAFLLTTTPRPVIVEPMEQF  179 (261)
T ss_dssp             HHSCEESSSSCCBCEEEECCCE
T ss_pred             cCCeEEecCCCceEEEeecccc
Confidence             555555   999999998754

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.26  E-value=1.3e-12  Score=133.71  Aligned_cols=55  Identities=16%  Similarity=0.381  Sum_probs=51.7

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+..+|||+|||+.+|+++|.++|..|    |.|..|.|+.++.+|.++|||||+|.+.
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~----G~I~~v~i~~d~~tg~~kG~aFV~F~~~  154 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVY----GPIKRIHMVYSKRSGKPRGYAFIEYEHE  154 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHc----CCeeEEEeeccCCCCCccceEEEeeccH
Confidence            456899999999999999999999999    9999999999999999999999999874

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.25  E-value=2e-11  Score=101.03  Aligned_cols=82  Identities=12%  Similarity=0.105  Sum_probs=67.6

Q ss_pred             CcccEEEEeCC--CccC--------CHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeC
Q 016231          223 KLLRTIFVGNL--PLKV--------KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFK  292 (393)
Q Consensus       223 ~~~rtVFVgNL--p~~~--------tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~  292 (393)
                      .+++.|.|.||  |..+        .+++|+.+|++||.|.+|.|++++....               +.++|||||+|.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~---------------~~~~G~~fV~f~   67 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVE---------------VPGCGKIFVEFT   67 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBC---------------CTTTTEEEEEES
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCC---------------cCCcEEEEEEEC
Confidence            35789999998  4343        3479999999999999999976542111               135699999999


Q ss_pred             CHHHHHHHH-HhcCceeCCeEEEEeecC
Q 016231          293 SEQSTEAAL-AFNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       293 s~e~A~~Al-~lng~~~~Gr~I~V~~a~  319 (393)
                      +.++|..|+ .|||..|.||.|.|.++.
T Consensus        68 ~~~~A~~Ai~~lnG~~f~GR~i~v~~~~   95 (105)
T 3v4m_A           68 SVFDCQKAMQGLTGRKFANRVVVTKYCD   95 (105)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CHHHHHHHHHHhCCCEeCCCEEEEEEeC
Confidence            999999999 799999999999999875

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.25  E-value=4e-12  Score=104.98  Aligned_cols=71  Identities=18%  Similarity=0.331  Sum_probs=60.4

Q ss_pred             EeCCCccCCHHHHHHHh------------cccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHH
Q 016231          230 VGNLPLKVKKKTLIKEF------------IKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQST  297 (393)
Q Consensus       230 VgNLp~~~tee~L~~~F------------s~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A  297 (393)
                      +.|||+.+++++|+++|            ++||.|.+|+|+++.   .               +.++|||||.|.+.++|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~---~---------------~~~~G~~fV~f~~~~~A   81 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL---G---------------DHLVGNVYVKFRREEDA   81 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS---S---------------SSSEEEEEEEESCHHHH
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC---C---------------CCccEEEEEEECCHHHH
Confidence            56788888888887777            999999999996543   1               23679999999999999


Q ss_pred             HHHH-HhcCceeCCeEEEEeec
Q 016231          298 EAAL-AFNMAVIGGNHIRLDRA  318 (393)
Q Consensus       298 ~~Al-~lng~~~~Gr~I~V~~a  318 (393)
                      ..|+ .|||..|.||.|.|.++
T Consensus        82 ~~A~~~lng~~~~Gr~i~v~~s  103 (104)
T 1jmt_A           82 EKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHTTCEETTEECCEEEC
T ss_pred             HHHHHHHCCCEECCEEEEEEEc
Confidence            9999 79999999999999886

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.24  E-value=7.7e-12  Score=98.03  Aligned_cols=54  Identities=15%  Similarity=0.254  Sum_probs=51.2

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +.++|||+|||+.+++++|+++|+.|    |.|..|+|+.++.+|.++|||||+|.+.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~----G~i~~~~i~~~~~~~~~~g~afV~f~~~   57 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPY----GKIVSTKAILDKTTNKCKGYGFVDFDSP   57 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTT----SCEEEEEEECCSSSCSCCSEEEEEESCH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEecCCCCCcCcEEEEEECCH
Confidence            56899999999999999999999999    9999999999999999999999999874

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.24  E-value=1.2e-11  Score=113.87  Aligned_cols=76  Identities=17%  Similarity=0.155  Sum_probs=63.9

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCe--eEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEI--DSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I--~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      +.++|||+|||+.+|+++|+++|+.||.|  .+|+++.+.    +.               ++|||||+|.+.++|..||
T Consensus       122 p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~----~~---------------~~g~gfV~f~~~~~A~~Ai  182 (205)
T 3tyt_A          122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK----SE---------------RSSSGLLEWDSKSDALETL  182 (205)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC----SS---------------SSEEEEEECSSHHHHHHHH
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC----CC---------------CceEEEEEeCCHHHHHHHH
Confidence            46899999999999999999999999999  888884432    11               3489999999999999999


Q ss_pred             -HhcCceeCCe----EEEEeec
Q 016231          302 -AFNMAVIGGN----HIRLDRA  318 (393)
Q Consensus       302 -~lng~~~~Gr----~I~V~~a  318 (393)
                       .||+..|.|+    ++.|.+|
T Consensus       183 ~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          183 GFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             HHHTTCEECCSSSSSCEECEEE
T ss_pred             HHhCCCCccCCCCCcceEEEec
Confidence             7999999886    4555543

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.23  E-value=1.3e-11  Score=100.75  Aligned_cols=56  Identities=21%  Similarity=0.405  Sum_probs=52.7

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|+|++++.+|.++|||||+|.++
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~v~~v~i~~~~~~g~~~g~afV~f~~~   68 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQY----GEVVDCVIMKDKTTNQSRGFGFVKFKDP   68 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTT----SCEEEEEEEECSSSCCEEEEEEEEESST
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEeeCCCCCCcceEEEEEECCH
Confidence            4567899999999999999999999999    9999999999999999999999999875

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.23  E-value=1e-11  Score=101.97  Aligned_cols=56  Identities=34%  Similarity=0.555  Sum_probs=52.4

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~g~~~g~afV~f~~~   67 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQF----GDLKYVRVVLHPDTEHSKGCAFAQFMTQ   67 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTT----SCEEEEECCBCSSSCCBCSEEEEEESSH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhc----CCeEEEEEEecCCCCCCccEEEEEECCH
Confidence            4467899999999999999999999999    9999999999999999999999999864

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.23  E-value=1e-11  Score=97.43  Aligned_cols=55  Identities=24%  Similarity=0.408  Sum_probs=50.6

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+.++|||+|||+++++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~   58 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPF----GRISDARVVKDMATGKSKGYGFVSFFNK   58 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhc----CCEeEEEEEecCCCCccceEEEEEECCH
Confidence            356899999999999999999999999    9999999999998999999999999864

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.23  E-value=1.1e-11  Score=96.32  Aligned_cols=52  Identities=25%  Similarity=0.427  Sum_probs=49.7

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+|||+|||+++++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~----G~i~~~~i~~~~~~~~~~g~afV~f~~~   53 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDF----PSYLSGHVMWDMQTGSSRGYGFVSFTSQ   53 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTS----TTEEEEEEEECTTTCCEEEEEEEEESCH
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhc----CCeeEEEEEEcCCCCCccceEEEEECCH
Confidence            589999999999999999999999    9999999999999999999999999874

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.23  E-value=4.6e-11  Score=101.10  Aligned_cols=83  Identities=17%  Similarity=0.164  Sum_probs=68.4

Q ss_pred             cccEEEEeCCCc--cC---CHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHH
Q 016231          224 LLRTIFVGNLPL--KV---KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE  298 (393)
Q Consensus       224 ~~rtVFVgNLp~--~~---tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~  298 (393)
                      ++++|+|.||-.  .+   .+++|++.|++||.|.+|.|++++......             +.++|||||+|.+.++|.
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~-------------~~~~G~~FV~F~~~e~A~   85 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEED-------------AEIIVKIFVEFSIASETH   85 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTT-------------CEEEEEEEEEESSHHHHH
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccC-------------CcceEEEEEEECCHHHHH
Confidence            479999999932  22   378999999999999999998876321111             235699999999999999


Q ss_pred             HHH-HhcCceeCCeEEEEeecC
Q 016231          299 AAL-AFNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       299 ~Al-~lng~~~~Gr~I~V~~a~  319 (393)
                      .|+ .|||..|.||.|.|.++.
T Consensus        86 ~Ai~~LnGr~f~GR~i~v~~~~  107 (118)
T 3ue2_A           86 KAIQALNGRWFAGRKVVAEVYD  107 (118)
T ss_dssp             HHHHHHTTCEETTEECEEEEEC
T ss_pred             HHHHHHCCCEECCcEEEEEEcC
Confidence            999 799999999999999875

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.23  E-value=8.5e-12  Score=97.49  Aligned_cols=55  Identities=20%  Similarity=0.393  Sum_probs=51.7

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+.++|||+|||+++++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.++
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~   59 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPF----GDITDIQIPLDYETEKHRGFAFVEFELA   59 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGG----SCEEEEECCEETTTTEECSEEEEEESSH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcc----CCEEEEEEEECCCCCccccEEEEEECCH
Confidence            457899999999999999999999999    9999999999999999999999999874

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.22  E-value=4.6e-12  Score=100.89  Aligned_cols=52  Identities=19%  Similarity=0.347  Sum_probs=47.3

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCC--CeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLES--SVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G--~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+|||+|||+++++++|+++|+.|    |  .|..|+|++++.+|.++|||||+|.+.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~----G~~~v~~v~i~~~~~~g~~kG~afV~f~~~   55 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSL----GVNDILEIKFFENRANGQSKGFALVGVGSE   55 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTT----TCCCCCCEEEEECTTTCCEEEEEEECC-CH
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHh----CCCceEEEEEEecCCCCccCcEEEEEECCH
Confidence            489999999999999999999999    8  999999999999999999999999874

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.22  E-value=1.3e-11  Score=100.36  Aligned_cols=56  Identities=20%  Similarity=0.365  Sum_probs=52.2

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~g~~~g~afV~f~~~   67 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTF----GEVLMVQVKKDLKTGHSKGFGFVRFTEY   67 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGG----SCEEEEEEEECSSSCSEEEEEEEEESSH
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhc----CCeEEEEEEecCCCCCccceEEEEECCH
Confidence            4456899999999999999999999999    9999999999999999999999999864

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.22  E-value=1.6e-11  Score=99.83  Aligned_cols=56  Identities=29%  Similarity=0.462  Sum_probs=52.6

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|.|+.++.+|.++|||||+|.+.
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~   65 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKY----GRVGDVYIPREPHTKAPRGFAFVRFHDR   65 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTT----SCEEEEECCBCSSSCSBCSCEEEEESSS
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEEeCCCCCCCCeEEEEEECCH
Confidence            4567899999999999999999999999    9999999999999999999999999874

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.22  E-value=9.9e-12  Score=102.87  Aligned_cols=56  Identities=21%  Similarity=0.455  Sum_probs=50.1

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+++++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~----G~i~~v~i~~~~~tg~~kg~afV~f~~~   77 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQF----GEVKECLVMRDPLTKRSRGFGFVTFMDQ   77 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTT----SCEEEEEECCCTTTCCCTTCEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcc----CCeEEEEEEECCCCCCcCcEEEEEECCH
Confidence            3456899999999999999999999999    9999999999999999999999999864

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.22  E-value=1.1e-11  Score=99.57  Aligned_cols=54  Identities=24%  Similarity=0.570  Sum_probs=50.8

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +.++|||+|||..+++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~g~~~g~afV~f~~~   54 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNV----GPVINLKMMFDPQTGRSKGYAFIEFRDL   54 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTT----SCEEEEECCBCTTTCCBCSEEEEEESSH
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhc----CCEEEEEEEeCCCCCccceEEEEEECCH
Confidence            35799999999999999999999999    9999999999999999999999999864

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.22  E-value=1.4e-11  Score=99.34  Aligned_cols=56  Identities=18%  Similarity=0.356  Sum_probs=52.2

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeE-EEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVE-AVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~-~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+++++++|+++|..|    |.|. .|+|++++.+|.++|||||+|.++
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~~v~i~~~~~~g~~~g~afV~f~~~   62 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATM----GETVMSVKIIRNRLTGIPAGYCFVEFADL   62 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHT----TCCCCEEEEEECSSSCCEEEEEEEECSCH
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHh----CCcceEEEEeecCCCCCcCCEEEEEeCCH
Confidence            4467899999999999999999999999    9999 999999999999999999999874

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.22  E-value=1.5e-11  Score=99.14  Aligned_cols=56  Identities=21%  Similarity=0.349  Sum_probs=52.1

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~   60 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAY----GPLSELHYPIDSLTKKPKGFAFVTFMFP   60 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTT----SCEEEEECCCCTTTCCCCSEEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEeEEEEEecCCCCCcCeEEEEEECCH
Confidence            3457899999999999999999999999    9999999999988999999999999874

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.22  E-value=1.8e-11  Score=96.48  Aligned_cols=53  Identities=28%  Similarity=0.542  Sum_probs=50.5

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .++|||+|||+++++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~   58 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGC----GSVNRVTILCDKFSGHPKGFAYIEFSDK   58 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGG----CCEEEEEEEESCSSSSCCEEEEEEESST
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhC----CCEEEEEEEecCCCCCcceEEEEEECCH
Confidence            5799999999999999999999999    9999999999999999999999999874

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.22  E-value=1.8e-11  Score=97.70  Aligned_cols=54  Identities=15%  Similarity=0.457  Sum_probs=51.2

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +.++|||+|||+.+++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.++
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~----G~v~~v~i~~~~~~~~~~g~afV~f~~~   57 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPF----GKIDNIVLMKDSDTGRSKGYGFITFSDS   57 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTT----SCEEEEEEECCSSSCCCCSEEEEEESCH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhc----CCEeEEEEeecCCCCceeeEEEEEECCH
Confidence            56899999999999999999999999    9999999999999999999999999874

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.21  E-value=6.8e-12  Score=96.21  Aligned_cols=52  Identities=23%  Similarity=0.531  Sum_probs=49.4

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ++|||+|||+++++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~----G~v~~v~i~~~~~~~~~~g~afV~f~~~   52 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQF----GEVKECLVMRDPLTKRSRGFGFVTFMDQ   52 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTT----SCCCCEEEECCCCSSSCSSEEEECCCCT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEecCCCCCCcCceEEEEEcCH
Confidence            479999999999999999999999    9999999999999999999999999875

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.21  E-value=2.1e-11  Score=97.23  Aligned_cols=56  Identities=18%  Similarity=0.322  Sum_probs=52.5

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|.|++++.+|.++|||||+|.++
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~----G~v~~v~i~~~~~~~~~~g~afV~f~~~   67 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKY----GPIADVSIVYDQQSRRSRGFAFVYFENV   67 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTT----SCEEEEEEEECSSSSSEEEEEEEEESSH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhc----CCeeEEEEEEcCCCCCcccEEEEEECCH
Confidence            4567899999999999999999999999    9999999999999999999999999874

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.21  E-value=6.9e-12  Score=106.95  Aligned_cols=55  Identities=20%  Similarity=0.377  Sum_probs=51.3

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEE--EEEeecCCCCCCccEEEEEeee
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEA--VRVIRHPHMRVGKGIAYVLFKT  391 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~--VrI~~d~~tg~~kGfaFVeF~t  391 (393)
                      ..+.++|||+|||+++|+++|+++|..|    |.|..  |+|++|+.+|.++|||||+|.+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~----G~v~~~~v~i~~d~~tg~~rG~aFV~f~~   76 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPY----AVLSSSNVRVIKDKQTQLNRGFAFIQLST   76 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGG----CCCCTTTEECCBCSSSSSBCSCEEEECCH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHh----CCcceeeEEEEEcCCCCCcceEEEEEECC
Confidence            3467899999999999999999999999    99977  9999999999999999999986

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.21  E-value=6.4e-12  Score=96.03  Aligned_cols=51  Identities=27%  Similarity=0.558  Sum_probs=48.8

Q ss_pred             eeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       338 tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +|||+|||+++++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~   51 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGF----GEVESIELPMDNKTNKRRGFCFITFKEE   51 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHH----SCCSEECCCCSCCCSSSCCCEEEECSSS
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEecCCCCCcCCEEEEEECCH
Confidence            69999999999999999999999    9999999999999999999999999874

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.20  E-value=4.8e-12  Score=103.06  Aligned_cols=54  Identities=17%  Similarity=0.194  Sum_probs=50.9

Q ss_pred             CcceeeeCCCCC------CCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPF------DVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~------~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++|||+|||+      ++++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.++
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~----G~i~~v~i~~d~~tg~~kG~afV~f~~~   64 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKA----GKVVNMEFPIDEATGKTKGFLFVECGSM   64 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTT----SCEEEEECCEETTTTEECSEEEEEESSH
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhc----CCEeEEEEEEcCCCCccceEEEEEECCH
Confidence            357999999999      99999999999999    9999999999999999999999999874

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.20  E-value=9.2e-12  Score=95.26  Aligned_cols=51  Identities=20%  Similarity=0.443  Sum_probs=48.6

Q ss_pred             eeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       338 tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +|||+|||+++++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.++
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~   51 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQF----GKVDDAMLMFDKTTNRHRGFGFVTFESE   51 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTT----SCCSEECCCBCSSSTTSCBEEEEECSCH
T ss_pred             CEEEecCCCCCCHHHHHHHHHhc----CCEEEEEEEecCCCCCcCcEEEEEECCH
Confidence            59999999999999999999999    9999999999998999999999999874

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.20  E-value=2.5e-11  Score=96.72  Aligned_cols=56  Identities=32%  Similarity=0.691  Sum_probs=52.2

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|+|+.++.+|.++|||||+|.++
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~----G~v~~v~i~~~~~~~~~~g~afV~f~~~   68 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKY----GKVVKVTIMKDKDTRKSKGVAFILFLDK   68 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTT----SCEEEEEECCCSSSCCCTTCEEEEESCH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhc----CCeEEEEEEeCCCCCCcccEEEEEECCH
Confidence            4457899999999999999999999999    9999999999999999999999999874

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.20  E-value=2.4e-11  Score=98.78  Aligned_cols=55  Identities=29%  Similarity=0.494  Sum_probs=51.1

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhc-CCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCG-LNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~-~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+..+|||+|||+++++++|+++|.. |    |.|..|+|++++ +|.++|||||+|.+.
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~----G~v~~v~i~~~~-~g~~~g~afV~f~~~   61 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVY----PSCRGGKVVLDQ-TGVSKGYGFVKFTDE   61 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHC----TTEEEEEEEECT-TCCEEEEEEEEESCH
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhC----CCeEEEEEEECC-CCCccceEEEEECCH
Confidence            345689999999999999999999999 9    999999999998 999999999999874

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.20  E-value=1.2e-11  Score=100.80  Aligned_cols=56  Identities=18%  Similarity=0.427  Sum_probs=52.2

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~g~~~g~afV~f~~~   65 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEF----GKIYELTVLKDRFTGMHKGCAFLTYCER   65 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHH----SCCCEEECCCCSSSCSCCSEEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeeEEEEEecCCCCCcceEEEEEECCH
Confidence            4457899999999999999999999999    9999999999999999999999999863

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.19  E-value=2.6e-11  Score=98.68  Aligned_cols=56  Identities=21%  Similarity=0.337  Sum_probs=52.3

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~   67 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQA----GPVVNTHMPKDRVTGQHQGYGFVEFLSE   67 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTT----SCEEEEECCBCSSSCSBCSCEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEecCCCCcCCcEEEEEECCH
Confidence            4467899999999999999999999999    9999999999998999999999999874

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.19  E-value=2.4e-11  Score=100.63  Aligned_cols=55  Identities=31%  Similarity=0.475  Sum_probs=51.5

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...++|||+|||+.+++++|+++|..|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~g~~~g~afV~f~~~   77 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAV----GKVRDVRIISDRNSRRSKGIAYVEFCEI   77 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTT----SCEEEEEECCSCCSSSCCCCEEEEESCG
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhC----CCEeEEEEEecCCCCccCcEEEEEeCcH
Confidence            346899999999999999999999999    9999999999999999999999999874

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.19  E-value=2e-11  Score=98.92  Aligned_cols=56  Identities=23%  Similarity=0.501  Sum_probs=52.4

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+++++++|+++|..|    |.|..|+|++++.++.++|||||+|.++
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~   64 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKY----GQISEVVVVKDRETQRSRGFGFVTFENI   64 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHH----SCCCEEEECCCSSSCSCCSEEEEECSSH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhc----CCeEEEEEEeCCCCCCcccEEEEEECCH
Confidence            4567899999999999999999999999    9999999999999999999999999874

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.19  E-value=2.9e-11  Score=98.33  Aligned_cols=55  Identities=35%  Similarity=0.564  Sum_probs=51.3

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+++++++|+++|..|    | |..|+|++++.+|.++|||||+|.+.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----g-i~~v~i~~~~~~g~~~g~afV~f~~~   66 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDL----S-IRSVRLVRDKDTDKFKGFCYVEFDEV   66 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTS----C-EEEEEEEECSSSCSEEEEEEEEESSH
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhC----C-ceEEEEeecCCCCccceEEEEEECCH
Confidence            4567899999999999999999999999    7 99999999999999999999999864

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.19  E-value=2.8e-11  Score=100.49  Aligned_cols=56  Identities=25%  Similarity=0.501  Sum_probs=52.3

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|+|++++.++.++|||||+|.+.
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~   69 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGF----GDIEEAVVITDRQTGKSRGYGFVTMADR   69 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTT----SCEEEEEESCCSSSCCCCSEEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhC----CCeeEEEEEEcCCCCccceEEEEEECCH
Confidence            4467899999999999999999999999    9999999999999999999999999864

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.19  E-value=2.3e-11  Score=99.25  Aligned_cols=56  Identities=16%  Similarity=0.182  Sum_probs=52.1

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|.|++++.+|.++|||||+|.+.
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~   75 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEY----GEIKNIHLNLDRRTGYLKGYTLVEYETY   75 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTSSEEEEEEEEESCH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcc----CCeEEEEEEecCCCCceeeEEEEEECCH
Confidence            3456899999999999999999999999    9999999999999999999999999874

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.19  E-value=2.2e-11  Score=98.31  Aligned_cols=56  Identities=21%  Similarity=0.234  Sum_probs=52.2

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEE--------EEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEA--------VRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~--------VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+..+|||+|||+++++++|+++|+.|    |.|..        |+|++++.+|.++|||||+|.+.
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~   73 (99)
T 2la6_A           10 HSDNNTIFVQGLGENVTIESVADYFKQI----GIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP   73 (99)
T ss_dssp             CCCCSEEEEECCCSSCCHHHHHHHHTTT----SCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHh----CCEeeccccccccEEEEecCCCCCeeeEEEEEECCH
Confidence            4567899999999999999999999999    99999        99999999999999999999864

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.19  E-value=7.9e-12  Score=108.79  Aligned_cols=95  Identities=18%  Similarity=0.192  Sum_probs=47.9

Q ss_pred             eEEEEeeCCHHHHHHHHHhcCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCC
Q 016231          285 VHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLE  364 (393)
Q Consensus       285 G~AFVeF~s~e~A~~Al~lng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~  364 (393)
                      |+||.+|..+..+..++..-...+.|....-.....       ..........+|||+|||+++|+++|+++|..|    
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~gg~~~g~~~g~~-------~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~----   70 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSGDS-------EFTVQSTTGHCVHMRGLPYKATENDIYNFFSPL----   70 (139)
T ss_dssp             --------------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSC----
T ss_pred             CcccccccCccccchhcccchhccCCCCCCCCCCCc-------ccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhc----
Confidence            688999988877766653222223333221111000       001123356799999999999999999999999    


Q ss_pred             CCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          365 SSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       365 G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      | |..|+|++|+. |.++|||||+|.++
T Consensus        71 G-i~~v~i~~d~~-g~srGfaFV~F~~~   96 (139)
T 2hgn_A           71 N-PVRVHIEIGPD-GRVTGEADVEFATH   96 (139)
T ss_dssp             C-CSEEECCCSSS-SCSSCCCEEECSHH
T ss_pred             C-CeEEEEEECCC-CCCceEEEEEeCCH
Confidence            8 67999999975 99999999999864

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.19  E-value=5.1e-11  Score=99.13  Aligned_cols=56  Identities=18%  Similarity=0.296  Sum_probs=52.3

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+++++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~~~i~~~~~~g~~~g~afV~f~~~   92 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPF----GNVISAKVFIDKQTSLSKCFGFVSFDNP   92 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTS----CEEEEEEECCCSSSSCCCCEEEEEEESS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEEeCCCCCCcCcEEEEEECCH
Confidence            4456899999999999999999999999    9999999999999999999999999874

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.19  E-value=2.6e-11  Score=99.27  Aligned_cols=55  Identities=29%  Similarity=0.393  Sum_probs=50.3

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEE-EEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEA-VRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~-VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .....+|||+|||+++++++|+++|..|    |.|.. |+|+.+ .+|.++|||||+|.++
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~----G~v~~~v~i~~~-~~g~~~G~afV~F~~~   67 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGL----EIVPNGMTLPVD-FQGRSTGEAFVQFASQ   67 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTC----CEEEEEEECCBC-SSSCBCSEEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCcceeEEEEEC-CCCCcceEEEEEECCH
Confidence            4456899999999999999999999999    89987 999999 7999999999999874

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.18  E-value=3.4e-11  Score=99.70  Aligned_cols=56  Identities=25%  Similarity=0.424  Sum_probs=52.3

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~   67 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPF----GRISDARVVKDMATGKSKGYGFVSFFNK   67 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEEcCCCCCcceEEEEEECCH
Confidence            4467899999999999999999999999    9999999999998999999999999864

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.18  E-value=1.5e-11  Score=98.44  Aligned_cols=54  Identities=22%  Similarity=0.519  Sum_probs=51.0

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEE-EEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAV-RVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~V-rI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +.++|||+|||+.+++++|+++|+.|    |.|..| +|++++.+|.++|||||+|.++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~~~~i~~~~~~g~~~g~afV~f~~~   58 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAF----GVILQTPKIMRDPDTGNSKGYAFINFASF   58 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTT----SCBSSCCEECCCTTTCSCCSEEEEEBSSH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc----CCeeEEEEEEEcCCCCCcCeEEEEEECCH
Confidence            56899999999999999999999999    999999 9999999999999999999874

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.18  E-value=2.3e-11  Score=98.62  Aligned_cols=54  Identities=31%  Similarity=0.533  Sum_probs=50.5

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...++|||+|||+++++++|+++|+.|    |.|..|+|++++ +|.++|||||+|.+.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~~-~g~~~g~afV~f~~~   60 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARY----GSVKEVKIITDR-TGVSKGYGFVSFYND   60 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGG----SCEEEEEEEECT-TSCEEEEEEEEESSC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhC----CCeEEEEEEECC-CCCccceEEEEECCH
Confidence            356899999999999999999999999    999999999998 999999999999874

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.18  E-value=2.4e-11  Score=98.70  Aligned_cols=56  Identities=25%  Similarity=0.425  Sum_probs=52.3

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~   67 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPF----GSISRIYLAKDKTTGQSKGFAFISFHRR   67 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTT----CCEEEEEEEECSSSCSEEEEEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhC----CCeEEEEEeecCCCCceeeEEEEEECCH
Confidence            4467899999999999999999999999    9999999999999999999999999864

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.17  E-value=4.1e-11  Score=97.73  Aligned_cols=56  Identities=25%  Similarity=0.511  Sum_probs=52.0

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeec-CCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRH-PHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d-~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|+|+++ ..+|.++|||||+|.+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~~g~afV~f~~~   68 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTF----GELKTVRLPKKMTGTGAHRGFGFVDFITK   68 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTT----SCEEEEECCCCCSSSCSSCSEEEEEESSH
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHcc----CCeEEEEEecCCCCCCCcCceEEEEECCH
Confidence            4467899999999999999999999999    99999999999 78999999999999874

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.17  E-value=1.7e-11  Score=99.25  Aligned_cols=56  Identities=20%  Similarity=0.373  Sum_probs=52.4

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~   64 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPF----GDITDIQIPLDYETEKHRGFAFVEFELA   64 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTT----SCCCCEECCCCSSSCCCSSEEEECCSSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcc----CCEEEEEEEecCCCCCcceEEEEEECCH
Confidence            4567899999999999999999999999    9999999999999999999999999864

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.17  E-value=4.6e-11  Score=97.20  Aligned_cols=54  Identities=28%  Similarity=0.517  Sum_probs=50.4

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+.++|||+|||+.+++++|+++|+.|    |.|..|+|++++ +|.++|||||+|.+.
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~~-~g~~~g~afV~f~~~   66 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPF----GVIDECTVLRGP-DGSSKGCAFVKFSSH   66 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTT----SCEEEEEEEECS-SSCEEEEEEEEESSH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEECC-CCCcCcEEEEEeCCH
Confidence            457899999999999999999999999    999999999997 799999999999864

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.17  E-value=5.2e-11  Score=96.19  Aligned_cols=55  Identities=25%  Similarity=0.472  Sum_probs=50.9

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|+|+.++ +|.++|||||+|.+.
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~-~g~~~g~afV~f~~~   68 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAH----GTVKDLRLVTNR-AGKPKGLAYVEYENE   68 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTT----SCEEEEEEEECT-TSCEEEEEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhC----CCeEEEEEEECC-CCCEEeEEEEEECCH
Confidence            3457899999999999999999999999    999999999997 899999999999874

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.17  E-value=2.4e-11  Score=107.38  Aligned_cols=54  Identities=19%  Similarity=0.340  Sum_probs=50.1

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCC--CeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLES--SVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G--~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++|||+|||+.+++++|+++|..|    |  .|..|+|++|+.+|.++|||||+|.++
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~----G~i~v~~v~i~~d~~tg~skGfaFV~f~~~  109 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSI----GVYDVVELKFAENRANGQSKGYAEVVVASE  109 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHT----TCCCEEEEEEEECTTTCCEEEEEEEEESCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHH----CCccEEEEEEEecCCCCccceEEEEEECCH
Confidence            45799999999999999999999999    9  999999999999999999999999874

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.17  E-value=3e-11  Score=99.87  Aligned_cols=56  Identities=16%  Similarity=0.426  Sum_probs=52.3

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.++
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~----G~i~~v~i~~~~~~g~~~g~afV~F~~~   78 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPF----GRIESIQLMMDSETGRSKGYGFITFSDS   78 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTT----SCEEEEEEEEETTTTEEEEEEEEEESCH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEEcCCCCccceEEEEEECCH
Confidence            4467899999999999999999999999    9999999999999999999999999874

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.16  E-value=4e-11  Score=95.68  Aligned_cols=55  Identities=31%  Similarity=0.522  Sum_probs=50.7

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|+|++++. |.++|||||+|.++
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~----G~i~~v~i~~~~~-g~~~g~afV~f~~~   67 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQA----GPLTKVTICKDRE-GKPKSFGFVCFKHP   67 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGG----SCEEEEEEEECTT-SCEEEEEEEEESST
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhc----CCEEEEEEEECCC-CCCceEEEEEECCH
Confidence            4467899999999999999999999999    9999999999975 99999999999874

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.16  E-value=2.9e-11  Score=98.51  Aligned_cols=55  Identities=40%  Similarity=0.654  Sum_probs=50.9

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCC-CCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHM-RVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~t-g~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+++++++|+++|..|    | |..|+|++++.+ |.++|||||+|.+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G-i~~v~i~~~~~~~g~~~g~afV~f~~~   67 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGL----N-ISAVRLPREPSNPERLKGFGYAEFEDL   67 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTS----C-EEEEECCBCSSCTTSBCSCEEEEESSH
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHC----C-ceEEEEecCCCCCCCcCeEEEEEECCH
Confidence            3467899999999999999999999999    9 999999999987 99999999999864

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.16  E-value=3.2e-11  Score=99.08  Aligned_cols=56  Identities=20%  Similarity=0.338  Sum_probs=52.1

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|+|+.++.+|.++|||||+|.+.
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~   78 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDY----GEIKNIHLNLDRRTGFSKGYALVEYETH   78 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGG----SCEEEEECCBCTTTSSBCSEEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEEecCCCCCcceEEEEEECCH
Confidence            3456899999999999999999999999    9999999999999999999999999874

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.16  E-value=2.7e-11  Score=100.52  Aligned_cols=56  Identities=18%  Similarity=0.366  Sum_probs=51.9

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+++++++|+++|..|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~g~~~g~afV~f~~~   77 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPF----GNVVSAKVFIDKQTNLSKCFGFVSYDNP   77 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGG----SCCSEEEEEECSSSCSEEEEEEEECSSH
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEECCCCCCcCccEEEEECCH
Confidence            3456899999999999999999999999    9999999999998999999999999864

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.16  E-value=2.6e-11  Score=96.89  Aligned_cols=51  Identities=29%  Similarity=0.433  Sum_probs=45.1

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+..+|||+|||+++|+++|+++|+.|    |.|..|+|+++     ++|||||+|.++
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~----G~i~~v~i~~~-----srGfaFV~F~~~   58 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQY----GEVVDVFIPKP-----FRAFAFVTFADD   58 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTT----SCEEEEECCSS-----CCSEEEEEESCH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcc----CCEEEEEEeeC-----CCCEEEEEECCH
Confidence            3456899999999999999999999999    99999999886     799999999874

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.16  E-value=2.9e-11  Score=100.46  Aligned_cols=55  Identities=20%  Similarity=0.512  Sum_probs=51.4

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+.++|||+|||+.+++++|+++|..|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~----G~i~~v~i~~~~~~g~~~g~afV~f~~~   79 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQW----GKLTDCVVMRDPASKRSRGFGFVTFSSM   79 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSS----CCCSEEEEECCTTTSSCCSEEEEECSSH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEEECCCCCCcCceEEEEeCCH
Confidence            346899999999999999999999999    9999999999999999999999999864

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.16  E-value=1.3e-11  Score=100.18  Aligned_cols=55  Identities=22%  Similarity=0.542  Sum_probs=51.5

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+.++|||+|||+.+++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~----G~i~~~~i~~~~~~g~~~g~afV~f~~~   60 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEV----GPVVSFRLVYDRETGKPKGYGFCEYQDQ   60 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTT----SCCSEEEEEEETTTTEEEEEEEEECSCH
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhc----CCeeEEEEEeCCCCCccceEEEEEECCH
Confidence            356899999999999999999999999    9999999999999999999999999864

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.15  E-value=2.1e-11  Score=101.48  Aligned_cols=55  Identities=27%  Similarity=0.431  Sum_probs=50.6

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCe-EEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSV-EAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I-~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+++++++|+++|..|    |.| ..|+|++++ +|.++|||||+|.+.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----g~v~~~v~i~~d~-~g~~~G~afV~F~~~   67 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGI----PVDENAVHVLVDN-NGQGLGQALVQFKNE   67 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTS----CCCSTTEEECCCT-TSSCSSCEEEECSSH
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhC----CCcCCeEEEEECC-CCCcceEEEEEECCH
Confidence            3456899999999999999999999999    899 899999997 999999999999864

>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=99.15  E-value=2.8e-11  Score=100.99  Aligned_cols=51  Identities=22%  Similarity=0.511  Sum_probs=46.7

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+|||+|||+++++++|+++|+.|    |.|.+|+|+++.  +.++|||||+|.++
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~----G~v~~v~i~~d~--~~~kg~afV~f~~~   55 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAF----GNILSCKVVCDE--NGSKGYGFVHFETQ   55 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEEET--TEEEEEEEEEESCH
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhcc----CCEEEEEEeecC--CCCCceEEEEECCH
Confidence            4689999999999999999999999    999999999995  45899999999874

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.15  E-value=2.4e-11  Score=97.64  Aligned_cols=54  Identities=17%  Similarity=0.426  Sum_probs=49.8

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCC---CCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPH---MRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~---tg~~kGfaFVeF~t~  392 (393)
                      +.++|||+|||+++++++|+++|+.|    |.|..|+|++++.   ++.++|||||+|.+.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~   60 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKV----GAIKSCTISKKKNKAGVLLSMGFGFVEYKKP   60 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTT----SCEEEEEEEEEECTTCCEEEEEEEEEEESSH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEecCCCCCCcCcccEEEEEECCH
Confidence            56899999999999999999999999    9999999999876   668999999999864

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.14  E-value=7.1e-11  Score=100.93  Aligned_cols=56  Identities=18%  Similarity=0.322  Sum_probs=52.5

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|+|++++.+|.++|||||+|.++
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~----G~I~~v~i~~d~~tg~~~G~afV~F~~~   98 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKY----GPIADVSIVYDQQSRRSRGFAFVYFENV   98 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTT----SCEEEEEEECCSSSSCCCCEEEEEESCH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEecCCCCccceEEEEEECCH
Confidence            4567899999999999999999999999    9999999999999999999999999874

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.14  E-value=2.5e-11  Score=105.13  Aligned_cols=55  Identities=16%  Similarity=0.190  Sum_probs=50.2

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCC---eEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESS---VEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~---I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .....+|||+|||+++|+++|+++|..|    |.   |..|+|++|+. |.++|||||+|.++
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~----G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~   98 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDC----TIHDGAAGVHFIYTRE-GRQSGEAFVELGSE   98 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTC----CCSSSSTTEEEEECSS-SCEEEEEEEECSSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHh----CCcCceeEEEEEECCC-CCCCeEEEEEECCH
Confidence            3456899999999999999999999999    88   89999999987 99999999999874

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.14  E-value=3.8e-11  Score=98.45  Aligned_cols=53  Identities=26%  Similarity=0.385  Sum_probs=48.3

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ....+|||+|||+++|+++|+++|..|    |. ..|+|++++ +|.++|||||+|.++
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~----G~-~~v~i~~d~-~g~~~G~afV~F~~~   65 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPL----NP-MRVHIEIGP-DGRVTGEADVEFATH   65 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSC----CC-SEEEEEESS-SSCEEEEEEEECSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHc----Cc-eEEEEEECC-CCCEeeEEEEEECCH
Confidence            456899999999999999999999999    84 499999997 899999999999874

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.13  E-value=1.4e-11  Score=97.56  Aligned_cols=52  Identities=25%  Similarity=0.531  Sum_probs=49.7

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ++|||+|||+++++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~   53 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQF----GKVFNVKLIYDRETKKPKGFGFVEMQEE   53 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHH----TCCSEEEECCCSSSCCCCEEEEEEECTT
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhc----CCEEEEEEEEcCCCCCcceEEEEEECCH
Confidence            589999999999999999999999    9999999999999999999999999874

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.13  E-value=6.3e-11  Score=96.75  Aligned_cols=55  Identities=25%  Similarity=0.382  Sum_probs=51.3

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|+|++++ +|.++|||||+|.+.
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~-~g~~~g~afV~f~~~   80 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEF----GTLKKAAVHYDR-SGRSLGTADVHFERK   80 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTT----SCEEEEEEEECT-TSCEEEEEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEECC-CCCcceEEEEEECCH
Confidence            4567899999999999999999999999    999999999998 999999999999864

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.12  E-value=5.3e-11  Score=97.51  Aligned_cols=54  Identities=24%  Similarity=0.357  Sum_probs=50.3

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCC-eEEEEEe-ecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESS-VEAVRVI-RHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~-I~~VrI~-~d~~tg~~kGfaFVeF~t~  392 (393)
                      +.++|||+|||+.+++++|+++|..|    |. |..|.|+ .+..+|.++|||||+|.+.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~----G~~v~~v~i~~~~~~~g~~~g~afV~f~~~   62 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKV----TEGVLDVIVYASAADKMKNRGFAFVEYESH   62 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHH----STTEEEEECCSSSCTTTTTCCEEEEEESSH
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHh----cCCceEEEEEccCCCCCCcCcEEEEEecCH
Confidence            56899999999999999999999999    88 9999999 8888899999999999864

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.12  E-value=2.8e-11  Score=98.23  Aligned_cols=55  Identities=40%  Similarity=0.661  Sum_probs=48.6

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecC-CCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP-HMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~-~tg~~kGfaFVeF~t~  392 (393)
                      ....++|||+|||+++++++|+++|+.|    | |..|+|++++ .+|.++|||||+|.+.
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G-i~~v~i~~~~~~~g~~~g~afV~f~~~   71 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGL----N-ISAVRLPREPSNPERLKGFGYAEFEDL   71 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSS----C-EEEEECSCCTTTTCCCCSCEEEEECCH
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhc----C-CeEEEEEecCCcCCccCeEEEEEECCH
Confidence            4457899999999999999999999999    9 9999999998 6899999999999874

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.12  E-value=8e-11  Score=99.00  Aligned_cols=56  Identities=27%  Similarity=0.356  Sum_probs=51.8

Q ss_pred             CcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       332 ~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .....++|||+|||+.+++++|+++|+.|    |.|..|+|+++. +|.++|||||+|.+.
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~v~~v~i~~~~-~g~~~g~afV~f~~~   86 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEF----GTLKKAAVDYDR-SGRSLGTADVHFERR   86 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTT----SCCSEEEEECCS-SSSCCSEEEEEESSH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeeEEEEEECC-CCCEeeEEEEEECCH
Confidence            35567899999999999999999999999    999999999998 999999999999874

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.12  E-value=1.1e-10  Score=96.48  Aligned_cols=55  Identities=15%  Similarity=0.440  Sum_probs=50.9

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|+|++++ +|.++|||||+|.+.
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~~~i~~~~-~g~~~g~afV~f~~~   76 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPF----GQVISTRILRDS-SGTSRGVGFARMEST   76 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTT----SCEEEEEEEECS-SSCEEEEEEEEESCH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEEECC-CCCcceEEEEEECCH
Confidence            3456899999999999999999999999    999999999997 899999999999864

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.11  E-value=9e-11  Score=95.27  Aligned_cols=54  Identities=20%  Similarity=0.353  Sum_probs=50.0

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|+|+.+  +|.++|||||+|.+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~--~g~~~g~afV~f~~~   65 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPF----GTITSAKVMME--GGRSKGFGFVCFSSP   65 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTT----SCEEEEEEEEC--SSSEEEEEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEEcC--CCCcCEEEEEEECCH
Confidence            4467899999999999999999999999    99999999998  899999999999864

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.11  E-value=1.4e-10  Score=98.74  Aligned_cols=56  Identities=20%  Similarity=0.373  Sum_probs=52.5

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|+|++++.+|.++|||||+|.++
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~  115 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPF----GDITDIQIPLDYETEKHRGFAFVEFELA  115 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGG----SCEEEEECCCCTTTCCCCSEEEEEESCH
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhc----CCEEEEEEeecCCCCCcCcEEEEEECCH
Confidence            4567899999999999999999999999    9999999999999999999999999874

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.11  E-value=5e-11  Score=100.02  Aligned_cols=54  Identities=24%  Similarity=0.473  Sum_probs=51.0

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++|||+|||+++++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~   88 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSC----GSINRITILCDKFSGHPKGYAYIEFAER   88 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTT----SCEEEEEEEEECTTSSCEEEEEEEESSH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEEecCCCCCcccEEEEEECCH
Confidence            45899999999999999999999999    9999999999999999999999999864

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.11  E-value=7.4e-11  Score=98.73  Aligned_cols=54  Identities=19%  Similarity=0.421  Sum_probs=50.3

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...++|||+|||+++++++|+++|+.|    |.|..|.|+.+. +|.++|||||+|.+.
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~~-~g~~~g~afV~F~~~   58 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKH----GPISEVLLIKDR-TSKSRGFAFITFENP   58 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTS----SCCSEEEEECST-TTTCCCEEEEECSSH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEEECC-CCCcccEEEEEECCH
Confidence            356899999999999999999999999    999999999997 999999999999864

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.11  E-value=1.2e-10  Score=92.34  Aligned_cols=54  Identities=24%  Similarity=0.242  Sum_probs=49.3

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|+|+++  +|.++|||||+|.+.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~----G~v~~~~i~~~--~g~~~g~afV~f~~~   58 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNEC----GHVLYADIKME--NGKSKGCGVVKFESP   58 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTT----SCEEEEEEEES--SSCEEEEEEEEESSH
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEEcc--CCCcceEEEEEECCH
Confidence            3467899999999999999999999999    99999999985  789999999999864

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.11  E-value=7.5e-11  Score=97.99  Aligned_cols=49  Identities=20%  Similarity=0.365  Sum_probs=44.8

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+..+|||+|||+++|+++|+++|+.|    |.|.+|+|+++      ||||||+|.++
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~f----G~V~~v~i~~~------kGfaFVeF~~~   62 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPF----GKVTNLLMLKG------KNQAFIEMNTE   62 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHH----CCEEEEEEETT------TTEEEEEESSH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEEcC------CCEEEEEECCH
Confidence            356899999999999999999999999    99999999875      79999999864

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.11  E-value=7.4e-11  Score=99.23  Aligned_cols=56  Identities=16%  Similarity=0.182  Sum_probs=52.0

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|.|+.++.+|.++|||||+|.+.
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~   74 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEY----GEIKNIHLNLDRRTGYLKGYTLVEYETY   74 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTT----SCEEEEECCBCTTTSSBCSCEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEecCCCCccceEEEEEECCH
Confidence            3456899999999999999999999999    9999999999999999999999999874

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.10  E-value=1.3e-10  Score=115.41  Aligned_cols=75  Identities=16%  Similarity=0.272  Sum_probs=63.2

Q ss_pred             CCCcccEEEEeC--CCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHH
Q 016231          221 EGKLLRTIFVGN--LPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE  298 (393)
Q Consensus       221 ~~~~~rtVFVgN--Lp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~  298 (393)
                      ...++++|||||  |++.+|+++|+++|++||.|.+|.+..                       ++|||||+|.+.++|+
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-----------------------~kgfaFV~f~~~~~A~   70 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----------------------NKPYSFARYRTTEESK   70 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-----------------------TCSEEEEEESSHHHHH
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----------------------CCCEEEEEECCHHHHH
Confidence            355689999999  588999999999999999999887621                       3489999999999999


Q ss_pred             HHH-HhcCcee---CCe--EEEEeec
Q 016231          299 AAL-AFNMAVI---GGN--HIRLDRA  318 (393)
Q Consensus       299 ~Al-~lng~~~---~Gr--~I~V~~a  318 (393)
                      +|+ .|||..+   .|+  .|.|.++
T Consensus        71 ~Ai~~lnG~~~~~~~g~~~~ly~~~~   96 (345)
T 3tht_A           71 RAYVTLNGKEVVDDLGQKITLYLNFV   96 (345)
T ss_dssp             HHHHHTTTCEEECTTSCEEECEEEEC
T ss_pred             HHHHHhCCCccccccCCceEEEEEEe
Confidence            999 7999987   355  5777766

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.10  E-value=6.1e-11  Score=101.44  Aligned_cols=56  Identities=23%  Similarity=0.495  Sum_probs=52.2

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ....++|||+|||+++++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~   94 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERY----GPIESVKIVCDRETRQSRGYGFVKFQSG   94 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHH----SCEEEEEEEEETTTTEEEEEEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEEcCCCCCcceEEEEEECCH
Confidence            4456899999999999999999999999    9999999999999999999999999864

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.10  E-value=4.9e-11  Score=100.14  Aligned_cols=54  Identities=19%  Similarity=0.254  Sum_probs=49.5

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCC---eEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESS---VEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~---I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ....+|||+|||+++|+++|+++|..|    |.   |..|+|++++. |.++|||||+|.++
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~----G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~   71 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDC----TIHDGVAGVHFIYTRE-GRQSGEAFVELESE   71 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTS----CBTTGGGGEEEEECSS-SCEEEEEEEEBSSH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHc----CCccCceeEEEEECCC-CCCCeEEEEEECCH
Confidence            456899999999999999999999999    77   89999999976 99999999999874

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.10  E-value=6.1e-11  Score=92.36  Aligned_cols=50  Identities=14%  Similarity=0.181  Sum_probs=45.7

Q ss_pred             ceeeeCCCCCCC------CHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          337 KTVFVGNLPFDV------KDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~------teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ++|||+|||+.+      ++++|+++|+.|    |.|..|+|+  +.+|.++|||||+|.+.
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~----G~i~~v~i~--~~~g~~~g~afV~f~~~   57 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKF----GKITNDFYP--EEDGKTKGYIFLEYASP   57 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTT----CCEEEEECC--CBTTBCCCEEEEEESSH
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhc----CCeEEEEec--CCCCcEeEEEEEEECCH
Confidence            689999999999      779999999999    999999998  35899999999999864

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.10  E-value=5.1e-11  Score=99.13  Aligned_cols=54  Identities=30%  Similarity=0.458  Sum_probs=49.2

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCC---CCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHM---RVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~t---g~~kGfaFVeF~t~  392 (393)
                      ...++|||+|||+++++++|+++|+.|    |.|. +.++.+..+   |.++|||||+|.++
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~----G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~   62 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRF----GPLV-VDWPHKAESKSYFPPKGYAFLLFQEE   62 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTT----CCCC-EECTTSSSSCCCSCTTSEEEECCSSH
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhc----CCEE-EEEeecCCCCCCCCcccEEEEEECCH
Confidence            346899999999999999999999999    9999 999998877   79999999999874

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.10  E-value=4.8e-11  Score=93.61  Aligned_cols=53  Identities=23%  Similarity=0.400  Sum_probs=49.2

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCC-CccEEEEEeeec
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRV-GKGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~-~kGfaFVeF~t~  392 (393)
                      .++|||+|||+++++++|+++|+.|    |.|..|+|+.+..++. ++|||||+|.+.
T Consensus         4 ~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~~~i~~~~~~~~~~~g~afV~f~~~   57 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDHIMEIFSTY----GKIKMIDMPVERMHPHLSKGYAYVEFENP   57 (88)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTT----SCEEEEECCEETTEEEEECSEEEEEESSH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhC----CCEEEEEEEeCCCCCCCCCcEEEEEEecH
Confidence            4799999999999999999999999    9999999999987776 899999999874

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.09  E-value=7.8e-11  Score=97.23  Aligned_cols=56  Identities=16%  Similarity=0.188  Sum_probs=51.5

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeE--------EEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVE--------AVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~--------~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|    |.|.        .|+|+.++.+|.++|||||+|.+.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~   75 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQC----GVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP   75 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTT----SCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSH
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhc----CCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCH
Confidence            3456899999999999999999999999    8999        699999999999999999999874

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.09  E-value=3.2e-11  Score=96.23  Aligned_cols=55  Identities=25%  Similarity=0.402  Sum_probs=50.1

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+..+|||+|||+.+++++|+++|..|    |.|..+.++.++.+|.++|||||+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~~~~~~~~~~g~~~g~afV~f~~~   67 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGY----QVIPGSVCLKYNEKGMPTGEAMVAFESR   67 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTS----CBCTTCCEEEECTTSCEEEEEEEEESSH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc----CCccceEEEEeCCCCCEeeEEEEEECCH
Confidence            346899999999999999999999999    9999999999999999999999999864

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.08  E-value=1.3e-10  Score=95.83  Aligned_cols=55  Identities=24%  Similarity=0.341  Sum_probs=50.5

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|+|++++ +|.++|||||+|.+.
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~----G~i~~~~i~~~~-~g~~~g~afV~f~~~   66 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMA----GVVVRADILEDK-DGKSRGIGTVTFEQS   66 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTT----SCEEEEEEEECT-TCSEEEEEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEECC-CCCeeeEEEEEECCH
Confidence            3457899999999999999999999999    999999999997 699999999999874

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.08  E-value=4.5e-11  Score=98.34  Aligned_cols=55  Identities=13%  Similarity=0.216  Sum_probs=49.8

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCC---eEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESS---VEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~---I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .....+|||+|||+++|+++|+++|..|    |.   |..|+|++++. |.++|||||+|.+.
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~----g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~   65 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDC----RIRNGENGIHFLLNRD-GKRRGDALIEMESE   65 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTS----CBTTTTTTEECCCCTT-STTCSEEEEEBSSH
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhc----CCcCCcceEEEEECCC-CCEeeEEEEEECCH
Confidence            3456899999999999999999999998    66   89999999987 99999999999864

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.08  E-value=1.3e-10  Score=99.48  Aligned_cols=53  Identities=30%  Similarity=0.463  Sum_probs=48.0

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeE--EEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVE--AVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~--~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ....+|||+|||+++|+++|+++|+.|    + |.  .|+|++|+. |.++|||||+|.++
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~----~-i~~~~v~i~~d~~-GrsrGfaFV~F~~~   94 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL----E-IVPNGITLPVDPE-GKITGEAFVQFASQ   94 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS----C-EEEEEEECCCCSS-SSSCSEEEEEESST
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC----C-ceeeEEEEEECCC-CCCceEEEEEECCH
Confidence            456789999999999999999999999    4 55  999999986 99999999999875

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.08  E-value=6.7e-11  Score=99.72  Aligned_cols=56  Identities=21%  Similarity=0.353  Sum_probs=49.9

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .....+|||+|||+++|+++|+++|..|    |.|..+.++.+..+|.++|||||+|.+.
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~----G~v~~~~~~~~~~~g~~~G~afV~F~~~   77 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKL----DIVEDSIYIAYGPNGKATGEGFVEFRNE   77 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSS----CBCTTTCEEEECTTSSEEEEEEEEBSSS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhc----CCccceEEEEECCCCCCCeEEEEEECCH
Confidence            4456899999999999999999999999    8998877777778999999999999874

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.07  E-value=1.6e-10  Score=100.89  Aligned_cols=56  Identities=25%  Similarity=0.465  Sum_probs=52.3

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|+|++++.++.++|||||+|.+.
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~   91 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKS----GDIKKIIMGLDKMKKTACGFCFVEYYSR   91 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEecCCCCccceEEEEEECCH
Confidence            3467899999999999999999999999    9999999999999999999999999874

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.07  E-value=9.2e-11  Score=100.95  Aligned_cols=51  Identities=10%  Similarity=0.180  Sum_probs=48.9

Q ss_pred             ceeeeCCC----CCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeee
Q 016231          337 KTVFVGNL----PFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT  391 (393)
Q Consensus       337 ~tLfVgNL----p~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t  391 (393)
                      ..|||+||    |+.+++.+|+++|+.|    |.|.+|.++.||.||.++|||||+|.+
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~f----GeV~~~~li~Dp~Tg~slGfgfVef~d   57 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKY----GEISHFEAFNDPNSALPLHVYLIKYAS   57 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTT----SCCSEEEEEECTTTCCEEEEEEEECC-
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhc----CCeEEEEEEecCCCCceeeEEEEEECC
Confidence            58999999    9999999999999999    999999999999999999999999985

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.07  E-value=1.1e-10  Score=97.35  Aligned_cols=54  Identities=24%  Similarity=0.391  Sum_probs=48.3

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .....+|||+|||+++++++|+++|+.|     .|..|+|++|+. |+++|||||+|.++
T Consensus        13 ~~~~~~v~V~nLp~~~te~dl~~~F~~~-----~v~~v~i~~d~~-g~~~G~afV~F~~~   66 (109)
T 2dnn_A           13 NPDDLYVSVHGMPFSAMENDVRDFFHGL-----RVDAVHLLKDHV-GRNNGNGLVKFLSP   66 (109)
T ss_dssp             CHHHHEEEEECCCSSCCHHHHHHHTTTS-----CCCEEEECCCTT-CCCCSEEEEECSSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhccC-----CeeEEEEEECCC-CCCCeEEEEEECCH
Confidence            3345799999999999999999999998     488999999975 99999999999874

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.07  E-value=1.5e-10  Score=98.32  Aligned_cols=51  Identities=20%  Similarity=0.316  Sum_probs=46.3

Q ss_pred             CcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       332 ~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...+.++|||+|||+++++++|+++|+.|    |.|..|+|+++      +|||||+|.+.
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~f----G~V~~v~i~~~------kG~AFVeF~~~   77 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPF----GKVTNLLMLKG------KNQAFIEMNTE   77 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTT----SCCCEEEEEGG------GTEEEEECSCH
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEeCC------CCEEEEEECCH
Confidence            35567899999999999999999999999    99999999876      79999999874

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.07  E-value=6.6e-11  Score=95.11  Aligned_cols=56  Identities=25%  Similarity=0.379  Sum_probs=51.3

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .....+|||+|||+.+++++|+++|..|    |.|..+.++.++.+|.++|||||+|.++
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~----G~v~~~~~~~~~~~g~~~g~afV~f~~~   67 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGY----QVIPGSVCLKYNEKGMPTGEAMVAFESR   67 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTS----CCCTTTCEEEECSSSCEEEEEEEEESCH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHc----CCccceEEEEECCCCCeeeEEEEEECCH
Confidence            3456899999999999999999999999    8999999999999999999999999864

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.07  E-value=1.3e-10  Score=108.82  Aligned_cols=54  Identities=19%  Similarity=0.338  Sum_probs=50.1

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCC--CeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLES--SVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G--~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++|||+|||+.+|+++|+++|..|    |  .|..|+|++|+.+|.++|||||+|.+.
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~----G~~~v~~v~i~~d~~tg~skGfaFV~f~~~  122 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSL----GVNDILEIKFFENRANGQSKGFALVGVGSE  122 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTT----TCCCEEEEEEEECTTTCCEEEEEEEEESCT
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHH----CCcceEEEEEEecCCCCccceEEEEEECCH
Confidence            35789999999999999999999999    9  999999999999999999999999875

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.06  E-value=1.8e-10  Score=94.83  Aligned_cols=51  Identities=18%  Similarity=0.156  Sum_probs=45.8

Q ss_pred             CcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          332 LYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       332 ~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...++++|||+|||+++|+++|+++|++|    |.|.+|+|++      .||||||+|.+.
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~f----G~V~~v~i~~------~kg~AFVef~~~   67 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEF----GPISYVVVMP------KKRQALVEFEDV   67 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEET------TTTEEEEEESSH
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhcc----CCEEEEEEEc------CCCEEEEEECCH
Confidence            35578899999999999999999999999    9999999985      379999999863

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.06  E-value=3.4e-10  Score=91.83  Aligned_cols=54  Identities=26%  Similarity=0.509  Sum_probs=48.7

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|+|++++.  .++|||||+|.+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~----G~v~~v~i~~~~~--~~~g~afV~f~~~   65 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQF----GKILDVEIIFNER--GSKGFGFVTFENS   65 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGT----SCEEEEEEECCTT--TTCCEEEEEESCH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEecCC--CCcEEEEEEECCH
Confidence            4457899999999999999999999999    9999999999864  3899999999864

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.06  E-value=7.7e-11  Score=100.39  Aligned_cols=57  Identities=23%  Similarity=0.293  Sum_probs=48.0

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...+|||+|||+++|+++|+++|..|+...|.|..|+|+.+ .+|+++|||||+|.++
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~   78 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACE   78 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCH
Confidence            45799999999999999999999999211123479999999 5899999999999874

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.05  E-value=2.1e-10  Score=94.30  Aligned_cols=50  Identities=18%  Similarity=0.282  Sum_probs=45.5

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|+|+++      +|||||+|.+.
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~f----G~v~~v~i~~~------kg~aFVef~~~   61 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPF----GKVTNILMLKG------KNQAFLELATE   61 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTT----SCEEEEEEETT------TTEEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEECC------CCEEEEEECCH
Confidence            4567899999999999999999999999    99999999865      89999999864

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.05  E-value=2.3e-10  Score=92.82  Aligned_cols=54  Identities=26%  Similarity=0.415  Sum_probs=48.4

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|+|+++..  .++|||||+|.+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~i~~~~~--~~~g~afV~f~~~   65 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQI----GPCKSCKMITEHT--SNDPYCFVEFYEH   65 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHH----SCEEEEEEECCCC--SSCCEEEEEESSH
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhc----CCEeEEEEEecCC--CCCCEEEEEECCH
Confidence            4467899999999999999999999999    9999999999954  3799999999864

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.05  E-value=2.2e-10  Score=90.92  Aligned_cols=54  Identities=22%  Similarity=0.386  Sum_probs=48.9

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .....+|||+|||+++++++|+++|+.|     .|..|+|+++ .+|.++|||||+|.+.
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-----~i~~v~i~~~-~~g~~~g~afV~f~~~   60 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-----KPVAIRIVRN-AHGNKTGYIFVDFSNE   60 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-----CCSEEEEEEC-TTSCEEEEEEEECSSH
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-----CceEEEEEEC-CCCCCceEEEEEECCH
Confidence            3456899999999999999999999998     4889999999 7899999999999874

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.04  E-value=9.1e-11  Score=92.67  Aligned_cols=49  Identities=24%  Similarity=0.369  Sum_probs=45.1

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +.++|||+|||+++++++|+++|+.|    |.|..|+|+++     ++|||||+|.+.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~----G~i~~v~i~~~-----~~g~afV~f~~~   52 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQY----GDVMDVFIPKP-----FRAFAFVTFADD   52 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTT----SCCCEEECCSS-----CCSCCEEECSCH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHc----CCeeEEEEecC-----CCCEEEEEECCH
Confidence            46899999999999999999999999    99999999876     689999999874

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.04  E-value=2.8e-10  Score=93.22  Aligned_cols=52  Identities=15%  Similarity=0.203  Sum_probs=47.4

Q ss_pred             CcceeeeCCCCCCC------CHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDV------KDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~------teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++|||+|||+.+      ++++|+++|+.|    |.|..|+|+  ..+|.++|||||+|.+.
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~----G~v~~v~i~--~~~g~~~G~afV~f~~~   71 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKF----GKITNDFYP--EEDGKTKGYIFLEYASP   71 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGG----SCEEEEECC--CBTTBSCCEEEEEECSS
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcC----CCEEEEEee--CCCCCeeeEEEEEECCH
Confidence            46799999999999      789999999999    999999998  36899999999999875

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.03  E-value=4.6e-10  Score=92.67  Aligned_cols=50  Identities=18%  Similarity=0.195  Sum_probs=45.3

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|+|+++      ||||||+|.+.
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~f----G~V~~v~i~~~------kg~aFVef~~~   61 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKF----GTICYVMMMPF------KRQALVEFENI   61 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTT----SCEEEEEEETT------TTEEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhC----CCEEEEEEECC------CCEEEEEECCH
Confidence            4567899999999999999999999999    99999999764      79999999863

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.01  E-value=3.6e-10  Score=90.98  Aligned_cols=53  Identities=19%  Similarity=0.231  Sum_probs=47.8

Q ss_pred             cCCcceeeeCCCCCCCCHHHHH----HHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIY----QLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~----e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .....+|||+|||+.+++++|+    ++|+.|    |.|..|+|++++.+   +|||||+|.++
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~----G~v~~v~i~~~~~~---rg~afV~f~~~   62 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARH----GKVKSVELSPHTDY---QLKAVVQMENL   62 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHH----SCEEEEEECSCCST---TCCEEEEESSH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccc----CcEEEEEEEeCCCC---CeEEEEEECCH
Confidence            4456899999999999999999    999999    99999999999765   89999999864

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.00  E-value=1.8e-10  Score=95.01  Aligned_cols=50  Identities=10%  Similarity=0.161  Sum_probs=45.1

Q ss_pred             cCCcceeeeCCCCC-CCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPF-DVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~-~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+ .+++++|+++|+.|    |.|.+|+|+++      +|||||+|.++
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~f----G~V~~v~i~~~------kg~aFVef~~~   62 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPF----GVISNHLILNK------INEAFIEMATT   62 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGG----SCEEEEEECSS------SSCEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhc----CCEEEEEEEcC------CCEEEEEECCH
Confidence            34678999999999 99999999999999    99999999865      58999999864

>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=98.99  E-value=1e-09  Score=92.23  Aligned_cols=76  Identities=17%  Similarity=0.124  Sum_probs=63.2

Q ss_pred             CcccEEEEeCCCcc----------CCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeC
Q 016231          223 KLLRTIFVGNLPLK----------VKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFK  292 (393)
Q Consensus       223 ~~~rtVFVgNLp~~----------~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~  292 (393)
                      .+++.|.|.||=.-          -.+++|+..|++||.|.+|.|+++.                     .+|||||.|.
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~---------------------~~G~~fV~f~   63 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS---------------------AQGNVYVKCP   63 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC---------------------TTCCEEEECS
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC---------------------CcEEEEEEEC
Confidence            35788999998321          1256899999999999999984321                     3489999999


Q ss_pred             CHHHHHHHH-HhcCceeCCeEEEEeecC
Q 016231          293 SEQSTEAAL-AFNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       293 s~e~A~~Al-~lng~~~~Gr~I~V~~a~  319 (393)
                      +.++|..|+ .|||..|.||.|.|.++.
T Consensus        64 ~~e~A~~Ai~~lnG~~f~GR~i~v~~~~   91 (114)
T 3s6e_A           64 SIAAAIAAVNALHGRWFAGKMITAAYVP   91 (114)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CHHHHHHHHHHhCCCEECCEEEEEEEEc
Confidence            999999999 799999999999999985

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.99  E-value=4.4e-10  Score=92.78  Aligned_cols=54  Identities=28%  Similarity=0.527  Sum_probs=48.8

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ....++|||+|||.++++++|+++|+.|    |.|..|+|+++.  +.++|||||+|.+.
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~----G~i~~v~i~~~~--~~~kg~afV~f~~~   79 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQF----GKILDVEIIFNE--RGSKGFGFVTFENS   79 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGT----CCCSCEEECCBT--TBCTTEEEEECCCS
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhc----CCEEEEEEEECC--CCCceEEEEEECCH
Confidence            4467899999999999999999999999    999999999985  45899999999874

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=98.99  E-value=3.2e-10  Score=103.36  Aligned_cols=95  Identities=15%  Similarity=0.186  Sum_probs=65.7

Q ss_pred             CHHHHHHHHH-h--cCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEE
Q 016231          293 SEQSTEAALA-F--NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEA  369 (393)
Q Consensus       293 s~e~A~~Al~-l--ng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~  369 (393)
                      +...+..|+. .  ....+.+....|.+...................++|||+|||+++++++|+++|+.|    |.|..
T Consensus        63 d~~~I~~Al~~S~~~~lev~ed~~~vrR~~~~p~p~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~----G~v~~  138 (193)
T 2voo_A           63 DFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDK----GQVLN  138 (193)
T ss_dssp             CHHHHHHHHHTCSSCCEEECTTSSEEEECTTSCCCCCCHHHHHHHHHTEEEEECCCTTCCHHHHHHHHTTS----CCEEE
T ss_pred             CHHHHHHHHhhcccceEEEecccceEEecccCCCcccchhhhhccccCEEEecCCCCcCCHHHHHHHHhcC----CCEEE
Confidence            4566777774 4  344566655566554211000000000001235799999999999999999999999    99999


Q ss_pred             EEEeecCCCCCCccEEEEEeeec
Q 016231          370 VRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       370 VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      |+|+++. +|.++|||||+|.++
T Consensus       139 v~i~~~~-~~~~kG~aFVeF~~~  160 (193)
T 2voo_A          139 IQMRRTL-HKAFKGSIFVVFDSI  160 (193)
T ss_dssp             EEEEECT-TCCEEEEEEEEESSH
T ss_pred             EEEEECC-CCCcccEEEEEECCH
Confidence            9999996 599999999999874

>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=98.98  E-value=5.6e-10  Score=92.30  Aligned_cols=52  Identities=25%  Similarity=0.652  Sum_probs=46.9

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+.++|||+|||+.+++++|+++|+.|    |.|..|+|+++   +.++|||||+|.+.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~v~~v~i~~~---~~~~g~afV~f~~~   57 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKY----GPIRQIRVGNT---PETRGTAYVVYEDI   57 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTT----SCEEEEEEECS---TTTTTCEEEEESSH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEeeC---CCCCcEEEEEECCH
Confidence            456899999999999999999999999    99999999976   45699999999864

>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=98.97  E-value=7.7e-10  Score=90.73  Aligned_cols=53  Identities=25%  Similarity=0.484  Sum_probs=47.1

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+++++++|+++|..|    |.|..|+|+.+   +.++|||||+|.+.
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~v~~~~i~~~---~~~~g~afV~f~~~   71 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKY----GAIRDIDLKNR---RGGPPFAFVEFEDP   71 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEECCS---SSSSCCEEEEESCH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEEC---CCCCcEEEEEECCH
Confidence            3456899999999999999999999999    99999999655   55899999999874

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=98.51  E-value=6.3e-11  Score=98.52  Aligned_cols=55  Identities=22%  Similarity=0.251  Sum_probs=51.2

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEE--------EEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEA--------VRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~--------VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+.++|||+|||+.+++++|+++|+.|    |.|..        |+|++++.+|.++|||||+|.+.
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~   67 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQI----GIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP   67 (116)
Confidence            356899999999999999999999999    99999        99999999999999999999874

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.96  E-value=4.5e-09  Score=86.30  Aligned_cols=74  Identities=15%  Similarity=0.123  Sum_probs=59.7

Q ss_pred             ccEEEEeCCC-------ccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHH
Q 016231          225 LRTIFVGNLP-------LKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQST  297 (393)
Q Consensus       225 ~rtVFVgNLp-------~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A  297 (393)
                      ..+|.|.-.+       ..+++++|+.+|++||.|..|+|+.                      .++|||||+|.+.++|
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~----------------------~~rGfaFVeF~~~~~A   67 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSS----------------------KKPGTAVVEFATVKAA   67 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEES----------------------SSSSEEEEEESCHHHH
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEcc----------------------CCCCEEEEEECCHHHH
Confidence            4556665543       4689999999999999999999841                      1569999999999999


Q ss_pred             HHHHHhcCceeCCeEEEEeecCCC
Q 016231          298 EAALAFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       298 ~~Al~lng~~~~Gr~I~V~~a~~~  321 (393)
                      ..||.. +..+.|+.|.|.++.++
T Consensus        68 ~~Ai~~-~~~~~g~~l~V~~a~~~   90 (100)
T 2d9o_A           68 ELAVQN-EVGLVDNPLKISWLEGQ   90 (100)
T ss_dssp             HHHHHT-CCBCSSSBCEEECSSCC
T ss_pred             HHHHHh-cCCCCCCeEEEEEccCC
Confidence            999953 34468999999998754

>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=98.93  E-value=1.7e-09  Score=84.38  Aligned_cols=50  Identities=20%  Similarity=0.448  Sum_probs=45.2

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|+|+++      +|||||+|.+.
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~----G~i~~~~~~~~------kg~afV~f~~~   58 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQF----GEIRTITVVQR------QQCAFIQFATR   58 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTT----SCEEEEEEEGG------GTEEEEEESSH
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhC----CCEeEEEEECC------CCEEEEEECCH
Confidence            4456899999999999999999999999    99999999864      79999999874

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.93  E-value=9e-11  Score=94.95  Aligned_cols=54  Identities=17%  Similarity=0.217  Sum_probs=48.7

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+.++|||+|||+++++++|+++|..|    |.|.. .++.+..+|.++|||||+|.+.
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~v~~-~~~~~~~~g~~~g~afV~f~~~   68 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISEL----FAKND-LAVVDVRTGTNRKFGYVDFESA   68 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHH----HHHHT-CCCCEEEEETTTTEEEEEESSH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHh----CCcce-EEEecCCCCCcCcEEEEEECCH
Confidence            356899999999999999999999999    88888 7778878899999999999864

>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=98.92  E-value=5.4e-10  Score=92.43  Aligned_cols=55  Identities=22%  Similarity=0.265  Sum_probs=48.7

Q ss_pred             CCcceeeeCCCCCCCCHHHHH---HHhhcCCCCCCCeEEEEEeecCCCC---CCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIY---QLFCGLNDLESSVEAVRVIRHPHMR---VGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~---e~F~~~~~~~G~I~~VrI~~d~~tg---~~kGfaFVeF~t~  392 (393)
                      ...++|||+|||+++++++|+   ++|..|    |.|..|+|+++..++   .++|||||+|.++
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~----G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~   73 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKF----GKIHKVVINNSTSYAGSQGPSASAYVTYIRS   73 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTT----SCEEEEEEECCSSCCSSSCCCEEEEEEESSH
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhcc----CCEEEEEEecCCCcCccCCCCeEEEEEECcH
Confidence            346799999999999999999   999999    999999999997654   5669999999864

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.92  E-value=8.4e-10  Score=89.16  Aligned_cols=52  Identities=21%  Similarity=0.376  Sum_probs=46.0

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|    |.|   +|+.+ .+|.++|||||+|.+.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----g~v---~~~~~-~~g~~~g~afV~f~~~   63 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKA----TFI---KVPQN-QNGKSKGYAFIEFASF   63 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSC----SEE---ECCBC-SSSCBCSEEEEECSSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhC----CEE---EEEEC-CCCCEeeEEEEEECCH
Confidence            4467899999999999999999999999    866   67777 6899999999999864

>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=98.91  E-value=1.7e-09  Score=88.85  Aligned_cols=49  Identities=20%  Similarity=0.189  Sum_probs=44.6

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .....+|||+|||+++++++|+++|..|    |.|..|+|+.+       |||||+|.+.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~~~i~~~-------g~afV~f~~~   60 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREA----GDVCYADVYRD-------GTGVVEFVRK   60 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGG----SCEEEEEEETT-------TEEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEeEEEEecC-------CEEEEEECCH
Confidence            3456899999999999999999999999    99999999877       8999999874

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.91  E-value=1.9e-09  Score=85.31  Aligned_cols=48  Identities=27%  Similarity=0.452  Sum_probs=43.8

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+++++++|+++|+.|    |.|..|+|+        +|||||+|.+.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~~~--------~g~afV~f~~~   52 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQY----GKVLECDII--------KNYGFVHIEDK   52 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTS----SCEEEEEEE--------TTEEEEEESSH
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhC----CCEEEEEEE--------CCEEEEEECCH
Confidence            3467899999999999999999999999    999999997        68999999874

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.91  E-value=1.3e-09  Score=87.98  Aligned_cols=53  Identities=26%  Similarity=0.417  Sum_probs=47.4

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+++++++|+++|..|    +   .|+++.++.++.++|||||+|.+.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----~---~~~~~~~~~~~~~~g~afV~f~~~   64 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGS----V---RARIVTDRETGSSKGFGFVDFNSE   64 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTC----S---EEEEEECSSSCSEEEEEEEECSSH
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCC----e---EEEEEecCCCCCcCcEEEEEECCH
Confidence            4567899999999999999999999987    3   688889988999999999999864

>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=98.91  E-value=5.7e-10  Score=93.66  Aligned_cols=50  Identities=20%  Similarity=0.388  Sum_probs=44.8

Q ss_pred             cCCcceeeeCCCCCC-CCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFD-VKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~-~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||++ +++++|+++|+.|    |.|..|+|++      ++|||||+|.+.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~f----G~V~~v~i~~------~kg~aFVef~~~   72 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPY----GKIKNYILMR------MKSQAFIEMETR   72 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTT----SCCSEEEEET------TTTEEEEECSSH
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhc----CCEEEEEEec------CCCEEEEEECCH
Confidence            446789999999998 9999999999999    9999999974      489999999863

>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=98.90  E-value=3.1e-10  Score=93.76  Aligned_cols=56  Identities=16%  Similarity=0.283  Sum_probs=45.3

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|.+..+..+|.++|||||+|.+.
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~----G~v~~~~~~~~~~~g~~~g~afV~f~~~   77 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARF----QEKKGPPIQFRMMTGRMRGQAFITFPNK   77 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHH----HHSSSSCCEEEEECSSSCSEEEEECSSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHh----CCccceEEEEEcCCCccceEEEEEECCH
Confidence            3467899999999999999999999999    8884433333333788999999999863

>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=98.90  E-value=1.4e-09  Score=89.49  Aligned_cols=66  Identities=27%  Similarity=0.453  Sum_probs=51.2

Q ss_pred             CCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCC-CCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEE
Q 016231          309 GGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFD-VKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYV  387 (393)
Q Consensus       309 ~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~-~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFV  387 (393)
                      .|..|.|..+.....      .......++|||+|||+. +++++|+++|..|    |.|..|.|        ++|||||
T Consensus         6 ~g~~~~~~~s~~~~~------~~~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~----G~v~~v~i--------~~g~afV   67 (110)
T 1wf1_A            6 SGMSLKLQASNVTNK------NDPKSINSRVFIGNLNTALVKKSDVETIFSKY----GRVAGCSV--------HKGYAFV   67 (110)
T ss_dssp             CSCCCCCCCCCSCCS------CCCTTCSSEEEECSCCCSSCCHHHHHHHHGGG----SCCSEEEE--------ETTEEEE
T ss_pred             CCcccccccCCCCCC------CCCCCCCcEEEEeCCCcccCCHHHHHHHHHhC----CCeEEEEE--------eCCEEEE
Confidence            456666665543221      112334589999999999 9999999999999    99999999        5899999


Q ss_pred             Eeeec
Q 016231          388 LFKTR  392 (393)
Q Consensus       388 eF~t~  392 (393)
                      +|.+.
T Consensus        68 ~f~~~   72 (110)
T 1wf1_A           68 QYSNE   72 (110)
T ss_dssp             ECSSS
T ss_pred             EECCH
Confidence            99874

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=98.90  E-value=1.2e-09  Score=98.27  Aligned_cols=55  Identities=27%  Similarity=0.389  Sum_probs=50.9

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+..+|||+|||+.+++++|+++|+.|    |.|..|.|+.++ +|.++|||||+|.+.
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~----G~I~~v~i~~d~-~g~~kG~afV~F~~~  139 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEF----GTLKKAAVDYDR-SGRSLGTADVHFERR  139 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHT----SCCSEEEECCCT-TSSCSCCEEEEESCH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEEECC-CCCEeeEEEEEeCCH
Confidence            3456899999999999999999999999    999999999997 899999999999864

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=98.89  E-value=1.5e-09  Score=92.86  Aligned_cols=53  Identities=21%  Similarity=0.296  Sum_probs=45.8

Q ss_pred             cCCcceeeeCCCCCCCCHHHHH----HHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIY----QLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~----e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+..+|||+|||+.+++++|+    ++|+.|    |.|..|.+.+   +|.++|||||+|.+.
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~----G~I~~v~i~~---~~~~rG~aFV~F~~~   82 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQ----GDILDIVVDL---SDDNSGKAYIVFATQ   82 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHH----SCEEEEEECC---CCSSCCCEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccC----CCeEEEEecc---CCCcCCEEEEEECCH
Confidence            4457899999999999999876    799999    9999998854   578999999999863

>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=98.89  E-value=4.9e-10  Score=89.65  Aligned_cols=53  Identities=25%  Similarity=0.422  Sum_probs=46.8

Q ss_pred             cCCcceeeeCCCCCCCCHHHHH----HHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIY----QLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~----e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+++++++|+    ++|+.|    |.|..|+|++   +|.++|||||+|.+.
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~----G~i~~v~i~~---~~~~~g~afV~f~~~   61 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRF----GQILDILVSR---SLKMRGQAFVIFKEV   61 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGG----SCEEEEECCH---HHHHTTCEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhC----CCEEEEEEEc---CCCcCcEEEEEeCCH
Confidence            3467899999999999999999    999999    9999999974   477899999999864

>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=98.88  E-value=1.7e-09  Score=86.85  Aligned_cols=50  Identities=14%  Similarity=0.303  Sum_probs=44.7

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|.|+++      +|||||+|.+.
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~v~~v~~~~~------~g~afV~f~~~   63 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRF----GSIRTIDHVKG------DSFAYIQYESL   63 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTT----SCEEEEEECSS------SCCEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeeEEEEeCC------CCEEEEEECCH
Confidence            3456899999999999999999999999    99999999754      78999999864

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=98.87  E-value=1.2e-09  Score=88.16  Aligned_cols=47  Identities=28%  Similarity=0.437  Sum_probs=43.8

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+|||+|||+++++++|+++|+.|    |.|..|+|+++     ++|||||+|.+.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~----G~i~~v~i~~~-----~~g~afV~f~~~   47 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYY----GPLRTVWIARN-----PPGFAFVEFEDP   47 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHH----CCCSEEEEESS-----SSSEEEEECSSH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEeeC-----CCCEEEEEECCH
Confidence            379999999999999999999999    99999999987     789999999874

>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=98.87  E-value=2e-09  Score=86.69  Aligned_cols=50  Identities=32%  Similarity=0.632  Sum_probs=45.1

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..|+|+++      +|||||+|.+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~i~~v~~~~~------kg~afV~f~~~   61 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKY----GKAGEVFIHKD------KGFGFIRLETR   61 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTT----CCCSEEEEETT------TTEEEEECSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhc----CCeEEEEEecC------CCEEEEEECCH
Confidence            4567899999999999999999999999    99999999854      79999999874

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=98.87  E-value=1.5e-09  Score=87.48  Aligned_cols=48  Identities=17%  Similarity=0.208  Sum_probs=43.8

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+..|||+||++.+|+++|+++|.+|    |.|.+++|+.      ++|||||+|.++
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~----G~V~~~~l~~------~kGfaFVey~~~   53 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQH----GPLVSFHPYL------NQGIALCKYTTR   53 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHH----SCEEEEEEET------TTTEEEEEESSH
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhh----CCEEEEEEcC------CCcEEEEEECCH
Confidence            35789999999999999999999999    9999999965      699999999874

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=98.86  E-value=2.7e-09  Score=86.13  Aligned_cols=48  Identities=19%  Similarity=0.422  Sum_probs=43.6

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++|||+|||.++++++|+++|..|    |.|..|+|+      .++|||||+|.+.
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~----G~i~~~~~~------~~~g~afV~f~~~   73 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNF----GFILDFKHY------PEKGCCFIKYDTH   73 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTT----SCCSEEEEE------TTTTEEEEECSSH
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhC----CCEEEEEEe------cCCCEEEEEECCH
Confidence            45799999999999999999999999    999999997      3589999999863

>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=98.86  E-value=2.4e-09  Score=87.92  Aligned_cols=49  Identities=27%  Similarity=0.469  Sum_probs=44.8

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...++|||+|||+.+++++|+++|..|    |.|..|+|+++      +|||||+|.+.
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~----G~i~~v~i~~~------~g~afV~f~~~   71 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPF----GQIMEIRVFPE------KGYSFVRFSTH   71 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHH----SCEEEEEEETT------TTEEEEEESSH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEeCC------CCEEEEEECCH
Confidence            346899999999999999999999999    99999999876      79999999874

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=98.81  E-value=3.9e-09  Score=84.76  Aligned_cols=48  Identities=21%  Similarity=0.606  Sum_probs=42.5

Q ss_pred             cCCcceeeeCCCCC-CCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPF-DVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~-~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+ .+++++|+++|+.|    |.|..|+|.        +|||||+|.+.
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~----G~v~~v~i~--------~g~afV~f~~~   55 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPY----GHIMQINIK--------NAFGFIQFDNP   55 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTT----CCCCEEEEE--------TTEEEEEESCH
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhc----CCEEEEEEe--------CCEEEEEECCH
Confidence            44678999999999 99999999999999    999999994        78999999874

>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=98.81  E-value=5.6e-09  Score=84.34  Aligned_cols=48  Identities=21%  Similarity=0.641  Sum_probs=43.4

Q ss_pred             cCCcceeeeCCCCC-CCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPF-DVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~-~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+ .+++++|+++|+.|    |.|..|+|.        +|||||+|.+.
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~----G~v~~v~i~--------~g~afV~f~~~   67 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPY----GHIMQINIK--------NAFGFIQFDNP   67 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGG----SCEEEEEEC--------SSEEEEEESSH
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhc----CCEEEEEEe--------CCEEEEEECCH
Confidence            44678999999998 99999999999999    999999993        79999999864

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=98.81  E-value=4.6e-09  Score=86.70  Aligned_cols=48  Identities=25%  Similarity=0.564  Sum_probs=43.8

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|+|+        +|||||+|.+.
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~----G~i~~v~i~--------kg~afV~f~~~   75 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPF----GPMKEVKIL--------NGFAFVEFEEA   75 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTT----SCCCEEEEE--------TTEEEEECSSH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhc----CCEEEEEEE--------CCEEEEEECCH
Confidence            4457899999999999999999999999    999999997        78999999863

>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=98.80  E-value=5e-09  Score=85.06  Aligned_cols=48  Identities=29%  Similarity=0.463  Sum_probs=43.3

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+++++++|+++|..|    |.|..|+|+        +|||||+|.++
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~----G~i~~v~~~--------~~~afV~f~~~   55 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQF----GKLERVKKL--------KDYAFIHFDER   55 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHH----SCEEEEEEC--------SSCEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEE--------CCEEEEEeCCH
Confidence            4567899999999999999999999999    999999986        56999999874

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.80  E-value=4e-09  Score=84.75  Aligned_cols=51  Identities=24%  Similarity=0.395  Sum_probs=44.0

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ....++|||+|||+.+++++|+++|..|    |.|. ++++.+    .++|||||+|.+.
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~----G~v~-~~~~~~----~~~g~afV~f~~~   66 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALREL----GSVP-LRLTWQ----GPRRRAFLHYPDS   66 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHT----TCCC-SEEEEE----TTTTEEEEECSSH
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhc----CCEE-EEEEcC----CCCcEEEEEECCH
Confidence            3346899999999999999999999999    8887 777754    5799999999864

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.80  E-value=9e-09  Score=82.16  Aligned_cols=49  Identities=22%  Similarity=0.331  Sum_probs=42.9

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++|||+|||+++++++|+++|..|    |.|..|  +.++.+|.   ||||+|.++
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~----G~v~~v--~~~~~~g~---~afV~f~~~   55 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAF----GPVASV--VMDKDKGV---FAIVEMGDV   55 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGT----SCEEEE--EECSSSCC---EEEEEESSH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhc----CCeEEE--EEcCCCCc---EEEEEECCH
Confidence            45799999999999999999999999    999987  66666665   999999874

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=98.79  E-value=2.5e-09  Score=89.38  Aligned_cols=50  Identities=16%  Similarity=0.080  Sum_probs=44.3

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCC-CeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLES-SVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G-~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...+|||+|||+++++++|+++|..|    | .|..|.|+.+    .++|||||+|.++
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~----G~~v~~v~i~~~----~~rGfaFV~F~~~   77 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLAREN----SLETTFSSVNTR----DFDGTGALEFPSE   77 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHH----TCCCSEEECSSC----SSSCCEEEEESSH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHh----CCeeEEEEEEcC----CCCCEEEEEECCH
Confidence            35799999999999999999999999    8 8999998643    4799999999864

>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=98.79  E-value=3.6e-09  Score=87.70  Aligned_cols=48  Identities=27%  Similarity=0.288  Sum_probs=43.3

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++|||+|||+.+++++|+++|..|    |.|..|+|+.      ++|||||+|.+.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~----G~i~~v~i~~------~~g~afV~f~~~   56 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRF----GSLGRVLLPE------GGITAIVEFLEP   56 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTT----SCEEEEECCS------SSSCEEEEESCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc----CCEEEEEEeC------CCCEEEEEeCCH
Confidence            35799999999999999999999999    9999999874      578999999864

>1fjc_A Nucleolin RBD2, 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=86.57  Aligned_cols=51  Identities=27%  Similarity=0.514  Sum_probs=44.3

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|    |.|..+     ..+|.++|||||+|.+.
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~----g~v~~~-----~~~~~~~g~afV~f~~~   63 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDA----LEIRLV-----SQDGKSKGIAYIEFKSE   63 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSE----EEECCE-----EETTEEEEEEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhC----CcEEEe-----CCCCCcceEEEEEECCH
Confidence            4467899999999999999999999999    877665     35788999999999864

>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=98.77  E-value=7.1e-10  Score=95.42  Aligned_cols=53  Identities=17%  Similarity=0.275  Sum_probs=44.7

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEE--------EEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAV--------RVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~V--------rI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+..+|||+|||+.+|+++|+.+|..|    |.|..|        ++.   .+|.++|||||+|.+.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~----G~i~~~~~~~~~di~~~---~~g~~~g~afV~f~~~  102 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRY----VDFSSETQRIMFDIRLM---KEGRMKGQAFIGLPNE  102 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGG----CCTTCHHHHHHCEEEEE---EETTTEEEEEEECSSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHh----CCcccccccceeeEEec---cCCCcccEEEEEeCCH
Confidence            3456899999999999999999999999    888764        333   4688999999999863

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.76  E-value=1.6e-08  Score=81.39  Aligned_cols=50  Identities=30%  Similarity=0.462  Sum_probs=43.5

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|..|+.  |.|..|+++        +|||||+|.+.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~--g~v~~~~~~--------~g~afV~f~~~   61 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKP--GAVERVKKI--------RDYAFVHFSNR   61 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTST--TCEEEEEEC--------SSEEEEEESSH
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCC--cceEEEEEe--------CCeEEEEeCCH
Confidence            456789999999999999999999999853  789988874        67999999864

>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=98.76  E-value=3.8e-09  Score=87.97  Aligned_cols=47  Identities=21%  Similarity=0.212  Sum_probs=42.2

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...+|||+|||+++++++|+++|..|    |.|..|.|+.+       |||||+|.+.
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~----G~v~~~~i~~~-------g~afV~f~~~   61 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREA----GDVCYADVYRD-------GTGVVEFVRK   61 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGG----SCEEEEEECTT-------SEEEEEESSH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEecC-------CEEEEEECCH
Confidence            45799999999999999999999999    99999999876       8999999873

>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=98.76  E-value=4.3e-09  Score=88.58  Aligned_cols=50  Identities=16%  Similarity=0.241  Sum_probs=44.0

Q ss_pred             cCCcceeee--CCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFV--GNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfV--gNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++++|||  +||++++++++|+++|+.|    |.|..|.|+.      .||||||+|.++
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~f----G~v~~v~i~~------~rgfaFV~f~~~   73 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKC----GLVDALLMPP------NKPYSFARYRTT   73 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHH----SCEEEEECCT------TCSCEEEEESSH
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhc----CCeEEEEEeC------CCCEEEEEECCH
Confidence            446789999  7799999999999999999    9999998864      379999999874

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.75  E-value=1e-08  Score=81.36  Aligned_cols=48  Identities=19%  Similarity=0.289  Sum_probs=43.0

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|+|+        +|||||+|.+.
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~v~~v~~~--------~~~afV~f~~~   54 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEY----GPVIECDIV--------KDYAFVHMERA   54 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTT----SCCCEEEEC--------SSEEEEEESCH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----CCeEEEEEE--------CCEEEEEECCH
Confidence            4467899999999999999999999999    999999996        44999999874

>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=98.73  E-value=7.6e-09  Score=80.81  Aligned_cols=52  Identities=27%  Similarity=0.572  Sum_probs=43.6

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCC-------CeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLES-------SVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G-------~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +.++|||+|||+++++++|+++|..|+...|       .|..|+++++      +|||||+|.++
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~   63 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSV   63 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCH
Confidence            4689999999999999999999999821114       7999999755      79999999874

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.72  E-value=3.2e-08  Score=79.84  Aligned_cols=73  Identities=19%  Similarity=0.264  Sum_probs=61.5

Q ss_pred             CcccEEEEeCCCc----cCCH----HHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCH
Q 016231          223 KLLRTIFVGNLPL----KVKK----KTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSE  294 (393)
Q Consensus       223 ~~~rtVFVgNLp~----~~te----e~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~  294 (393)
                      ++..||+|.-+|.    ..-.    .+|...|++||.|..+++..                         +.+||+|.+.
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~-------------------------d~~fVtF~d~   59 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVE-------------------------DKMWVTFLEG   59 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECS-------------------------SSEEEEESSH
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEec-------------------------CCEEEEECCh
Confidence            4567899988762    3333    57899999999999999944                         3489999999


Q ss_pred             HHHHHHHHhcCceeCCeEEEEeecCC
Q 016231          295 QSTEAALAFNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       295 e~A~~Al~lng~~~~Gr~I~V~~a~~  320 (393)
                      ++|.+||.|||..+.||.|+|..+++
T Consensus        60 ~sAlaAi~mnG~~v~Gr~LkV~lkt~   85 (91)
T 2dnr_A           60 SSALNVLSLNGKELLNRTITIALKSP   85 (91)
T ss_dssp             HHHHHGGGGTTCEETTEEEEEEECCC
T ss_pred             HHHHHHHhcCCeEeCCeEEEEEeCCC
Confidence            99999999999999999999999864

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.71  E-value=1.4e-08  Score=80.26  Aligned_cols=48  Identities=25%  Similarity=0.345  Sum_probs=42.9

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+.+++++|+++|+.|    |.|..|+|+        +|||||+|.+.
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~v~~~~~~--------~~~afV~f~~~   53 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERR----GRVIECDVV--------KDYAFVHMEKE   53 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHH----SCEEEEEEC--------SSCEEEEESCH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcC----CCEEEEEEE--------CCEEEEEECCH
Confidence            3456899999999999999999999999    999999997        44999999874

>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=98.70  E-value=5.5e-09  Score=83.04  Aligned_cols=48  Identities=21%  Similarity=0.380  Sum_probs=41.2

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCC-eEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESS-VEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~-I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+.++|||+|||+++++++|+++|..|    |. |..+.+.       ++|||||+|.++
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~vv~~~~~~-------~~g~afV~f~~~   54 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDR----KLPLAGQVLL-------KSGYAFVDYPDQ   54 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHT----TCCCSSCEEE-------ETTEEEECCSCH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHc----CCceEEEEEc-------CCCEEEEEECCH
Confidence            456899999999999999999999999    88 6666662       489999999874

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.65  E-value=6.2e-08  Score=82.33  Aligned_cols=73  Identities=11%  Similarity=0.037  Sum_probs=62.3

Q ss_pred             cccEEEEeCCCcc-CCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCC-HHHHHHHH
Q 016231          224 LLRTIFVGNLPLK-VKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKS-EQSTEAAL  301 (393)
Q Consensus       224 ~~rtVFVgNLp~~-~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s-~e~A~~Al  301 (393)
                      ..+.|||+||++. ++.++|+.+|+.||.|..|.+.++.                       -.|||.|.+ ..+|..|+
T Consensus        17 ~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~-----------------------~tgfVrf~~~~~~A~~av   73 (121)
T 1owx_A           17 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA-----------------------KEGIILFKEKAKEALGKA   73 (121)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC-----------------------SEEEEEESSCHHHHHHHH
T ss_pred             CCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-----------------------CEEEEEECCChHHHHHHH
Confidence            4688999999999 9999999999999999999985432                       269999999 88899888


Q ss_pred             -Hh--cCceeCCeEEEEeecC
Q 016231          302 -AF--NMAVIGGNHIRLDRAC  319 (393)
Q Consensus       302 -~l--ng~~~~Gr~I~V~~a~  319 (393)
                       .+  ++..|.|..+.+....
T Consensus        74 ~~ln~~~~~i~g~~~~~evL~   94 (121)
T 1owx_A           74 KDANNGNLQLRNKEVTWEVLE   94 (121)
T ss_dssp             HHTTTSCBCTTSSSEEEEECC
T ss_pred             HHhhcCCcEEeCcEEEEEECC
Confidence             67  4778899888887654

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.64  E-value=1.6e-08  Score=80.64  Aligned_cols=51  Identities=16%  Similarity=0.249  Sum_probs=44.4

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEE-EeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVR-VIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~Vr-I~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...++|||+|||+.+++++|+++|..|    |.|..|+ |+.++.+|    .|||+|.+.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~----G~v~~~~~i~~~~~~~----~afV~f~~~   64 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQY----GVVESCEQVNTDSETA----VVNVTYSSK   64 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHH----SCEEEEEEECCSSSSE----EEEEEESSH
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhc----CCeEEEEEeecCCCCC----EEEEEECCH
Confidence            346899999999999999999999999    9999995 88886544    499999864

>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=98.63  E-value=1.5e-08  Score=79.96  Aligned_cols=47  Identities=23%  Similarity=0.247  Sum_probs=41.3

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++|||+|||+.+++++|+++|..|     .|..|+|.      .++|||||+|.++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-----~v~~~~i~------~~~g~afV~f~~~   50 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-----DLKYCYVD------RNKRTAFVTLLNG   50 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-----CCCCEEEE------GGGTEEEECCSCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-----CeEEEEEe------CCCcEEEEEECCH
Confidence            35799999999999999999999998     47888884      5799999999864

>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=98.62  E-value=4.2e-08  Score=87.62  Aligned_cols=50  Identities=16%  Similarity=0.185  Sum_probs=44.2

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...+|||+||++.+|+++|+++|+.|    |.|..|.|+.+.    ++|||||+|.++
T Consensus        45 ~vl~l~VgNL~~~vted~L~~~Fs~f----G~V~~V~i~~k~----~rgfAFVeF~d~   94 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTLDVLHQIFSKF----GTVLKIITFTKN----NQFQALLQYADP   94 (164)
T ss_dssp             CEEEEEECSCCSCCCHHHHHHHHHHH----SCEEEEEEEESS----SCEEEEEEESCH
T ss_pred             ceEEEEEeCcCCCCCHHHHHHHHHhc----CCEEEEEEEeCC----CCCEEEEEECCH
Confidence            34679999999999999999999999    999999997552    589999999864

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.58  E-value=8.5e-08  Score=76.84  Aligned_cols=48  Identities=13%  Similarity=0.164  Sum_probs=42.0

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+||  ++++++|+++|..|    |.|..|.|.      .++|||||+|.+.
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~----G~i~~v~i~------~~~g~afV~f~~~   59 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPF----GNIIDLSMD------PPRNCAFVTYEKM   59 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTT----SCEEEEEEE------TTTTEEEEEESSH
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhC----CCEEEEEec------CCCCEEEEEECCH
Confidence            345689999996  89999999999999    999999994      4689999999863

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=98.57  E-value=6.2e-08  Score=83.31  Aligned_cols=49  Identities=16%  Similarity=0.238  Sum_probs=43.4

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccE-EEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGI-AYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGf-aFVeF~t~  392 (393)
                      ....|||+||++.+|+++|+++|+.|    |.|..|+|+.+     .+|| |||+|.+.
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~y----G~V~~V~i~~~-----~~gfqAFVef~~~   76 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKF----GTVLKIITFTK-----NNQFQALLQYADP   76 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTS----SCEEEEEEEEE-----TTEEEEEEEESCH
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCc----CCEEEEEEEcC-----CCCcEEEEEECCH
Confidence            44688999999999999999999999    99999999875     3688 99999864

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.52  E-value=1.4e-07  Score=76.48  Aligned_cols=73  Identities=19%  Similarity=0.267  Sum_probs=61.1

Q ss_pred             CCcccEEEEeCCCcc-----CCH----HHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeC
Q 016231          222 GKLLRTIFVGNLPLK-----VKK----KTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFK  292 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~-----~te----e~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~  292 (393)
                      .++..||+|.-++..     +-.    .+|.+.|..||.|..|+|..+                         -+||+|.
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d-------------------------~~fVtF~   66 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG-------------------------QMLVTFA   66 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT-------------------------EEEEECS
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecC-------------------------cEEEEEc
Confidence            345689999988743     222    468899999999999999542                         3999999


Q ss_pred             CHHHHHHHHHhcCceeCCeEEEEeecC
Q 016231          293 SEQSTEAALAFNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       293 s~e~A~~Al~lng~~~~Gr~I~V~~a~  319 (393)
                      +.++|.+||.|||..+.||.|+|..-.
T Consensus        67 d~~sAl~AI~ldG~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           67 DSHSALSVLDVDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             CSHHHHHHHHGGGSEETTEEEEEECCC
T ss_pred             ChHHHHHHHhcCCeeeCCeEEEEeccC
Confidence            999999999999999999999998754

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.52  E-value=2.1e-07  Score=85.52  Aligned_cols=70  Identities=19%  Similarity=0.199  Sum_probs=59.1

Q ss_pred             CCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-HhcCceeCCeEEEE
Q 016231          237 VKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRL  315 (393)
Q Consensus       237 ~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~lng~~~~Gr~I~V  315 (393)
                      -.+++|...|++||.|.+|.|+++...+..             ++.++|++||+|.+.++|.+|+ .|||..|.||.|.|
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~-------------~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~  207 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEE-------------DAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVA  207 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSST-------------TCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCccc-------------CcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEE
Confidence            356899999999999999999876532211             2347799999999999999999 79999999999999


Q ss_pred             eecC
Q 016231          316 DRAC  319 (393)
Q Consensus       316 ~~a~  319 (393)
                      .++.
T Consensus       208 ~~~~  211 (222)
T 3dxb_A          208 EVYD  211 (222)
T ss_dssp             EECC
T ss_pred             EEcC
Confidence            9874

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=98.50  E-value=1.6e-07  Score=77.35  Aligned_cols=55  Identities=13%  Similarity=0.029  Sum_probs=46.5

Q ss_pred             CCcceeeeCCCCC-----CCCHHHHHHHhhcCCCCCCCeEEEEEeecCCC-CCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPF-----DVKDEEIYQLFCGLNDLESSVEAVRVIRHPHM-RVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~-----~~teedL~e~F~~~~~~~G~I~~VrI~~d~~t-g~~kGfaFVeF~t~  392 (393)
                      .++++|+|+||..     +-++++|+++|+.|    |.|..|.|++++.+ +.++|||||+|.+.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~----G~V~~v~i~~~~~~~~~~~G~~FV~f~~~   66 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKY----GKVGKCVIFEIPGAPDDEAVRIFLEFERV   66 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGG----SCEEEEEEEECSSCCTTTSEEEEEEESSH
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhc----CCEEEEEEecCCCCCCCCcEEEEEEECCH
Confidence            4678999999963     23789999999999    99999999998754 68999999999864

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.50  E-value=1.8e-07  Score=79.63  Aligned_cols=46  Identities=17%  Similarity=0.348  Sum_probs=40.3

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccE-EEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGI-AYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGf-aFVeF~t~  392 (393)
                      ..|||+||++.+++++|+++|+.|    |.|..|+|+..      .|| |||+|.+.
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~y----G~V~~v~i~~~------~Gf~aFVef~~~   72 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPV----GKVQRIVIFKR------NGIQAMVEFESV   72 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTT----SCEEEEEEEES------SSEEEEEEESSH
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhc----CCEEEEEEEeC------CCCEEEEEECCH
Confidence            457899999999999999999999    99999999753      286 99999863

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=98.44  E-value=1.1e-07  Score=89.95  Aligned_cols=50  Identities=24%  Similarity=0.450  Sum_probs=44.7

Q ss_pred             cCCcceeeeCCCCCCC---------CHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDV---------KDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~---------teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ....++|||+||+..+         ++++|+.+|+.|    |.|..|+|+.      ++|||||+|.++
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~f----G~I~~v~v~~------~kG~AFV~F~~~  189 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRL----GDIDRIRYVE------SKNCGFVKFKYQ  189 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTT----SCEEEEEEEG------GGTEEEEEESSH
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHcc----CCEEEEEEEC------CCCEEEEEeCCH
Confidence            4457899999999998         799999999999    9999999985      389999999874

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.40  E-value=2.9e-07  Score=74.95  Aligned_cols=46  Identities=20%  Similarity=0.191  Sum_probs=37.5

Q ss_pred             CCcce-eeeCCCCCCCCHHH----HHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKT-VFVGNLPFDVKDEE----IYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~t-LfVgNLp~~~teed----L~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .++.| |||+|||+.+++++    |+++|..|+   |.|..|       +|   |||||.|.+.
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yG---G~Vl~V-------tg---G~AfV~F~~~   56 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCG---GKVLSI-------TG---CSAILRFINQ   56 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTT---CCEEEC-------CT---TCEEEEESSH
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcC---CeeEEE-------ec---CEEEEEECCH
Confidence            34556 99999999999888    568999992   399988       34   9999999863

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=98.32  E-value=3.1e-07  Score=91.08  Aligned_cols=50  Identities=16%  Similarity=0.223  Sum_probs=43.8

Q ss_pred             cCCcceeeeCC--CCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGN--LPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgN--Lp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++.+|||+|  |++.+|+++|+++|+.|    |.|.+|.|+.      +||||||+|.+.
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~----G~V~~v~~~~------~kgfaFV~f~~~   66 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKC----GLVDALLMPP------NKPYSFARYRTT   66 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTT----SCEEEEECCT------TCSEEEEEESSH
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhc----CCeEEEEEeC------CCCEEEEEECCH
Confidence            56788999999  57899999999999999    9999988853      489999999763

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.15  E-value=5.2e-06  Score=67.90  Aligned_cols=38  Identities=18%  Similarity=0.126  Sum_probs=34.2

Q ss_pred             CCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          346 FDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       346 ~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+++++|+++|++|    |.|..|+|+     +.++|||||+|.++
T Consensus        27 ~~~te~~L~~~F~~~----G~V~~v~i~-----~~~rGfaFVeF~~~   64 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKY----GEVLNLVLS-----SKKPGTAVVEFATV   64 (100)
T ss_dssp             CSCCHHHHHHHHHTT----SCEEEEEEE-----SSSSSEEEEEESCH
T ss_pred             CCCCHHHHHHHHHhc----CCEEEEEEc-----cCCCCEEEEEECCH
Confidence            568999999999999    999999998     36899999999864

>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=98.10  E-value=1.9e-06  Score=70.88  Aligned_cols=54  Identities=17%  Similarity=0.214  Sum_probs=44.8

Q ss_pred             CcceeeeCCC--CCCCC--------HHHHHHHhhcCCCCCCCeEEEEEeecCCC--CCCccEEEEEeeec
Q 016231          335 IKKTVFVGNL--PFDVK--------DEEIYQLFCGLNDLESSVEAVRVIRHPHM--RVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNL--p~~~t--------eedL~e~F~~~~~~~G~I~~VrI~~d~~t--g~~kGfaFVeF~t~  392 (393)
                      |++.|+|.|+  |..+.        .++|++.|+.|    |.|.+|.|+++..+  +.++|||||+|.+.
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~----G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~   69 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKY----GLVKSIEIPRPVDGVEVPGCGKIFVEFTSV   69 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTT----SCEEEEECCCCBTTBCCTTTTEEEEEESSH
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHcc----CCEEEEEEeccCCCCCcCCcEEEEEEECCH
Confidence            5789999998  44443        47899999999    99999999998754  36899999999874

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.10  E-value=1e-05  Score=67.30  Aligned_cols=71  Identities=20%  Similarity=0.139  Sum_probs=64.0

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhccc-----CCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHH
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKF-----GEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~-----G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~  299 (393)
                      .++|-+-|||-.++...|+.++..+     |.|..|.|+.+.                       |-|+|+|.+...|-+
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH-----------------------~GAivef~d~~~AgK   77 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF-----------------------NGAIIIFRDSKFAAK   77 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT-----------------------TEEEEECSCHHHHHH
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC-----------------------CceEEEEccchhhHH
Confidence            5899999999999999999999999     999999885543                       689999999999988


Q ss_pred             HH-HhcCceeCCeEEEEeec
Q 016231          300 AL-AFNMAVIGGNHIRLDRA  318 (393)
Q Consensus       300 Al-~lng~~~~Gr~I~V~~a  318 (393)
                      |. .|+|..|.||.|+|...
T Consensus        78 asLaL~G~ef~gr~Lr~gTv   97 (117)
T 2l9w_A           78 MLMILNGSQFQGKVIRSGTI   97 (117)
T ss_dssp             HHHHHSSEEETTEEEEEECH
T ss_pred             HHhhcCCeeecCeEEEecCH
Confidence            86 99999999999999754

>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=98.07  E-value=2.1e-06  Score=72.29  Aligned_cols=54  Identities=13%  Similarity=0.097  Sum_probs=44.4

Q ss_pred             CcceeeeCCCC--CCC---CHHHHHHHhhcCCCCCCCeEEEEEeecCC----CCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLP--FDV---KDEEIYQLFCGLNDLESSVEAVRVIRHPH----MRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp--~~~---teedL~e~F~~~~~~~G~I~~VrI~~d~~----tg~~kGfaFVeF~t~  392 (393)
                      ++++|+|.|+-  .++   -+++|++.|+.|    |.|.+|.|++++.    ++.++|||||+|.+.
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~----G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~   81 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKF----GAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIA   81 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTT----SCEEEEEEEEEEESSSTTCEEEEEEEEEESSH
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhcc----CCEeEEEEeecCCCcccCCcceEEEEEEECCH
Confidence            57899999983  223   368999999999    9999999999864    456789999999864

>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=98.07  E-value=3.3e-06  Score=69.54  Aligned_cols=52  Identities=13%  Similarity=0.215  Sum_probs=41.5

Q ss_pred             cCCcceeeeCCCCCCCC-----------HHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVK-----------DEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~t-----------eedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++++|+|.||.....           +++|+++|+.|    |.|..|.| .+.   .++|||||+|.++
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~----G~v~~v~i-~~~---~~~G~afV~f~~~   74 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKF----GQIRKLLL-FDR---HPDGVASVSFRDP   74 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGT----SCCSEEEE-ETT---CTTCEEEEECSCH
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHcc----CCEeEEEE-ecC---CCCEEEEEEECCH
Confidence            34678999999944432           58999999999    99999966 553   3799999999864

>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=98.01  E-value=8.9e-07  Score=72.67  Aligned_cols=47  Identities=23%  Similarity=0.239  Sum_probs=39.6

Q ss_pred             eCCCCCCCCHHHHHHHh------------hcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          341 VGNLPFDVKDEEIYQLF------------CGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       341 VgNLp~~~teedL~e~F------------~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +.|||+.+++++|+++|            +.|    |.|..|.|+++. +|.++|||||+|.++
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~----G~V~~v~i~~~~-~~~~~G~~fV~f~~~   78 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKY----GEVEEMNVCDNL-GDHLVGNVYVKFRRE   78 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT----CCEEEEEECCSS-SSSSEEEEEEEESCH
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccC----CceEEEEEEeCC-CCCccEEEEEEECCH
Confidence            66788888888777766            999    999999999985 488999999999864

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.85  E-value=0.00011  Score=60.47  Aligned_cols=88  Identities=20%  Similarity=0.190  Sum_probs=72.5

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcc-----cCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHH
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIK-----FGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE  298 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~-----~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~  298 (393)
                      ..++|.|.|||..+.++.|.-+|..     -|+|.+|..  .+                       +-|+|+|.+...|+
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~--~~-----------------------~~AvItF~d~~va~   61 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQR--LG-----------------------CGGVLTFREPADAE   61 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEE--ET-----------------------TEEEEEESSHHHHH
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEE--cC-----------------------CcEEEEEcChHHHH
Confidence            3578999999999999999999986     267887776  11                       36999999999999


Q ss_pred             HHHHhcCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCC
Q 016231          299 AALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVK  349 (393)
Q Consensus       299 ~Al~lng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~t  349 (393)
                      ..|+...+.|.|..|.|....+.             ...+|++.||++.++
T Consensus        62 rVL~k~~H~L~~~~LsV~P~~~~-------------~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           62 RVLAQADHELHGAQLSLRPAPPR-------------APARLLLQGLPPGTS   99 (104)
T ss_dssp             HHHTCSCCBSSSSBCEEEECCCC-------------CCCCCCCCSCCCCCC
T ss_pred             HHhcCCcceecCeEEEEEcCCCC-------------CcceEeeecCCCCCC
Confidence            99987778889999999775432             347899999998875

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.84  E-value=1.5e-05  Score=67.64  Aligned_cols=49  Identities=18%  Similarity=0.187  Sum_probs=44.6

Q ss_pred             cCCcceeeeCCCCCC-CCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeee
Q 016231          333 YDIKKTVFVGNLPFD-VKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT  391 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~-~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t  391 (393)
                      ..+...|||+||+.. ++.++|+++|+.|    |.|.+|.|+++..      .|||.|.+
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~----G~V~~Vd~~~g~~------tgfVrf~~   64 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNH----GEIKWIDFVRGAK------EGIILFKE   64 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSS----CCEEEEECCTTCS------EEEEEESS
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhc----CCEEEEEEecCCC------EEEEEECC
Confidence            556789999999999 9999999999999    9999999998854      59999987

>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=97.19  E-value=0.00033  Score=58.42  Aligned_cols=50  Identities=12%  Similarity=0.112  Sum_probs=39.2

Q ss_pred             CcceeeeCCCC--CCC--------CHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLP--FDV--------KDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp--~~~--------teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +++.|.|.||=  ...        .+++|++.|+.|    |.|..|.|+++.    ++|||||+|.+.
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kf----G~V~~v~i~~~~----~~G~~fV~f~~~   65 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKH----GGVIHIYVDKNS----AQGNVYVKCPSI   65 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTT----TCCSEEEECTTC----TTCCEEEECSSH
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhcc----CCEEEEEEecCC----CcEEEEEEECCH
Confidence            56789999872  221        146889999999    999999997763    599999999863

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=96.74  E-value=0.0044  Score=50.39  Aligned_cols=52  Identities=19%  Similarity=0.342  Sum_probs=43.9

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      .+.++| ++|..+.-.||..+|+.||.|. |+++-+.                        .|||.|.+.+.|..||.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv~-I~WidDT------------------------sAlvvf~~~~~a~~al~   67 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT------------------------SAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSCC-CEEEETT------------------------EEEEECSCHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCEE-EEEEcCC------------------------eEEEEecCHHHHHHHHH
Confidence            455666 9999999999999999999765 7775432                        79999999999999985

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=96.51  E-value=0.011  Score=48.60  Aligned_cols=74  Identities=12%  Similarity=0.049  Sum_probs=60.0

Q ss_pred             ccEEEEeCCCccC-C----HHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHH
Q 016231          225 LRTIFVGNLPLKV-K----KKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (393)
Q Consensus       225 ~rtVFVgNLp~~~-t----ee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~  299 (393)
                      ..+|+|.||+..+ .    .+.++.+|..|+++.+..+..                       |-.-..|.|.+.++|..
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lk-----------------------SFRRirv~F~~~~~A~~   61 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK-----------------------SFKRVRINFSNPLSAAD   61 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET-----------------------TTTEEEEECSSTTHHHH
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecC-----------------------cceEEEEEeCChHHHHH
Confidence            5789999999876 2    357899999999987765521                       11247999999999999


Q ss_pred             HH-HhcCceeCCeEEEEeecCCC
Q 016231          300 AL-AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       300 Al-~lng~~~~Gr~I~V~~a~~~  321 (393)
                      |- .||+..|+|+.|+|-++.+.
T Consensus        62 AR~~Lh~~~f~g~~~r~YFgq~~   84 (104)
T 1wey_A           62 ARLRLHKTEFLGKEMKLYFAQTL   84 (104)
T ss_dssp             HHHTSTTSEETTEECEEECCCCS
T ss_pred             HHHHhccceecCceeEEEecCCC
Confidence            97 89999999999999998743

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=96.42  E-value=0.015  Score=46.69  Aligned_cols=69  Identities=22%  Similarity=0.235  Sum_probs=51.3

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hhc
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~ln  304 (393)
                      ..|.|++||+.+|++++++.++.+..+....++.-.  .+..+             ..-+-|||.|.+.+++.... .++
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~--~s~~~-------------~~~SRaYi~f~~~e~v~~f~~~~~   66 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSND--TSLYP-------------HMYARAYINFKNQEDIILFRDRFD   66 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESC--CSSTT-------------CCCEEEEEEESSSHHHHHHHHHHT
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCc--cCCCC-------------CcceEEEEEeCCHHHHHHHHHHhC
Confidence            468999999999999999999998876555543221  11111             23367999999999888877 689


Q ss_pred             CceeC
Q 016231          305 MAVIG  309 (393)
Q Consensus       305 g~~~~  309 (393)
                      |..|.
T Consensus        67 g~~F~   71 (91)
T 1uw4_A           67 GYVFL   71 (91)
T ss_dssp             TCEEE
T ss_pred             CcEEE
Confidence            88773

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.36  E-value=0.018  Score=48.38  Aligned_cols=72  Identities=15%  Similarity=0.161  Sum_probs=58.3

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHh
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~l  303 (393)
                      ..+.|-|-+.|+.. ...|..+|++||.|.+....      .+                 ..+.+|.|.+..+|+.||..
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~------~~-----------------~NWihI~Y~s~~~A~rAL~k   78 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS------NT-----------------GNWMHIRYQSKLQARKALSK   78 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC------SS-----------------SSEEEEEESSHHHHHHHHTT
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC------CC-----------------CCeEEEEeCCHHHHHHHHHh
Confidence            35789999999986 56677889999999887651      11                 13899999999999999999


Q ss_pred             cCceeCC-eEEEEeecC
Q 016231          304 NMAVIGG-NHIRLDRAC  319 (393)
Q Consensus       304 ng~~~~G-r~I~V~~a~  319 (393)
                      ||..|.| -.|-|.++.
T Consensus        79 NG~ii~g~~mIGV~p~~   95 (119)
T 1wwh_A           79 DGRIFGESIMIGVKPCI   95 (119)
T ss_dssp             TTCEETTTEECEEEECC
T ss_pred             CCeEecCCEEEEEEECC
Confidence            9999985 667777764

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=95.90  E-value=0.0062  Score=49.60  Aligned_cols=51  Identities=20%  Similarity=0.372  Sum_probs=42.3

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      +.++| ++|..+.-.+|..+|+.||.|. |+++-+.                        .|||.|.+.+.|..||.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv~-I~WidDT------------------------sAlvvf~~~~~a~~al~   57 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT------------------------SAFVSLSQPEQVKIAVN   57 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEEE-EEEEETT------------------------EEEEEEEEECHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCEE-EEEEcCC------------------------eEEEEecCHHHHHHHHH
Confidence            34555 9999999999999999999544 7774432                        79999999999999985

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=95.53  E-value=0.0092  Score=54.21  Aligned_cols=41  Identities=12%  Similarity=0.028  Sum_probs=34.5

Q ss_pred             CCHHHHHHHhhcCCCCCCCeEEEEEeecCC----CCCCccEEEEEeeec
Q 016231          348 VKDEEIYQLFCGLNDLESSVEAVRVIRHPH----MRVGKGIAYVLFKTR  392 (393)
Q Consensus       348 ~teedL~e~F~~~~~~~G~I~~VrI~~d~~----tg~~kGfaFVeF~t~  392 (393)
                      -.+++|++.|..|    |.|.+|.|+++..    +|.++||+||+|.+.
T Consensus       141 e~~~dl~~e~~~~----G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~  185 (222)
T 3dxb_A          141 DLEGEVTEECGKF----GAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIA  185 (222)
T ss_dssp             THHHHHHHHHTTT----SCEEEEEEEEEECCSSTTCCEEEEEEEEESSH
T ss_pred             HHHHHHHHHHHcc----CCeEEEEEecCCCCcccCcCceeEEEEEECCH
Confidence            4578999999999    9999999996653    458999999999763

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=95.08  E-value=0.025  Score=45.31  Aligned_cols=45  Identities=24%  Similarity=0.338  Sum_probs=35.3

Q ss_pred             CcceeeeCCCC----CCCCH----HHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeee
Q 016231          335 IKKTVFVGNLP----FDVKD----EEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT  391 (393)
Q Consensus       335 ~~~tLfVgNLp----~~~te----edL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t  391 (393)
                      +.-||+|.-++    .++-.    .+|.+.|.+|    |.|..++|+.+.        |||+|.+
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~----G~Vi~vr~~~d~--------~fVtF~d   58 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASF----GEVILIRFVEDK--------MWVTFLE   58 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTT----CCEEEEEECSSS--------EEEEESS
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhC----CCeEEEEEecCC--------EEEEECC
Confidence            45688888766    23444    6788999999    999999998873        8999975

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=94.60  E-value=0.015  Score=59.49  Aligned_cols=56  Identities=20%  Similarity=0.274  Sum_probs=41.2

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~l  303 (393)
                      .|+|||. .|..+++.+|.++|++||+|.++.+-.    +.+                  -||.|+|.+.+++..++..
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~----~~g------------------~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYE----SFG------------------LYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEEC----SSS------------------EEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEc----cCC------------------eEEEEEeCCHHHHHHHHhc
Confidence            5889997 799999999999999999999988721    111                  4999999999999988743

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=94.46  E-value=0.086  Score=44.98  Aligned_cols=89  Identities=19%  Similarity=0.057  Sum_probs=56.1

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeeccc-CCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhc
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPII-DTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~-~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~ln  304 (393)
                      ..|.|=+.|..... .|..+|++||.|..-.-+..+.. .+...+    -.+++..-....+..|.|.+..+|..||..|
T Consensus         8 ~~VtVFGFp~~~~~-~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~----~~k~yP~f~g~NWikItYds~~~A~rAL~~N   82 (132)
T 3p3d_A            8 LAILVFGYPETMAN-QVIAYFQEFGTILEDFEVLRKPQAMTVGLQ----DRQFVPIFSGNSWTKITYDNPASAVDALLEN   82 (132)
T ss_dssp             CEEEEECCCGGGHH-HHHHHHGGGSCBCSCCGGGCCC---------------CCCCCEETTEEEEEBSSHHHHHHHHTTT
T ss_pred             eEEEEEecCHHHHH-HHHHHHHhhceEeeeccccccccccccccc----cccccCccCCCcEEEEEcCCHHHHHHHHHhC
Confidence            45777788777654 56678999999865211000000 000000    0011111123468999999999999999999


Q ss_pred             CceeCCeEEEEeecC
Q 016231          305 MAVIGGNHIRLDRAC  319 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~  319 (393)
                      |..|.|.-|-|.++.
T Consensus        83 G~ii~G~mIGV~Py~   97 (132)
T 3p3d_A           83 GAVFNGVLLGVIPYT   97 (132)
T ss_dssp             TCEETTEECEEEECC
T ss_pred             CeEeCcEEEEEEECC
Confidence            999999988888875

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=93.43  E-value=0.097  Score=42.38  Aligned_cols=70  Identities=13%  Similarity=0.126  Sum_probs=46.7

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      +..|.|+.||+.+|++++.+.++.+-.+   .+..  +.....+.+          ...-.-|||.|.+.+++..-. .+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~---d~~~--fv~G~~s~~----------~~~~SRAYI~F~~~edv~~F~~~f   73 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAH---DYFE--FFAADLSLY----------PHLYSRAYINFRNPDDILLFRDRF   73 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSE---EECC--CCCCCSSSC----------CSCCCCCEEEESCHHHHHHHHHHS
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCcc---ceEE--EeCCccCCC----------CCcceEEEEEeCCHHHHHHHHHHc
Confidence            4579999999999999988777765443   2211  111111110          112257999999999988877 68


Q ss_pred             cCceeC
Q 016231          304 NMAVIG  309 (393)
Q Consensus       304 ng~~~~  309 (393)
                      +|..|.
T Consensus        74 ~g~~F~   79 (97)
T 2l08_A           74 DGYIFL   79 (97)
T ss_dssp             TTEEEE
T ss_pred             CCcEEE
Confidence            888773

>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=93.25  E-value=0.057  Score=43.57  Aligned_cols=47  Identities=19%  Similarity=0.145  Sum_probs=37.2

Q ss_pred             cCCcceeeeCCCCCC-----CCH----HHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeee
Q 016231          333 YDIKKTVFVGNLPFD-----VKD----EEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT  391 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~-----~te----edL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t  391 (393)
                      -++.-||+|.-++.+     +-.    .+|.+.|..|    |.|..|||+.|.        +||+|.+
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~----G~Vilvr~v~d~--------~fVtF~d   67 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSY----GTIVLVRINQGQ--------MLVTFAD   67 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHH----SCCSEEEEETTE--------EEEECSC
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHC----CCEEEEEEecCc--------EEEEEcC
Confidence            345679999988743     333    5688999999    999999999884        9999975

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=93.21  E-value=0.18  Score=40.32  Aligned_cols=52  Identities=15%  Similarity=0.222  Sum_probs=41.0

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCC--CccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRV--GKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~--~kGfaFVeF~t~  392 (393)
                      .+|.|++||+.+|++++.+.+..+    ..+.+.+++....+..  .-.-|||.|.+.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~----~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~   55 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPM----PEHDYFEFFSNDTSLYPHMYARAYINFKNQ   55 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSC----CCEEEEEEEESCCSSTTCCCEEEEEEESSS
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCc----ccceEEEEeCCccCCCCCcceEEEEEeCCH
Confidence            478999999999999999999998    6788888766543322  235789999763

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=90.83  E-value=0.63  Score=38.00  Aligned_cols=49  Identities=20%  Similarity=0.089  Sum_probs=39.0

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCC-CCCCCeEEEEEeecCCCCCCccEEEEEeee
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLN-DLESSVEAVRVIRHPHMRVGKGIAYVLFKT  391 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~-~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t  391 (393)
                      ...+|.|.|||+.+.++.|.-.|+.-. +=.|.|..|....        +-|+|+|.+
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d   56 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFRE   56 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESS
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcC
Confidence            457999999999999999999998721 1139999998753        358999976

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=90.08  E-value=0.48  Score=38.37  Aligned_cols=44  Identities=23%  Similarity=0.478  Sum_probs=34.9

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...++| ++|..|...||.++|+.|    |.| .|+++-|-       -|||.|.++
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~f----ggv-~I~WidDT-------sAlvvf~~~   59 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAF----GNI-QISWIDDT-------SAFVSLSQP   59 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTT----CSC-CCEEEETT-------EEEEECSCH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhcc----CCE-EEEEEcCC-------eEEEEecCH
Confidence            456777 999999999999999999    533 56666662       599999764

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=88.92  E-value=0.71  Score=37.47  Aligned_cols=43  Identities=23%  Similarity=0.441  Sum_probs=35.4

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++| ++|..|...||.++|+.|    |. ..|+++-|-       -|||.|.++
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~f----gg-v~I~WidDT-------sAlvvf~~~   49 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAF----GN-IQISWIDDT-------SAFVSLSQP   49 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTS----EE-EEEEEEETT-------EEEEEEEEE
T ss_pred             eEEEE-eCChhhhhHHHHHHHhcc----CC-EEEEEEcCC-------eEEEEecCH
Confidence            45677 999999999999999999    63 467777662       599999875

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=84.57  E-value=2.6  Score=43.42  Aligned_cols=54  Identities=19%  Similarity=0.308  Sum_probs=43.0

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      ...++|+ +|..+...+|..+|+.||.| .|+++.+                        ..|||.|.+.+.|..++ .+
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd------------------------t~a~V~~~~~~~a~~~l~~~  493 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD------------------------TSAFVSLSQPEQVQIAVNTS  493 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS------------------------SEEEEECSCHHHHHHHHHHH
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC------------------------CeEEEEECCHHHHHHHHHHH
Confidence            4567776 88899999999999999964 4666332                        27999999999999998 45


Q ss_pred             c
Q 016231          304 N  304 (393)
Q Consensus       304 n  304 (393)
                      +
T Consensus       494 ~  494 (507)
T 3d45_A          494 K  494 (507)
T ss_dssp             T
T ss_pred             H
Confidence            3

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=82.21  E-value=0.73  Score=47.10  Aligned_cols=48  Identities=13%  Similarity=0.190  Sum_probs=37.2

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++|||. .|..+++.+|.+.|++|    |.|.++.+..+.  |   -||.|+|.+.
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~----g~i~~~~~~~~~--g---~~~~vef~~~   99 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQF----GPINNHFFYESF--G---LYAVVEFCQK   99 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGG----SCCCCEEEECSS--S---EEEEEECC--
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhc----CCcceEEEEccC--C---eEEEEEeCCH
Confidence            35899997 79999999999999999    999999887652  2   6999999874

---

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	393
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	5e-09
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-08
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	0.001
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	4e-08
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	0.001
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-07
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-07
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	3e-05
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-07
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-07
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	0.003
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-07
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-06
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	4e-07
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	8e-04
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	5e-07
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-05
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-07
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-06
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	0.004
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-06
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-06
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	3e-04
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-06
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-04
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-06
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	0.002
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-06
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-06
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-04
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-06
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	0.001
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	4e-06
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-05
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	4e-06
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-04
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	4e-06
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	3e-05
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	4e-06
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	0.002
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	5e-06
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	0.002
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	8e-06
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-04
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-05
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-05
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	0.003
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-05
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.004
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-05
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.001
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-05
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-05
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-05
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	8e-05
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-05
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-04
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-05
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-04
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	3e-05
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	8e-04
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	4e-05
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	4e-05
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	0.002
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	4e-05
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	8e-04
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	7e-05
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-04
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	0.001
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-04
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	7e-04
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-04
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	3e-04
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	1e-04
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	7e-04
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-04
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	4e-04
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-04
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-04
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	9e-04
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-04
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-04
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-04
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-04
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	4e-04
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	6e-04
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	9e-04
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	0.001
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	0.001
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	0.001
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	0.001
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	0.002
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	0.002
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	0.002
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	0.003

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.5 bits (127), Expect = 5e-09
 Identities = 25/168 (14%), Positives = 58/168 (34%), Gaps = 24/168 (14%)

Query: 225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADS 284
           LR +F+G L  +   ++L   F ++G +    +                  +  N     
Sbjct: 6   LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV-----------------MRDPNTKRSR 48

Query: 285 VHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNL 344
              ++ + + +  +AA+      + G  +   RA     +   +    +   K +FVG +
Sbjct: 49  GFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA---VSREDSQRPGAHLTVKKIFVGGI 105

Query: 345 PFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
             D ++  +   F         +E + ++        +G A+V F   
Sbjct: 106 KEDTEEHHLRDYFEQ----YGKIEVIEIMTDRGSGKKRGFAFVTFDDH 149

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.4 bits (117), Expect = 2e-08
 Identities = 17/93 (18%), Positives = 38/93 (40%), Gaps = 12/93 (12%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           R ++VGN+P  + ++ ++  F     +  +       +              +  N D  
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPV------------LAVQINQDKN 49

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRA 318
            A++ F+S   T  A+AF+  +  G  +++ R 
Sbjct: 50  FAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRP 82

>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 = 35.5 bits (81), Expect = 0.001
 Identities = 11/57 (19%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLES-SVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           + ++VGN+PF + +E +   F     L   +      +    +   K  A++ F++ 
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 58

>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 = 48.1 bits (114), Expect = 4e-08
 Identities = 23/110 (20%), Positives = 43/110 (39%), Gaps = 18/110 (16%)

Query: 217 GFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQK 276
           G   E     T++VG L  KV +  L + F++ G + +  +                  K
Sbjct: 1   GPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHM-----------------PK 43

Query: 277 QINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKL 325
                    + ++ F SE+  + A+   +M  + G  IR+++A    K L
Sbjct: 44  DRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNL 93

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.4 bits (81), Expect = 0.001
 Identities = 8/20 (40%), Positives = 13/20 (65%)

Query: 338 TVFVGNLPFDVKDEEIYQLF 357
           TV+VG L   V +  +++LF
Sbjct: 11  TVYVGGLDEKVSEPLLWELF 30

>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 = 47.0 bits (111), Expect = 1e-07
 Identities = 20/100 (20%), Positives = 39/100 (39%), Gaps = 20/100 (20%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           RT++VGNL   V +  +++ F + G   S                    +      ++  
Sbjct: 9   RTLYVGNLSRDVTEVLILQLFSQIGPCKSC-------------------KMITEHTSNDP 49

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKK 324
           + ++ F   +   AAL A N   I G  ++++ A  P  +
Sbjct: 50  YCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQ 89

>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 = 46.5 bits (110), Expect = 1e-07
 Identities = 21/93 (22%), Positives = 38/93 (40%), Gaps = 18/93 (19%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVH 286
           +++VG+L   V +  L ++F   G I S+R+                  + +       +
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRV-----------------CRDMITRRSLGY 44

Query: 287 AYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRA 318
           AY+ F+     E AL   N  VI G  +R+  +
Sbjct: 45  AYVNFQQPADAERALDTMNFDVIKGKPVRIMWS 77

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.9 bits (93), Expect = 3e-05
 Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 4/55 (7%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           +++VG+L  DV +  +Y+ F     + S    +RV R    R   G AYV F+  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILS----IRVCRDMITRRSLGYAYVNFQQP 52

>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 = 46.6 bits (110), Expect = 1e-07
 Identities = 16/97 (16%), Positives = 31/97 (31%), Gaps = 15/97 (15%)

Query: 228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHA 287
           +F+ NL     ++TL   F K G I S  I                   +          
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKK--------------NKAGVLLSMGFG 46

Query: 288 YIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRK 323
           ++ +K  +  + AL       + G+ + +  +    K
Sbjct: 47  FVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATK 83

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.6 bits (110), Expect = 2e-07
 Identities = 25/100 (25%), Positives = 40/100 (40%), Gaps = 18/100 (18%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           R ++VG L  +V  K L   FI FG+I  ++I                            
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI-----------------PLDYETEKHRG 48

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKK 324
            A++ F+  +   AA+   N + + G  IR++ A P R K
Sbjct: 49  FAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIK 88

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.6 bits (79), Expect = 0.003
 Identities = 9/43 (20%), Positives = 18/43 (41%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHM 378
           K+ ++VG L  +V D+ ++  F    D+      +      H 
Sbjct: 5   KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR 47

>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 = 46.9 bits (111), Expect = 2e-07
 Identities = 22/115 (19%), Positives = 38/115 (33%), Gaps = 17/115 (14%)

Query: 211 VHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRK 270
           V    +    E +  RT+F   L  +++ + L   F   G++  VRI             
Sbjct: 4   VREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRI------------- 50

Query: 271 GAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKL 325
                   N       AY+ F   QS   A+      + G  I +  +   + +L
Sbjct: 51  ----ISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEKNRL 101

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.5 bits (102), Expect = 2e-06
 Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 4/72 (5%)

Query: 321 PRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRV 380
           P ++     +P     +TVF   L   ++  ++   F  +      V  VR+I   + R 
Sbjct: 3   PVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGK----VRDVRIISDRNSRR 58

Query: 381 GKGIAYVLFKTR 392
            KGIAYV F   
Sbjct: 59  SKGIAYVEFCEI 70

>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 = 45.0 bits (106), Expect = 4e-07
 Identities = 17/95 (17%), Positives = 33/95 (34%), Gaps = 18/95 (18%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVH 286
            + V  LP  +  + L   F   G I++ RI                  +         +
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRI-----------------MRDYKTGYSYGY 46

Query: 287 AYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACP 320
           A++ F SE  ++ A+   N   +    +++  A P
Sbjct: 47  AFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP 81

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 36.1 bits (83), Expect = 8e-04
 Identities = 9/20 (45%), Positives = 12/20 (60%)

Query: 338 TVFVGNLPFDVKDEEIYQLF 357
            + V  LP D+ D E+Y LF
Sbjct: 4   NLIVNYLPQDMTDRELYALF 23

>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 = 45.0 bits (106), Expect = 5e-07
 Identities = 14/91 (15%), Positives = 29/91 (31%), Gaps = 17/91 (18%)

Query: 228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHA 287
           +F+G L  +  ++ L + F +FGE+    +   P                          
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDP-----------------LTKRSRGFG 45

Query: 288 YIVFKSEQSTEAALAFNMAVIGGNHIRLDRA 318
           ++ F  +   +  LA +   +    I    A
Sbjct: 46  FVTFMDQAGVDKVLAQSRHELDSKTIDPKVA 76

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.7 bits (95), Expect = 2e-05
 Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 4/54 (7%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           +F+G L +    E + + F    +    V+   V+R P  +  +G  +V F  +
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGE----VKECLVMRDPLTKRSRGFGFVTFMDQ 52

>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 = 45.6 bits (108), Expect = 5e-07
 Identities = 23/113 (20%), Positives = 43/113 (38%), Gaps = 27/113 (23%)

Query: 217 GFDDEGKLLRTIFVGNL-PLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQ 275
           G  D   +   +F+GNL  L VKK  +   F K+G+I    +                  
Sbjct: 7   GKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKG--------------- 51

Query: 276 KQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKG 327
                      A++ + +E++  AA+   +  +I G  + ++ A  P+    G
Sbjct: 52  ----------FAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVNRSG 94

>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 = 44.2 bits (104), Expect = 1e-06
 Identities = 18/97 (18%), Positives = 35/97 (36%), Gaps = 24/97 (24%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             +FVGNLP  + ++ + K F K+G+                         ++  + D  
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEKYGK-----------------------AGEVFIHKDKG 45

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPP 321
             +I  ++    E A    +   + G  +R+  AC  
Sbjct: 46  FGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS 82

>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 = 34.2 bits (78), Expect = 0.004
 Identities = 11/23 (47%), Positives = 17/23 (73%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFC 358
           +  +FVGNLP D+ +EE+ +LF 
Sbjct: 8   RSRLFVGNLPPDITEEEMRKLFE 30

>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 = 44.4 bits (104), Expect = 1e-06
 Identities = 15/96 (15%), Positives = 34/96 (35%), Gaps = 10/96 (10%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             I+V  L   V    L   F + G +   +    P+I   + ++               
Sbjct: 9   SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE---------TGKPKG 59

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACP 320
            A + ++   + +AA+  F+     G+ +++  A  
Sbjct: 60  DATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARK 95

>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 = 43.6 bits (102), Expect = 1e-06
 Identities = 14/96 (14%), Positives = 31/96 (32%), Gaps = 18/96 (18%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             + V  LP  + ++     F   GEI+S ++                  +         
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKL-----------------VRDKITGQSLG 45

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACP 320
           + ++ +   +  E A+   N   +    I++  A P
Sbjct: 46  YGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP 81

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.0 bits (85), Expect = 3e-04
 Identities = 8/23 (34%), Positives = 11/23 (47%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFC 358
           K  + V  LP ++  EE   LF 
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFG 24

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (104), Expect = 2e-06
 Identities = 22/102 (21%), Positives = 37/102 (36%), Gaps = 17/102 (16%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
            T F+GNLP  V ++++ + F           R     + +  +                
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPR--EPSNPERLKG--------------- 58

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKG 327
             Y  F+   S  +AL+ N   +G   IR+D A   + K  G
Sbjct: 59  FGYAEFEDLDSLLSALSLNEESLGNKRIRVDVADQAQDKDSG 100

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.4 bits (86), Expect = 3e-04
 Identities = 12/23 (52%), Positives = 16/23 (69%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCG 359
            T F+GNLP+DV +E I + F G
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRG 38

>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 = 43.2 bits (101), Expect = 2e-06
 Identities = 16/91 (17%), Positives = 29/91 (31%), Gaps = 17/91 (18%)

Query: 228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHA 287
           IFVG L +    + +   F +FG++D   +                       N      
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAML-----------------MFDKTTNRHRGFG 44

Query: 288 YIVFKSEQSTEAALAFNMAVIGGNHIRLDRA 318
           ++ F+SE   E     +   I    +   +A
Sbjct: 45  FVTFESEDIVEKVCEIHFHEINNKMVECKKA 75

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.3 bits (78), Expect = 0.002
 Identities = 10/54 (18%), Positives = 21/54 (38%), Gaps = 4/54 (7%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           +FVG L  +   E++   F         V+   ++        +G  +V F++ 
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGK----VDDAMLMFDKTTNRHRGFGFVTFESE 51

>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 = 43.5 bits (102), Expect = 2e-06
 Identities = 16/102 (15%), Positives = 32/102 (31%), Gaps = 23/102 (22%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             +FVG     + +  L + F ++G++  V I                            
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRA---------------------- 43

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKG 327
            A++ F  +Q  ++       +I G  + +  A P      G
Sbjct: 44  FAFVTFADDQIAQSLCG-EDLIIKGISVHISNAEPKHNSNSG 84

>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 = 43.1 bits (101), Expect = 2e-06
 Identities = 15/99 (15%), Positives = 33/99 (33%), Gaps = 18/99 (18%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             +F+G LP  +    + +    FG + +  +       T + +                
Sbjct: 2   HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS--ATGLSKG--------------- 44

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRK 323
           +A+  +     T+ A+   N   +G   + + RA    K
Sbjct: 45  YAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK 83

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.1 bits (83), Expect = 7e-04
 Identities = 10/54 (18%), Positives = 25/54 (46%), Gaps = 4/54 (7%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           +F+G LP  + D+++ +L          ++A  +++     + KG A+  +   
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGP----LKAFNLVKDSATGLSKGYAFCEYVDI 53

>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 = 42.6 bits (100), Expect = 3e-06
 Identities = 16/91 (17%), Positives = 33/91 (36%), Gaps = 17/91 (18%)

Query: 228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHA 287
           IFVG L     ++ + + F  FGE++S+ +      + +                     
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRG-----------------FC 44

Query: 288 YIVFKSEQSTEAALAFNMAVIGGNHIRLDRA 318
           +I FK E+  +  +      +G +   +  A
Sbjct: 45  FITFKEEEPVKKIMEKKYHNVGLSKCEIKVA 75

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.3 bits (81), Expect = 0.001
 Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 4/54 (7%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           +FVG L  D  +E+I + F G       VE++ +         +G  ++ FK  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFG----EVESIELPMDNKTNKRRGFCFITFKEE 51

>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 = 43.1 bits (101), Expect = 4e-06
 Identities = 18/100 (18%), Positives = 37/100 (37%), Gaps = 17/100 (17%)

Query: 221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINE 280
           E +  R +F+G L  +  +++L   + ++G++    +   P        +G         
Sbjct: 16  EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASK---RSRG--------- 63

Query: 281 NADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACP 320
                  ++ F S    +AA+A     I G  +   RA  
Sbjct: 64  -----FGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVA 98

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.4 bits (94), Expect = 3e-05
 Identities = 14/73 (19%), Positives = 29/73 (39%), Gaps = 8/73 (10%)

Query: 320 PPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMR 379
            P ++ K E        + +F+G L F+  +E +   +         +    V+R P  +
Sbjct: 8   VPLERKKREKEQF----RKLFIGGLSFETTEESLRNYYEQWGK----LTDCVVMRDPASK 59

Query: 380 VGKGIAYVLFKTR 392
             +G  +V F + 
Sbjct: 60  RSRGFGFVTFSSM 72

>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 = 42.4 bits (99), Expect = 4e-06
 Identities = 24/101 (23%), Positives = 39/101 (38%), Gaps = 19/101 (18%)

Query: 228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHA 287
           IF+GNL  ++ +K L   F  FG I                     + +  +      +A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTP----------------KIMRDPDTGNSKGYA 44

Query: 288 YIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKG 327
           +I F S  +++AA+ A N   +    I +  A    K  KG
Sbjct: 45  FINFASFDASDAAIEAMNGQYLCNRPITVSYAFK--KDSKG 83

>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 = 37.8 bits (87), Expect = 2e-04
 Identities = 12/53 (22%), Positives = 27/53 (50%), Gaps = 3/53 (5%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
           +F+GNL  ++ ++ +Y  F     +    +  +++R P     KG A++ F +
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVIL---QTPKIMRDPDTGNSKGYAFINFAS 50

>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 = 42.3 bits (99), Expect = 4e-06
 Identities = 17/94 (18%), Positives = 36/94 (38%), Gaps = 17/94 (18%)

Query: 225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADS 284
           LR +F+G L  +   ++L   F ++G +    +   P  +TK  R               
Sbjct: 6   LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDP--NTKRSRG-------------- 49

Query: 285 VHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRA 318
              ++ + + +  +AA+      + G  +   RA
Sbjct: 50  -FGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA 82

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.0 bits (93), Expect = 3e-05
 Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 4/56 (7%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           + +F+G L F+  DE +   F     L        V+R P+ +  +G  +V + T 
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTD----CVVMRDPNTKRSRGFGFVTYATV 58

>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 = 42.2 bits (99), Expect = 4e-06
 Identities = 12/92 (13%), Positives = 26/92 (28%), Gaps = 19/92 (20%)

Query: 228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHA 287
           + V NL   V    + + F +FG +    +                             A
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAV------------------HYDRSGRSLGTA 44

Query: 288 YIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRA 318
            + F+ +     A+  +N   + G  + +   
Sbjct: 45  DVHFERKADALKAMKQYNGVPLDGRPMNIQLV 76

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.9 bits (80), Expect = 0.002
 Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 5/54 (9%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           + V NL F V D +I +LF     L+ +      + +       G A V F+ +
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKA-----AVHYDRSGRSLGTADVHFERK 51

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.6 bits (100), Expect = 5e-06
 Identities = 17/99 (17%), Positives = 34/99 (34%), Gaps = 18/99 (18%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
            T++VGNL     ++ + + F K G+I  + +    +  T                    
Sbjct: 8   CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG----------------- 50

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRK 323
             ++ + S    E A+   N   +    IR D     ++
Sbjct: 51  FCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKE 89

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.3 bits (81), Expect = 0.002
 Identities = 11/21 (52%), Positives = 16/21 (76%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF 357
            T++VGNL F   +E+IY+LF
Sbjct: 8   CTLYVGNLSFYTTEEQIYELF 28

>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 = 41.8 bits (98), Expect = 8e-06
 Identities = 16/95 (16%), Positives = 34/95 (35%), Gaps = 18/95 (18%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             I V N+P +  ++ + + F  FGE+ +VR+                            
Sbjct: 9   SKILVRNIPFQANQREIRELFSTFGELKTVRL----PKKMTGTGAH------------RG 52

Query: 286 HAYIVFKSEQSTEAALA--FNMAVIGGNHIRLDRA 318
             ++ F ++Q  + A     +   + G  + L+ A
Sbjct: 53  FGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWA 87

>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 = 37.2 bits (86), Expect = 3e-04
 Identities = 12/57 (21%), Positives = 20/57 (35%), Gaps = 3/57 (5%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
              + V N+PF     EI +LF   +            +       +G  +V F T+
Sbjct: 8   TSKILVRNIPFQANQREIRELF---STFGELKTVRLPKKMTGTGAHRGFGFVDFITK 61

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.7 bits (97), Expect = 1e-05
 Identities = 11/102 (10%), Positives = 27/102 (26%), Gaps = 19/102 (18%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             + +  LP +  +  +   F     +                           +   + 
Sbjct: 16  HCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIG-------------------PDGRVTG 56

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKG 327
            A + F + +   AA+A + A +   ++ L           G
Sbjct: 57  EADVEFATHEDAVAAMAKDKANMQHRYVELFLNSTAGTSGSG 98

>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 = 41.2 bits (96), Expect = 1e-05
 Identities = 16/96 (16%), Positives = 37/96 (38%), Gaps = 18/96 (18%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             +FV ++  + ++  + ++F  +GEI ++ +                            
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKG----------------- 50

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACP 320
           +A + +++ +   AA  A N A I G  I++D    
Sbjct: 51  YALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFV 86

>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 = 34.7 bits (79), Expect = 0.003
 Identities = 6/21 (28%), Positives = 14/21 (66%)

Query: 338 TVFVGNLPFDVKDEEIYQLFC 358
            +FV ++  + +++EI + FC
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFC 29

>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 = 41.2 bits (96), Expect = 1e-05
 Identities = 13/100 (13%), Positives = 29/100 (29%), Gaps = 18/100 (18%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             +FV NL     ++ L K F  +G +  +      +                       
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKG----------------- 51

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKK 324
            A++ F   +    A    +  V  G  + +  +   ++ 
Sbjct: 52  FAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEA 91

>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 = 34.3 bits (78), Expect = 0.004
 Identities = 12/56 (21%), Positives = 22/56 (39%), Gaps = 4/56 (7%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
             +FV NL +   +E++ +LF         +  +        +  KG A+V F   
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGP----LSELHYPIDSLTKKPKGFAFVTFMFP 60

>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 = 40.7 bits (95), Expect = 1e-05
 Identities = 21/91 (23%), Positives = 33/91 (36%), Gaps = 17/91 (18%)

Query: 228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHA 287
           +F+G L     KK L   F KFGE+    ++  P   T   R                  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDP--ITGRSRG---------------FG 44

Query: 288 YIVFKSEQSTEAALAFNMAVIGGNHIRLDRA 318
           +++FK  +S +  +      + G  I   RA
Sbjct: 45  FVLFKESESVDKVMDQKEHKLNGKVIDPKRA 75

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.3 bits (81), Expect = 0.001
 Identities = 11/54 (20%), Positives = 22/54 (40%), Gaps = 4/54 (7%)

Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           +F+G L +D   +++   F    ++        +   P     +G  +VLFK  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVD----CTLKLDPITGRSRGFGFVLFKES 51

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.9 bits (95), Expect = 1e-05
 Identities = 15/93 (16%), Positives = 34/93 (36%), Gaps = 17/93 (18%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           + IFVG +    ++  L   F ++G+I+ + I +      K                   
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRG----------------- 45

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRA 318
            A++ F    S +  +      + G++  + +A
Sbjct: 46  FAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA 78

>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 = 40.9 bits (95), Expect = 2e-05
 Identities = 20/95 (21%), Positives = 40/95 (42%), Gaps = 15/95 (15%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           R I + NL  ++  + L++E   F    S+   ++P    +                 + 
Sbjct: 5   REIMIRNLSTELLDENLLRES--FEGFGSIEKINIPAGQKEHSFN-------------NC 49

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACP 320
            A++VF+++ S E AL  N +++G   I +  A  
Sbjct: 50  CAFMVFENKDSAERALQMNRSLLGNREISVSLADK 84

>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 = 40.7 bits (95), Expect = 2e-05
 Identities = 15/96 (15%), Positives = 30/96 (31%), Gaps = 20/96 (20%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             ++V NLP  +    L   F K+G I                     + +         
Sbjct: 7   TNLYVTNLPRTITDDQLDTIFGKYGSI-----------------VQKNILRDKLTGRPRG 49

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNH--IRLDRA 318
            A++ +   +  + A+ A N  +  G    + +  A
Sbjct: 50  VAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 85

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 38.8 bits (90), Expect = 8e-05
 Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 5/60 (8%)

Query: 334 DIKKT-VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
            IK T ++V NLP  + D+++  +F        S+    ++R       +G+A+V +  R
Sbjct: 3   SIKDTNLYVTNLPRTITDDQLDTIFGKY----GSIVQKNILRDKLTGRPRGVAFVRYNKR 58

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.2 bits (96), Expect = 2e-05
 Identities = 18/104 (17%), Positives = 39/104 (37%), Gaps = 21/104 (20%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           R +++ NLP K+  + +   F K+G I  +R+ + P        +G              
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP------ETRG-------------- 47

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKKLKGE 328
            AY+V++     + A    +   +   ++ +      R   K +
Sbjct: 48  TAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMD 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 = 39.2 bits (91), Expect = 1e-04
 Identities = 14/56 (25%), Positives = 28/56 (50%), Gaps = 7/56 (12%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           + +++ NLP+ +  EE+Y +F            +R IR  +    +G AYV+++  
Sbjct: 8   RILYIRNLPYKITAEEMYDIF-------GKYGPIRQIRVGNTPETRGTAYVVYEDI 56

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.8 bits (95), Expect = 2e-05
 Identities = 18/101 (17%), Positives = 38/101 (37%), Gaps = 18/101 (17%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVH 286
            +F+G +P   K++ +++E  K  E     +        K+  +G               
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVL-DVIVYASAADKMKNRG--------------F 47

Query: 287 AYIVFKSEQSTEAA---LAFNMAVIGGNHIRLDRACPPRKK 324
           A++ ++S ++   A   L      + G+ I +D A P    
Sbjct: 48  AFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDV 88

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.7 bits (87), Expect = 3e-04
 Identities = 11/55 (20%), Positives = 22/55 (40%), Gaps = 2/55 (3%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
            +F+G +P   K EEI +    + +    V              +G A+V +++ 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKN--RGFAFVEYESH 55

>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 = 40.4 bits (94), Expect = 3e-05
 Identities = 19/99 (19%), Positives = 34/99 (34%), Gaps = 21/99 (21%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             I+VGNLP  ++ K +   F K+G I  +                       N      
Sbjct: 15  CRIYVGNLPPDIRTKDIEDVFYKYGAIRDID--------------------LKNRRGGPP 54

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRK 323
            A++ F+  +  E A+   +     G  +R++     R 
Sbjct: 55  FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRG 93

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.2 bits (83), Expect = 8e-04
 Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 7/55 (12%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
            ++VGNLP D++ ++I  +F           A+R I   + R G   A+V F+  
Sbjct: 16  RIYVGNLPPDIRTKDIEDVF-------YKYGAIRDIDLKNRRGGPPFAFVEFEDP 63

>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 = 39.7 bits (92), Expect = 4e-05
 Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 4/55 (7%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
            + V N+PF V  +EI   F G   +  SV     +++    +  G A V F++R
Sbjct: 11  IIKVQNMPFTVSIDEILDFFYGYQVIPGSV----CLKYNEKGMPTGEAMVAFESR 61

>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 = 40.0 bits (93), Expect = 4e-05
 Identities = 15/109 (13%), Positives = 39/109 (35%), Gaps = 24/109 (22%)

Query: 213 RKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGA 272
           R E+  +       T++ G +   +  + + + F  FG+I  +R+               
Sbjct: 6   RFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRV--------------- 50

Query: 273 ILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACP 320
                     +  ++++ F + +S   A+ + N   I G+ ++      
Sbjct: 51  --------FPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE 91

>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 = 34.9 bits (80), Expect = 0.002
 Identities = 8/41 (19%), Positives = 15/41 (36%), Gaps = 4/41 (9%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHM 378
           TV+ G +   + D+ + Q F     +      +RV      
Sbjct: 20  TVYCGGIASGLTDQLMRQTFSPFGQIME----IRVFPEKGY 56

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 41.0 bits (95), Expect = 4e-05
 Identities = 21/125 (16%), Positives = 44/125 (35%), Gaps = 18/125 (14%)

Query: 201 KADNETEDMLVHRKEEGFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSV 260
           +     +    H      + E  +LR + V  +P  V +  L + F ++G I+SV+I   
Sbjct: 18  QLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKI--- 74

Query: 261 PIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRAC 319
                                    + ++ F+S  S + A+   N   I    +++  A 
Sbjct: 75  --------------VCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA 120

Query: 320 PPRKK 324
              ++
Sbjct: 121 SGHQR 125

>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 = 37.2 bits (85), Expect = 8e-04
 Identities = 8/39 (20%), Positives = 17/39 (43%)

Query: 320 PPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFC 358
             +     +  P  D+ + + V  +P  V + ++ QLF 
Sbjct: 26  QQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFE 64

>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 = 39.2 bits (91), Expect = 7e-05
 Identities = 18/99 (18%), Positives = 39/99 (39%), Gaps = 20/99 (20%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVH 286
            IF+ NL   +  K L   F  FG I S ++                     +EN    +
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGNILSCKV-------------------VCDENGSKGY 50

Query: 287 AYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKK 324
            ++ F+++++ E A+   N  ++    + + R    +++
Sbjct: 51  GFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKER 89

>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 = 38.9 bits (90), Expect = 1e-04
 Identities = 16/96 (16%), Positives = 28/96 (29%), Gaps = 18/96 (18%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
            TI V NL    ++  L + F  FG I  + +                            
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKG----------------- 51

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACP 320
            A+I F   +    A+   +        + ++ A P
Sbjct: 52  FAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKP 87

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.8 bits (82), Expect = 0.001
 Identities = 8/24 (33%), Positives = 14/24 (58%)

Query: 334 DIKKTVFVGNLPFDVKDEEIYQLF 357
           D   T+ V NL  D ++ ++ +LF
Sbjct: 6   DDNATIRVTNLSEDTRETDLQELF 29

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.5 bits (89), Expect = 1e-04
 Identities = 17/90 (18%), Positives = 28/90 (31%), Gaps = 18/90 (20%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             + V  L L   ++ L + F K+G I  V I                            
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSI-----------------VYDQQSRRSRG 52

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIR 314
            A++ F++    + A    N   + G  IR
Sbjct: 53  FAFVYFENVDDAKEAKERANGMELDGRRIR 82

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.2 bits (83), Expect = 7e-04
 Identities = 3/22 (13%), Positives = 9/22 (40%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFC 358
             + V  L     + ++ ++F 
Sbjct: 10  CCLGVFGLSLYTTERDLREVFS 31

>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 = 38.2 bits (88), Expect = 1e-04
 Identities = 12/96 (12%), Positives = 25/96 (26%), Gaps = 18/96 (18%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
            T+++ N P    ++ +         +           +T                    
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRR----------------- 44

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACP 320
            AYI   S++     +   N   I G  +    + P
Sbjct: 45  FAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP 80

>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 = 37.1 bits (85), Expect = 3e-04
 Identities = 5/21 (23%), Positives = 8/21 (38%)

Query: 338 TVFVGNLPFDVKDEEIYQLFC 358
           T+++ N P       I  L  
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQ 23

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 38.3 bits (88), Expect = 1e-04
 Identities = 19/92 (20%), Positives = 28/92 (30%), Gaps = 19/92 (20%)

Query: 227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVH 286
           T+ V NLP    +  + K F   G I  V +                     +   +   
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVAD-------------------SLKKNFRF 42

Query: 287 AYIVFKSEQSTEAALAFNMAVIGGNHIRLDRA 318
           A I F       AA+     V+G N I +   
Sbjct: 43  ARIEFARYDGALAAITKTHKVVGQNEIIVSHL 74

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 36.0 bits (82), Expect = 7e-04
 Identities = 10/50 (20%), Positives = 14/50 (28%), Gaps = 4/50 (8%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYV 387
           TV V NLP      ++Y+ F         +  V V               
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGP----IIHVDVADSLKKNFRFARIEF 47

>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 = 38.4 bits (89), Expect = 1e-04
 Identities = 10/56 (17%), Positives = 22/56 (39%), Gaps = 4/56 (7%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
             + V  LP+   ++++ + F    ++      V+V +       KG  +V F   
Sbjct: 9   SDLIVLGLPWKTTEQDLKEYFSTFGEVLM----VQVKKDLKTGHSKGFGFVRFTEY 60

>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 = 36.9 bits (85), Expect = 4e-04
 Identities = 13/99 (13%), Positives = 30/99 (30%), Gaps = 18/99 (18%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             + V  LP K  ++ L + F  FGE+  V+++                           
Sbjct: 9   SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKG----------------- 51

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKK 324
             ++ F   ++    ++    +I G           + +
Sbjct: 52  FGFVRFTEYETQVKVMS-QRHMIDGRWCDCKLPNSKQSQ 89

>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 = 39.0 bits (90), Expect = 1e-04
 Identities = 19/101 (18%), Positives = 40/101 (39%), Gaps = 18/101 (17%)

Query: 225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADS 284
           LR++FVGN+P +  ++ L   F + G + S R+                           
Sbjct: 8   LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRL-----------------VYDRETGKPK 50

Query: 285 VHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKK 324
            + +  ++ +++  +A+   N     G  +R+D A   + K
Sbjct: 51  GYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNK 91

>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 = 38.5 bits (89), Expect = 1e-04
 Identities = 22/98 (22%), Positives = 27/98 (27%), Gaps = 23/98 (23%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           RT+   NL   + +  L + F    EI  V                              
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEIRLVSQD----------------------GKSKG 54

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPR 322
            AYI FKSE   E  L     A I G  + L       
Sbjct: 55  IAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG 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 = 36.2 bits (83), Expect = 9e-04
 Identities = 6/21 (28%), Positives = 15/21 (71%)

Query: 337 KTVFVGNLPFDVKDEEIYQLF 357
           +T+   NL F++ ++E+ ++F
Sbjct: 17  RTLLAKNLSFNITEDELKEVF 37

>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 = 38.1 bits (88), Expect = 1e-04
 Identities = 20/106 (18%), Positives = 39/106 (36%), Gaps = 24/106 (22%)

Query: 219 DDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQI 278
           +D    ++ ++V NL L   ++ + KEF         R++                    
Sbjct: 2   EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------------------- 42

Query: 279 NENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRK 323
                  +A++ F + +    A+ A N  V+ G+ I +  A P  K
Sbjct: 43  ----IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK 84

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.1 bits (88), Expect = 2e-04
 Identities = 17/96 (17%), Positives = 35/96 (36%), Gaps = 20/96 (20%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           + + V N+P + +   L + F +FG+I  V                   +   NE     
Sbjct: 12  KRLHVSNIPFRFRDPDLRQMFGQFGKILDV-------------------EIIFNERGSKG 52

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACP 320
             ++ F++    + A    +  V+ G  I ++ A  
Sbjct: 53  FGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA 88

>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 = 37.3 bits (86), Expect = 3e-04
 Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 4/55 (7%)

Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
            ++V  LP  +  +E+ QLF     + +     R++      V +G+ ++ F  R
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIIT----SRILVDQVTGVSRGVGFIRFDKR 58

>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 = 37.3 bits (86), Expect = 3e-04
 Identities = 16/91 (17%), Positives = 28/91 (30%), Gaps = 18/91 (19%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             ++V  LP  + +K L + F ++G I + RI    +                       
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRG----------------- 49

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRL 315
             +I F      E A+   N     G    +
Sbjct: 50  VGFIRFDKRIEAEEAIKGLNGQKPSGATEPI 80

>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 = 37.1 bits (85), Expect = 4e-04
 Identities = 11/106 (10%), Positives = 30/106 (28%), Gaps = 17/106 (16%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
               + N+P  + K  +++        ++       ++D      G              
Sbjct: 9   VCAHITNIPFSITKMDVLQFLEGIPVDENAVH---VLVDNNGQGLG-------------- 51

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAP 331
            A + FK+E     +   +   + G    +        +   ++ P
Sbjct: 52  QALVQFKNEDDARKSERLHRKKLNGREAFVHVVTLEDMREIEKNPP 97

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.6 bits (84), Expect = 6e-04
 Identities = 20/100 (20%), Positives = 38/100 (38%), Gaps = 18/100 (18%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             +FVG L     +++L + F K+G+I  V +            +G              
Sbjct: 6   GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVV---VKDRETQRSRG-------------- 48

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRACPPRKK 324
             ++ F++    + A+ A N   + G  IR+D+A      
Sbjct: 49  FGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDN 88

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.2 bits (83), Expect = 9e-04
 Identities = 4/22 (18%), Positives = 9/22 (40%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFC 358
             ++VG L  +     + + F 
Sbjct: 18  TRLWVGGLGPNTSLAALAREFD 39

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.9 bits (82), Expect = 0.001
 Identities = 6/57 (10%), Positives = 21/57 (36%), Gaps = 5/57 (8%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
            ++V++   P D   ++I +       + +      + +     +     +V+F + 
Sbjct: 6   NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSI-----FVVFDSI 57

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.9 bits (82), Expect = 0.001
 Identities = 8/93 (8%), Positives = 28/93 (30%), Gaps = 18/93 (19%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           R++++   P       + +     G++ +++                   ++    A   
Sbjct: 7   RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ------------------MRRTLHKAFKG 48

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRA 318
             ++VF S +S +  +           + +   
Sbjct: 49  SIFVVFDSIESAKKFVETPGQKYKETDLLILFK 81

>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 = 35.9 bits (82), Expect = 0.001
 Identities = 18/98 (18%), Positives = 30/98 (30%), Gaps = 17/98 (17%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             IFVG LP      +L K F  FG+I+   + +                          
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRG----------------- 53

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRK 323
           + ++      + E A      +I G    ++ A    K
Sbjct: 54  YGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLGAK 91

>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 = 35.4 bits (81), Expect = 0.001
 Identities = 18/94 (19%), Positives = 31/94 (32%), Gaps = 17/94 (18%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
            TI++ NL  K+KK  L K                 ++   +  +G              
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFS--RFGQILDILVSRSLKMRG-------------- 47

Query: 286 HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRA 318
            A+++FK   S   AL +          +R+  A
Sbjct: 48  QAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 81

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.6 bits (79), Expect = 0.002
 Identities = 12/57 (21%), Positives = 25/57 (43%), Gaps = 3/57 (5%)

Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
             T+++ NL   +K +E+ +     + + S    +  I        +G A+V+FK  
Sbjct: 3   NHTIYINNLNEKIKKDELKKSL---HAIFSRFGQILDILVSRSLKMRGQAFVIFKEV 56

>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 = 35.6 bits (81), Expect = 0.002
 Identities = 17/102 (16%), Positives = 39/102 (38%), Gaps = 24/102 (23%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
           +T+F+ NL    +++ L +   +FG++  VR+   P  +                     
Sbjct: 9   KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKG----------------- 51

Query: 286 HAYIVFKSEQSTEAALA-------FNMAVIGGNHIRLDRACP 320
            A+  F ++++ +  LA            + G  +++D A  
Sbjct: 52  CAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVT 93

>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 = 35.2 bits (80), Expect = 0.002
 Identities = 21/56 (37%), Positives = 31/56 (55%), Gaps = 4/56 (7%)

Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
           KTVF+ NL FD ++E + ++     DL+     VRV+ HP     KG A+  F T+
Sbjct: 9   KTVFIRNLSFDSEEEALGEVLQQFGDLKY----VRVVLHPDTEHSKGCAFAQFMTQ 60

>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 = 34.5 bits (78), Expect = 0.003
 Identities = 16/93 (17%), Positives = 30/93 (32%), Gaps = 18/93 (19%)

Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
             +F+GNL        L     +    + + +  V     +                   
Sbjct: 14  FNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRK------------------ 55

Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRA 318
             Y+ F+S +  E AL      + GN I+L++ 
Sbjct: 56  FGYVDFESAEDLEKALELTGLKVFGNEIKLEKP 88

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	393
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.95
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.75
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.75
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.74
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.74
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.74
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.74
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.74
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.74
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.74
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.73
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.73
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.73
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.73
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.72
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.72
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.72
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.72
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.71
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.71
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.71
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.71
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.71
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.71
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.71
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.71
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.71
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.7
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.7
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.7
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.69
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.69
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.69
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.68
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.68
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.68
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.68
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.68
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.68
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.68
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.67
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.67
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.66
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.66
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.66
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.65
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.65
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.65
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.65
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.65
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.64
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.64
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.64
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.63
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.63
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.63
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.63
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.63
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.63
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.62
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.61
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.61
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.61
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.6
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.6
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.59
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.59
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.58
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.58
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.57
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.56
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.56
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.55
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.54
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.54
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.52
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.51
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.5
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.49
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.47
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.43
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.41
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.4
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.39
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.37
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.37
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.36
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.36
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.35
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.35
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.34
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.33
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.33
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.33
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.33
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.33
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.32
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.32
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.32
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.31
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.31
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.3
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.3
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.3
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.3
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.29
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.29
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.28
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.27
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.26
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.26
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.24
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.24
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.24
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.24
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.22
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.21
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.2
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.19
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.18
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.17
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.16
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.15
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.14
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.13
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.13
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.11
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.11
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.11
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.1
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.09
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.08
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.05
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.04
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.04
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.04
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.03
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.03
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.0
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.0
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.0
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.97
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	98.96
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	98.96
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	98.95
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	98.93
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	98.93
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.92
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	98.91
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.91
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	98.89
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	98.88
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	98.87
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	98.87
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.86
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	98.84
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	98.82
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.81
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	98.81
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	98.79
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.75
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	98.7
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	98.68
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.68
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	98.65
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	98.65
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	98.55
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	98.23
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	98.19
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.1
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	97.6
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	97.56
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.78
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.23
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	95.26
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	93.89
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	90.67

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=3.2e-27  Score=209.90  Aligned_cols=145  Identities=18%  Similarity=0.362  Sum_probs=126.0

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHh
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~l  303 (393)
                      ..|+|||||||+.+|+++|+++|++||.|.+|.++++..  +               +.++|||||+|.+.++|..|+.+
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~--~---------------~~~~g~afv~f~~~~~a~~a~~~   67 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN--T---------------KRSRGFGFVTYATVEEVDAAMNA   67 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT--T---------------CCEEEEEEEEESSHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeeccc--C---------------CCccCceecccCCHHHHHHHHHh
Confidence            358999999999999999999999999999999977542  2               34669999999999999999998


Q ss_pred             cCceeCCeEEEEeecCCCcccCCCCCCCCcCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCcc
Q 016231          304 NMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKG  383 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~~~~~~~~~~~~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kG  383 (393)
                      ++..+.++.+.+.+..+.......   ......++|||+|||+.+|+++|+++|..|    |.|..|.|+.+..+|.++|
T Consensus        68 ~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~i~V~~lp~~~te~~L~~~f~~~----G~v~~~~i~~~~~~~~~~g  140 (183)
T d1u1qa_          68 RPHKVDGRVVEPKRAVSREDSQRP---GAHLTVKKIFVGGIKEDTEEHHLRDYFEQY----GKIEVIEIMTDRGSGKKRG  140 (183)
T ss_dssp             CSCEETTEECEEEECCCTTGGGST---TTTCCCSEEEEECCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTCCEEE
T ss_pred             cCCcccccchhhhhhhhccccccc---ccccccceeEEccCCCcCCHHHHhhhhccC----CceeeeeeecccccCccce
Confidence            999999999999887654433222   224456899999999999999999999999    9999999999999999999


Q ss_pred             EEEEEeeec
Q 016231          384 IAYVLFKTR  392 (393)
Q Consensus       384 faFVeF~t~  392 (393)
                      ||||+|.++
T Consensus       141 ~~fV~f~~~  149 (183)
T d1u1qa_         141 FAFVTFDDH  149 (183)
T ss_dssp             EEEEEESCH
T ss_pred             eEEEEECCH
Confidence            999999874

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=3e-18  Score=137.22  Aligned_cols=81  Identities=20%  Similarity=0.279  Sum_probs=72.6

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      .++||||+|||+++|+++|+.+|+.||+|.+|+|+.++.  +               +.++|||||+|.+.++|..|| .
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~--~---------------~~~kg~afV~f~~~~~A~~Ai~~   68 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM--K---------------KTACGFCFVEYYSRADAENAMRY   68 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT--T---------------CCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccc--c---------------ccccceEEEEECCHHHHHHHHHH
Confidence            478999999999999999999999999999999977652  2               236699999999999999999 6


Q ss_pred             hcCceeCCeEEEEeecCCC
Q 016231          303 FNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~  321 (393)
                      ||+..|.|+.|.|.|+...
T Consensus        69 l~g~~~~gr~i~V~~a~~~   87 (93)
T d1h2vz_          69 INGTRLDDRIIRTDWDAGF   87 (93)
T ss_dssp             TTTSEETTEECEEEEESCC
T ss_pred             hCCCEECCEEEEEEEcCCC
Confidence            9999999999999998643

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=1.5e-18  Score=137.69  Aligned_cols=81  Identities=30%  Similarity=0.460  Sum_probs=72.5

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..+||||+|||+++|+++|+++|+.||.|.+|+|++++  .+               +.++|||||+|.+.++|..|+ .
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~--~~---------------~~~kg~afV~f~~~~~A~~ai~~   66 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY--ET---------------EKHRGFAFVEFELAEDAAAAIDN   66 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCS--SS---------------CCCSSEEEECCSSHHHHHHHHHH
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEeccccccc--cc---------------ccccceeEEEECCHHHHHHHHHH
Confidence            36899999999999999999999999999999997654  22               346699999999999999999 7


Q ss_pred             hcCceeCCeEEEEeecCCC
Q 016231          303 FNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~  321 (393)
                      ||+..|.|+.|.|.++.+.
T Consensus        67 l~~~~i~g~~l~v~~a~p~   85 (89)
T d2cqba1          67 MNESELFGRTIRVNLAKPM   85 (89)
T ss_dssp             HTTEEETTEEEEEEECCCC
T ss_pred             cCCCEECCEEEEEEEeCCC
Confidence            9999999999999999754

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=4.5e-18  Score=133.76  Aligned_cols=79  Identities=19%  Similarity=0.423  Sum_probs=71.2

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHh
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~l  303 (393)
                      ..++|||+|||+++|+++|+++|+.||.|.+|+|++++  .+               +.++|||||+|.+.++|+.||.+
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~--~t---------------g~~kG~afV~f~~~~~a~~ai~~   67 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDP--NT---------------KRSRGFGFVTYATVEEVDAAMNA   67 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT--TT---------------CCEEEEEEEEESSHHHHHHHHHT
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccc--cC---------------CCcccEEEEEEcCHHHHHHHHHh
Confidence            35899999999999999999999999999999998765  22               34669999999999999999999


Q ss_pred             cCceeCCeEEEEeecC
Q 016231          304 NMAVIGGNHIRLDRAC  319 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~  319 (393)
                      ++..|.|+.|.|.+|.
T Consensus        68 ~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1          68 RPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             CSCEETTEECEEEECC
T ss_pred             CCCEECCEEEEEEeee
Confidence            9999999999999874

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.74  E-value=2.6e-18  Score=133.80  Aligned_cols=79  Identities=23%  Similarity=0.340  Sum_probs=71.0

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      .++|||+|||+++|+++|+++|++||.|.+|+|++++  .+               +.++|||||+|.+.++|+.|| .|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~---------------g~~~g~afV~f~~~~~A~~ai~~l   64 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDY--KT---------------GYSYGYAFVDFTSEMDSQRAIKVL   64 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEET--TT---------------TEECSEEEEEESSHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeec--cc---------------CCccccceEEECCHHHHHHHHHHh
Confidence            4689999999999999999999999999999997764  22               236699999999999999999 69


Q ss_pred             cCceeCCeEEEEeecCC
Q 016231          304 NMAVIGGNHIRLDRACP  320 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~  320 (393)
                      |+..|.|+.|+|.++.|
T Consensus        65 ng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1          65 NGITVRNKRLKVSYARP   81 (82)
T ss_dssp             TTCEETTEECEEEECCC
T ss_pred             CCCEECCEEEEEEEcCC
Confidence            99999999999999864

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=5.4e-18  Score=134.69  Aligned_cols=82  Identities=24%  Similarity=0.405  Sum_probs=72.3

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....+||||+|||+++|+++|+++|+.||+|.+|+|+++..                   ..+|||||+|.+.++|..|+
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~-------------------~~~~~afV~f~~~~~A~~A~   65 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT-------------------SNDPYCFVEFYEHRDAAAAL   65 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC-------------------SSCCEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccC-------------------ccceeeEEEECCHHHHHHHH
Confidence            34478999999999999999999999999999999966431                   13489999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCCc
Q 016231          302 -AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~~  322 (393)
                       .+|+..|.|+.|+|.++.++.
T Consensus        66 ~~l~~~~~~g~~i~v~~a~~~~   87 (90)
T d2cqia1          66 AAMNGRKILGKEVKVNWATTPS   87 (90)
T ss_dssp             HHHTTEEETTEEEEEEECCCTT
T ss_pred             HHcCCCEECCEEEEEEEcCCCC
Confidence             699999999999999997653

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=1.3e-18  Score=141.65  Aligned_cols=79  Identities=24%  Similarity=0.276  Sum_probs=71.3

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHh
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~l  303 (393)
                      ..+||||+|||+++|+++|+.+|+.||.|.+|+|+++.  .               +++++|||||+|.+.++|..||.|
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~--~---------------tg~~kG~afV~F~~~e~a~~A~~l   79 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDR--N---------------SRRSKGIAYVEFCEIQSVPLAIGL   79 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSC--C---------------SSSCCCCEEEEESCGGGHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecC--C---------------CccccceEEEEECCHHHHHHHHHH
Confidence            35899999999999999999999999999999997654  2               234679999999999999999999


Q ss_pred             cCceeCCeEEEEeecC
Q 016231          304 NMAVIGGNHIRLDRAC  319 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~  319 (393)
                      ||..|.|+.|.|.++.
T Consensus        80 ~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          80 TGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             TTEEETTEEEEEEEHH
T ss_pred             CCCEECCEEEEEEECC
Confidence            9999999999999875

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=5.8e-18  Score=131.69  Aligned_cols=79  Identities=20%  Similarity=0.317  Sum_probs=70.6

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      ..+|||+|||+++++++|+++|+.||.|.+|+|++++.  .               +.++|||||+|.+.++|+.|+ .|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~--~---------------~~~~g~afv~f~~~~~a~~a~~~l   64 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKI--T---------------GQSLGYGFVNYIDPKDAEKAINTL   64 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTT--T---------------CCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeecc--C---------------CCceeeEEEEECCHHHHHHHHHHh
Confidence            35799999999999999999999999999999976541  2               246799999999999999999 69


Q ss_pred             cCceeCCeEEEEeecCC
Q 016231          304 NMAVIGGNHIRLDRACP  320 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~  320 (393)
                      ||..|.|+.|.|.++.|
T Consensus        65 ~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1          65 NGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             TTCEETTEECEEEECCC
T ss_pred             CCCEECCEEEEEEEeeC
Confidence            99999999999999864

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=5.1e-18  Score=131.19  Aligned_cols=77  Identities=18%  Similarity=0.385  Sum_probs=69.4

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhc
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~ln  304 (393)
                      .++|||||||+++|+++|+++|++||.|..+.++.++.                 ++.++|||||+|.+.+++.+|+.+|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~-----------------~~~~~g~afV~f~~~e~~~~al~~~   64 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRG-----------------SGKKRGFAFVTFDDHDSVDKIVIQK   64 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTT-----------------TCCEEEEEEEEESSHHHHHHHHHCS
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCC-----------------CcccccEEEEEEcCHHHHHHHHHhC
Confidence            47899999999999999999999999999999876542                 2346799999999999999999999


Q ss_pred             CceeCCeEEEEeec
Q 016231          305 MAVIGGNHIRLDRA  318 (393)
Q Consensus       305 g~~~~Gr~I~V~~a  318 (393)
                      +..|.|+.|.|..|
T Consensus        65 ~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2          65 YHTVNGHNCEVRKA   78 (79)
T ss_dssp             CCEETTEECEEEEC
T ss_pred             CCEECCEEEEEEEC
Confidence            99999999999876

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=5.7e-18  Score=131.67  Aligned_cols=76  Identities=30%  Similarity=0.436  Sum_probs=69.4

Q ss_pred             EEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-HhcC
Q 016231          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNM  305 (393)
Q Consensus       227 tVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~lng  305 (393)
                      +|||||||+.+|+++|+.+|+.||+|.+|+|++++.  +               +.++|||||+|.+.++|..|| .|||
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~--t---------------g~~~g~aFV~f~~~~~a~~ai~~l~g   64 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMI--T---------------RRSLGYAYVNFQQPADAERALDTMNF   64 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT--T---------------CCEEEEEEEEESSHHHHHHHHTTSTT
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEeccc--c---------------cCCCCceEEEECCHHHHHHHHHHcCC
Confidence            699999999999999999999999999999987652  2               346799999999999999999 6999


Q ss_pred             ceeCCeEEEEeecC
Q 016231          306 AVIGGNHIRLDRAC  319 (393)
Q Consensus       306 ~~~~Gr~I~V~~a~  319 (393)
                      ..|.|+.|+|.++.
T Consensus        65 ~~~~gr~i~v~~a~   78 (80)
T d1cvja1          65 DVIKGKPVRIMWSQ   78 (80)
T ss_dssp             CEETTEECEEEECC
T ss_pred             CEECCEEEEEEEeC
Confidence            99999999999984

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=5.1e-18  Score=135.84  Aligned_cols=84  Identities=23%  Similarity=0.338  Sum_probs=73.7

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+++|+++|+.+|++||.|.+|+|++++  .+               +.++|||||+|.+.++|+.||
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~--~t---------------g~~kg~afV~f~~~~~A~~Ai   68 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDR--VT---------------GQHQGYGFVEFLSEEDADYAI   68 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCS--SS---------------CSBCSCEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecc--cc---------------cccccceEEEECCHHHHHHHH
Confidence            3346899999999999999999999999999999997654  22               346699999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCCc
Q 016231          302 -AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~~  322 (393)
                       .||+..|.|+.|+|.+|.+..
T Consensus        69 ~~l~g~~~~g~~l~V~~A~~~~   90 (93)
T d1x5ua1          69 KIMDMIKLYGKPIRVNKASAHN   90 (93)
T ss_dssp             HHSSSCBCSSCBCEEEETTTTS
T ss_pred             HHcCCCEECCEEEEEEEcCCCC
Confidence             699999999999999997653

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=3.5e-18  Score=139.68  Aligned_cols=80  Identities=20%  Similarity=0.409  Sum_probs=72.1

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhc
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~ln  304 (393)
                      .++|||||||+++|+++|+.+|++||.|..|.|++++.  +               +.++|||||+|.+.++|.+||.++
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~--~---------------~~~kg~aFV~f~~~~~a~~al~~~   82 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPA--S---------------KRSRGFGFVTFSSMAEVDAAMAAR   82 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTT--T---------------SSCCSEEEEECSSHHHHHHHHTSC
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeeccccc--C---------------CCccCeEEEEECCHHHHHHHHHhC
Confidence            47899999999999999999999999999999977652  2               236799999999999999999999


Q ss_pred             CceeCCeEEEEeecCCC
Q 016231          305 MAVIGGNHIRLDRACPP  321 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~~  321 (393)
                      +..|.|+.|.|.++.+.
T Consensus        83 ~~~l~G~~i~V~~a~~k   99 (103)
T d1x4ba1          83 PHSIDGRVVEPKRAVAR   99 (103)
T ss_dssp             SEEETTEEEEEECCSSC
T ss_pred             CCeECCEEEEEEECccc
Confidence            99999999999998754

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.73  E-value=6.4e-18  Score=133.82  Aligned_cols=80  Identities=21%  Similarity=0.279  Sum_probs=71.5

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      +.++|||+|||+++|+++|+++|+.||.|.+|+|++++.  +               +.++|||||+|.+.++|+.|+ .
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~--t---------------g~~~g~afV~f~~~~~A~~A~~~   68 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR--T---------------GFSKGYALVEYETHKQALAAKEA   68 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT--T---------------SSEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCccccccccccc--c---------------cccccceeEEECCHHHHHHHHHH
Confidence            468999999999999999999999999999999977652  2               346799999999999999999 6


Q ss_pred             hcCceeCCeEEEEeecCC
Q 016231          303 FNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~  320 (393)
                      |||..|.|+.|.|.+|.+
T Consensus        69 lng~~l~g~~l~V~~a~~   86 (88)
T d1rk8a_          69 LNGAEIMGQTIQVDWCFV   86 (88)
T ss_dssp             HTTCEETTEECEEEESEE
T ss_pred             cCCCEECCEEEEEEEecC
Confidence            999999999999999854

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=8.7e-18  Score=133.49  Aligned_cols=81  Identities=21%  Similarity=0.228  Sum_probs=72.3

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ...+|||+|||+++|+++|+++|+.||.|.+|+|+.++  .+               +.++|||||+|.+.++|..|| .
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~--~t---------------~~~rg~afV~f~~~~~A~~Ai~~   69 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDK--TT---------------GQSKGFAFISFHRREDAARAIAG   69 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECS--SS---------------CSEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccc--cc---------------cccccceeEEECCHHHHHHHHHH
Confidence            35789999999999999999999999999999997754  22               346799999999999999999 6


Q ss_pred             hcCceeCCeEEEEeecCCC
Q 016231          303 FNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~  321 (393)
                      |||..|.|+.|.|.++.+.
T Consensus        70 l~g~~~~g~~i~v~~akp~   88 (90)
T d2cq0a1          70 VSGFGYDHLILNVEWAKPS   88 (90)
T ss_dssp             TTTCEETTEECEEEESSCC
T ss_pred             hCCCEECCEEEEEEeeeCC
Confidence            9999999999999999754

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1.1e-17  Score=130.71  Aligned_cols=77  Identities=22%  Similarity=0.249  Sum_probs=68.7

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      +.+.++|||+|||+.+|+++|+++|+.||.|.+|+|++++  .+               +.++|||||+|.+.++|..||
T Consensus         6 p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~--~~---------------~~~~g~afV~f~~~~~A~~Ai   68 (83)
T d2cqca1           6 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQ--QS---------------RRSRGFAFVYFENVDDAKEAK   68 (83)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECS--SS---------------SSEEEEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccc--cc---------------cccccceEEEECCHHHHHHHH
Confidence            3457899999999999999999999999999999997754  22               236699999999999999999


Q ss_pred             -HhcCceeCCeEEEE
Q 016231          302 -AFNMAVIGGNHIRL  315 (393)
Q Consensus       302 -~lng~~~~Gr~I~V  315 (393)
                       .||+..|.|+.|+|
T Consensus        69 ~~l~g~~~~gr~i~V   83 (83)
T d2cqca1          69 ERANGMELDGRRIRV   83 (83)
T ss_dssp             HHHTTEEETTEEEEE
T ss_pred             HHcCCCEECCEEeEC
Confidence             69999999999987

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1.8e-17  Score=132.11  Aligned_cols=80  Identities=18%  Similarity=0.251  Sum_probs=70.1

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHh
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~l  303 (393)
                      ..++|||+|||+++|+++|+.+|+.||.|.+|+|++++.  +               +.++|||||+|.+.++|..||. 
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~--t---------------g~srG~aFV~f~~~~~a~~al~-   68 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLK--T---------------GHSKGFGFVRFTEYETQVKVMS-   68 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSS--S---------------CSEEEEEEEEESSHHHHHHHHH-
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCC--C---------------cccCCEEEEEECCHHHHHHHHh-
Confidence            357899999999999999999999999999999988652  2               3467999999999999999996 


Q ss_pred             cCceeCCeEEEEeecCCC
Q 016231          304 NMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~  321 (393)
                      ++..|+|+.|.|.++.+.
T Consensus        69 ~~~~l~Gr~i~v~~a~~k   86 (90)
T d2cqga1          69 QRHMIDGRWCDCKLPNSK   86 (90)
T ss_dssp             SCEEETTEEEEEECCCTT
T ss_pred             cCCccCCEEeEEEeCCCC
Confidence            345899999999998764

>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=99.72  E-value=1.6e-17  Score=135.05  Aligned_cols=83  Identities=18%  Similarity=0.325  Sum_probs=73.3

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      .+.++|||+|||+++|+++|+.+|+.||.|.+|.++.++.                 ++.++|||||+|.+.++|..|| 
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~-----------------~g~~kG~afV~f~~~~~A~~Ai~   78 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQ-----------------TNLSKCFGFVSYDNPVSAQAAIQ   78 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSS-----------------SCSEEEEEEEECSSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecc-----------------cCCCccceEEEeCCHHHHHHHHH
Confidence            3467899999999999999999999999999999977542                 2346799999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCCc
Q 016231          302 AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      .||+..|.|+.|.|.++.+..
T Consensus        79 ~lng~~~~g~~i~V~~a~~k~   99 (102)
T d2cpza1          79 SMNGFQIGMKRLKVQLKRSKN   99 (102)
T ss_dssp             HHTTCEETTEECEEECCCCSC
T ss_pred             HhCCCEECCEEEEEEEeCCCC
Confidence            799999999999999997653

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=1.4e-17  Score=130.60  Aligned_cols=80  Identities=19%  Similarity=0.261  Sum_probs=70.1

Q ss_pred             EEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-HhcCc
Q 016231          228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMA  306 (393)
Q Consensus       228 VFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~lng~  306 (393)
                      |||+|||+++|+++|+.+|+.||.|.+|.|++++..  +..            +.++|||||+|.+.++|..|+ .||+.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~--~~~------------~~~kG~afV~f~~~~~A~~A~~~~~~~   66 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNK--AGV------------LLSMGFGFVEYKKPEQAQKALKQLQGH   66 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECT--TCC------------EEEEEEEEEEESSHHHHHHHHHHSTTC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceeccccc--ccc------------cccceEEEEEECCHHHHHHHHHHhCCC
Confidence            799999999999999999999999999999887632  211            136799999999999999999 79999


Q ss_pred             eeCCeEEEEeecCCC
Q 016231          307 VIGGNHIRLDRACPP  321 (393)
Q Consensus       307 ~~~Gr~I~V~~a~~~  321 (393)
                      .|.|+.|.|.++.+.
T Consensus        67 ~~~g~~i~V~~a~~~   81 (85)
T d2cpfa1          67 TVDGHKLEVRISERA   81 (85)
T ss_dssp             EETTEECEEECSSCS
T ss_pred             EECCEEEEEEECCCC
Confidence            999999999998643

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.71  E-value=3.2e-18  Score=132.63  Aligned_cols=76  Identities=21%  Similarity=0.368  Sum_probs=69.1

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhcC
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNM  305 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~lng  305 (393)
                      |+|||+|||+++|+++|+++|++||.|.+|+|++++.  ++               .++|||||+|.+.++|++||.+|+
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~--tg---------------~~kG~aFV~f~~~~~a~~al~~~~   63 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL--TK---------------RSRGFGFVTFMDQAGVDKVLAQSR   63 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCC--SS---------------SCSSEEEECCCCTTHHHHHHHTTT
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccC--CC---------------CccceEEEEECCHHHHHHHHHcCC
Confidence            5799999999999999999999999999999977652  22               366999999999999999999999


Q ss_pred             ceeCCeEEEEeec
Q 016231          306 AVIGGNHIRLDRA  318 (393)
Q Consensus       306 ~~~~Gr~I~V~~a  318 (393)
                      +.|+|+.|.|..|
T Consensus        64 ~~i~Gr~i~V~~A   76 (77)
T d1uawa_          64 HELDSKTIDPKVA   76 (77)
T ss_dssp             CCCSSCCCEEEEC
T ss_pred             CEECCeEEEEEEC
Confidence            9999999999876

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.71  E-value=2.3e-17  Score=140.91  Aligned_cols=83  Identities=24%  Similarity=0.388  Sum_probs=73.3

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+++|+++|+++|+.||.|.+|+|++++  .+               +.++|||||+|.+.++|..|| 
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~--~t---------------~~~rg~afV~f~~~~~A~~Ai~  102 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDR--ET---------------RQSRGYGFVKFQSGSSAQQAIA  102 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEET--TT---------------TEEEEEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhcccccccccccc--cc---------------ccccceeeEEECCHHHHHHHHH
Confidence            345799999999999999999999999999999998765  22               236699999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCCc
Q 016231          302 AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      .||+..|.|+.|+|.++.+..
T Consensus       103 ~lng~~~~gr~l~V~~a~~~~  123 (139)
T d1u6fa1         103 GLNGFNILNKRLKVALAASGH  123 (139)
T ss_dssp             HTTTEECSSCEEEEEESSCCC
T ss_pred             HhCCCEECCEEEEEEEcCCCC
Confidence            699999999999999987543

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=5.1e-18  Score=138.16  Aligned_cols=82  Identities=23%  Similarity=0.408  Sum_probs=72.9

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      +..+||||+|||+++|+++|+++|+.||.|.+|+|++++.  +               +.++|||||+|.+.++|..|| 
T Consensus         6 ~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~--t---------------g~~~g~afV~f~~~~~a~~ai~   68 (104)
T d1p1ta_           6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRE--T---------------GKPKGYGFCEYQDQETALSAMR   68 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETT--T---------------TEEEEEEEEECSCHHHHHHHHH
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccc--e---------------eccCCceEEEECCHHHHHHHHH
Confidence            3468999999999999999999999999999999987652  2               236799999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCC
Q 016231          302 AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~  321 (393)
                      .||+..|.|+.|.|.++.+.
T Consensus        69 ~l~~~~~~g~~i~V~~a~~~   88 (104)
T d1p1ta_          69 NLNGREFSGRALRVDNAASE   88 (104)
T ss_dssp             HSSSBSCSSSCBEEEETTCT
T ss_pred             HcCCCEECCEEEEEEECCCC
Confidence            69999999999999998653

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.71  E-value=9.5e-18  Score=130.39  Aligned_cols=78  Identities=15%  Similarity=0.167  Sum_probs=66.3

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hhc
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~ln  304 (393)
                      +||||+|||+++|+++|+++|+.||.|..+.++.+.  .               .+.++|||||+|.+.++|..|+ .||
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~--~---------------~~~~~g~afV~f~~~e~A~~Ai~~l~   64 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSL--R---------------FNTSRRFAYIDVTSKEDARYCVEKLN   64 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC------------------------CCEEEEECSSHHHHHHHHHHHT
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeeccc--c---------------cccccceeEEEECCHHHHHHHHHHhC
Confidence            799999999999999999999999999877764432  1               2346799999999999999999 699


Q ss_pred             CceeCCeEEEEeecCC
Q 016231          305 MAVIGGNHIRLDRACP  320 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~  320 (393)
                      |..|.|+.|.|.++.|
T Consensus        65 g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1          65 GLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             TCEETTEECEEEECCC
T ss_pred             CCEECCEEEEEEEccC
Confidence            9999999999999865

>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=99.71  E-value=1.4e-17  Score=133.54  Aligned_cols=82  Identities=22%  Similarity=0.391  Sum_probs=71.7

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      .+.+|||+|||+++++++|+.+|+.||.|.+|+|+++.. .               ++.++|||||+|.+.++|..|| .
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~-~---------------~g~~rg~afV~f~~~~~A~~Ai~~   70 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMT-G---------------TGAHRGFGFVDFITKQDAKKAFNA   70 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCS-S---------------SCSSCSEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccc-c---------------CCCcccEEEEEECCHHHHHHHHHH
Confidence            467899999999999999999999999999999866431 1               2346799999999999999999 5


Q ss_pred             h-cCceeCCeEEEEeecCCC
Q 016231          303 F-NMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       303 l-ng~~~~Gr~I~V~~a~~~  321 (393)
                      | |+..|.|+.|.|.+|...
T Consensus        71 l~~~~~~~Gr~l~V~~A~~~   90 (94)
T d2cpha1          71 LCHSTHLYGRRLVLEWADSE   90 (94)
T ss_dssp             HHTCCBSSSCBCEEEECCCC
T ss_pred             ccCCcEECCEEEEEEEcCCC
Confidence            7 899999999999999754

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=9.7e-18  Score=132.01  Aligned_cols=79  Identities=18%  Similarity=0.328  Sum_probs=71.0

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hhc
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~ln  304 (393)
                      .+|||+|||+++|+++|+.+|+.||+|.+|+|++++  .+               +.++|||||+|.+.++|..|+ .||
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~--~t---------------g~~rg~aFV~f~~~~~A~~a~~~l~   64 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS--AT---------------GLSKGYAFCEYVDINVTDQAIAGLN   64 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCC--SS---------------SCCCCEEEEEESSSHHHHHHHHTSS
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccc--cc---------------cccceeEEEEECCHHHHHHHHHHhC
Confidence            469999999999999999999999999999997765  22               346699999999999999999 599


Q ss_pred             CceeCCeEEEEeecCCC
Q 016231          305 MAVIGGNHIRLDRACPP  321 (393)
Q Consensus       305 g~~~~Gr~I~V~~a~~~  321 (393)
                      +..|.|+.|.|.++.+.
T Consensus        65 ~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_          65 GMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             SCCCSSSCCEEEECCCC
T ss_pred             CCEECCEEEEEEECCCC
Confidence            99999999999999754

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.71  E-value=9.9e-18  Score=132.16  Aligned_cols=81  Identities=26%  Similarity=0.414  Sum_probs=68.8

Q ss_pred             cccEEEEeCCCccCC-HHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          224 LLRTIFVGNLPLKVK-KKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~t-ee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      ..++|||+|||+++| +++|+++|+.||.|.+|+|++...                .++.++|||||+|.+.++|..||+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~----------------~~~~~kg~afV~f~~~~~a~~Al~   66 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQK----------------EHSFNNCCAFMVFENKDSAERALQ   66 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC-------------------CCCEEEEEEESSHHHHHHHGG
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccC----------------CccccceeeeEEECCHHHHHHHHh
Confidence            368999999999976 566999999999999999854321                123577999999999999999999


Q ss_pred             hcCceeCCeEEEEeecCC
Q 016231          303 FNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~  320 (393)
                      +|+..|.|+.|.|.++.+
T Consensus        67 ~n~~~~~gr~l~V~~a~~   84 (86)
T d2ghpa3          67 MNRSLLGNREISVSLADK   84 (86)
T ss_dssp             GTTEEETTEEEEEEECCC
T ss_pred             cCCCEECCEEEEEEEcCC
Confidence            999999999999999864

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=3.4e-17  Score=133.35  Aligned_cols=82  Identities=21%  Similarity=0.323  Sum_probs=70.2

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      ...++|||+|||+.+|+++|+++|+.||.|.+|+|++++  .               ++.++|||||+|.+.++|+.||+
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~--~---------------tg~~kg~afV~f~~~~~A~~Ai~   70 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDR--Q---------------TGKSRGYGFVTMADRAAAERACK   70 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCS--S---------------SCCCCSEEEEEESSHHHHHHHHT
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccc--c---------------ccccCCeEEEEECCHHHHHHHHH
Confidence            345789999999999999999999999999999997654  2               23467999999999999999995


Q ss_pred             hcCceeCCeEEEEeecCCC
Q 016231          303 FNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~  321 (393)
                      ..+..|.|+.|.|.++...
T Consensus        71 ~~~~~l~Gr~l~V~~a~~~   89 (103)
T d2cqda1          71 DPNPIIDGRKANVNLAYLG   89 (103)
T ss_dssp             CSSCEETTEECEEEESTTT
T ss_pred             HCCCcCCCEEEEEEEcCCC
Confidence            4445799999999998754

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=2.1e-17  Score=130.16  Aligned_cols=76  Identities=12%  Similarity=0.160  Sum_probs=69.1

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhc
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~ln  304 (393)
                      .++|||+|||+++|+++|+.+|+.||+|.+|+|++++   +               +.++|||||+|.+.++|.+||+++
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~---~---------------~~~kG~afV~f~~~e~a~~al~~~   67 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL---H---------------KAFKGSIFVVFDSIESAKKFVETP   67 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT---T---------------CCEEEEEEEEESCHHHHHHHHTCC
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec---c---------------CCcceEEEEEEcCHHHHHHHHHHC
Confidence            6899999999999999999999999999999986643   2               236699999999999999999999


Q ss_pred             CceeCCeEEEEeec
Q 016231          305 MAVIGGNHIRLDRA  318 (393)
Q Consensus       305 g~~~~Gr~I~V~~a  318 (393)
                      +..|.|+.|.|.+.
T Consensus        68 ~~~~~g~~l~v~~~   81 (85)
T d1zh5a2          68 GQKYKETDLLILFK   81 (85)
T ss_dssp             CCEETTEECEEEEG
T ss_pred             CCEECCEEEEEEEc
Confidence            99999999999885

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=1.2e-17  Score=128.49  Aligned_cols=75  Identities=28%  Similarity=0.484  Sum_probs=67.2

Q ss_pred             EEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhcCc
Q 016231          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMA  306 (393)
Q Consensus       227 tVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~lng~  306 (393)
                      .|||+|||+++|+++|.++|++||.|.+|+|++++.  +               +.++|||||+|.+.++|+.||.+++.
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~--t---------------~~~kg~afV~f~~~~~a~~Al~~~~~   63 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPI--T---------------GRSRGFGFVLFKESESVDKVMDQKEH   63 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTT--T---------------TBCCSEEEEEESSHHHHHHHHHTCCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCC--C---------------CCcCceEEEEECCHHHHHHHHhcCCC
Confidence            499999999999999999999999999999977552  2               23669999999999999999999999


Q ss_pred             eeCCeEEEEeec
Q 016231          307 VIGGNHIRLDRA  318 (393)
Q Consensus       307 ~~~Gr~I~V~~a  318 (393)
                      .|.|+.|.|.+|
T Consensus        64 ~l~Gr~i~V~rA   75 (75)
T d1hd0a_          64 KLNGKVIDPKRA   75 (75)
T ss_dssp             CBTTBCCEECCC
T ss_pred             EECCCEEEeeEC
Confidence            999999999764

>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=99.70  E-value=2.3e-17  Score=127.71  Aligned_cols=75  Identities=16%  Similarity=0.297  Sum_probs=67.7

Q ss_pred             EEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-HhcC
Q 016231          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNM  305 (393)
Q Consensus       227 tVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~lng  305 (393)
                      .|||+|||+++++++|+++|+.||.|.+|+|+.++   +               +.++|||||+|.+.++|..|+ .||+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~---~---------------g~~~g~afV~f~~~~~A~~Ai~~l~g   63 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR---S---------------GRSLGTADVHFERKADALKAMKQYNG   63 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS---C---------------CCSCCEEEEEESCHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee---c---------------cccceeEEEEECCHHHHHHHHHHhCC
Confidence            59999999999999999999999999999996543   2               346699999999999999999 6999


Q ss_pred             ceeCCeEEEEeecC
Q 016231          306 AVIGGNHIRLDRAC  319 (393)
Q Consensus       306 ~~~~Gr~I~V~~a~  319 (393)
                      ..|.|+.|.|.++.
T Consensus        64 ~~l~g~~l~V~~a~   77 (78)
T d1no8a_          64 VPLDGRPMNIQLVT   77 (78)
T ss_dssp             CEETTEECEEEEEC
T ss_pred             CEECCEEEEEEEee
Confidence            99999999999874

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.70  E-value=4.5e-17  Score=131.42  Aligned_cols=82  Identities=17%  Similarity=0.205  Sum_probs=72.6

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      .+++|||+|||+++|+++|+++|..||.|.+|+|++++  .+               +.++|||||+|.+.++|..|| .
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~--~t---------------g~~~g~afV~f~~~~~a~~A~~~   69 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDS--LT---------------KKPKGFAFVTFMFPEHAVKAYAE   69 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCT--TT---------------CCCCSEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccc--cc---------------cccCcceEEEECCHHHHHHHHHH
Confidence            36789999999999999999999999999999996654  22               236699999999999999999 6


Q ss_pred             hcCceeCCeEEEEeecCCCc
Q 016231          303 FNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~~  322 (393)
                      ||+..|.|+.|.|.++.+..
T Consensus        70 l~g~~~~gr~i~V~~a~~~~   89 (99)
T d1whwa_          70 VDGQVFQGRMLHVLPSTIKK   89 (99)
T ss_dssp             TTTEESSSCEEEEEECCCCS
T ss_pred             cCCCEECCEEEEEEECCCCC
Confidence            99999999999999998654

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=9.9e-17  Score=128.11  Aligned_cols=81  Identities=20%  Similarity=0.355  Sum_probs=71.9

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+.+++++|+++|+.||+|.+|+++.++    +.               ++|||||+|.+.++|..||
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~----~~---------------~kg~afV~f~~~~~a~~Ai   68 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE----RG---------------SKGFGFVTFENSADADRAR   68 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT----TT---------------TCCEEEEEESCHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc----cC---------------CcceeEEEECCHHHHHHHH
Confidence            3456889999999999999999999999999999996643    11               4589999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCCC
Q 016231          302 -AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~~  321 (393)
                       .||+..|.|+.|.|.+|.+.
T Consensus        69 ~~l~~~~~~g~~l~V~~A~~r   89 (93)
T d2cq3a1          69 EKLHGTVVEGRKIEVNNATAR   89 (93)
T ss_dssp             HHHTTCEETTEECEEEECCSS
T ss_pred             HHcCCCEECCEEEEEEecCcC
Confidence             69999999999999999754

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=4.4e-17  Score=134.43  Aligned_cols=77  Identities=19%  Similarity=0.342  Sum_probs=69.5

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      .+++|||+|||+++|+++|+++|+.||.|.+|+++.+.                    .++|||||+|.+.++|..|| .
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~--------------------~~kG~afV~f~~~~~A~~Ai~~   65 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP--------------------ETRGTAYVVYEDIFDAKNACDH   65 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECST--------------------TTTTEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccC--------------------CcCCeEEEEECCHHHHHHHHHH
Confidence            46899999999999999999999999999999985421                    25699999999999999999 7


Q ss_pred             hcCceeCCeEEEEeecCC
Q 016231          303 FNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~  320 (393)
                      |||..|.|+.|.|.++.+
T Consensus        66 l~g~~~~gr~l~V~~a~~   83 (114)
T d2f9da1          66 LSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             HTTCEETTEECEEEECCH
T ss_pred             hCCCEECCEEEEEEEcCC
Confidence            999999999999999854

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.69  E-value=5.4e-17  Score=127.37  Aligned_cols=78  Identities=22%  Similarity=0.292  Sum_probs=69.3

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|||+|||+++++++|+.+|+.||.|.+|+|++++  .+               +.++|||||+|.+.++|..|| .
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~--~~---------------g~~~g~afV~f~~~~~A~~Ai~~   67 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK--LT---------------GRPRGVAFVRYNKREEAQEAISA   67 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECT--TT---------------CCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeeccc--cc---------------ccCceeEEEEECCHHHHHHHHHH
Confidence            45789999999999999999999999999999998765  22               346699999999999999999 6


Q ss_pred             hcCceeCC--eEEEEeec
Q 016231          303 FNMAVIGG--NHIRLDRA  318 (393)
Q Consensus       303 lng~~~~G--r~I~V~~a  318 (393)
                      ||+..+.|  ++|.|.+|
T Consensus        68 l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2          68 LNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             HTTCCCTTCSSCCEEEEC
T ss_pred             HCCCEeCCCCeEEEEEEC
Confidence            99999977  88999886

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.68  E-value=1e-17  Score=133.64  Aligned_cols=81  Identities=20%  Similarity=0.273  Sum_probs=71.0

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ....++|||+|||+++|+++|+.+|+.||.|.+++|+...                  .+.++|||||+|.+.++|+.||
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~------------------~g~~kg~afv~F~~~e~a~~Al   71 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR------------------TGTNRKFGYVDFESAEDLEKAL   71 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEE------------------EETTTTEEEEEESSHHHHHHHH
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecC------------------CCCccEEeEEeeCCHHHHHHHH
Confidence            3446799999999999999999999999999888775432                  2346799999999999999999


Q ss_pred             HhcCceeCCeEEEEeecCC
Q 016231          302 AFNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~  320 (393)
                      +||+..|.|+.|.|.++..
T Consensus        72 ~~~g~~~~g~~i~V~~ak~   90 (91)
T d1fjeb1          72 ELTGLKVFGNEIKLEKPKG   90 (91)
T ss_dssp             HGGGEEETTEEEEEECCCC
T ss_pred             hcCCcEECCEEEEEEecCC
Confidence            9999999999999999863

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=4.3e-17  Score=129.09  Aligned_cols=80  Identities=25%  Similarity=0.464  Sum_probs=70.9

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      .++|||||||+++|+++|+++|+.||.|..|.++...  .+               +.++|||||+|.+.++|+.|| .|
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~--~~---------------~~~~g~afV~f~~~~~a~~Ai~~l   67 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDR--ET---------------QRSRGFGFVTFENIDDAKDAMMAM   67 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCS--SS---------------CSCCSEEEEECSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeecccc--cc---------------ccccceEEEEECCHHHHHHHHHHc
Confidence            5789999999999999999999999999999886543  22               236699999999999999999 79


Q ss_pred             cCceeCCeEEEEeecCCC
Q 016231          304 NMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~  321 (393)
                      |+..|.|+.|.|.++.+.
T Consensus        68 ~~~~~~g~~l~V~~a~~~   85 (90)
T d1x5sa1          68 NGKSVDGRQIRVDQAGKS   85 (90)
T ss_dssp             TTCCTTSCCCEEEEEECC
T ss_pred             CCCEECCEEEEEEEcCCC
Confidence            999999999999998654

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=7e-17  Score=126.91  Aligned_cols=77  Identities=25%  Similarity=0.324  Sum_probs=68.0

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      .++|||+|||+.+|+++|+.+|++||.|.+|+|++++  .+               +.++|||||+|.+.++|..|+ .|
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~---------------g~~kg~afV~f~~~~~a~~Ai~~l   68 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQ--VT---------------GVSRGVGFIRFDKRIEAEEAIKGL   68 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT--TT---------------CCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccccc--cc---------------ccCCCeeEEEEcCHHHHHHHHHHh
Confidence            4789999999999999999999999999999998764  22               236699999999999999999 69


Q ss_pred             cCceeCC--eEEEEeec
Q 016231          304 NMAVIGG--NHIRLDRA  318 (393)
Q Consensus       304 ng~~~~G--r~I~V~~a  318 (393)
                      ||..+.|  ++|.|.+|
T Consensus        69 ng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2          69 NGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TTCCCTTCSSCCEEEEC
T ss_pred             CCCEeCCCCEEEEEEeC
Confidence            9999998  55888875

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=8.6e-17  Score=130.63  Aligned_cols=82  Identities=29%  Similarity=0.410  Sum_probs=70.3

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHh
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~l  303 (393)
                      +.++|||+|||+++|+++|+++|+.|| |..++++.++.                ..+.++|||||+|.+.++|++|+.|
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~----------------~~g~~~g~afV~f~~~e~a~~~~~~   76 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPS----------------NPERLKGFGYAEFEDLDSLLSALSL   76 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSS----------------CTTSBCSCEEEEESSHHHHHHHHGG
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeec----------------cCCCcceeeeEEECCHHHHHHHHHc
Confidence            468999999999999999999999999 66777755431                1234679999999999999988899


Q ss_pred             cCceeCCeEEEEeecCCCc
Q 016231          304 NMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~  322 (393)
                      |+..|.|+.|+|.++.+..
T Consensus        77 ~~~~~~gr~l~V~~a~~~~   95 (104)
T d1wi8a_          77 NEESLGNKRIRVDVADQAQ   95 (104)
T ss_dssp             GTCEETTEECEEEECCCCC
T ss_pred             CCCEECCEEEEEEECCCCC
Confidence            9999999999999987653

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.68  E-value=3.3e-17  Score=125.10  Aligned_cols=75  Identities=23%  Similarity=0.387  Sum_probs=66.8

Q ss_pred             EEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhcCc
Q 016231          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMA  306 (393)
Q Consensus       227 tVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~lng~  306 (393)
                      .|||||||+++|+++|+++|+.||.|..+.+++++  .+               +.++|||||+|.+.++|+.||++|+.
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~--~~---------------~~~~~~afV~F~~~~~a~~al~~~~~   63 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDK--TT---------------NRHRGFGFVTFESEDIVEKVCEIHFH   63 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCT--TC---------------TTSCCEEEEECSCHHHHHHHHHCSSC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeec--cc---------------cccCceeEEEECCHHHHHHHHhcCCC
Confidence            49999999999999999999999999998886543  22               23669999999999999999999999


Q ss_pred             eeCCeEEEEeec
Q 016231          307 VIGGNHIRLDRA  318 (393)
Q Consensus       307 ~~~Gr~I~V~~a  318 (393)
                      .|.|+.|.|.+|
T Consensus        64 ~l~gr~i~V~~A   75 (75)
T d2msta_          64 EINNKMVECKKA   75 (75)
T ss_dssp             CBTTBCCEEEEC
T ss_pred             EECCeEEEEEEC
Confidence            999999999875

>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=99.68  E-value=4.4e-17  Score=127.14  Aligned_cols=77  Identities=31%  Similarity=0.430  Sum_probs=66.9

Q ss_pred             EEEeCCCccCCHHHHHHHhcccCCeeEE-EEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-HhcC
Q 016231          228 IFVGNLPLKVKKKTLIKEFIKFGEIDSV-RIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNM  305 (393)
Q Consensus       228 VFVgNLp~~~tee~L~~~Fs~~G~I~sV-ri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~lng  305 (393)
                      |||+|||+++|+++|+++|++||.|.++ +|++++  .               +++++|||||+|.+.++|..|| .||+
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~--~---------------~g~~~g~afV~f~~~~~a~~Ai~~~~g   63 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDP--D---------------TGNSKGYAFINFASFDASDAAIEAMNG   63 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCT--T---------------TCSCCSEEEEEBSSHHHHHHHHHTTTT
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeec--c---------------ccccCceEEEEECCHHHHHHHHHhCCC
Confidence            8999999999999999999999998654 665433  1               2346799999999999999999 6999


Q ss_pred             ceeCCeEEEEeecCCC
Q 016231          306 AVIGGNHIRLDRACPP  321 (393)
Q Consensus       306 ~~~~Gr~I~V~~a~~~  321 (393)
                      ..|.|+.|.|.++.+.
T Consensus        64 ~~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1          64 QYLCNRPITVSYAFKK   79 (83)
T ss_dssp             CEETTEECEEEESCCC
T ss_pred             cEECCEEEEEEEecCC
Confidence            9999999999999754

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.68  E-value=8.8e-17  Score=123.67  Aligned_cols=73  Identities=26%  Similarity=0.295  Sum_probs=66.5

Q ss_pred             EEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhcCc
Q 016231          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMA  306 (393)
Q Consensus       227 tVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~lng~  306 (393)
                      ||||+|||+++++++|+++|+.||.|..|+|+.++.                   ..+|||||+|.+.++|.+||.+|+.
T Consensus         2 tv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~-------------------~~~~~afV~F~~~~~a~~Al~~~~~   62 (75)
T d2ghpa2           2 TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK-------------------KNFRFARIEFARYDGALAAITKTHK   62 (75)
T ss_dssp             EEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT-------------------SSSEEEEEEESSHHHHHHHHTTTTC
T ss_pred             EEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc-------------------ccceEEEEEEcchHHhHHHHHhcCc
Confidence            799999999999999999999999999999976541                   1347999999999999999999999


Q ss_pred             eeCCeEEEEeec
Q 016231          307 VIGGNHIRLDRA  318 (393)
Q Consensus       307 ~~~Gr~I~V~~a  318 (393)
                      .|+|+.|.|..+
T Consensus        63 ~i~g~~i~V~~~   74 (75)
T d2ghpa2          63 VVGQNEIIVSHL   74 (75)
T ss_dssp             EETTEECEEEEC
T ss_pred             EECCEEEEEEEC
Confidence            999999999875

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=2.2e-17  Score=127.36  Aligned_cols=75  Identities=24%  Similarity=0.387  Sum_probs=66.9

Q ss_pred             EEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhcCc
Q 016231          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMA  306 (393)
Q Consensus       227 tVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~lng~  306 (393)
                      .|||||||+++|+++|+++|++||.|..|+|++++  .+               +.++|||||+|.+.++|++||..++.
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~--~t---------------~~~rG~~FV~f~~~~~a~~al~~~~~   63 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDN--KT---------------NKRRGFCFITFKEEEPVKKIMEKKYH   63 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCT--TT---------------CCTTCCEEEEESSSHHHHHHTTCSSC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccc--cc---------------cccccEEEEEECCHHHHHHHHhhCCC
Confidence            49999999999999999999999999999997764  22               34669999999999999999988888


Q ss_pred             eeCCeEEEEeec
Q 016231          307 VIGGNHIRLDRA  318 (393)
Q Consensus       307 ~~~Gr~I~V~~a  318 (393)
                      .++|+.|.|..|
T Consensus        64 ~i~g~~i~vk~A   75 (75)
T d1x0fa1          64 NVGLSKCEIKVA   75 (75)
T ss_dssp             CBTTBCCEEECC
T ss_pred             EECCEEeEEEEC
Confidence            999999998764

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1.8e-16  Score=124.43  Aligned_cols=76  Identities=24%  Similarity=0.343  Sum_probs=68.2

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|||+|||+++|+++|..+|+.||.|..+.+..                       ++|||||+|.+.++|..|| .
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~-----------------------~rg~afV~f~~~~~A~~Ai~~   63 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----------------------IRDYAFVHFSNREDAVEAMKA   63 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE-----------------------CSSEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc-----------------------ccEEEEEEeCCHHHHHHHHHH
Confidence            358999999999999999999999999988776622                       4589999999999999999 6


Q ss_pred             hcCceeCCeEEEEeecCCCc
Q 016231          303 FNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~~  322 (393)
                      ||+..|.|+.|.|.++.|+.
T Consensus        64 l~~~~i~g~~i~V~~akP~~   83 (86)
T d2cpda1          64 LNGKVLDGSPIEVTLAKPVD   83 (86)
T ss_dssp             HSSEEETTEEEEEECCCCCC
T ss_pred             cCCCEECCEEEEEEeccCCC
Confidence            99999999999999998654

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=7.7e-17  Score=129.88  Aligned_cols=92  Identities=17%  Similarity=0.199  Sum_probs=70.9

Q ss_pred             CCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       221 ~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      ++...++|||+|||+.+|+++|+++|..||.|..+.+.....  ....       ....++.++|||||+|.+.++|..|
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~--~~~~-------~d~~~~~~~g~afV~f~~~~~a~~A   74 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPM--IHIY-------LDKETGKPKGDATVSYEDPPTAKAA   74 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBS--EECC-------BCTTTCSBCSEEEEEBSSHHHHHHH
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccce--eEEe-------eccccccccceeeEEecCHHHHHHH
Confidence            345578999999999999999999999999986443322110  0000       0112345789999999999999999


Q ss_pred             H-HhcCceeCCeEEEEeecCCC
Q 016231          301 L-AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       301 l-~lng~~~~Gr~I~V~~a~~~  321 (393)
                      | .|||..|.|+.|.|.++.+.
T Consensus        75 i~~l~g~~~~gr~i~V~~a~~~   96 (101)
T d2cpea1          75 VEWFDGKDFQGSKLKVSLARKK   96 (101)
T ss_dssp             HHHHTTCEETTEECEEECSSCC
T ss_pred             HHHhCCCEECCEEEEEEEcCCC
Confidence            9 69999999999999999653

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.3e-16  Score=126.40  Aligned_cols=78  Identities=21%  Similarity=0.373  Sum_probs=69.8

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      ..+|||+|||+++|+++|+++|+.||.|.+|+|+.+.    +               .++|||||+|.+.++|+.|| .|
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~----~---------------~~kg~afV~f~~~~~A~~Ai~~l   68 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE----N---------------GSKGYGFVHFETQEAAERAIEKM   68 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT----T---------------BCCSCEEEEESCHHHHHHHTTSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec----C---------------CCcceeEEEECCHHHHHHHHHHc
Confidence            4679999999999999999999999999999996543    1               25689999999999999999 69


Q ss_pred             cCceeCCeEEEEeecCCC
Q 016231          304 NMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~  321 (393)
                      ||..|.|+.|.|.++.+.
T Consensus        69 ~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2          69 NGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             SEEEETTEEEEEEECCCT
T ss_pred             CCCEECCEEEEEEECCCC
Confidence            999999999999999754

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.66  E-value=2e-16  Score=126.62  Aligned_cols=82  Identities=22%  Similarity=0.391  Sum_probs=69.9

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+++|+++|+.+|+.||.|.+++++.+.  .               .+.++|||||+|.+.++|..|| 
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~--~---------------~~~~~g~afV~F~~~~~a~~ai~   68 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHP--D---------------TEHSKGCAFAQFMTQEAAQKCLA   68 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCS--S---------------SCCBCSEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeecccc--c---------------cccccceEEEEEcCHHHHHHHHH
Confidence            346899999999999999999999999999999886543  1               2236799999999999999999 


Q ss_pred             Hhc------CceeCCeEEEEeecCCC
Q 016231          302 AFN------MAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 ~ln------g~~~~Gr~I~V~~a~~~  321 (393)
                      .+|      +..|.|+.|.|.++.+.
T Consensus        69 ~l~~~~~~~g~~~~gr~l~v~~a~~k   94 (98)
T d1x4ha1          69 AASLEAEGGGLKLDGRQLKVDLAVTR   94 (98)
T ss_dssp             HHCTTTTTCCEESSSCEEEEECCCCC
T ss_pred             HcccccccCCcEECCEEEEEEECCCC
Confidence            465      67789999999998754

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=1.2e-16  Score=129.44  Aligned_cols=78  Identities=22%  Similarity=0.302  Sum_probs=68.7

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      .++|||+|||+++|+++|+.+|+.||.|..++++.+.   +               +.++|||||+|.+.++|..|| .|
T Consensus        18 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~---~---------------~~~~g~afV~f~~~~~A~~Ai~~l   79 (101)
T d1x5oa1          18 PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS---S---------------GTSRGVGFARMESTEKCEAVIGHF   79 (101)
T ss_dssp             TTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS---S---------------SCEEEEEEEEESCHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc---c---------------cccccceeEEeCCHHHHHHHHHHh
Confidence            5789999999999999999999999999999886542   1               236799999999999999999 69


Q ss_pred             cCceeCCeEEEEeecCC
Q 016231          304 NMAVIGGNHIRLDRACP  320 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~  320 (393)
                      ||..|.|+++.|.++.|
T Consensus        80 ng~~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          80 NGKFIKTPPGVSAPTEP   96 (101)
T ss_dssp             BTCCCCCCTTSCCCSSC
T ss_pred             CCCEECCcCCccCCCCC
Confidence            99999999998877643

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=3.1e-16  Score=125.59  Aligned_cols=79  Identities=22%  Similarity=0.387  Sum_probs=69.4

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+++|+++|+++|+.||.|..+.+....                    .++|||||+|.+.++|..|| 
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~--------------------~~~g~afV~f~~~e~a~~Ai~   71 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR--------------------GGPPFAFVEFEDPRDAEDAVY   71 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSS--------------------SSSCCEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccc--------------------cccceEEEEECCHHHHHHHHH
Confidence            446889999999999999999999999999988873321                    25589999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCC
Q 016231          302 AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~  321 (393)
                      .||+..|.|+.|.|.++.+.
T Consensus        72 ~l~g~~~~g~~l~V~~a~~~   91 (95)
T d1x4aa1          72 GRDGYDYDGYRLRVEFPRSG   91 (95)
T ss_dssp             HHTTCEETTEECEEECCCCC
T ss_pred             HhCCCEECCEEEEEEeccCC
Confidence            69999999999999998653

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=1.7e-16  Score=128.82  Aligned_cols=82  Identities=16%  Similarity=0.176  Sum_probs=70.3

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      .....+|||+|||+++|+++|+++|..||. ..|.++.+.                  .+.++|||||+|.+.++|+.||
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~------------------~g~~~G~afVeF~~~~~a~~Al   72 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP------------------DGRVTGEADVEFATHEDAVAAM   72 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS------------------SSCEEEEEEEECSSSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEec------------------CCcceEEEEEEECCHHHHHHHH
Confidence            345689999999999999999999999985 467775543                  1336699999999999999999


Q ss_pred             HhcCceeCCeEEEEeecCCCc
Q 016231          302 AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      ++|+..|.||.|.|.++.+..
T Consensus        73 ~~~~~~i~gR~I~V~~s~~~~   93 (102)
T d1weza_          73 AKDKANMQHRYVELFLNSTAG   93 (102)
T ss_dssp             TTSSCCSSSSCCEEEEECCCC
T ss_pred             HcCCCEECCEEEEEEEcCCCC
Confidence            999999999999999987653

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.65  E-value=8.1e-17  Score=131.80  Aligned_cols=76  Identities=18%  Similarity=0.273  Sum_probs=68.3

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      .+..++|||+|||+.+++++|+++|+.||.|..|.|..                       ++|||||+|.+.++|..||
T Consensus         7 ~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~-----------------------~kg~afV~f~~~~~A~~A~   63 (111)
T d1whxa_           7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----------------------GGITAIVEFLEPLEARKAF   63 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----------------------SSSCEEEEESCHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec-----------------------cCceEEEEEcCHHHHHHHH
Confidence            34568999999999999999999999999999988721                       4589999999999999999


Q ss_pred             -HhcCceeCCeEEEEeecCC
Q 016231          302 -AFNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~~a~~  320 (393)
                       .|||..|.|+.|.|.++..
T Consensus        64 ~~lng~~~~gr~l~v~~a~~   83 (111)
T d1whxa_          64 RHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             HHHTTCBSSSSBCEEEEEET
T ss_pred             HHHcCCccCCCeEEEEECCC
Confidence             7999999999999999853

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.65  E-value=2.1e-16  Score=126.76  Aligned_cols=77  Identities=29%  Similarity=0.301  Sum_probs=67.6

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...++|||+|||+++|+++|+++|+.||.|..++.       .               +.++|||||+|.+.++|..|+ 
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-------~---------------~~~~~~afV~f~~~~~A~~A~~   71 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-------D---------------GKSKGIAYIEFKSEADAEKNLE   71 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-------T---------------TEEEEEEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-------c---------------CccccEEEEEeCCHHHHHHHHH
Confidence            44789999999999999999999999998765543       1               236699999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCC
Q 016231          302 AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~  321 (393)
                      .||+..|.|+.|.|.++.+.
T Consensus        72 ~l~~~~~~gr~i~V~~a~~k   91 (96)
T d1fjca_          72 EKQGAEIDGRSVSLYYTGEK   91 (96)
T ss_dssp             HTTEEEETTEEEEEEECSSS
T ss_pred             HcCCCEECCEEEEEEEeCCC
Confidence            69999999999999999764

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=2.7e-16  Score=126.46  Aligned_cols=74  Identities=18%  Similarity=0.337  Sum_probs=68.1

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|||+|||..+++++|+.+|+.||.|.+|+|+.                       ++|||||+|.+.++|..|+ .
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~-----------------------~kg~afV~f~~~~~A~~Ai~~   73 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP-----------------------EKGYSFVRFSTHESAAHAIVS   73 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEET-----------------------TTTEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEe-----------------------cceEEEEEECCHHHHHHHHHH
Confidence            357999999999999999999999999999999853                       2489999999999999999 7


Q ss_pred             hcCceeCCeEEEEeecCC
Q 016231          303 FNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~  320 (393)
                      ||+..|.|+.|+|.|+.+
T Consensus        74 l~~~~i~g~~l~v~~ak~   91 (96)
T d1x4ga1          74 VNGTTIEGHVVKCYWGKE   91 (96)
T ss_dssp             HTTCEETTEECEEECCCC
T ss_pred             hCCCEECCEEEEEEEcCC
Confidence            999999999999999864

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=8.3e-17  Score=130.05  Aligned_cols=83  Identities=18%  Similarity=0.247  Sum_probs=72.7

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      .++++|||+|||+++++++|+.+|+.||.|..+.++.+..                 .+.++|||||+|.+.++|..|| 
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~-----------------~g~~~g~~fV~f~~~~~A~~Ai~   78 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM-----------------TGRMRGQAFITFPNKEIAWQALH   78 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE-----------------CSSSCSEEEEECSSHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccc-----------------cccccccceEEeccHHHHHHHHH
Confidence            3478999999999999999999999999998888766441                 2346699999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCCCc
Q 016231          302 AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      .|||..|.|+.|.|.++.+..
T Consensus        79 ~l~g~~~~g~~l~V~~ak~k~   99 (102)
T d2cpxa1          79 LVNGYKLYGKILVIEFGKNKK   99 (102)
T ss_dssp             HSTTCBCSSCBCEEEECCCCS
T ss_pred             HhCCCEECCEEEEEEeCCCcc
Confidence            699999999999999997643

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=4.4e-16  Score=125.77  Aligned_cols=75  Identities=27%  Similarity=0.466  Sum_probs=66.9

Q ss_pred             CCcccEEEEeCCC-ccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          222 GKLLRTIFVGNLP-LKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       222 ~~~~rtVFVgNLp-~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      ....++|||+||| ..+++++|+.+|++||.|.+|+|                         ++|||||+|.+.++|..|
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i-------------------------~rg~aFV~f~~~~~A~~A   66 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------------------------HKGFAFVQYVNERNARAA   66 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE-------------------------ETEEEEEEESSHHHHHHH
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE-------------------------eCCeEEEEECCHHHHHHH
Confidence            3445789999997 57889999999999999999988                         338999999999999999


Q ss_pred             H-HhcCceeCCeEEEEeecCCC
Q 016231          301 L-AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       301 l-~lng~~~~Gr~I~V~~a~~~  321 (393)
                      | .|||..|.|+.|+|.++.++
T Consensus        67 i~~lng~~~~g~~l~V~~a~~~   88 (98)
T d1wf2a_          67 VAGEDGRMIAGQVLDINLAAEP   88 (98)
T ss_dssp             HHTTTTCEETTEECEEEETTSC
T ss_pred             HHHcCCCEECCEEEEEEECCCC
Confidence            9 69999999999999999754

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=2.2e-16  Score=124.78  Aligned_cols=76  Identities=20%  Similarity=0.323  Sum_probs=67.3

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHh
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~l  303 (393)
                      .+++|||+|||+.+|+++|+++|+.||.|.+|+++.                      .++|||||+|.+.++|+.||. 
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~----------------------~~~gfafV~f~~~~~a~~a~~-   60 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK----------------------PFRAFAFVTFADDQIAQSLCG-   60 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS----------------------SCCSCCEEECSCHHHHHHTTT-
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee----------------------ccCceEEEEECCHHHHHHHHh-
Confidence            478999999999999999999999999999987622                      145899999999999999996 


Q ss_pred             cCceeCCeEEEEeecCCCc
Q 016231          304 NMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~  322 (393)
                      ++..|.|+.|.|.++.++.
T Consensus        61 ~~~~i~g~~l~v~~a~~k~   79 (88)
T d1wf0a_          61 EDLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             CEEEETTEEEEEECCCCCC
T ss_pred             CCCEECCEEeEEEeCCCCC
Confidence            7889999999999997654

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=2.4e-16  Score=124.18  Aligned_cols=74  Identities=27%  Similarity=0.481  Sum_probs=68.0

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      .++|||+|||+++++++|+.+|+.||.|.+|++.+                       ++|||||+|.+.++|..|+ .|
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~-----------------------~k~~afV~f~~~~~A~~A~~~l   64 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK-----------------------DKGFGFIRLETRTLAEIAKVEL   64 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEET-----------------------TTTEEEEECSSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeec-----------------------ccceEEEEECCHHHHHHHHHHh
Confidence            46899999999999999999999999999999843                       3489999999999999999 69


Q ss_pred             cCceeCCeEEEEeecCCC
Q 016231          304 NMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~  321 (393)
                      ||..|.|+.|.|.+|.+.
T Consensus        65 ~g~~i~g~~l~V~~A~~~   82 (86)
T d2cpja1          65 DNMPLRGKQLRVRFACHS   82 (86)
T ss_dssp             TTCCBTTBCCEEEESSCC
T ss_pred             CCCEECCEEEEEEECCCc
Confidence            999999999999999754

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=3.7e-16  Score=123.21  Aligned_cols=77  Identities=19%  Similarity=0.153  Sum_probs=67.0

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      .++++|||+|||+++|+++|+.+|+.||.|..+.++..                     .++|||||+|.+.++|..|+ 
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~---------------------~~~~~afV~f~~~~~A~~A~~   66 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---------------------KDRKMALIQMGSVEEAVQALI   66 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS---------------------SSTTCEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee---------------------cccceeEEEECCHHHHHHHHH
Confidence            35789999999999999999999999999987766321                     14589999999999999999 


Q ss_pred             HhcCcee-CCeEEEEeecCC
Q 016231          302 AFNMAVI-GGNHIRLDRACP  320 (393)
Q Consensus       302 ~lng~~~-~Gr~I~V~~a~~  320 (393)
                      .|||..+ .|+.|+|.++.+
T Consensus        67 ~l~~~~i~~g~~l~v~~sk~   86 (88)
T d2adca2          67 DLHNHDLGENHHLRVSFSKS   86 (88)
T ss_dssp             HHTTCBSSSSCBCEEEECSS
T ss_pred             hccCCEecCCCEEEEEeCCC
Confidence            7999887 589999999863

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=2.4e-16  Score=125.01  Aligned_cols=78  Identities=22%  Similarity=0.341  Sum_probs=67.1

Q ss_pred             ccEEEEeCCCccCCHHHH---HHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          225 LRTIFVGNLPLKVKKKTL---IKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L---~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      .++|||+|||+++++++|   .++|++||.|.+|.|++++.+.  ..            ...+|||||+|.+.++|..|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~--~~------------~~~~g~aFV~f~~~~~A~~Ai   73 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYA--GS------------QGPSASAYVTYIRSEDALRAI   73 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCC--SS------------SCCCEEEEEEESSHHHHHHHH
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcC--CC------------CCcceEEEEecccchhHHHHH
Confidence            467999999999999999   6789999999999998765322  11            125699999999999999999


Q ss_pred             -HhcCceeCCeEEEEe
Q 016231          302 -AFNMAVIGGNHIRLD  316 (393)
Q Consensus       302 -~lng~~~~Gr~I~V~  316 (393)
                       .|||..|.|+.|+|.
T Consensus        74 ~~lng~~~~gr~lkvS   89 (89)
T d2cpia1          74 QCVNNVVVDGRTLKAS   89 (89)
T ss_dssp             HHHTTEEETTEEEEEE
T ss_pred             HHhCCCEECCEEEEEC
Confidence             699999999999984

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.63  E-value=4.2e-16  Score=121.73  Aligned_cols=77  Identities=23%  Similarity=0.269  Sum_probs=67.4

Q ss_pred             CCCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          221 EGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       221 ~~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      +..+++||||+|||+++|+++|..+|+.||.|..|++++.                      .+|||||+|.+.++|..|
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~----------------------~~g~afV~f~~~~~A~~A   61 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN----------------------RHDIAFVEFTTELQSNAA   61 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT----------------------TCSCEEEEESSHHHHHHH
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc----------------------cceeEEEecCCHHHHHHH
Confidence            3455799999999999999999999999999999998321                      348999999999999999


Q ss_pred             H-HhcCcee-CCeEEEEeecC
Q 016231          301 L-AFNMAVI-GGNHIRLDRAC  319 (393)
Q Consensus       301 l-~lng~~~-~Gr~I~V~~a~  319 (393)
                      + .|||..| .|+.|.|.|+.
T Consensus        62 ~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1          62 KEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             HHHHTTCBSSTTCBCEEEECC
T ss_pred             HHHhCCcEeCCCcEEEEEEec
Confidence            9 6999888 56899999984

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=8.3e-16  Score=125.02  Aligned_cols=82  Identities=17%  Similarity=0.189  Sum_probs=69.7

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHh
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~l  303 (393)
                      ...+|||+|||+++|+++|++||..||.|..+.++...  .               .+.++|||||+|.+.++|++||.+
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~--~---------------~~~~kG~afV~F~~~e~a~~a~~~   76 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD--F---------------QGRSTGEAFVQFASQEIAEKALKK   76 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC--S---------------SSCBCSEEEEEESSHHHHHHHHTT
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeC--C---------------CCCcceEEEEEeCCHHHHHHHHhh
Confidence            35679999999999999999999999988775554322  1               223669999999999999999999


Q ss_pred             cCceeCCeEEEEeecCCCc
Q 016231          304 NMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~~  322 (393)
                      |+..|.||.|.|.++.+..
T Consensus        77 ~~~~i~gR~i~V~~~~~~~   95 (104)
T d1wg5a_          77 HKERIGHRYIEIFKSSRAE   95 (104)
T ss_dssp             TTCCSSSSCCEEEEECTTT
T ss_pred             CCCEEcceEEEEEECCHHH
Confidence            9999999999999997654

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=3.2e-16  Score=121.76  Aligned_cols=74  Identities=15%  Similarity=0.190  Sum_probs=65.3

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hhc
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~ln  304 (393)
                      .+|||||||+++|+++|+.+|++||.|.++++..                       ++|||||+|.+.++|..|+ .||
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~-----------------------~rg~aFV~f~~~~~A~~Ai~~ln   58 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-----------------------KSGYAFVDYPDQNWAIRAIETLS   58 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-----------------------ETTEEEECCSCHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec-----------------------ccceEEEEECCHHHHHHHHHHhC
Confidence            3699999999999999999999999987766633                       3489999999999999999 699


Q ss_pred             Cc-eeCCeEEEEeecCCCc
Q 016231          305 MA-VIGGNHIRLDRACPPR  322 (393)
Q Consensus       305 g~-~~~Gr~I~V~~a~~~~  322 (393)
                      |. .|.|+.|.|.++.+..
T Consensus        59 g~~~~~G~~i~V~~a~~k~   77 (80)
T d2cqha1          59 GKVELHGKIMEVDYSVSKK   77 (80)
T ss_dssp             TTCEETTEECEEEECCCCC
T ss_pred             CCeEECCEEEEEEEcCCcC
Confidence            86 6999999999998653

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=4.8e-16  Score=126.02  Aligned_cols=81  Identities=11%  Similarity=0.125  Sum_probs=67.7

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      ....+|||+|||+++|+++|+++|..||.|..+.++...  .               .+.++|||||+|.+.++|+.||.
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~--~---------------~g~~~G~afV~F~s~~~a~~Al~   68 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVD--N---------------NGQGLGQALVQFKNEDDARKSER   68 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCC--T---------------TSSCSSCEEEECSSHHHHHHHGG
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeC--C---------------CCCcCccEEEEECCHHHHHHHHh
Confidence            345779999999999999999999999988764332211  1               23467999999999999999999


Q ss_pred             hcCceeCCeEEEEeecCC
Q 016231          303 FNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~  320 (393)
                      +|+..|.|+.|.|.++..
T Consensus        69 ~n~~~i~gr~i~V~~~~~   86 (103)
T d2cpya1          69 LHRKKLNGREAFVHVVTL   86 (103)
T ss_dssp             GCSEEETTEEEEEEEECH
T ss_pred             cCCCeECCcEEEEEECCH
Confidence            999999999999998753

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=4.1e-16  Score=123.89  Aligned_cols=78  Identities=27%  Similarity=0.356  Sum_probs=67.6

Q ss_pred             CcccEEEEeCCCccCCHHHHHH----HhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIK----EFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE  298 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~----~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~  298 (393)
                      ++++||||+|||+.+++++|++    +|+.||.|.+|++...                    +.++|||||+|.+.++|.
T Consensus         1 ~P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~--------------------~~~~g~afV~F~~~~~A~   60 (91)
T d1nu4a_           1 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS--------------------LKMRGQAFVIFKEVSSAT   60 (91)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHH--------------------HHHTTCEEEEESSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeee--------------------ccCCCceEEEECCHHHHH
Confidence            3579999999999999998864    6899999999887321                    125699999999999999


Q ss_pred             HHH-HhcCceeCCeEEEEeecCC
Q 016231          299 AAL-AFNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       299 ~Al-~lng~~~~Gr~I~V~~a~~  320 (393)
                      .|+ .+|+..|.|+.|+|.++..
T Consensus        61 ~A~~~~~~~~~~g~~l~v~~ak~   83 (91)
T d1nu4a_          61 NALRSMQGFPFYDKPMRIQYAKT   83 (91)
T ss_dssp             HHHHHHTTCEETTEECEEEECSS
T ss_pred             HHHHHhCCCEECCEEEEEEEeCC
Confidence            999 6999999999999999964

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=7.1e-16  Score=123.55  Aligned_cols=82  Identities=20%  Similarity=0.323  Sum_probs=68.2

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCC-eeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGE-IDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~-I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      +|+|||||||.++|+++|+++|+.||+ |.+|+|+.++.                ..+.++|||||+|.+.++|..|+ .
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~----------------~~~~~rg~aFV~F~~~~~A~~Ai~~   64 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAA----------------DKMKNRGFAFVEYESHRAAAMARRK   64 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSC----------------TTTTTCCEEEEEESSHHHHHHHHTT
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeecc----------------ccccCCCeEEEEEcCHHHHHHHHHH
Confidence            368999999999999999999999996 88898865431                12347799999999999999999 5


Q ss_pred             hcC--ceeCCeEEEEeecCCCc
Q 016231          303 FNM--AVIGGNHIRLDRACPPR  322 (393)
Q Consensus       303 lng--~~~~Gr~I~V~~a~~~~  322 (393)
                      |++  ..+.|+.|.|.||.+..
T Consensus        65 l~~~~~~~~g~~i~V~~A~p~~   86 (96)
T d2disa1          65 LMPGRIQLWGHQIAVDWAEPEI   86 (96)
T ss_dssp             TTTCCSCBTTBCCEEEESCSSC
T ss_pred             HcCCCeEECCEEEEEEEcCCCC
Confidence            754  45679999999997643

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.2e-15  Score=124.33  Aligned_cols=75  Identities=20%  Similarity=0.293  Sum_probs=67.1

Q ss_pred             ccEEEEeCCCc-cCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          225 LRTIFVGNLPL-KVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       225 ~rtVFVgNLp~-~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      +++|||+|||+ .+|+++|+++|+.||.|..|.|+++                      .+|||||+|.+.++|..|| .
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~----------------------~kg~afV~f~~~~~A~~ai~~   59 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----------------------KKENALVQMADGNQAQLAMSH   59 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCT----------------------TSCCEEEEESCHHHHHHHHHH
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEec----------------------ccceEEEEECCHHHHHHHHHH
Confidence            57999999965 5999999999999999999999542                      2389999999999999999 7


Q ss_pred             hcCceeCCeEEEEeecCCC
Q 016231          303 FNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~  321 (393)
                      ||+..|.|+.|.|.++...
T Consensus        60 lng~~l~g~~l~v~~s~~~   78 (109)
T d2adca1          60 LNGHKLHGKPIRITLSKHQ   78 (109)
T ss_dssp             HTTCBCSSSBCEEECCSCC
T ss_pred             hCCCEECCEEEEEEECCCC
Confidence            9999999999999998644

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.60  E-value=1.4e-15  Score=119.21  Aligned_cols=77  Identities=21%  Similarity=0.283  Sum_probs=65.1

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEE-EEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSV-RIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sV-ri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      ...+|||+|||+++++++|+++|+.||.|... .+..+.                  ++.++|||||+|.+.++|..|| 
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~------------------~g~~~G~afV~f~~~e~a~~Ai~   69 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE------------------KGMPTGEAMVAFESRDEATAAVI   69 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECS------------------SSCEEEEEEEEESCHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCC------------------CCCcceEEEEEEcCcHHHHHHHH
Confidence            35679999999999999999999999998653 342221                  2346799999999999999999 


Q ss_pred             HhcCceeCCeEEEEeec
Q 016231          302 AFNMAVIGGNHIRLDRA  318 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a  318 (393)
                      .||+..|.||+|+|.++
T Consensus        70 ~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1          70 DLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             HTTTCEETTEECEEEES
T ss_pred             HcCCCEECCEEEEEEEC
Confidence            69999999999999864

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=1.1e-15  Score=118.32  Aligned_cols=73  Identities=16%  Similarity=0.272  Sum_probs=66.0

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      +..+||||+|||  +|+++|+++|++||.|.+|++..                       ++|||||+|.+.++|..|+ 
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~-----------------------~~~~afV~f~~~~~A~~Ai~   57 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDP-----------------------PRNCAFVTYEKMESADQAVA   57 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEET-----------------------TTTEEEEECSSHHHHHHHHH
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeecc-----------------------CCCEEEEEEcccHHHHHHHH
Confidence            457899999996  89999999999999999998832                       3489999999999999999 


Q ss_pred             HhcCceeCCeEEEEeecCC
Q 016231          302 AFNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       302 ~lng~~~~Gr~I~V~~a~~  320 (393)
                      .||+..|.|+.|+|.++.+
T Consensus        58 ~lng~~~~g~~l~V~~a~~   76 (79)
T d2bz2a1          58 ELNGTQVESVQLKVNIARK   76 (79)
T ss_dssp             HHTTCBCSSCBCEEEECCS
T ss_pred             HhCCCEECCEEEEEEEecC
Confidence            7999999999999999964

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=3.1e-15  Score=117.85  Aligned_cols=77  Identities=14%  Similarity=0.253  Sum_probs=68.2

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ..++++|||+|||+++++++|+++|+.||.|.+|++..                       ++|||||+|.+.++|..|+
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~-----------------------~~~~afV~f~~~e~A~~a~   61 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK-----------------------GKNQAFLELATEEAAITMV   61 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEET-----------------------TTTEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccc-----------------------cceEEEEEeCCHHHHHHHH
Confidence            45689999999999999999999999999999998843                       3479999999999999998


Q ss_pred             H---hcCceeCCeEEEEeecCCC
Q 016231          302 A---FNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 ~---lng~~~~Gr~I~V~~a~~~  321 (393)
                      .   +++..+.|+.|+|.++...
T Consensus        62 ~~~~~~~~~~~g~~l~v~~sk~~   84 (88)
T d2cq1a1          62 NYYSAVTPHLRNQPIYIQYSNHK   84 (88)
T ss_dssp             HHHHHSCCEETTEECEEEECSCS
T ss_pred             HHHccCCCccCCCEEEEEECCCC
Confidence            3   4678999999999999654

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=2.8e-15  Score=122.65  Aligned_cols=78  Identities=21%  Similarity=0.214  Sum_probs=68.8

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ...+|||+|||+.+|+++|+++|+.||.|..|.|++.+                     ++|||||+|.+.++|+.|| .
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~---------------------~~g~aFV~f~~~e~A~~Ai~~   64 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---------------------NQFQALLQYADPVSAQHAKLS   64 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET---------------------TEEEEEEEESCHHHHHHHHHH
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC---------------------CCCeEEEEECCHHHHHHHHHH
Confidence            45789999999999999999999999999999986542                     4589999999999999999 7


Q ss_pred             hcCcee--CCeEEEEeecCCCc
Q 016231          303 FNMAVI--GGNHIRLDRACPPR  322 (393)
Q Consensus       303 lng~~~--~Gr~I~V~~a~~~~  322 (393)
                      ||+..|  .|+.|.|.++.+..
T Consensus        65 ln~~~l~~~~~~l~v~~s~~~~   86 (108)
T d2adba1          65 LDGQNIYNACCTLRIDFSKLTS   86 (108)
T ss_dssp             HHSCCSSTTCCCCEEEECSSCS
T ss_pred             HCCCEeccCCcEEEEEecCCcc
Confidence            999988  57899999986543

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=8e-16  Score=116.66  Aligned_cols=70  Identities=17%  Similarity=0.254  Sum_probs=62.0

Q ss_pred             EEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-HhcCc
Q 016231          228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMA  306 (393)
Q Consensus       228 VFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~lng~  306 (393)
                      |||+|||+++|+++|+++|+.||.|..+++.+++  .+               +.++|||||+|.+.++|+.|+ .|||.
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~--~~---------------~~~~g~afV~f~~~~~A~~Ai~~lng~   63 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDK--TT---------------NKCKGYGFVDFDSPSAAQKAVTALKAS   63 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCS--SS---------------CSCCSEEEEEESCHHHHHHHHHHHHHH
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhcccccccccccc--cc---------------ccccceeEEEECCHHHHHHHHHHhCCC
Confidence            8999999999999999999999999999986654  22               236699999999999999999 79999


Q ss_pred             eeCCeEEE
Q 016231          307 VIGGNHIR  314 (393)
Q Consensus       307 ~~~Gr~I~  314 (393)
                      .|.|+.|+
T Consensus        64 ~~~Gr~~k   71 (72)
T d1x4ea1          64 GVQAQMAK   71 (72)
T ss_dssp             TCCEESCC
T ss_pred             EECCEECc
Confidence            99998763

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=5.8e-16  Score=122.06  Aligned_cols=69  Identities=10%  Similarity=0.098  Sum_probs=63.4

Q ss_pred             EEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-HhcC
Q 016231          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNM  305 (393)
Q Consensus       227 tVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~lng  305 (393)
                      +|||+|||+++++++|+++|+.||.|.+|+|++                        .|||||+|.+.++|+.|| .|||
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~------------------------~g~afV~f~~~~~a~~Ai~~l~g   57 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR------------------------DGTGVVEFVRKEDMTYAVRKLDN   57 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT------------------------TSEEEEEESSHHHHHHHHHHHTT
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhcccccccccc------------------------cceeeEEeCCHHHHHHHHHHhCC
Confidence            599999999999999999999999999998832                        279999999999999999 7999


Q ss_pred             ceeCCeEEEEeecC
Q 016231          306 AVIGGNHIRLDRAC  319 (393)
Q Consensus       306 ~~~~Gr~I~V~~a~  319 (393)
                      ..|.|+.|.|.++.
T Consensus        58 ~~~~g~~i~v~~~~   71 (87)
T d3begb1          58 TKFRSHEGETAYIR   71 (87)
T ss_dssp             CBCCCTTSCCCBCE
T ss_pred             CEECCcEeEEeEEe
Confidence            99999999988764

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=1.5e-15  Score=125.17  Aligned_cols=80  Identities=16%  Similarity=0.277  Sum_probs=67.9

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHh
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAF  303 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~l  303 (393)
                      ..++|||+|||+++|+++|.+||+.||.|..+.++...  .               .+.++|||||+|.+.++|++||.+
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~--~---------------~g~~~G~afVeF~~~e~a~~al~~   79 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYG--P---------------NGKATGEGFVEFRNEADYKAALCR   79 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEEC--T---------------TSSEEEEEEEEBSSSHHHHHHHTS
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecC--c---------------ccceeeEEEEEECCHHHHHHHHHc
Confidence            46799999999999999999999999988654443322  1               234669999999999999999999


Q ss_pred             cCceeCCeEEEEeecCC
Q 016231          304 NMAVIGGNHIRLDRACP  320 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~  320 (393)
                      |+..|+||.|.|..+.+
T Consensus        80 ~~~~i~gR~i~V~~~~~   96 (112)
T d1wela1          80 HKQYMGNRFIQVHPITK   96 (112)
T ss_dssp             CSBCSTTSCBEEEEECH
T ss_pred             CCCcCCCEEEEEEEcCh
Confidence            99999999999988753

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=6.1e-15  Score=116.51  Aligned_cols=73  Identities=12%  Similarity=0.205  Sum_probs=63.1

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hh
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AF  303 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~l  303 (393)
                      +.+|||+|||+++++++|+++|..||. ..+.+.                       .++|||||+|.+.++|+.|+ .|
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G~-~~~~~~-----------------------~~kg~afV~f~~~~~A~~Ai~~l   60 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYDL-KYCYVD-----------------------RNKRTAFVTLLNGEQAQNAIQMF   60 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSCC-CCEEEE-----------------------GGGTEEEECCSCHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcCc-eeeeee-----------------------ccCCceEEEECCHHHHHHHHHHh
Confidence            578999999999999999999999993 323331                       14589999999999999999 79


Q ss_pred             cCceeCCeEEEEeecCCC
Q 016231          304 NMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       304 ng~~~~Gr~I~V~~a~~~  321 (393)
                      |+..|.|+.|.|.++...
T Consensus        61 n~~~~~G~~l~V~~a~~~   78 (88)
T d1wg1a_          61 HQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             TTEEETTEEEEEEECCCC
T ss_pred             CCCEECCEEEEEEEcCCC
Confidence            999999999999998543

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.55  E-value=8.7e-15  Score=112.27  Aligned_cols=69  Identities=13%  Similarity=0.249  Sum_probs=61.0

Q ss_pred             EEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-HhcCc
Q 016231          228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMA  306 (393)
Q Consensus       228 VFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~lng~  306 (393)
                      |||+|||+++++++|+++|++|| +..+.+.                       .++|||||+|.+.++|..|+ .||+.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~-----------------------~~~g~afv~f~~~~~A~~Ai~~ln~~   56 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD-----------------------KYKGTAFVTLLNGEQAEAAINTFHQS   56 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE-----------------------TTTTEEEEEESSHHHHHHHHHHHTTE
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec-----------------------ccceeEEEEECCHHHHHHHHHHhCCc
Confidence            79999999999999999999999 4444441                       25589999999999999999 79999


Q ss_pred             eeCCeEEEEeecCC
Q 016231          307 VIGGNHIRLDRACP  320 (393)
Q Consensus       307 ~~~Gr~I~V~~a~~  320 (393)
                      .+.|+.|.|.++..
T Consensus        57 ~~~g~~l~V~~a~~   70 (75)
T d1wi6a1          57 RLRERELSVQLQPT   70 (75)
T ss_dssp             ESSSCEEEEEECCS
T ss_pred             cCCCCEEEEEEeCC
Confidence            99999999999853

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.54  E-value=6.7e-15  Score=118.15  Aligned_cols=75  Identities=27%  Similarity=0.414  Sum_probs=67.1

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-  301 (393)
                      .++++|||+|||+++++++|+++|+.||.|..|++.+                       ++|||||+|.+.++|..|+ 
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~-----------------------~~~~afV~f~~~~~A~~A~~   71 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK-----------------------GDSFAYIQYESLDAAQAACA   71 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECS-----------------------SSCCEEEEESSHHHHHHHHH
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeec-----------------------cccEEEeccCCHHHHHHHHH
Confidence            4579999999999999999999999999999998832                       3479999999999999999 


Q ss_pred             HhcCceeCC--eEEEEeecCC
Q 016231          302 AFNMAVIGG--NHIRLDRACP  320 (393)
Q Consensus       302 ~lng~~~~G--r~I~V~~a~~  320 (393)
                      .||+..|.|  ++|+|.++.+
T Consensus        72 ~l~~~~i~g~~~~l~v~~ak~   92 (97)
T d1whya_          72 KMRGFPLGGPDRRLRVDFAKS   92 (97)
T ss_dssp             HHTTCBCSSSSCBCEEEECCC
T ss_pred             HhCCCEeCCCceEEEEEeCCC
Confidence            799999976  5899999864

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.54  E-value=4.7e-15  Score=119.60  Aligned_cols=73  Identities=11%  Similarity=0.083  Sum_probs=66.5

Q ss_pred             cccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-H
Q 016231          224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-A  302 (393)
Q Consensus       224 ~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~  302 (393)
                      ..++|||+|||+.+++++|+++|+.||.|..|.|.+                        +|||||+|.+.++|+.|| .
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~------------------------~g~afV~f~~~~~a~~Ai~~   69 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK------------------------DGMGMVEYLRKEDMEYALRK   69 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET------------------------TTEEEEEESSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc------------------------cceEEEEECCHHHHHHHHHH
Confidence            467899999999999999999999999999998732                        279999999999999999 7


Q ss_pred             hcCceeCCeEEEEeecCC
Q 016231          303 FNMAVIGGNHIRLDRACP  320 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~  320 (393)
                      ||+..|.|+.|.|.++..
T Consensus        70 lng~~~~g~~i~v~~~~~   87 (98)
T d1wg4a_          70 LDDTKFRSHEGETSYIRV   87 (98)
T ss_dssp             HSSEEEECTTSCEEEEEE
T ss_pred             hCCCEeCCeEEEEEEEec
Confidence            999999999999998753

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.52  E-value=1e-14  Score=117.71  Aligned_cols=77  Identities=18%  Similarity=0.254  Sum_probs=67.5

Q ss_pred             CCcccEEEEeCCCcc-CCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLK-VKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAA  300 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~-~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~A  300 (393)
                      ...+++|||+|||.. +|+++|..+|+.||.|.+|++++                       ++|||||+|.+.++|..|
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~-----------------------~k~~afV~f~~~~~A~~A   71 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR-----------------------MKSQAFIEMETREDAMAM   71 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET-----------------------TTTEEEEECSSHHHHHHH
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEee-----------------------cCCcEEEEecchHHHHHH
Confidence            445789999999985 89999999999999999999843                       347999999999999999


Q ss_pred             HH---hcCceeCCeEEEEeecCCC
Q 016231          301 LA---FNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       301 l~---lng~~~~Gr~I~V~~a~~~  321 (393)
                      +.   +++..|.|+.|.|.++...
T Consensus        72 i~~~~~~~~~~~gr~l~V~~s~~~   95 (99)
T d1x4fa1          72 VDHCLKKALWFQGRCVKVDLSEKY   95 (99)
T ss_dssp             HHHHHHSCCCSSSSCCEEEEECSC
T ss_pred             HHHHhcCCceECCEEEEEEEcCCc
Confidence            83   7888999999999998643

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.51  E-value=4.4e-14  Score=114.72  Aligned_cols=77  Identities=18%  Similarity=0.183  Sum_probs=67.3

Q ss_pred             CCcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          222 GKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       222 ~~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ..++++|||+|||+.+|+++|..+|+.||.|..|+|.+                       .+|||||+|.+.++|..||
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~-----------------------~k~~AfV~f~~~e~A~~ai   68 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-----------------------FKRQALVEFENIDSAKECV   68 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET-----------------------TTTEEEEEESSHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEe-----------------------cceeEEEEeCCHHHHHHHH
Confidence            34589999999999999999999999999999998832                       3479999999999999999


Q ss_pred             -Hh--cCceeCCeEEEEeecCCC
Q 016231          302 -AF--NMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 -~l--ng~~~~Gr~I~V~~a~~~  321 (393)
                       .+  ++..+.|+.|.|.++...
T Consensus        69 ~~~~~~~~~~~g~~l~v~~s~~~   91 (104)
T d1wexa_          69 TFAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             HHHHHSCCBSSSSBCEEEECSSS
T ss_pred             HHHcCCCcEEeeEEEEEEEcCCC
Confidence             45  566789999999999654

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=2e-16  Score=125.30  Aligned_cols=82  Identities=21%  Similarity=0.423  Sum_probs=67.0

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhcC
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNM  305 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~lng  305 (393)
                      |+|||||||+++|+++|+++|+.||.|..+.+......            .....+.++|||||+|.+.++|+.|+.|||
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~------------~~~~~~~~kg~afV~f~~~e~a~~a~~l~g   69 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPV------------LAVQINQDKNFAFLEFRSVDETTQAMAFDG   69 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSE------------EECCEETTTTEEEEEESSCTTTTTGGGGSS
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEecccee------------eecccCCCceEEEEEeCCHHHHHHHHhhCC
Confidence            78999999999999999999999998877665322100            011234578999999999999999999999


Q ss_pred             ceeCCeEEEEeecC
Q 016231          306 AVIGGNHIRLDRAC  319 (393)
Q Consensus       306 ~~~~Gr~I~V~~a~  319 (393)
                      ..|.|+.|.|.++.
T Consensus        70 ~~~~Gr~l~V~r~k   83 (90)
T d1u2fa_          70 IIFQGQSLKIRRPH   83 (90)
T ss_dssp             CCSSSSCCCCBCTT
T ss_pred             cEECCEEEEECCCC
Confidence            99999999998654

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=5.1e-14  Score=123.64  Aligned_cols=82  Identities=17%  Similarity=0.365  Sum_probs=72.3

Q ss_pred             CcccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          223 KLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      ...++|||+|||+.+|+++|+.+|+.||.|..|.|+.+.  .+               +.++|||||+|.+.++|..||.
T Consensus        95 ~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~--~~---------------~~~~g~~fV~f~~~e~A~~Al~  157 (183)
T d1u1qa_          95 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR--GS---------------GKKRGFAFVTFDDHDSVDKIVI  157 (183)
T ss_dssp             CCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT--TT---------------CCEEEEEEEEESCHHHHHHHHT
T ss_pred             cccceeEEccCCCcCCHHHHhhhhccCCceeeeeeeccc--cc---------------CccceeEEEEECCHHHHHHHHH
Confidence            346899999999999999999999999999999997754  22               2366999999999999999999


Q ss_pred             hcCceeCCeEEEEeecCCC
Q 016231          303 FNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~~~  321 (393)
                      +++..|.|+.|.|.+|.++
T Consensus       158 ~~~~~~~G~~i~V~~A~~k  176 (183)
T d1u1qa_         158 QKYHTVNGHNCEVRKALSK  176 (183)
T ss_dssp             SSCEEETTEEEEEEECCCH
T ss_pred             hCCCeECCEEEEEEecCCc
Confidence            8999999999999998654

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.47  E-value=5.8e-14  Score=111.14  Aligned_cols=76  Identities=17%  Similarity=0.207  Sum_probs=66.4

Q ss_pred             CcccEEEEeCCCcc-CCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH
Q 016231          223 KLLRTIFVGNLPLK-VKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL  301 (393)
Q Consensus       223 ~~~rtVFVgNLp~~-~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al  301 (393)
                      ..+++|||+|||.. +|+++|.++|+.||.|.+|.++.                       +++||||+|.+.++|..|+
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~-----------------------~k~~afV~f~~~~~A~~A~   62 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN-----------------------KINEAFIEMATTEDAQAAV   62 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECS-----------------------SSSCEEEEESSHHHHHHHH
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeec-----------------------cceEEEEEEcchhhHHHHH
Confidence            34799999999986 88999999999999999999843                       2369999999999999999


Q ss_pred             H---hcCceeCCeEEEEeecCCC
Q 016231          302 A---FNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       302 ~---lng~~~~Gr~I~V~~a~~~  321 (393)
                      .   +++..+.|++|.|.++...
T Consensus        63 ~~l~~~~~~~~gr~l~V~~s~~~   85 (89)
T d1x4da1          63 DYYTTTPALVFGKPVRVHLSQKY   85 (89)
T ss_dssp             HHHHHSCCEETTEECEEEEECCC
T ss_pred             HHHhhCCCccCCceEEEEECCCc
Confidence            3   4677899999999998643

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.43  E-value=7.3e-14  Score=110.81  Aligned_cols=55  Identities=20%  Similarity=0.378  Sum_probs=51.6

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...++|||+|||+++|+++|+++|+.|    |.|..|+|++|+.+|.++|||||+|.++
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~----G~i~~v~i~~d~~tg~srG~aFV~f~~~   60 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTF----GEVLMVQVKKDLKTGHSKGFGFVRFTEY   60 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGG----SCEEEEEEEECSSSCSEEEEEEEEESSH
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhh----cccceeeeccCCCCcccCCEEEEEECCH
Confidence            345799999999999999999999999    9999999999999999999999999864

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.41  E-value=1.5e-13  Score=111.86  Aligned_cols=76  Identities=12%  Similarity=0.031  Sum_probs=66.4

Q ss_pred             cccEEEEeCCCccC-C----HHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHH
Q 016231          224 LLRTIFVGNLPLKV-K----KKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTE  298 (393)
Q Consensus       224 ~~rtVFVgNLp~~~-t----ee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~  298 (393)
                      ...+|||+||+.++ +    +++|..+|+.||.|.++++++                       ++|||||+|.+.++|.
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k-----------------------~~~~afV~f~~~~~A~   60 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK-----------------------SFKRVRINFSNPLSAA   60 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET-----------------------TTTEEEEECSSTTHHH
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec-----------------------CCCEEEEEECCHHHHH
Confidence            36789999999986 3    367999999999999998832                       4579999999999999


Q ss_pred             HHH-HhcCceeCCeEEEEeecCCCc
Q 016231          299 AAL-AFNMAVIGGNHIRLDRACPPR  322 (393)
Q Consensus       299 ~Al-~lng~~~~Gr~I~V~~a~~~~  322 (393)
                      .|+ .|||..|.|+.|.|.++.+..
T Consensus        61 ~Ai~~lng~~~~g~~l~v~~a~~~~   85 (104)
T d1weya_          61 DARLRLHKTEFLGKEMKLYFAQTLH   85 (104)
T ss_dssp             HHHHTSTTSEETTEECEEECCCCSS
T ss_pred             HHHHHhcccccCCCEeEEeecccCC
Confidence            999 799999999999999997553

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.40  E-value=1.3e-13  Score=107.78  Aligned_cols=54  Identities=24%  Similarity=0.537  Sum_probs=51.0

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++|||+|||+++|+++|+++|+.|    |.|..|+|++|+.+|.++|||||+|.++
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~----G~i~~v~i~~d~~tg~~kG~afV~f~~~   58 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQW----GTLTDCVVMRDPNTKRSRGFGFVTYATV   58 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhh----ccccceeecccccCCCcccEEEEEEcCH
Confidence            34799999999999999999999999    9999999999999999999999999874

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=1e-13  Score=106.41  Aligned_cols=51  Identities=27%  Similarity=0.558  Sum_probs=49.0

Q ss_pred             eeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       338 tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +|||+|||+++|+++|+++|+.|    |.|..|+|++++.+|.++|||||+|.+.
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~----G~I~~v~i~~d~~t~~~rG~~FV~f~~~   51 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGF----GEVESIELPMDNKTNKRRGFCFITFKEE   51 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHH----SCEEEEECCCCTTTCCTTCCEEEEESSS
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHh----CCcccccccccccccccccEEEEEECCH
Confidence            59999999999999999999999    9999999999999999999999999874

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.37  E-value=2.1e-13  Score=104.24  Aligned_cols=51  Identities=24%  Similarity=0.527  Sum_probs=49.0

Q ss_pred             eeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       338 tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +|||+|||+++|+++|+++|+.|    |.|..|+|++++.+|.++|||||+|.++
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~----G~i~~~~i~~d~~t~~~kg~afV~f~~~   51 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKF----GEVVDCTLKLDPITGRSRGFGFVLFKES   51 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTT----SCEEEEECCCBTTTTBCCSEEEEEESSH
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhh----ccccccccccCCCCCCcCceEEEEECCH
Confidence            59999999999999999999999    9999999999999999999999999874

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.37  E-value=3.2e-13  Score=109.27  Aligned_cols=54  Identities=31%  Similarity=0.486  Sum_probs=51.0

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++|||+|||+++++++|+++|+.|    |.|.+|+|+++..+|.++|||||+|.+.
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~----G~V~~v~i~~d~~tg~~kG~afV~F~~~   70 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAV----GKVRDVRIISDRNSRRSKGIAYVEFCEI   70 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTT----SCEEEEEECCSCCSSSCCCCEEEEESCG
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCC----CeEEEEEeeecCCCccccceEEEEECCH
Confidence            35789999999999999999999999    9999999999999999999999999874

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.36  E-value=4.3e-13  Score=104.08  Aligned_cols=55  Identities=18%  Similarity=0.347  Sum_probs=51.7

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+.++|||+|||+.+|+++|+++|+.|    |.|.+|+|++++.+|.++|||||+|.+.
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~----G~i~~v~i~~~~~~~~~~g~afV~f~~~   61 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKY----GPIADVSIVYDQQSRRSRGFAFVYFENV   61 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTT----SCEEEEEEEECSSSSSEEEEEEEEESSH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHh----CCCccccccccccccccccceEEEECCH
Confidence            456899999999999999999999999    9999999999999999999999999874

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.36  E-value=3.5e-13  Score=104.03  Aligned_cols=51  Identities=31%  Similarity=0.526  Sum_probs=49.0

Q ss_pred             eeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       338 tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +|||+|||+.+|+++|+++|+.|    |.|.+|+|++|+.+|.++|||||+|.++
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~----G~i~~v~i~~d~~tg~~~g~aFV~f~~~   52 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPA----GPILSIRVCRDMITRRSLGYAYVNFQQP   52 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHh----CCEeEEEEEecccccCCCCceEEEECCH
Confidence            69999999999999999999999    9999999999999999999999999874

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.35  E-value=2e-13  Score=105.13  Aligned_cols=51  Identities=24%  Similarity=0.559  Sum_probs=49.3

Q ss_pred             eeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       338 tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +|||+|||+++|+++|+++|+.|    |.|..|+|++|+.+|.++|||||+|.++
T Consensus         2 klfV~nLp~~~te~~l~~~F~~~----G~i~~v~i~~d~~tg~~kG~aFV~f~~~   52 (77)
T d1uawa_           2 KMFIGGLSWQTTQEGLREYFGQF----GEVKECLVMRDPLTKRSRGFGFVTFMDQ   52 (77)
T ss_dssp             CEEEESCCSSCCSHHHHHHHTTT----SCCCCEEEECCCCSSSCSSEEEECCCCT
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHh----CCcceeeeecccCCCCccceEEEEECCH
Confidence            69999999999999999999999    9999999999999999999999999875

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.35  E-value=2e-13  Score=107.51  Aligned_cols=54  Identities=20%  Similarity=0.401  Sum_probs=51.1

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++|||+|||+++++++|+++|+.|    |.|.+|+|++|+.+|.++|||||+|.++
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~----G~i~~v~i~~d~~~~~~kg~afV~f~~~   57 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPF----GDITDIQIPLDYETEKHRGFAFVEFELA   57 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTT----SCCCCEECCCCSSSCCCSSEEEECCSSH
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhC----CeEEecccccccccccccceeEEEECCH
Confidence            45799999999999999999999999    9999999999999999999999999874

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=5.7e-13  Score=104.17  Aligned_cols=52  Identities=19%  Similarity=0.496  Sum_probs=49.7

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+|||+|||+.+|+++|+++|+.|    |.|..|+|++|+.+|.++|||||+|.++
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~----G~v~~v~i~~d~~tg~~rg~aFV~f~~~   53 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSF----GPLKAFNLVKDSATGLSKGYAFCEYVDI   53 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSS----SCEEEEEEECCCSSSCCCCEEEEEESSS
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhc----CccceEEeeccccccccceeEEEEECCH
Confidence            479999999999999999999999    9999999999999999999999999874

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.33  E-value=7.1e-13  Score=105.34  Aligned_cols=55  Identities=25%  Similarity=0.473  Sum_probs=51.7

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.+|||+|||+++|+++|+++|+.|    |.|.+|+|++++.+|.++|||||+|.++
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~----G~i~~v~i~~~~~~~~~kg~afV~f~~~   59 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKS----GDIKKIIMGLDKMKKTACGFCFVEYYSR   59 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHH----CCcceeccccccccccccceEEEEECCH
Confidence            456799999999999999999999999    9999999999999999999999999874

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.33  E-value=6.5e-13  Score=103.77  Aligned_cols=53  Identities=23%  Similarity=0.508  Sum_probs=50.1

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+|||+|||+.+|+++|+++|+.|    |.|..|+|++|+.+|.++|||||+|.++
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~----G~v~~v~i~~d~~~g~~kg~afV~f~~~   58 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQY----GRIITSRILVDQVTGVSRGVGFIRFDKR   58 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHh----CCccccccccccccccCCCeeEEEEcCH
Confidence            3579999999999999999999999    9999999999999999999999999874

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.33  E-value=7.7e-13  Score=103.15  Aligned_cols=53  Identities=23%  Similarity=0.496  Sum_probs=50.2

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .++|||+|||+++++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.++
T Consensus         6 ~t~lfV~nlp~~~te~~l~~~F~~~----G~i~~~~~~~d~~~g~~~g~afV~f~~~   58 (85)
T d1b7fa2           6 DTNLYVTNLPRTITDDQLDTIFGKY----GSIVQKNILRDKLTGRPRGVAFVRYNKR   58 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHTSS----SCEEEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhh----CCEeeeeeecccccccCceeEEEEECCH
Confidence            4679999999999999999999999    9999999999999999999999999874

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.33  E-value=4.8e-13  Score=103.35  Aligned_cols=52  Identities=29%  Similarity=0.565  Sum_probs=49.8

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ++|||+|||+++++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.++
T Consensus         3 t~l~V~nLp~~~t~~~l~~~F~~~----G~v~~~~i~~~~~~g~~~g~afV~f~~~   54 (82)
T d1b7fa1           3 TNLIVNYLPQDMTDRELYALFRAI----GPINTCRIMRDYKTGYSYGYAFVDFTSE   54 (82)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHHTT----SCEEEEECCEETTTTEECSEEEEEESSH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHh----CCcceeeeeeecccCCccccceEEECCH
Confidence            589999999999999999999999    9999999999999999999999999874

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.33  E-value=7.7e-13  Score=102.07  Aligned_cols=52  Identities=21%  Similarity=0.424  Sum_probs=49.6

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ++|||+|||+++++++|+++|+.|    |.|..|+|++++.+|.++|||||+|.++
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~----G~v~~v~i~~~~~~~~~~g~afv~f~~~   54 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSI----GEIESCKLVRDKITGQSLGYGFVNYIDP   54 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTT----SCEEEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHh----CCcccccceeeccCCCceeeEEEEECCH
Confidence            579999999999999999999999    9999999999999999999999999874

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.32  E-value=1e-12  Score=106.33  Aligned_cols=53  Identities=26%  Similarity=0.551  Sum_probs=50.3

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .++|||+|||+.+++++|+++|+.|    |.|.+|+|++++.+|.++|||||+|.+.
T Consensus        10 ~~~lfV~nLp~~~te~~l~~~F~~~----G~i~~v~i~~d~~tg~~kg~afV~f~~~   62 (103)
T d2cqda1          10 FTKIFVGGLPYHTTDASLRKYFEGF----GDIEEAVVITDRQTGKSRGYGFVTMADR   62 (103)
T ss_dssp             SSEEEEECCCSSCCHHHHHHHHHTT----SCEEEEEESCCSSSCCCCSEEEEEESSH
T ss_pred             CcEEEEeCCCCcCcHHHHHHHHhhc----ccccceeccccccccccCCeEEEEECCH
Confidence            4679999999999999999999999    9999999999999999999999999874

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.32  E-value=6.7e-13  Score=107.78  Aligned_cols=53  Identities=21%  Similarity=0.526  Sum_probs=50.5

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .++|||+|||+++++++|+++|..|    |.|..|.|++|+.++.++|||||+|.++
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~----G~i~~~~i~~d~~~~~~kg~aFV~f~~~   72 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQW----GKLTDCVVMRDPASKRSRGFGFVTFSSM   72 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSS----CCCSEEEEECCTTTSSCCSEEEEECSSH
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhh----CcccceeecccccCCCccCeEEEEECCH
Confidence            4799999999999999999999999    9999999999999999999999999874

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.32  E-value=1e-12  Score=103.27  Aligned_cols=54  Identities=20%  Similarity=0.380  Sum_probs=50.7

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++|||+|||+.+++++|+++|+.|    |.|.+|+|++|+.+|.++|||||+|.+.
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~----G~i~~v~i~~d~~tg~~~g~afV~f~~~   59 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDY----GEIKNIHLNLDRRTGFSKGYALVEYETH   59 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEEEECTTTSSEEEEEEEEESSH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHc----CCcccccccccccccccccceeEEECCH
Confidence            45799999999999999999999999    9999999999999999999999999874

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.31  E-value=1.2e-12  Score=104.88  Aligned_cols=55  Identities=22%  Similarity=0.367  Sum_probs=51.2

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ....+|||+|||+.+++++|+++|..|    |.|..|+|++|+.+|.++|||||+|.+.
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~----g~v~~v~i~~d~~tg~~~g~afV~f~~~   60 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAY----GPLSELHYPIDSLTKKPKGFAFVTFMFP   60 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTT----SCEEEEECCCCTTTCCCCSEEEEEESSH
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhc----CCceeeeecccccccccCcceEEEECCH
Confidence            345789999999999999999999999    9999999999999999999999999864

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.31  E-value=1.1e-12  Score=100.53  Aligned_cols=53  Identities=21%  Similarity=0.453  Sum_probs=50.3

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .++|||+|||+++|+++|+++|+.|    |.|..+.++.++.++.++|||||+|.++
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~----G~i~~~~~~~~~~~~~~~g~afV~f~~~   54 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQY----GKIEVIEIMTDRGSGKKRGFAFVTFDDH   54 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTT----SCEEEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHh----ccccccccccCCCCcccccEEEEEEcCH
Confidence            3689999999999999999999999    9999999999999999999999999864

>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=99.30  E-value=1.2e-12  Score=104.21  Aligned_cols=55  Identities=25%  Similarity=0.525  Sum_probs=50.3

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCC-CCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPH-MRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~-tg~~kGfaFVeF~t~  392 (393)
                      ....+|||+|||+++++++|+++|+.|    |.|.+|+|++++. +|.++|||||+|.+.
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~----G~i~~v~i~~~~~~~g~~rg~afV~f~~~   61 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTF----GELKTVRLPKKMTGTGAHRGFGFVDFITK   61 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTT----SCEEEEECCCCCSSSCSSCSEEEEEESSH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHh----CCceEEEEEeccccCCCcccEEEEEECCH
Confidence            456799999999999999999999999    9999999999864 899999999999874

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.30  E-value=2.5e-13  Score=110.57  Aligned_cols=74  Identities=15%  Similarity=0.219  Sum_probs=65.9

Q ss_pred             EEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-HhcC
Q 016231          227 TIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNM  305 (393)
Q Consensus       227 tVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~lng  305 (393)
                      .++|++++..+++++|.++|++||.|.+|+|+++.                  +++++|||||+|.+.++|..|+ .|||
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~------------------~~~~~G~~fV~f~~~~~A~~Ai~~lng   90 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL------------------GDHLVGNVYVKFRREEDAEKAVIDLNN   90 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS------------------SSSSEEEEEEEESCHHHHHHHHHHHTT
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC------------------CCCEeeEEEEEEechhHHHHHHHHHCC
Confidence            48889999999999999999999999999995432                  2346799999999999999999 7999


Q ss_pred             ceeCCeEEEEeec
Q 016231          306 AVIGGNHIRLDRA  318 (393)
Q Consensus       306 ~~~~Gr~I~V~~a  318 (393)
                      ..|.||.|.|.++
T Consensus        91 ~~~~gr~i~v~~s  103 (104)
T d1jmta_          91 RWFNGQPIHAELS  103 (104)
T ss_dssp             CEETTEECCEEEC
T ss_pred             CEECCEEEEEEEC
Confidence            9999999999875

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.30  E-value=2.9e-12  Score=99.71  Aligned_cols=72  Identities=17%  Similarity=0.179  Sum_probs=61.4

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHHhc
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFN  304 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~ln  304 (393)
                      .+.|||+|||++++++.| .+|++||.|.++++.+                       ++|||||.|.+.++|+.||.+|
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~-----------------------~~~~~fV~f~~~~~A~~Al~~n   59 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN-----------------------TGNWMHIRYQSKLQARKALSKD   59 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS-----------------------SSSEEEEEESSHHHHHHHHTTT
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC-----------------------CCCEEEEEEcccHHHHHHHhcC
Confidence            467999999999997655 5899999999998721                       3489999999999999999999


Q ss_pred             CceeCCeE-EEEeecCC
Q 016231          305 MAVIGGNH-IRLDRACP  320 (393)
Q Consensus       305 g~~~~Gr~-I~V~~a~~  320 (393)
                      |..|.|+. |.|.++..
T Consensus        60 G~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1          60 GRIFGESIMIGVKPCID   76 (81)
T ss_dssp             TCEETTTEECEEEECCC
T ss_pred             CCeECCcEEEEEEeCCC
Confidence            99999985 56877753

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.30  E-value=1.4e-12  Score=103.58  Aligned_cols=54  Identities=22%  Similarity=0.347  Sum_probs=50.9

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++|||+|||+.+|+++|+++|+.|    |.|.+|+|++++.+|.++|||||+|.++
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~----G~v~~v~~~~d~~tg~~kg~afV~f~~~   61 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQA----GPVVNTHMPKDRVTGQHQGYGFVEFLSE   61 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTT----SCEEEEECCBCSSSCSBCSCEEEEESSH
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHh----CCccccceeecccccccccceEEEECCH
Confidence            34799999999999999999999999    9999999999999999999999999864

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.29  E-value=1.3e-12  Score=103.05  Aligned_cols=55  Identities=25%  Similarity=0.446  Sum_probs=51.5

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ++..+|||+|||.++++++|+++|+.|    |.|..|+|++|+.+|.++|||||+|.+.
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~----G~v~~v~i~~d~~t~~~rg~afV~f~~~   60 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPF----GSISRIYLAKDKTTGQSKGFAFISFHRR   60 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTT----CCEEEEEEEECSSSCSEEEEEEEEESSH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHh----cccccccccccccccccccceeEEECCH
Confidence            356799999999999999999999999    9999999999999999999999999863

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.29  E-value=2e-12  Score=106.46  Aligned_cols=72  Identities=17%  Similarity=0.167  Sum_probs=60.8

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCH-HHHHHHH-H
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSE-QSTEAAL-A  302 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~-e~A~~Al-~  302 (393)
                      ...+||||||+.+|+++|+.+|+.||+|.+|+|++                       .+|||||.|.+. ++|..|+ .
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~-----------------------~kg~gfV~F~~~~~~A~~a~~~   67 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR-----------------------GAKEGIILFKEKAKEALGKAKD   67 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCT-----------------------TCSEEEEEESSCHHHHHHHHHH
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEec-----------------------CCceEEEEecCcHHHHHHHHHH
Confidence            45679999999999999999999999999999843                       348999999985 6787787 7


Q ss_pred             hcCceeCCeEEEEeecC
Q 016231          303 FNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       303 lng~~~~Gr~I~V~~a~  319 (393)
                      +|+..+.++.+.|.+..
T Consensus        68 ~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          68 ANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             TTTSCBCTTSSSEEEEE
T ss_pred             hcCCceecCceEEEEee
Confidence            99998887777776653

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.28  E-value=7.9e-13  Score=106.84  Aligned_cols=54  Identities=22%  Similarity=0.554  Sum_probs=50.7

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++|||+|||+++++++|+++|+.|    |.|.+|+|++++.+|.++|||||+|.+.
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~----G~i~~v~i~~~~~tg~~~g~afV~f~~~   60 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEV----GPVVSFRLVYDRETGKPKGYGFCEYQDQ   60 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTT----SCCSEEEEEEETTTTEEEEEEEEECSCH
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhcc----ccccccccccccceeccCCceEEEECCH
Confidence            34789999999999999999999999    9999999999999999999999999874

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.27  E-value=3e-12  Score=103.49  Aligned_cols=64  Identities=16%  Similarity=0.293  Sum_probs=55.8

Q ss_pred             CCcccEEEEeC--CCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHH
Q 016231          222 GKLLRTIFVGN--LPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEA  299 (393)
Q Consensus       222 ~~~~rtVFVgN--Lp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~  299 (393)
                      ..+.++|||+|  ||+++|+++|+.+|++||.|..|+++.                       ++|||||+|.+.++|..
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~-----------------------~k~~aFV~f~~~e~A~~   71 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----------------------NKPYSFARYRTTEESKR   71 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT-----------------------TCSCEEEEESSHHHHHH
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeecc-----------------------CccEEEEEECCHHHHHH
Confidence            44578899955  999999999999999999999988732                       34799999999999999


Q ss_pred             HH-HhcCcee
Q 016231          300 AL-AFNMAVI  308 (393)
Q Consensus       300 Al-~lng~~~  308 (393)
                      |+ .|||..+
T Consensus        72 A~~~lng~~i   81 (101)
T d2cq2a1          72 AYVTLNGKEV   81 (101)
T ss_dssp             HHHHTTTCEE
T ss_pred             HHHHhCCCCC
Confidence            99 7999876

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.26  E-value=2.8e-12  Score=101.94  Aligned_cols=55  Identities=35%  Similarity=0.572  Sum_probs=51.2

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...++|||+|||+++|+++|+++|..|    |.|..+.++.+..++.++|||||+|.+.
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~----G~v~~~~~~~~~~~~~~~g~afV~F~~~   60 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQF----GDLKYVRVVLHPDTEHSKGCAFAQFMTQ   60 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTT----SCEEEEECCBCSSSCCBCSEEEEEESSH
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhcc----ccceeeeeccccccccccceEEEEEcCH
Confidence            345799999999999999999999999    9999999999999999999999999864

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.26  E-value=9.1e-12  Score=100.16  Aligned_cols=79  Identities=18%  Similarity=0.281  Sum_probs=66.4

Q ss_pred             CCcccEEEEeCC--CccC---------CHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEe
Q 016231          222 GKLLRTIFVGNL--PLKV---------KKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIV  290 (393)
Q Consensus       222 ~~~~rtVFVgNL--p~~~---------tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVe  290 (393)
                      .+.+++|+|.||  |.++         .+++|+..|+.||.|..|.++..                     ..+|||||.
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~---------------------~~~G~~fV~   63 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR---------------------HPDGVASVS   63 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT---------------------CTTCEEEEE
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC---------------------CCccEEEEE
Confidence            356899999999  6543         24689999999999999987432                     145899999


Q ss_pred             eCCHHHHHHHH-HhcCceeCCeEEEEeecCCC
Q 016231          291 FKSEQSTEAAL-AFNMAVIGGNHIRLDRACPP  321 (393)
Q Consensus       291 F~s~e~A~~Al-~lng~~~~Gr~I~V~~a~~~  321 (393)
                      |.+.++|..|+ .|||..|.||.|.|.++.+.
T Consensus        64 f~~~e~A~~A~~~lng~~~~gr~i~v~~~~g~   95 (99)
T d2dita1          64 FRDPEEADYCIQTLDGRWFGGRQITAQAWDGT   95 (99)
T ss_dssp             CSCHHHHHHHHHHSTTCEETTEECEEEECCSC
T ss_pred             ECCHHHHHHHHHHhCCcEECCEEEEEEEeCCc
Confidence            99999999999 79999999999999998643

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.24  E-value=3.8e-12  Score=99.42  Aligned_cols=52  Identities=19%  Similarity=0.365  Sum_probs=48.5

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .++|||+|||+++|+++|+++|+.|    |.|..|+|+++. +|.++|||||+|.++
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~----G~v~~v~l~~~~-~~~~kG~afV~f~~~   57 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDK----GQVLNIQMRRTL-HKAFKGSIFVVFDSI   57 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTS----CCEEEEEEEECT-TCCEEEEEEEEESCH
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHh----cccccceeeeec-cCCcceEEEEEEcCH
Confidence            4799999999999999999999999    999999998884 899999999999874

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.24  E-value=2.7e-12  Score=100.83  Aligned_cols=54  Identities=24%  Similarity=0.530  Sum_probs=50.5

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++|||+|||+++++++|+++|..|    |.|..|.++++..+|.++|||||+|.++
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~----G~i~~~~~~~~~~~~~~~g~afV~f~~~   57 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKY----GQISEVVVVKDRETQRSRGFGFVTFENI   57 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHH----SCCCEEEECCCSSSCSCCSEEEEECSSH
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhcc----ccccceeeccccccccccceEEEEECCH
Confidence            35689999999999999999999999    9999999999999999999999999874

>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=99.24  E-value=4.3e-12  Score=102.39  Aligned_cols=55  Identities=18%  Similarity=0.396  Sum_probs=51.4

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+..+|||+|||+++++++|+++|+.|    |.|..|.++.++.+|.++|||||+|.++
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~----G~i~~~~~~~~~~~g~~kG~afV~f~~~   70 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPF----GNVVSAKVFIDKQTNLSKCFGFVSYDNP   70 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGG----SCCSEEEEEECSSSCSEEEEEEEECSSH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhh----ccccccceeeecccCCCccceEEEeCCH
Confidence            356789999999999999999999999    9999999999999999999999999874

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.24  E-value=2.7e-12  Score=108.87  Aligned_cols=55  Identities=24%  Similarity=0.523  Sum_probs=51.3

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...++|||+|||+++|+++|+++|+.|    |.|.+|+|++++.+|.++|||||+|.+.
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~----G~i~~v~i~~d~~t~~~rg~afV~f~~~   94 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERY----GPIESVKIVCDRETRQSRGYGFVKFQSG   94 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHH----SCEEEEEEEEETTTTEEEEEEEEEESSH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhh----ccccccccccccccccccceeeEEECCH
Confidence            345789999999999999999999999    9999999999999999999999999873

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.22  E-value=4.4e-12  Score=95.52  Aligned_cols=50  Identities=16%  Similarity=0.309  Sum_probs=48.2

Q ss_pred             eeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       339 LfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      |||+|||+++|+++|+++|..|    |.|..+++++++.++.++|||||+|.++
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~----G~v~~~~~~~~~~~~~~~g~afV~f~~~   50 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPY----GKIVSTKAILDKTTNKCKGYGFVDFDSP   50 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTT----SCEEEEEEECCSSSCSCCSEEEEEESCH
T ss_pred             CEEeCCCCcCCHHHHHHHHhhh----ccccccccccccccccccceeEEEECCH
Confidence            7999999999999999999999    9999999999999999999999999874

>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=99.21  E-value=6.3e-12  Score=96.46  Aligned_cols=50  Identities=28%  Similarity=0.428  Sum_probs=47.3

Q ss_pred             eeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       338 tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +|||+|||+++++++|+++|+.|    |.|..|+|++++ +|.++|||||+|.++
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~----G~v~~~~i~~~~-~g~~~g~afV~f~~~   51 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEF----GTLKKAAVHYDR-SGRSLGTADVHFERK   51 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHH----SCEEEEEESCSS-CCCSCCEEEEEESCH
T ss_pred             EEEEECCCCCCCHHHHHHHHHHh----CCCeEEEEEEee-ccccceeEEEEECCH
Confidence            69999999999999999999999    999999999995 899999999999874

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.20  E-value=4.1e-12  Score=96.15  Aligned_cols=51  Identities=20%  Similarity=0.443  Sum_probs=48.6

Q ss_pred             eeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       338 tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +|||+|||+++|+++|+++|+.|    |.|..+.+++++.+|.++|||||+|.++
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~----G~i~~~~~~~~~~~~~~~~~afV~F~~~   51 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQF----GKVDDAMLMFDKTTNRHRGFGFVTFESE   51 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTT----SCCSEECCBCCTTCTTSCCEEEEECSCH
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHh----CCcceeeeeeeccccccCceeEEEECCH
Confidence            59999999999999999999999    9999999999999999999999999874

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.19  E-value=5.4e-12  Score=98.07  Aligned_cols=50  Identities=18%  Similarity=0.486  Sum_probs=46.0

Q ss_pred             eeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCC---CCccEEEEEeeec
Q 016231          339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMR---VGKGIAYVLFKTR  392 (393)
Q Consensus       339 LfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg---~~kGfaFVeF~t~  392 (393)
                      |||+|||+++|+++|+++|+.|    |.|.+|.|++++.++   .++|||||+|.++
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~----G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~   53 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKV----GAIKSCTISKKKNKAGVLLSMGFGFVEYKKP   53 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTT----SCEEEEEEEEEECTTCCEEEEEEEEEEESSH
T ss_pred             CEEcCCCCCCCHHHHHHHHHHh----CCccccceecccccccccccceEEEEEECCH
Confidence            7999999999999999999999    999999999987665   4689999999874

>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=99.18  E-value=5.6e-12  Score=97.51  Aligned_cols=50  Identities=24%  Similarity=0.584  Sum_probs=46.3

Q ss_pred             eeeCCCCCCCCHHHHHHHhhcCCCCCCCeEE-EEEeecCCCCCCccEEEEEeeec
Q 016231          339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEA-VRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       339 LfVgNLp~~~teedL~e~F~~~~~~~G~I~~-VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      |||+|||+++|+++|+++|+.|    |.|.. ++|++++.+|.++|||||+|.+.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~----G~i~~~~~i~~~~~~g~~~g~afV~f~~~   51 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAF----GVILQTPKIMRDPDTGNSKGYAFINFASF   51 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTT----SCBSSCCEECCCTTTCSCCSEEEEEBSSH
T ss_pred             CEEcCCCCcCcHHHHHHHHHHh----CceeeeEEEEeeccccccCceEEEEECCH
Confidence            7999999999999999999999    88865 58999999999999999999874

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.17  E-value=1.5e-11  Score=96.72  Aligned_cols=52  Identities=27%  Similarity=0.446  Sum_probs=47.0

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +.++|||+|||+++|+++|+++|+.|    |.|..|+|+++..+  .+|||||+|.+.
T Consensus         7 ~~~tl~V~nLp~~~te~~l~~~F~~~----G~i~~v~i~~d~~~--~~~~afV~f~~~   58 (90)
T d2cqia1           7 QPRTLYVGNLSRDVTEVLILQLFSQI----GPCKSCKMITEHTS--NDPYCFVEFYEH   58 (90)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHH----SCEEEEEEECCCCS--SCCEEEEEESSH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhc----CCceeeeeecccCc--cceeeEEEECCH
Confidence            45799999999999999999999999    99999999999654  489999999863

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.16  E-value=8.3e-12  Score=96.10  Aligned_cols=52  Identities=15%  Similarity=0.270  Sum_probs=42.2

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+|||+|||+++|+++|+++|+.|    |.|..+.++.+..+|.++|||||+|.++
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~----G~v~~~~~~~~~~~~~~~g~afV~f~~~   53 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDI----NVVALSIRLPSLRFNTSRRFAYIDVTSK   53 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHT----TCCCCEEECC-------CCEEEEECSSH
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHh----CcEEeeeeecccccccccceeEEEECCH
Confidence            489999999999999999999999    9999998888888999999999999874

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.15  E-value=2.2e-11  Score=99.56  Aligned_cols=51  Identities=25%  Similarity=0.647  Sum_probs=46.2

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+++|||+|||..+++++|+++|+.|    |.|..|+|+.+   +.++|||||+|.+.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~----G~v~~i~~~~~---~~~kG~afV~f~~~   56 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKY----GPIRQIRVGNT---PETRGTAYVVYEDI   56 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTT----SCEEEEEEECS---TTTTTEEEEEESSH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhc----CCeEeeccccc---CCcCCeEEEEECCH
Confidence            46899999999999999999999999    99999999865   56799999999864

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.14  E-value=4.6e-11  Score=94.55  Aligned_cols=53  Identities=28%  Similarity=0.558  Sum_probs=47.6

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...++|||+|||+++++++|+++|+.|    |.|.+|+|+.+.  +.++|||||+|.++
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~----G~v~~v~~~~~~--~~~kg~afV~f~~~   61 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQF----GKILDVEIIFNE--RGSKGFGFVTFENS   61 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGT----SCEEEEEEECCT--TTTCCEEEEEESCH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhc----ceeeeccccccc--cCCcceeEEEECCH
Confidence            345789999999999999999999999    999999999986  34799999999874

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.13  E-value=1.1e-11  Score=96.92  Aligned_cols=53  Identities=15%  Similarity=0.380  Sum_probs=44.4

Q ss_pred             cceeeeCCCCCCCC-HHHHHHHhhcCCCCCCCeEEEEEeec-CCCCCCccEEEEEeeec
Q 016231          336 KKTVFVGNLPFDVK-DEEIYQLFCGLNDLESSVEAVRVIRH-PHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~~~t-eedL~e~F~~~~~~~G~I~~VrI~~d-~~tg~~kGfaFVeF~t~  392 (393)
                      .++|||+|||++++ +++|+++|+.|    |.|.+|+|+.+ ..+|.++|||||+|.+.
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~----G~i~~v~i~~~~~~~~~~kg~afV~f~~~   58 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGF----GSIEKINIPAGQKEHSFNNCCAFMVFENK   58 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGG----SCEEEEECCSCCC---CCCEEEEEEESSH
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhh----hhccceeeecccCCccccceeeeEEECCH
Confidence            57999999999986 56699999999    99999999875 46899999999999864

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.13  E-value=4e-11  Score=97.02  Aligned_cols=82  Identities=12%  Similarity=0.086  Sum_probs=66.9

Q ss_pred             CcccEEEEeCC--Ccc--------CCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeC
Q 016231          223 KLLRTIFVGNL--PLK--------VKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFK  292 (393)
Q Consensus       223 ~~~rtVFVgNL--p~~--------~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~  292 (393)
                      .+++.|.|.||  |..        ...++|++.|++||.|.+|.|++++..  ...             ...|+|||.|.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~--~~~-------------~~~g~vfV~f~   66 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDG--VEV-------------PGCGKIFVEFT   66 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTS--SSC-------------TTCCEEEEEES
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCC--Ccc-------------CCceEEEEEEC
Confidence            35789999999  433        345689999999999999999664421  111             25589999999


Q ss_pred             CHHHHHHHH-HhcCceeCCeEEEEeecC
Q 016231          293 SEQSTEAAL-AFNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       293 s~e~A~~Al-~lng~~~~Gr~I~V~~a~  319 (393)
                      +.++|..|+ .|||..|+||.|.|.++.
T Consensus        67 ~~e~A~~A~~~l~Gr~f~gR~v~v~f~~   94 (104)
T d1o0pa_          67 SVFDCQKAMQGLTGRKFANRVVVTKYCD   94 (104)
T ss_dssp             CHHHHHHHHHHHSSCCSSSSCCEEEEEC
T ss_pred             CHHHHHHHHHHHCCCEECCeEEEEEEcC
Confidence            999999999 799999999999999875

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.11  E-value=5.3e-11  Score=96.01  Aligned_cols=56  Identities=29%  Similarity=0.357  Sum_probs=49.6

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .....+|||+|||+++|+++|+++|..|    |.|..+.++.+..++.++|||||+|.++
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~----g~v~~~v~~~~~~~~~~kG~afV~F~~~   67 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGL----EIVPNGMTLPVDFQGRSTGEAFVQFASQ   67 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTC----CEEEEEEECCBCSSSCBCSEEEEEESSH
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhc----CCceEEEEEEeCCCCCcceEEEEEeCCH
Confidence            4455689999999999999999999999    8888877777778999999999999874

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.11  E-value=4e-11  Score=96.44  Aligned_cols=55  Identities=40%  Similarity=0.661  Sum_probs=48.4

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecC-CCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP-HMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~-~tg~~kGfaFVeF~t~  392 (393)
                      ..+..+|||+|||+++|+++|+++|+.|    | |..++++.+. .+|.++|||||+|.+.
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~----g-~~~~~~~~~~~~~g~~~g~afV~f~~~   67 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGL----N-ISAVRLPREPSNPERLKGFGYAEFEDL   67 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTS----C-EEEEECCBCSSCTTSBCSCEEEEESSH
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHh----c-cccceeeeeeccCCCcceeeeEEECCH
Confidence            4467899999999999999999999999    7 7788888776 4788999999999863

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.11  E-value=3.4e-11  Score=94.47  Aligned_cols=51  Identities=22%  Similarity=0.499  Sum_probs=46.2

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+|||+|||+++++++|+++|+.|    |.|..|+|+.+.  +.++|||||+|.+.
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~----G~v~~~~i~~~~--~~~kg~afV~f~~~   58 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAF----GNILSCKVVCDE--NGSKGYGFVHFETQ   58 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTT----SCEEEEEECCBT--TBCCSCEEEEESCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhc----CCceEEEEEeec--CCCcceeEEEECCH
Confidence            3579999999999999999999999    999999999985  44789999999874

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.10  E-value=3.9e-11  Score=96.38  Aligned_cols=53  Identities=15%  Similarity=0.464  Sum_probs=48.8

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++|||+|||+++++++|+++|+.|    |.|..++++.+ .++.++|||||+|.+.
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~----G~i~~~~~~~~-~~~~~~g~afV~f~~~   69 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPF----GQVISTRILRD-SSGTSRGVGFARMEST   69 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTT----SCEEEEEEEEC-SSSCEEEEEEEEESCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhc----ccccceeeecc-cccccccceeEEeCCH
Confidence            35789999999999999999999999    99999999998 5889999999999874

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.09  E-value=3.4e-11  Score=95.66  Aligned_cols=52  Identities=25%  Similarity=0.395  Sum_probs=47.2

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCC-eEEEEEeecC-CCCCCccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESS-VEAVRVIRHP-HMRVGKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~-I~~VrI~~d~-~tg~~kGfaFVeF~t~  392 (393)
                      .+|||+|||.++++++|+++|+.|    |. |..|+|++++ .+|.++|||||+|.+.
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~----g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~   55 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKV----TEGVLDVIVYASAADKMKNRGFAFVEYESH   55 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHH----STTEEEEECCSSSCTTTTTCCEEEEEESSH
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHh----CCcceEEEEeeeccccccCCCeEEEEEcCH
Confidence            379999999999999999999999    74 9999999986 4689999999999874

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.08  E-value=5.2e-11  Score=90.71  Aligned_cols=50  Identities=24%  Similarity=0.295  Sum_probs=45.2

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ++|||+|||+++++++|+++|..|    |.|..|+|+.++.  ..+|||||+|.++
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~----G~I~~v~~~~~~~--~~~~~afV~F~~~   50 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHC----GPIIHVDVADSLK--KNFRFARIEFARY   50 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGG----SCEEEEEEEECTT--SSSEEEEEEESSH
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcC----CceEEEEEEeecc--ccceEEEEEEcch
Confidence            489999999999999999999999    9999999999864  3568999999874

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.05  E-value=7.9e-11  Score=93.90  Aligned_cols=54  Identities=17%  Similarity=0.199  Sum_probs=48.4

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCe--------EEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSV--------EAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I--------~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++|||+|||+.+|+++|+++|..|    |.|        ..+.+.++..+|.++|||||+|.++
T Consensus         7 ~~~~i~V~nLp~~~te~~l~~~F~~~----G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~   68 (101)
T d2cpea1           7 DNSAIYVQGLNDSVTLDDLADFFKQC----GVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP   68 (101)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHTTT----SCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSH
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHHC----ceEEEeeecccceeEEeeccccccccceeeEEecCH
Confidence            45799999999999999999999999    776        4678888889999999999999874

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.04  E-value=5.4e-11  Score=97.37  Aligned_cols=56  Identities=21%  Similarity=0.353  Sum_probs=48.8

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .....+|||+|||+++|+++|+++|..|    |.|..+.++.+..+|.++|||||+|.+.
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~----g~~~~~~~~~~~~~g~~~G~afVeF~~~   70 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKL----DIVEDSIYIAYGPNGKATGEGFVEFRNE   70 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSS----CBCTTTCEEEECTTSSEEEEEEEEBSSS
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhc----cccccceeeecCcccceeeEEEEEECCH
Confidence            4456799999999999999999999999    8887766666667899999999999874

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.04  E-value=9.9e-12  Score=98.30  Aligned_cols=53  Identities=19%  Similarity=0.270  Sum_probs=48.3

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++|||+|||+++++++|+++|+.|    |.|..|+|+.+ .+|.++|||||+|.++
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~----G~i~~~~v~~~-~~g~~kg~afv~F~~~   64 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISEL----FAKNDLAVVDV-RTGTNRKFGYVDFESA   64 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHH----HHHHTCCCCEE-EEETTTTEEEEEESSH
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcC----CcEEEeeeeec-CCCCccEEeEEeeCCH
Confidence            45799999999999999999999999    99999998765 6899999999999874

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.04  E-value=1.2e-10  Score=90.01  Aligned_cols=51  Identities=25%  Similarity=0.440  Sum_probs=45.6

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..|+++|||+|||.++++++|+++|+.|    |.|..|+|+++     .+|||||+|.++
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~----G~i~~v~~~~~-----~~g~afV~f~~~   55 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQF----PGFKEVRLVPN-----RHDIAFVEFTTE   55 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTS----TTEEEEEECTT-----TCSCEEEEESSH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccC----ccEEEeeeecc-----cceeEEEecCCH
Confidence            3467899999999999999999999999    99999999865     378999999874

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.03  E-value=1.5e-11  Score=98.43  Aligned_cols=56  Identities=16%  Similarity=0.283  Sum_probs=51.7

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++++|||+|||.++++++|+++|+.|    |.|..+.++.+..+|.++|||||+|.++
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~l~~~f~~~----G~v~~~~~~~~~~~g~~~g~~fV~f~~~   70 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERDLVSLFARF----QEKKGPPIQFRMMTGRMRGQAFITFPNK   70 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHH----HHSSSSCCEEEEECSSSCSEEEEECSSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhc----cceeeEEeecccccccccccceEEeccH
Confidence            4467899999999999999999999999    8999999999888999999999999874

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.03  E-value=6.5e-11  Score=95.14  Aligned_cols=55  Identities=24%  Similarity=0.366  Sum_probs=46.8

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ....+|||+|||+++|+++|+++|..|    |.|..+.++.+..+|.++|||||+|.+.
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~----g~i~~~~~~~~~~~g~~~G~afV~F~s~   60 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGI----PVDENAVHVLVDNNGQGLGQALVQFKNE   60 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTS----CCCSTTEEECCCTTSSCSSCEEEECSSH
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhccc----ceEEEEEEEEeCCCCCcCccEEEEECCH
Confidence            345789999999999999999999999    8887654445547899999999999874

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.00  E-value=7.1e-11  Score=92.45  Aligned_cols=49  Identities=24%  Similarity=0.369  Sum_probs=43.7

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+++|||+|||+++|+++|+++|+.|    |.|..|+++.+     ++|||||+|.+.
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~----G~v~~v~~~~~-----~~gfafV~f~~~   52 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQY----GDVMDVFIPKP-----FRAFAFVTFADD   52 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTT----SCCCEEECCSS-----CCSCCEEECSCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHc----CCceEEEEeec-----cCceEEEEECCH
Confidence            46899999999999999999999999    99999987544     689999999863

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.00  E-value=1.6e-10  Score=92.81  Aligned_cols=53  Identities=26%  Similarity=0.372  Sum_probs=46.7

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ....+|||+|||+++|+++|+++|..|    | |..|+++.+. +|.++|||||+|.++
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~----~-~~~v~~~~~~-~g~~~G~afVeF~~~   65 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPL----N-PMRVHIEIGP-DGRVTGEADVEFATH   65 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSC----C-CSEEEEEESS-SSCEEEEEEEECSSS
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhcc----C-cceeeeEEec-CCcceEEEEEEECCH
Confidence            345799999999999999999999998    6 5588888885 689999999999875

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.00  E-value=7e-11  Score=92.84  Aligned_cols=53  Identities=23%  Similarity=0.298  Sum_probs=46.6

Q ss_pred             cceeeeCCCCCCCCHHHH---HHHhhcCCCCCCCeEEEEEeecCCCCCC---ccEEEEEeeec
Q 016231          336 KKTVFVGNLPFDVKDEEI---YQLFCGLNDLESSVEAVRVIRHPHMRVG---KGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL---~e~F~~~~~~~G~I~~VrI~~d~~tg~~---kGfaFVeF~t~  392 (393)
                      .++|||+|||+++++++|   .++|+.|    |.|..|.|++++.++.+   +|||||+|.++
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~----G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~   66 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKF----GKIHKVVINNSTSYAGSQGPSASAYVTYIRS   66 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTT----SCEEEEEEECCSSCCSSSCCCEEEEEEESSH
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhccc----CCceEEEEeeccCcCCCCCcceEEEEecccc
Confidence            468999999999999999   6679998    99999999999877654   49999999874

>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=98.97  E-value=3.7e-10  Score=89.43  Aligned_cols=53  Identities=25%  Similarity=0.484  Sum_probs=46.2

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+..+|||+|||+++++++|+++|..|    |.|..|.+..+   +.++|||||+|.+.
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~----G~v~~~~~~~~---~~~~g~afV~f~~~   63 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKY----GAIRDIDLKNR---RGGPPFAFVEFEDP   63 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGG----SCEEEEEECCS---SSSSCCEEEEESCH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcC----CceEEEEeccc---ccccceEEEEECCH
Confidence            3455689999999999999999999999    99999998655   45799999999874

>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=98.96  E-value=1.3e-10  Score=90.25  Aligned_cols=53  Identities=28%  Similarity=0.424  Sum_probs=45.1

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEE-EEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEA-VRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~-VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...+|||+|||+++++++|+++|..|    |.|.. +.+..+ .+|.++|||||+|.++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~----~~~~~~~~~~~~-~~g~~~G~afV~f~~~   61 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGY----QVIPGSVCLKYN-EKGMPTGEAMVAFESR   61 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTS----CCCTTTCEEEEC-SSSCEEEEEEEEESCH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhc----ccceeEEEEEeC-CCCCcceEEEEEEcCc
Confidence            45689999999999999999999999    77765 455555 6899999999999874

>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=98.96  E-value=3.9e-10  Score=87.96  Aligned_cols=50  Identities=18%  Similarity=0.282  Sum_probs=45.1

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..|+++|||+|||+++++++|+++|+.|    |.|..|++.++      +|||||+|.++
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~----G~i~~v~~~~~------~~~afV~f~~~   54 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPF----GKVTNILMLKG------KNQAFLELATE   54 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTT----SCEEEEEEETT------TTEEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcc----ccccccccccc------ceEEEEEeCCH
Confidence            4578999999999999999999999999    99999998755      58999999874

>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=98.95  E-value=2.9e-10  Score=92.13  Aligned_cols=51  Identities=16%  Similarity=0.184  Sum_probs=46.2

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+..+|||+|||+.+|+++|+++|+.|    |.|..|.|+++.    ++|||||+|.++
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~----G~i~~~~i~~~~----~~g~aFV~f~~~   55 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKF----GTVLKIITFTKN----NQFQALLQYADP   55 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTT----SCEEEEEEEEET----TEEEEEEEESCH
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccC----CcEEEEEEEeeC----CCCeEEEEECCH
Confidence            456899999999999999999999999    999999998874    589999999874

>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=98.93  E-value=3.9e-10  Score=89.76  Aligned_cols=48  Identities=27%  Similarity=0.483  Sum_probs=43.9

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...+|||+|||..+++++|+++|+.|    |.|.+|+|+++      +|||||+|.++
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~f----G~i~~v~i~~~------kg~afV~f~~~   64 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPF----GQIMEIRVFPE------KGYSFVRFSTH   64 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHH----SCEEEEEEETT------TTEEEEEESSH
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHh----CCceEEEEEec------ceEEEEEECCH
Confidence            34689999999999999999999999    99999999866      78999999874

>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=98.93  E-value=5.7e-10  Score=86.90  Aligned_cols=52  Identities=17%  Similarity=0.246  Sum_probs=44.7

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..|+++|||+|||+++++++|+++|+.|    |.|..+.+...    .++|||||+|.+.
T Consensus         7 ~pPs~tL~V~NLp~~~te~~l~~~F~~~----G~v~~~~~~~~----~~~~~afV~f~~~   58 (88)
T d2adca2           7 FPPSATLHLSNIPPSVSEEDLKVLFSSN----GGVVKGFKFFQ----KDRKMALIQMGSV   58 (88)
T ss_dssp             CCSCSEEEEECCCTTCCHHHHHHHHHTT----SCCEEEEEECS----SSTTCEEEEESSH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHhhcc----CCEEEEEEeee----cccceeEEEECCH
Confidence            3567899999999999999999999999    88988877544    3589999999863

>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=98.92  E-value=2.6e-10  Score=89.00  Aligned_cols=45  Identities=22%  Similarity=0.226  Sum_probs=41.0

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ++|||+|||+++++++|+++|+.|    |.|..|+|+++       |||||+|.+.
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~----G~v~~~~i~~~-------g~afV~f~~~   45 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREA----GDVCYADVYRD-------GTGVVEFVRK   45 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGG----SCEEEEEECTT-------SEEEEEESSH
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhh----ccccccccccc-------ceeeEEeCCH
Confidence            379999999999999999999999    99999998654       7999999874

>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=98.91  E-value=5.8e-10  Score=88.67  Aligned_cols=49  Identities=14%  Similarity=0.325  Sum_probs=44.4

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .|+++|||+|||+++++++|+++|+.|    |.|..|++.++      +|||||+|.+.
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~----G~i~~~~~~~~------~~~afV~f~~~   63 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRF----GSIRTIDHVKG------DSFAYIQYESL   63 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTT----SCEEEEEECSS------SCCEEEEESSH
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhh----cccceEeeecc------ccEEEeccCCH
Confidence            467899999999999999999999999    99999999754      68999999874

>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=98.91  E-value=3.8e-10  Score=91.21  Aligned_cols=48  Identities=27%  Similarity=0.288  Sum_probs=42.8

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++|||+|||+.+++++|+++|+.|    |.|..|.|..      .+|||||+|.+.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~f----G~I~~v~l~~------~kg~afV~f~~~   56 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRF----GSLGRVLLPE------GGITAIVEFLEP   56 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTT----SCEEEEECCS------SSSCEEEEESCH
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhcc----CCccEEEeec------cCceEEEEEcCH
Confidence            35799999999999999999999999    9999998842      579999999864

>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=98.89  E-value=7.4e-10  Score=86.25  Aligned_cols=47  Identities=34%  Similarity=0.650  Sum_probs=42.9

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+|||+|||+++++++|+++|+.|    |.|..|+++++      +|||||+|.++
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~----G~i~~i~~~~~------k~~afV~f~~~   54 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKY----GKAGEVFIHKD------KGFGFIRLETR   54 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTT----CCCSEEEEETT------TTEEEEECSSS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHh----CCceEeeeecc------cceEEEEECCH
Confidence            4579999999999999999999999    99999999865      68999999874

>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=98.88  E-value=1.6e-09  Score=87.18  Aligned_cols=50  Identities=18%  Similarity=0.195  Sum_probs=45.1

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++++|||+|||+.+++++|.++|..|    |.|..|+|.++      +|||||+|.+.
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~f----G~I~~~~~~~~------k~~AfV~f~~~   61 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKF----GTICYVMMMPF------KRQALVEFENI   61 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTT----SCEEEEEEETT------TTEEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhc----ccceEEEEEec------ceeEEEEeCCH
Confidence            4578899999999999999999999999    99999999754      78999999864

>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=98.87  E-value=7.1e-10  Score=89.40  Aligned_cols=48  Identities=23%  Similarity=0.321  Sum_probs=42.9

Q ss_pred             cceeeeCCCCC-CCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          336 KKTVFVGNLPF-DVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~-~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      +.+|||+|||+ .+|+++|+++|+.|    |.|..|.|+++     .+|||||+|.+.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~f----G~I~~v~i~~~-----~kg~afV~f~~~   50 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVY----GDVQRVKILFN-----KKENALVQMADG   50 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHH----TCEEEEEECCT-----TSCCEEEEESCH
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhc----cccceEEEEec-----ccceEEEEECCH
Confidence            46999999965 59999999999999    99999999987     379999999874

>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=98.87  E-value=3e-10  Score=89.26  Aligned_cols=51  Identities=25%  Similarity=0.464  Sum_probs=43.6

Q ss_pred             CcceeeeCCCCCCCCHHHHHH----HhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQ----LFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e----~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      |+++|||+|||+.+++++|++    +|+.|    |.|.+|++..   ++.++|||||+|.++
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~----G~i~~i~~~~---~~~~~g~afV~F~~~   56 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRF----GQILDILVSR---SLKMRGQAFVIFKEV   56 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGG----SCEEEEECCH---HHHHTTCEEEEESSH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhccc----ccccceEEee---eccCCCceEEEECCH
Confidence            468999999999999999864    57888    9999999864   467899999999874

>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=98.86  E-value=1.2e-10  Score=91.24  Aligned_cols=52  Identities=19%  Similarity=0.493  Sum_probs=44.3

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEe-----ecCCCCCCccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVI-----RHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~-----~d~~tg~~kGfaFVeF~t~  392 (393)
                      ++|||+|||+.+|+++|+++|+.|    |.|..+.+.     .+..++.++|||||+|.++
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~----g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~   58 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQ----MRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV   58 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHH----HTTTTSCCSSSCSEEECCEETTTTEEEEEESSC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhh----CcEEEEEEeccceeeecccCCCceEEEEEeCCH
Confidence            689999999999999999999999    666665553     4557788999999999875

>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=98.84  E-value=2e-09  Score=83.32  Aligned_cols=49  Identities=27%  Similarity=0.329  Sum_probs=42.3

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...++|||+|||+++++++|+++|+.|    |.|..+++.      .++|||||+|.++
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~----g~i~~~~~~------~~rg~afV~f~~~   54 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNI----KPGAVERVK------KIRDYAFVHFSNR   54 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTT----STTCEEEEE------ECSSEEEEEESSH
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhccc----ceeeeEEEc------cccEEEEEEeCCH
Confidence            345799999999999999999999999    888877773      3589999999874

>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=98.82  E-value=8e-10  Score=87.61  Aligned_cols=51  Identities=27%  Similarity=0.493  Sum_probs=43.6

Q ss_pred             cCCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..+.++|||+|||+++|+++|+++|..|    |.|..++.     +|.++|||||+|.+.
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~----g~v~~~~~-----~~~~~~~afV~f~~~   63 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDA----LEIRLVSQ-----DGKSKGIAYIEFKSE   63 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSE----EEECCEEE-----TTEEEEEEEEEESSH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc----ccceeeee-----cCccccEEEEEeCCH
Confidence            4457899999999999999999999999    87765542     578899999999874

>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=98.81  E-value=1.9e-09  Score=86.13  Aligned_cols=50  Identities=20%  Similarity=0.402  Sum_probs=44.1

Q ss_pred             cCCcceeeeCCCCCC-CCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFD-VKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~-~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++++|||+|||.+ +|+++|.++|+.|    |.|..|+|+++      +|||||+|.+.
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~f----G~V~~v~~~~~------k~~afV~f~~~   65 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPY----GKIKNYILMRM------KSQAFIEMETR   65 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTT----SCCSEEEEETT------TTEEEEECSSH
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccc----cceeEEEEeec------CCcEEEEecch
Confidence            456789999999985 8999999999999    99999999755      68999999874

>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=98.81  E-value=5.6e-10  Score=85.74  Aligned_cols=46  Identities=26%  Similarity=0.411  Sum_probs=40.5

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+|||+|||+++|+++|+++|+.|    |.|..+++..      ++|||||+|.++
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~----G~i~~~~~~~------~rg~aFV~f~~~   47 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDR----KLPLAGQVLL------KSGYAFVDYPDQ   47 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHT----TCCCSSCEEE------ETTEEEECCSCH
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHh----CcEEEeEEec------ccceEEEEECCH
Confidence            479999999999999999999999    8888777765      479999999874

>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=98.79  E-value=3.8e-09  Score=84.21  Aligned_cols=48  Identities=17%  Similarity=0.176  Sum_probs=42.9

Q ss_pred             CCcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ....+|||+|||+.+++++|+++|+.|    |.|..|.|.+       +|||||+|.++
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~----G~v~~~~i~~-------~g~afV~f~~~   60 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREA----GDVCYADVQK-------DGMGMVEYLRK   60 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTS----SCEEEEEEET-------TTEEEEEESSH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhh----cccccccccc-------cceEEEEECCH
Confidence            345789999999999999999999999    9999999863       58999999874

>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=98.75  E-value=3.3e-09  Score=86.68  Aligned_cols=47  Identities=21%  Similarity=0.315  Sum_probs=42.8

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...+||||||+.+|+++|+++|+.|    |.|.+|+|+++      +|||||.|.++
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~f----G~V~~v~i~~~------kg~gfV~F~~~   57 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNH----GEIKWIDFVRG------AKEGIILFKEK   57 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSS----CCEEEEECCTT------CSEEEEEESSC
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhc----CChheEEEecC------CceEEEEecCc
Confidence            5678999999999999999999999    99999999854      79999999874

>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=98.70  E-value=5.2e-09  Score=83.40  Aligned_cols=47  Identities=28%  Similarity=0.548  Sum_probs=40.8

Q ss_pred             CCcceeeeCCCC-CCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNLP-FDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNLp-~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ....+|||+||| ..+++++|+++|..|    |.|..|+|        ++|||||+|.++
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~----G~i~~~~i--------~rg~aFV~f~~~   60 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKY----GKIVGCSV--------HKGFAFVQYVNE   60 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTS----SCEEEEEE--------ETEEEEEEESSH
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhc----CCEEEEEE--------eCCeEEEEECCH
Confidence            345689999997 578899999999999    99999998        478999999874

>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=98.68  E-value=5.6e-09  Score=79.68  Aligned_cols=45  Identities=11%  Similarity=0.186  Sum_probs=40.0

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .++|||+||+  +|+++|+++|+.|    |.|..|++.++      +|||||+|.++
T Consensus         5 ~~ti~V~~~~--~te~~L~~~F~~~----G~I~~v~~~~~------~~~afV~f~~~   49 (79)
T d2bz2a1           5 GNTLYVYGED--MTPTLLRGAFSPF----GNIIDLSMDPP------RNCAFVTYEKM   49 (79)
T ss_dssp             CCEEEEECSS--CCHHHHHHHHSTT----CCCSCEEEETT------TTEEEEECSSH
T ss_pred             CCEEEEECCC--CCHHHHHHHHhcc----CccceeeeccC------CCEEEEEEccc
Confidence            5799999996  8999999999999    99999999754      68999999864

>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=98.68  E-value=5e-09  Score=82.05  Aligned_cols=50  Identities=10%  Similarity=0.159  Sum_probs=44.2

Q ss_pred             cCCcceeeeCCCCCC-CCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVGNLPFD-VKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVgNLp~~-~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+++++|||+|||.. +|++||.++|+.|    |.|..|+|+.+      ++||||+|.+.
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~f----G~I~~i~i~~~------k~~afV~f~~~   55 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPF----GVISNHLILNK------INEAFIEMATT   55 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGG----SCEEEEEECSS------SSCEEEEESSH
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhh----CCeEEEEeecc------ceEEEEEEcch
Confidence            456789999999986 7899999999999    99999999765      56999999863

>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=98.65  E-value=6.1e-09  Score=81.26  Aligned_cols=47  Identities=23%  Similarity=0.272  Sum_probs=38.6

Q ss_pred             CcceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      .+++|||+|||+++++++|+++|+.|    | +..+.+      +.++|||||+|.+.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~----G-~~~~~~------~~~kg~afV~f~~~   50 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDY----D-LKYCYV------DRNKRTAFVTLLNG   50 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS----C-CCCEEE------EGGGTEEEECCSCH
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhc----C-ceeeee------eccCCceEEEECCH
Confidence            35799999999999999999999999    7 333443      34689999999874

>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=98.65  E-value=1.2e-08  Score=77.13  Aligned_cols=43  Identities=26%  Similarity=0.397  Sum_probs=36.8

Q ss_pred             eeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       339 LfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      |||+|||+++++++|+++|+.|    | +..+.+      +.++|||||+|.++
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~----g-~~~~~~------~~~~g~afv~f~~~   43 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDY----E-LKYCFV------DKYKGTAFVTLLNG   43 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTS----C-EEEEEE------ETTTTEEEEEESSH
T ss_pred             CEEeCCCCcCCHHHHHHHHhcc----c-ccceee------cccceeEEEEECCH
Confidence            7999999999999999999999    7 555554      45789999999874

>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=98.55  E-value=1.8e-08  Score=80.78  Aligned_cols=50  Identities=14%  Similarity=0.206  Sum_probs=43.2

Q ss_pred             cCCcceeeeC--CCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          333 YDIKKTVFVG--NLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       333 ~~~~~tLfVg--NLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++++|||+  |||..+|+++|+++|+.|    |.|..|+++.+      +|||||+|.+.
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~----G~i~~i~~~~~------k~~aFV~f~~~   66 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKC----GLVDALLMPPN------KPYSFARYRTT   66 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHH----SCEEEEECCTT------CSCEEEEESSH
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhh----CcccEEeeccC------ccEEEEEECCH
Confidence            4567788885  599999999999999999    99999998755      67999999873

>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=98.23  E-value=4.7e-08  Score=78.65  Aligned_cols=51  Identities=18%  Similarity=0.087  Sum_probs=47.0

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ..++|++++..+++++|+++|+.|    |.|..|+|+++ .+|.++|||||+|.+.
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~----G~I~~v~I~~~-~~~~~~G~~fV~f~~~   78 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKY----GEVEEMNVCDN-LGDHLVGNVYVKFRRE   78 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHT----CCEEEEEECCS-SSSSSEEEEEEEESCH
T ss_pred             chHHhhhhhhhhhHHHHHHHhccC----CCEEEEEeecC-CCCCEeeEEEEEEech
Confidence            569999999999999999999999    99999999988 5899999999999864

>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=98.19  E-value=2.7e-07  Score=74.06  Aligned_cols=48  Identities=10%  Similarity=0.024  Sum_probs=40.6

Q ss_pred             CcceeeeCCCCCCC-C----HHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          335 IKKTVFVGNLPFDV-K----DEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNLp~~~-t----eedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...+|||+||+.++ +    +++|+++|+.|    |.|..|++.+      ++|||||+|.+.
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~----G~i~~~~~~k------~~~~afV~f~~~   56 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTY----DKDTTFQYFK------SFKRVRINFSNP   56 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTT----CSSCEEEEET------TTTEEEEECSST
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhccc----ccceEEEEec------CCCEEEEEECCH
Confidence            45789999999886 3    35699999999    9999999974      478999999875

>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=98.10  E-value=9.2e-07  Score=67.81  Aligned_cols=46  Identities=9%  Similarity=0.045  Sum_probs=38.5

Q ss_pred             cceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       336 ~~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...|+|+|||++++++.| .+|+.|    |.|.++++.+      .+|||||+|.++
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~----G~I~~~~~~~------~~~~~fV~f~~~   49 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQY----GNILKHVMSN------TGNWMHIRYQSK   49 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTT----SCEEEEEECS------SSSEEEEEESSH
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhh----hhhheEEecC------CCCEEEEEEccc
Confidence            467999999999986555 579999    9999998853      478999999875

>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=97.60  E-value=1.9e-05  Score=62.25  Aligned_cols=51  Identities=18%  Similarity=0.368  Sum_probs=40.7

Q ss_pred             CCcceeeeCCC--CCCCC---------HHHHHHHhhcCCCCCCCeEEEEEeecCCCCCCccEEEEEeeec
Q 016231          334 DIKKTVFVGNL--PFDVK---------DEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR  392 (393)
Q Consensus       334 ~~~~tLfVgNL--p~~~t---------eedL~e~F~~~~~~~G~I~~VrI~~d~~tg~~kGfaFVeF~t~  392 (393)
                      ...++|+|.||  |.++.         .++|++.|+.|    |.|..|.++.+    .++|||||+|.++
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~----G~V~~v~~~~~----~~~G~~fV~f~~~   67 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKF----GQIRKLLLFDR----HPDGVASVSFRDP   67 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGT----SCCSEEEEETT----CTTCEEEEECSCH
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCc----ccEEEEeccCC----CCccEEEEEECCH
Confidence            35689999999  55432         36889999999    99999998765    3689999999874

>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=97.56  E-value=1.5e-05  Score=63.34  Aligned_cols=54  Identities=17%  Similarity=0.214  Sum_probs=43.3

Q ss_pred             CcceeeeCCC--CCCCC--------HHHHHHHhhcCCCCCCCeEEEEEeecCCCC--CCccEEEEEeeec
Q 016231          335 IKKTVFVGNL--PFDVK--------DEEIYQLFCGLNDLESSVEAVRVIRHPHMR--VGKGIAYVLFKTR  392 (393)
Q Consensus       335 ~~~tLfVgNL--p~~~t--------eedL~e~F~~~~~~~G~I~~VrI~~d~~tg--~~kGfaFVeF~t~  392 (393)
                      |+++|+|.||  |..+.        .+||++.|+.|    |.|..|.|++++.+.  ...|++||+|.+.
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~----G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~   68 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKY----GLVKSIEIPRPVDGVEVPGCGKIFVEFTSV   68 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTT----SCEEEEECCCCTTSSSCTTCCEEEEEESCH
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhccc----CceEEEEEeecCCCCccCCceEEEEEECCH
Confidence            5789999999  55443        45789999999    999999999877543  4569999999874

>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=96.78  E-value=0.0017  Score=50.03  Aligned_cols=72  Identities=18%  Similarity=0.286  Sum_probs=57.0

Q ss_pred             CcccEEEEeCCCccCCH---------HHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCC
Q 016231          223 KLLRTIFVGNLPLKVKK---------KTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKS  293 (393)
Q Consensus       223 ~~~rtVFVgNLp~~~te---------e~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s  293 (393)
                      ++.-||.|.=..+...+         .+|.+.|..||+|.-||++.                         +-..|+|.+
T Consensus        13 PpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~-------------------------d~mwVTF~d   67 (95)
T d1ufwa_          13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQ-------------------------GQMLVTFAD   67 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEET-------------------------TEEEEECSC
T ss_pred             CCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeC-------------------------CeEEEEECC
Confidence            34567878555433322         46778899999999898844                         468999999


Q ss_pred             HHHHHHHHHhcCceeCCeEEEEeecC
Q 016231          294 EQSTEAALAFNMAVIGGNHIRLDRAC  319 (393)
Q Consensus       294 ~e~A~~Al~lng~~~~Gr~I~V~~a~  319 (393)
                      -++|-+|+.+++..+.|+.|.|....
T Consensus        68 G~SAL~al~l~g~~v~G~~l~It~~~   93 (95)
T d1ufwa_          68 SHSALSVLDVDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             SHHHHHHHHGGGSEETTEEEEEECCC
T ss_pred             cHHHHHHhccCCeEEcceEEEEecCC
Confidence            99999999999999999999997653

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.23  E-value=0.01  Score=45.70  Aligned_cols=69  Identities=22%  Similarity=0.235  Sum_probs=52.7

Q ss_pred             cEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-Hhc
Q 016231          226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFN  304 (393)
Q Consensus       226 rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~ln  304 (393)
                      ..|.|++||+++|++++.+.++..|.+.....+.-.  .+..+             ..-.-|||.|.+.+++.... .++
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk--~s~~~-------------~~~SRAYi~F~~~~~v~~F~~~f~   66 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSND--TSLYP-------------HMYARAYINFKNQEDIILFRDRFD   66 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESC--CSSTT-------------CCCEEEEEEESSSHHHHHHHHHHT
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCC--cCCCC-------------CcceEEEEEeCCHHHHHHHHHHcC
Confidence            368999999999999999999999988766654322  11111             12358999999999988877 688


Q ss_pred             CceeC
Q 016231          305 MAVIG  309 (393)
Q Consensus       305 g~~~~  309 (393)
                      |..|.
T Consensus        67 g~~F~   71 (91)
T d1uw4a_          67 GYVFL   71 (91)
T ss_dssp             TCEEE
T ss_pred             CcEEE
Confidence            88773

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.26  E-value=0.035  Score=40.57  Aligned_cols=60  Identities=22%  Similarity=0.321  Sum_probs=48.9

Q ss_pred             HHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHH-HhcCceeCCeEEEEeec
Q 016231          240 KTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDRA  318 (393)
Q Consensus       240 e~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al-~lng~~~~Gr~I~V~~a  318 (393)
                      +.|...|..+|.|.++.|..  .++ +.                 -.|-|...+.++|..|+ .|+...|++++|.|.++
T Consensus        11 q~L~~~f~~h~~V~sv~l~~--~~d-g~-----------------~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~   70 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSP--HTD-YQ-----------------LKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLA   70 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECS--CCS-TT-----------------CCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             HHHHHHHHhheeEEEEEEEe--ccC-Cc-----------------EEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEe
Confidence            45667889999999998822  222 11                 27999999999999999 79999999999999987


Q ss_pred             C
Q 016231          319 C  319 (393)
Q Consensus       319 ~  319 (393)
                      .
T Consensus        71 ~   71 (73)
T d2dgxa1          71 T   71 (73)
T ss_dssp             C
T ss_pred             c
Confidence            4

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.89  E-value=0.049  Score=41.72  Aligned_cols=52  Identities=15%  Similarity=0.222  Sum_probs=41.8

Q ss_pred             ceeeeCCCCCCCCHHHHHHHhhcCCCCCCCeEEEEEeecCCCCC--CccEEEEEeeec
Q 016231          337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRV--GKGIAYVLFKTR  392 (393)
Q Consensus       337 ~tLfVgNLp~~~teedL~e~F~~~~~~~G~I~~VrI~~d~~tg~--~kGfaFVeF~t~  392 (393)
                      ++|.|+.||+++|++++.+.++..    |.+.+........+..  .-.-|||.|.+.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~----~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~   55 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPM----PEHDYFEFFSNDTSLYPHMYARAYINFKNQ   55 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSC----CCEEEEEEEESCCSSTTCCCEEEEEEESSS
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCc----CceEEEEEeCCCcCCCCCcceEEEEEeCCH
Confidence            479999999999999999999987    8999998877654332  225689999764

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.67  E-value=0.35  Score=37.25  Aligned_cols=53  Identities=17%  Similarity=0.300  Sum_probs=44.3

Q ss_pred             ccEEEEeCCCccCCHHHHHHHhcccCCeeEEEEeeecccCCCCCccchhhhhhcccCCCceEEEEeeCCHHHHHHHHH
Q 016231          225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHAYIVFKSEQSTEAALA  302 (393)
Q Consensus       225 ~rtVFVgNLp~~~tee~L~~~Fs~~G~I~sVri~~~~~~~~~~~rkga~~~~k~~~~~srG~AFVeF~s~e~A~~Al~  302 (393)
                      ..-||.-..|.....-+|.++|+.||.|. |-++-+.                        -|||...+.++|..++.
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT------------------------Sa~V~L~~~e~~~~v~~   67 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT------------------------SAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT------------------------EEEEECSCHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc------------------------eEEEEecCHHHHHHHHH
Confidence            45599999999999999999999999876 5553221                        69999999999998884